Local supercoil-stabilized DNA structures.

The DNA double helix exhibits local sequence-dependent polymorphism at the level of the single base pair and dinucleotide step. Curvature of the DNA molecule occurs in DNA regions with a specific type of nucleotide sequence periodicities. Negative supercoiling induces in vitro local nucleotide sequence-dependent DNA structures such as cruciforms, left-handed DNA, multistranded structures, etc. Techniques based on chemical probes have been proposed that make it possible to study DNA local structures in cells. Recent results suggest that the local DNA structures observed in vitro exist in the cell, but their occurrence and structural details are dependent on the DNA superhelical density in the cell and can be related to some cellular processes.

[1]  R. Wells,et al.  The B- to Z-DNA equilibrium in vivo is perturbed by biological processes. , 1988, Proceedings of the National Academy of Sciences of the United States of America.

[2]  Y. Kohwi,et al.  Magnesium ion-dependent triple-helix structure formed by homopurine-homopyrimidine sequences in supercoiled plasmid DNA. , 1988, Proceedings of the National Academy of Sciences of the United States of America.

[3]  Z. Wang,et al.  Genomic footprinting in mammalian cells with ultraviolet light. , 1989, Proceedings of the National Academy of Sciences of the United States of America.

[4]  H. Weintraub,et al.  Detection of an altered DNA conformation at specific sites in chromatin and supercoiled DNA. , 1983, Proceedings of the National Academy of Sciences of the United States of America.

[5]  J. Dahlberg,et al.  Single strands, triple strands, and kinks in H-DNA. , 1988, Science.

[6]  N. Rousseau,et al.  A study of the B-Z transition of the AC-rich region of the repeat unit of a satellite DNA from Cebus by means of chemical probes. , 1988, Journal of Biological Chemistry.

[7]  D. Patterson,et al.  Transverse alternating field electrophoresis and applications to mammalian genome mapping , 1989, Electrophoresis.

[8]  R. Tjian,et al.  Transcription factors that activate the Ultrabithorax promoter in developmentally staged extracts , 1988, Cell.

[9]  Nikos Panayotatos,et al.  Cruciform structures in supercoiled DNA , 1981, Nature.

[10]  T. Kimura,et al.  Nuclease S1-sensitive sites on superhelical DNA molecules carrying the LTR region of Moloney murine leukemia virus. , 1987, Biochimica et biophysica acta.

[11]  C J Benham.  Theoretical analysis of conformational equilibria in superhelical DNA. , 1985, Annual review of biophysics and biophysical chemistry.

[12]  R. Watson,et al.  Early and late helix-coil transitions in closed circular DNA. The number of superhelical turns in polyoma DNA. , 1968, Journal of molecular biology.

[13]  P. Hagerman,et al.  Sequence-directed curvature of DNA. , 1986, Nature.

[14]  E. Paleček,et al.  Unusual protonated structure in the homopurine.homopyrimidine tract of supercoiled and linearized plasmids recognized by chemical probes. , 1987, Journal of biomolecular structure & dynamics.

[15]  E. Stoll,et al.  Scanning tunneling microscopy of recA-DNA complexes coated with a conducting film , 1988 .

[16]  T. Lohman,et al.  E. coli single strand binding protein: a new look at helix-destabilizing proteins. , 1988, Trends in biochemical sciences.

[17]  S. Linn.  [31] An endonuclease from Neurospora crassa specific for polynucleotides lacking an ordered structure , 1967 .

[18]  J. S. Lee,et al.  Polypurine DNAs and RNAs form secondary structures which may be tetra-stranded. , 1980, Nucleic acids research.

[19]  J. Casasnovas,et al.  DNA-sequence and metal-ion specificity of the formation of *H-DNA. , 1990, Nucleic acids research.

[20]  C R Cantor,et al.  Pulsed-field gel electrophoresis of very large DNA molecules. , 1988, Annual review of biophysics and biophysical chemistry.

[21]  M. D. Shetlar.  Cross-Linking of Proteins to Nucleic Acids by Ultraviolet Light , 1980 .

[22]  D. Natale,et al.  Stable DNA unwinding, not "breathing," accounts for single-strand-specific nuclease hypersensitivity of specific A+T-rich sequences. , 1988, Proceedings of the National Academy of Sciences of the United States of America.

[23]  S. Bram.  The Polymorphism of DNA , 1976 .

[24]  M. Waring,et al.  Differences between sites of binding to DNA and strand cleavage for complexes of bleomycin with iron of cobalt , 1989, Journal of molecular recognition : JMR.

[25]  J. Langowski,et al.  Configurational and dynamic properties of different length superhelical DNAs measured by dynamic light scattering. , 1989, Biophysical chemistry.

[26]  D. Lilley.  DNA supercoiling and DNA structure. , 1986, Biochemical Society transactions.

[27]  A. Nordheim,et al.  Chemical footprinting of the interaction between left-handed Z-DNA and anti-Z-DNA antibodies by diethylpyrocarbonate carbethoxylation. , 1986, Journal of molecular biology.

[28]  H. Miles,et al.  Poly(I) helix formation. Dependence on size-specific complexing to alkali metal ions , 1978 .

[29]  E. Blackburn,et al.  S1 nuclease sensitivity of a double-stranded telomeric DNA sequence. , 1987, Nucleic acids research.

[30]  A. Ciccodicola,et al.  Locations and contexts of sequences that hybridize to poly(dG-dT).(dC-dA) in mammalian ribosomal DNAs and two X-linked genes. , 1988, Nucleic acids research.

[31]  J. Barton,et al.  Chiral probe for A-form helixes of DNA and RNA: tris(tetramethylphenanthroline)ruthenium(II) , 1986 .

[32]  J. Casasnovas,et al.  Structural polymorphism of homopurine–homopyrimidine sequences: the secondary DNA structure adopted by a d(GA.CT)22 sequence in the presence of zinc ions. , 1989, The EMBO journal.

[33]  J. Van De Sande,et al.  Left-handed DNA: from synthetic polymers to chromosomes. , 1983, Journal of biomolecular structure & dynamics.

[34]  E. Paleček,et al.  Site-specific OsO4 modification of the B-Z junctions formed at the (dA-dC)32 region in supercoiled DNA. , 1986, The Journal of biological chemistry.

[35]  J. E. Larson,et al.  Methylation of cytosine in the 5-position alters the structural and energetic properties of the supercoil-induced Z-helix and of B-Z junctions. , 1988, Biochemistry.

[36]  J. Gralla,et al.  DNA supercoiling promotes formation of a bent repression loop in lac DNA. , 1987, Journal of molecular biology.

[37]  M. A. Gama Sosa,et al.  Slipped DNA structures within the enhancer region of the Moloney murine leukemia virus. , 1988, Biochemical and Biophysical Research Communications - BBRC.

[38]  S. J. Flint,et al.  Site-specific oligonucleotide binding represses transcription of the human c-myc gene in vitro. , 1988, Science.

[39]  J. Lebowitz,et al.  Carbodiimide inactivation of Escherichia coli RNA polymerase promoters on supercoiled simian virus 40 and ColE1 DNAs occurs by a one-hit process at salt concentrations in the physiological range. , 1983, The Journal of biological chemistry.

[40]  E. Paleček,et al.  Premelting changes in DNA conformation. , 1976, Progress in nucleic acid research and molecular biology.

[41]  C. Marck,et al.  Protonated polynucleotides structures - 22.CD study of the acid-base titration of poly(dG).poly(dC). , 1978, Nucleic Acids Research.

[42]  Alexander Rich,et al.  FORMATION OF A THREE-STRANDED POLYNUCLEOTIDE MOLECULE , 1957 .

[43]  P. Dervan.  Sequence Specific Recognition of Double Helical DNA. A Synthetic Approach , 1988 .

[44]  K. Rippe,et al.  A parallel stranded linear DNA duplex incorporating dG.dC base pairs. , 1990, Journal of biomolecular structure & dynamics.

[45]  J. Dodgson,et al.  Action of single-strand specific nucleases on model DNA heteroduplexes of defined size and sequence. , 1977, Biochemistry.

[46]  Y. Lyubchenko,et al.  A sharp structural transition in pA03 plasmid DNA caused by increased superhelix density , 1982, FEBS letters.

[47]  B. Révet,et al.  Location of B- and Z-DNA in the chromosomes of a primitive eukaryote dinoflagellate , 1990, The Journal of cell biology.

[48]  K. Rippe,et al.  Substrate properties of 25-nt parallel-stranded linear DNA duplexes. , 1989, Biochemistry.

[49]  T M Jovin,et al.  Recognition mechanisms of DNA-specific enzymes. , 1976, Annual review of biochemistry.

[50]  R. Hand.  Eucaryotic DNA: Organization of the genome for replication , 1978, Cell.

[51]  I. Madshus,et al.  Regulation of intracellular pH in eukaryotic cells. , 1988, The Biochemical journal.

[52]  J. Feigon,et al.  Triple-strand formation in the homopurine:homopyrimidine DNA oligonucleotides d(G-A)4 and d(T-C)4 , 1989, Nature.

[53]  R. Dickerson,et al.  A stochastic model for helix bending in B-DNA. , 1983, Journal of biomolecular structure & dynamics.

[54]  E. Paleček,et al.  B-Z junctions in supercoiled pRW751 DNA contain unpaired bases or non-Watson-Crick base pairs. , 1987, Journal of biomolecular structure & dynamics.

[55]  P. Miškovský,et al.  The Z-conformation of poly(dA-dT).poly(dA-dT) in solution as studied by ultraviolet resonance Raman spectroscopy. , 1989, Journal of biomolecular structure & dynamics.

[56]  D. Lilley.  Bacterial chromatin: A new twist to an old story , 1986, Nature.

[57]  N. Heintz,et al.  Intramolecular DNA triplexes, bent DNA and DNA unwinding elements in the initiation region of an amplified dihydrofolate reductase replicon. , 1990, Journal of molecular biology.

[58]  H. Noller,et al.  Chemical probing of conformation in large RNA molecules. Analysis of 16 S ribosomal RNA using diethylpyrocarbonate. , 1984, Journal of molecular biology.

[59]  J. Lown,,et al.  α-DNA-V. Parallel annealing, handedness and conformation of the duplex of the unnatural α-hexadeoxyribonucleotide α-[d(CpApTpGpCpG)] with its β-complement β-[d(GpTpApCpGpC)] deduced from high field 1H-NMR , 1987 .

[60]  C. Hélène,et al.  Oligo(alpha-deoxynucleotide)s covalently linked to intercalating agents: differential binding to ribo- and deoxyribopolynucleotides and stability towards nuclease digestion. , 1987, Proceedings of the National Academy of Sciences of the United States of America.

[61]  D. Brown.  1 – CHEMICAL REACTIONS OF POLYNUCLEOTIDES AND NUCLEIC ACIDS , 1974 .

[62]  L. Loeb,et al.  An E. coli promoter that regulates transcription by DNA superhelix-induced cruciform extrusion. , 1988, Science.

[63]  J M Gale,et al.  UV-induced formation of pyrimidine dimers in nucleosome core DNA is strongly modulated with a period of 10.3 bases. , 1987, Proceedings of the National Academy of Sciences of the United States of America.

[64]  A. Heeger,et al.  Nature of the open state in long polynucleotide double helices: possibility of soliton excitations. , 1980, Proceedings of the National Academy of Sciences of the United States of America.

[65]  R. Portalier,et al.  Acid shock proteins of Escherichia coli , 1990 .

[66]  J. Sullivan,et al.  Site-directed chemical modification for probing DNA-protein interactions. Osmium tetroxide modification of the -10 site of the lacUV5 promoter enhances open complex formation. , 1989, Journal of Biological Chemistry.

[67]  F. Blattner,et al.  Mapping using gene encyclopaedias , 1987, Nature.

[68]  D. Lilley,et al.  Stress‐induced cruciform formation in a cloned d(CATG)10 sequence. , 1986, The EMBO journal.

[69]  M. Waring,et al.  Echinomycin-induced hypersensitivity to osmium tetroxide of DNA fragments incapable of forming Hoogsteen base pairs. , 1989, Proceedings of the National Academy of Sciences of the United States of America.

[70]  E. Behrman,et al.  The reaction of osmium tetroxide-pyridine complexes with nucleic acid components , 1971 .

[71]  H. Pelham,et al.  Association of an S1 nuclease-sensitive structure with short direct repeats 5′ of Drosophila heat shock genes , 1983, Nature.

[72]  R. Wells,et al.  Unusual DNA Structures and the Probes Used for their Detection , 1988 .

[73]  S. Mirkin,et al.  DNA H form requires a homopurine–homopyrimidine mirror repeat , 1987, Nature.

[74]  R. Wells,et al.  B-Z DNA junctions are neither highly flexible nor strongly bent. , 1987, Biopolymers.

[75]  L. Naylor,et al.  d(TG)n.d(CA)n sequences upstream of the rat prolactin gene form Z-DNA and inhibit gene transcription. , 1990, Nucleic acids research.

[76]  Marc Nadal,et al.  Positively supercoiled DNA in a virus-like particle of an archaebacterium , 1986, Nature.

[77]  R. Hay,et al.  Detection of Z DNA binding proteins in tissue culture cells. , 1988, Nucleic acids research.

[78]  D Riesner,et al.  Temperature‐Gradient gel electrophoresis of nucleic acids: Analysis of conformational transitions, sequence variations, and protein‐nucleic acid interactions , 1989, Electrophoresis.

[79]  F. B. Fuller.  The writhing number of a space curve. , 1971, Proceedings of the National Academy of Sciences of the United States of America.

[80]  U. Heinemann,et al.  The conformation of a B‐DNA decamer is mainly determined by its sequence and not by crystal environment. , 1991, The EMBO journal.

[81]  J. S. Lee,et al.  Poly(pyrimidine) . poly(purine) synthetic DNAs containing 5-methylcytosine form stable triplexes at neutral pH. , 1984, Nucleic acids research.

[82]  D. Eilat.  Anti-DNA antibodies: problems in their study and interpretation. , 1986, Clinical and experimental immunology.

[83]  E. I. Budowsky,et al.  G-DNA: a twice-folded DNA structure adopted by single-stranded oligo(dG) and its implications for telomeres. , 1990, Proceedings of the National Academy of Sciences of the United States of America.

[84]  S. A. Salisbury,et al.  Structure of the deoxytetranucleotide d‐pApTpApT and a sequence‐dependent model for poly(dA‐dT) , 1982, Biopolymers.

[85]  H. M. Sobell,et al.  beta-kinked DNA--a structure that gives rise to drug intercalation and DNA breathing--and its wider significance in determining the premelting and melting behavior of DNA. , 1983, Cold Spring Harbor Symposia on Quantitative Biology.

[86]  J. R. Fresco,et al.  Formation of the triple-stranded polynucleotide helix, poly(A.A.U). , 1987, Proceedings of the National Academy of Sciences of the United States of America.

[87]  Pulleyblank De,et al.  A structural basis for S1 nuclease sensitivity of double-stranded DNA , 1985 .

[88]  R. Sinden,et al.  Perfect palindromic lac operator DNA sequence exists as a stable cruciform structure in supercoiled DNA in vitro but not in vivo. , 1983, Proceedings of the National Academy of Sciences of the United States of America.

[89]  M. Vojtíṥková,et al.  Electron microscopy of supercoiled pEJ4 DNA containing homopurine.homopyrimidine sequences. , 1989, Journal of biomolecular structure & dynamics.

[90]  P. Nielsen,et al.  Site specificity of psoralen-DNA interstrand cross-linking determined by nuclease Bal31 digestion. , 1986, Biochemistry.

[91]  D. Riesner,et al.  Temperature-gradient gel electrophoresis. Thermodynamic analysis of nucleic acids and proteins in purified form and in cellular extracts. , 1987, Biophysical chemistry.

[92]  M. Riley,et al.  Physical and chemical characterization of two- and three-stranded adenine-thymine and adenine-uracil homopolymer complexes. , 1966, Journal of molecular biology.

[93]  K. Rippe,et al.  Spectroscopic properties and helical stabilities of 25-nt parallel-stranded linear DNA duplexes. , 1989, Biochemistry.

[94]  M. Linial,et al.  Bent DNA structures associated with several origins of replication are recognized by a unique enzyme from trypanosomatids. , 1988, Nucleic acids research.

[95]  S. Mirkin,et al.  A structural transition in d(AT)n.d(AT)n inserts within superhelical DNA. , 1985, Journal of biomolecular structure & dynamics.

[96]  E. Taillandier,et al.  Z form of poly d(A-T).poly d(A-T) in solution studied by CD and UV spectroscopies. , 1987, Journal of biomolecular structure & dynamics.

[97]  P. Nielsen,et al.  Detection of intercalation‐induced changes in DNA structure by reaction with diethyl pyrocarbonate or potassium permanganate Evidence against the induction of Hoogsteen base pairing by echinomycin , 1988, FEBS letters.

[98]  C. Cantor,et al.  Possible structures of homopurine-homopyrimidine S1-hypersensitive sites. , 1984, Nucleic acids research.

[99]  R. Dulbecco,et al.  VIRUS-CELL INTERACTION WITH A TUMOR-PRODUCING VIRUS. , 1960, Proceedings of the National Academy of Sciences of the United States of America.

[100]  J. Rossi,et al.  Synthesis and use of synthetic oligonucleotides. , 1984, Annual review of biochemistry.

[101]  J. Lebowitz,et al.  Physical and Topological Properties of Circular DNA , 1966, The Journal of general physiology.

[102]  J. M. Collins.  Deoxyribonucleic acid structure in human diploid fibroblasts stimulated to proliferate. , 1977, The Journal of biological chemistry.

[103]  D. Pettijohn,et al.  The folded genome of Escherichia coli isolated in a protein-DNA-RNA complex. , 1971, Proceedings of the National Academy of Sciences of the United States of America.

[104]  D M Crothers,et al.  Bent helical structure in kinetoplast DNA. , 1982, Proceedings of the National Academy of Sciences of the United States of America.

[105]  B. Crombrugghe,et al.  A sequence conserved in both the chicken and mouse alpha 2(I) collagen promoter contains sites sensitive to S1 nuclease. , 1984, The Journal of biological chemistry.

[106]  A. Gierer.  Model for DNA and Protein Interactions and the Function of the Operator , 1966, Nature.

[107]  E. Paleček,et al.  Osmium tetroxide probing of local DNA structure in linear and supercoiled plasmids containing curvature-inducing sequences. , 1988, General physiology and biophysics.

[108]  M. Price,et al.  Use of the hydroxyl radical and gel electrophoresis to study DNA structure , 1989, Electrophoresis.

[109]  G. Carrea,et al.  Chemical modification of 3 alpha,20 beta-hydroxysteroid dehydrogenase with diethyl pyrocarbonate. Evidence for an essential, highly reactive, lysyl residue. , 1987, Biochemistry.

[110]  W. Bauer,et al.  Calculation of the twist and the writhe for representative models of DNA. , 1986, Journal of molecular biology.

[111]  H R Drew,et al.  Structure of a B-DNA dodecamer. II. Influence of base sequence on helix structure. , 1981, Journal of molecular biology.

[112]  E. Paleček,et al.  Probing of B-Z junctions in recombinant plasmids in vitro and in the cell with different osmium tetroxide complexes. , 1989, General physiology and biophysics.

[113]  D. Stuart,et al.  The crystal and molecular structure of an osmium bispyridine adduct of thymine. , 1976, Biochimica et biophysica acta.

[114]  P. Hagerman,et al.  Sequence dependence of the curvature of DNA: a test of the phasing hypothesis. , 1985, Biochemistry.

[115]  E. Paleček,et al.  CHANGES IN OSCILLOPOLAROGRAPHIC BEHAVIOUR OF DEOXYRIBONUCLEIC ACIDS AT TEMPERATURES BELOW DENATURATION TEMPERATURE. , 1965, Journal of molecular biology.

[116]  Structural interconversion of alternating purine-pyrimidine inverted repeats cloned in supercoiled plasmids. , 1988, Nucleic acids research.

[117]  W. Christens-Barry,et al.  Raman spectroscopy of supercoiled and nicked ColE1 plasmid , 1989, Biopolymers.

[118]  Highly recurring sequence elements identified in eukaryotic DNAs by computer analysis are often homologous to regulatory sequences or protein binding sites. , 1987, Nucleic acids research.

[119]  C. Chang,et al.  Reactions of cytosine and 5-methylcytosine with osmium(VIII) reagents: Synthesis and deamination to uracil and thymine derivatives , 1981 .

[120]  M. A. Gama Sosa,et al.  Unusual DNA structures at the integration site of an HIV provirus. , 1989, Biochemical and biophysical research communications.

[121]  I. Lehman,et al.  AN ENDONUCLEASE FROM NEUROSPORA CRASSA SPECIFIC FOR POLYNUCLEOTIDES LACKING AN ORDERED STRUCTURE. I. PURIFICATION AND PROPERTIES OF THE ENZYME. , 1965, The Journal of biological chemistry.

[122]  B. Stollar.  Antibodies to DNA. , 1986, CRC critical reviews in biochemistry.

[123]  C. Cantor,et al.  A stable complex between homopyrimidine oligomers and the homologous regions of duplex DNAs. , 1988, Nucleic acids research.

[124]  W. Sauerbier,et al.  Flanking AT-rich sequences may lower the activation energy of cruciform extrusion in supercoiled DNA. , 1989, Biochemical and biophysical research communications.

[125]  H. Drew.  Structural specificities of five commonly used DNA nucleases. , 1984, Journal of molecular biology.

[126]  Y. Tsao,et al.  Transcription-driven supercoiling of DNA: Direct biochemical evidence from in vitro studies , 1989, Cell.

[127]  B. Johnston.  Chemical probing of the B-Z transition in negatively supercoiled DNA. , 1988, Journal of biomolecular structure & dynamics.

[128]  C. Marck,et al.  Z‐DNA and other non‐B‐DNA structures are reversed to B‐DNA by interaction with netropsin , 1983, FEBS letters.

[129]  J. Langowski,et al.  Neutron and light-scattering studies of DNA gyrase and its complex with DNA. , 1990, Journal of molecular biology.

[130]  A. Revzin,et al.  Studies of DNA‐protein interactions by gel electrophoresis , 1989, Electrophoresis.

[131]  D. Lilley,et al.  Fluorescence energy transfer shows that the four-way DNA junction is a right-handed cross of antiparallel molecules , 1989, Nature.

[132]  K. Burton,et al.  Selective degradation of thymidine and thymine deoxynucleotides. , 1966, The Biochemical journal.

[133]  H. Manor,et al.  Unusual sequence element found at the end of an amplicon. , 1987, Molecular and cellular biology.

[134]  W. Bauer,et al.  Temperature dependence of the gel electrophoretic mobility of superhelical DNA. , 1985, Nucleic acids research.

[135]  E. Paleček,et al.  Recognition of the structural distortions at the junctions between B and Z segments in negatively supercoiled DNA by osmium tetroxide. , 1985, Journal of biomolecular structure & dynamics.

[136]  D. Kowalski,et al.  Action of mung bean nuclease on supercoiled PM2 DNA. , 1982, The Journal of biological chemistry.

[137]  K. Fox.  Long (dA)n.(dT)n tracts can form intramolecular triplexes under superhelical stress. , 1990, Nucleic acids research.

[138]  D. Tautz,et al.  Simple sequences are ubiquitous repetitive components of eukaryotic genomes. , 1984, Nucleic acids research.

[139]  D. Kowalski.  Changes in site specificity of single-strand-specific endonucleases on supercoiled PM2 DNA with temperature and ionic environment. , 1984, Nucleic acids research.

[140]  G. A. Thomas,et al.  A duplex of the oligonucleotides d(GGGGGTTTTT) and d(AAAAACCCCC) forms an A to B conformational junction in concentrated salt solutions. , 1989, Journal of biomolecular structure & dynamics.

[141]  M. Liszewski,et al.  Antibodies specific for modified nucleosides: an immunochemical approach for the isolation and characterization of nucleic acids. , 1980, Progress in nucleic acid research and molecular biology.

[142]  J. Michael Schurr,et al.  Deformational dynamics and nmr relaxation of supercoiled DNAs , 1985, Biopolymers.

[143]  M. Gellert,et al.  DNA Supercoiling as a Regulator of Bacterial Gene Expression , 1987 .

[144]  R. Dickerson,et al.  X-ray structure of a DNA hairpin molecule , 1988, Nature.

[145]  A. Klug,et al.  The structure of an oligo(dA)·oligo(dT) tract and its biological implications , 1987, Nature.

[146]  M. Churchill,et al.  Mapping functional regions of transcription factor TFIIIA , 1988, Molecular and cellular biology.

[147]  D. Lilley,et al.  DNA bending induced by cruciform formation , 1985, Nature.

[148]  M. Leng.  Left-handed Z-DNA. , 1985, Biochimica et biophysica acta.

[149]  A. Travers,et al.  DNA conformation and protein binding. , 1989, Annual review of biochemistry.

[150]  S. Bram,et al.  Polymorphism of natural DNA. , 1972, Nature: New biology.

[151]  L. Koole,et al.  A parallel right-handed duplex of the hexamer d(TpTpTpTpTpT) with phosphate triester linkages. , 1987 .

[152]  D. Crothers,et al.  Chemical determinants of DNA bending at adenine-thymine tracts. , 1987, Biochemistry.

[153]  D. Greaves,et al.  RecBC, sbcB independent, (AT)n-mediated deletion of sequences flanking a Xenopus laevis beta globin gene on propagation in E. coli. , 1986, Nucleic acids research.

[154]  H. Hayatsu,et al.  The selective degradation of pyrimidines in nucleic acids by permanganate oxidation. , 1967, Biochemical and biophysical research communications.

[155]  G. A. van der Marel,et al.  Triple helix formation by oligopurine-oligopyrimidine DNA fragments. Electrophoretic and thermodynamic behavior. , 1990, Journal of molecular biology.

[156]  M. Laskowski,et al.  Sugar-unspecific mung bean nuclease I. , 1968, The Journal of biological chemistry.

[157]  J. Feigon,et al.  NMR studies of triple-strand formation from the homopurine-homopyrimidine deoxyribonucleotides d(GA)4 and d(TC)4. , 1989, Biochemistry.

[158]  B. Stollar.  Immunochemical approaches to the definition of unusual nucleic acid structures , 1988 .

[159]  S. Mirkin,et al.  A pH-dependent structural transition in the homopurine-homopyrimidine tract in superhelical DNA. , 1985, Journal of biomolecular structure & dynamics.

[160]  J. Francois,et al.  Inhibition of restriction endonuclease cleavage via triple helix formation by homopyrimidine oligonucleotides. , 1989, Biochemistry.

[161]  S. Heywood,et al.  A long polypyrimidine/polypurine tract induces an altered DNA conformation on the 3' coding region of the adjacent myosin heavy chain gene. , 1987, Nucleic acids research.

[162]  D. Thiele,et al.  Four-stranded nucleic acid structures 25 years later: from guanosine gels to telomer DNA. , 1990, Journal of biomolecular structure & dynamics.

[163]  P. Nielsen.  Chemical and photochemical probing of DNA complexes , 1990, Journal of molecular recognition : JMR.

[164]  R. Wells,et al.  Unusual DNA Structures , 2011, Springer New York.

[165]  E. Westhof,et al.  Unusual helical packing in crystals of DNA bearing a mutation hot spot , 1989, Nature.

[166]  C. W. Hilbers,et al.  Effects of base sequence on the loop folding in DNA hairpins. , 1989, Biochemistry.

[167]  J. Lebowitz,et al.  Through the looking glass: the discovery of supercoiled DNA. , 1990, Trends in biochemical sciences.

[168]  B. Haas,et al.  Interaction of oligoribocytidylates with T7 DNA in neutral and acid media. , 1977, Biochemistry.

[169]  E. Paleček,et al.  Probing of DNA polymorphic structure in the cell with osmium tetroxide. , 1988, Biochemical and biophysical research communications.

[170]  D. Crothers,et al.  Equilibria and kinetics of lac repressor-operator interactions by polyacrylamide gel electrophoresis. , 1981, Nucleic acids research.

[171]  W. Herr,et al.  Nucleotide sequence of the 3' half of AKV. , 1982, Nucleic acids research.

[172]  R. Anand.  Pulsed field gel electrophoresis: a technique for fractionating large DNA molecules , 1986 .

[173]  M. Gellert,et al.  Slow cruciform transitions in palindromic DNA. , 1983, Proceedings of the National Academy of Sciences of the United States of America.

[174]  H. Buc,et al.  Correlation between the conformation of Escherichia coli −10 hexamer sequences and promoter strength: use of orthophenanthroline cuprous complex as a structural index. , 1988, The EMBO journal.

[175]  W. Hunter,et al.  Structural variation in d(CTCTAGAG). Implications for protein-DNA interactions. , 1989, Biochemistry.

[176]  R. Ratliff,et al.  CD of six different conformational rearrangements of poly[d(A-G).d(C-T)] induced by low pH. , 1988, Nucleic acids research.

[177]  N. Rousseau,et al.  Chloroacetaldehyde reacts with Z-DNA. , 1988, Journal of molecular biology.

[178]  B. Moss,et al.  Molecular cloning and sequence of the concatemer junction from vaccinia virus replicative DNA. Viral nuclease cleavage sites in cruciform structures. , 1988, Journal of molecular biology.

[179]  S. Shen,et al.  Human globin ψB2 is not a globin-related sequence , 1982 .

[180]  G. Scott,et al.  The gene for rat atrial natriuretic factor. , 1985, The Journal of biological chemistry.

[181]  A. Rich,et al.  The level of Z-DNA in metabolically active, permeabilized mammalian cell nuclei is regulated by torsional strain , 1989, The Journal of cell biology.

[182]  S. Zimmerman.  The three-dimensional structure of DNA. , 1982, Annual review of biochemistry.

[183]  R. Rownd,et al.  Denaturation and Renaturation of Deoxyribonucleic Acid12 , 1963 .

[184]  D. Lilley,et al.  Localized chemical hyperreactivity in supercoiled DNA: evidence for base unpairing in sequences that induce low-salt cruciform extrusion. , 1989, Biochemistry.

[185]  A. Rich,et al.  Z-DNA and the polytene chromosome. , 1983, Cold Spring Harbor symposia on quantitative biology.

[186]  M. Laskowski,et al.  Mung bean nuclease I. II. Resistance of double stranded deoxyribonucleic acid and susceptibility of regions rich in adenosine and thymidine to enzymatic hydrolysis. , 1970, The Journal of biological chemistry.

[187]  M. Fried.  Measurement of protein‐DNA interaction parameters by electrophoresis mobility shift assay , 1989, Electrophoresis.

[188]  E. Kmiec,et al.  Homologous pairing of DNA molecules by ustilago rec1 protein is promoted by sequences of Z-DNA , 1986, Cell.

[189]  R. Wells,et al.  Unusual DNA structures in the adenovirus genome. , 1986, The Journal of biological chemistry.

[190]  D. Rabinovich,et al.  The effect of the base sequence on the fine structure of the DNA double helix. , 1986, Progress in biophysics and molecular biology.

[191]  J. Dubochet,et al.  Direct visualization of supercoiled DNA molecules in solution. , 1990, The EMBO journal.

[192]  E Westhof,et al.  Water: an integral part of nucleic acid structure. , 1988, Annual review of biophysics and biophysical chemistry.

[193]  W. Hillen,et al.  Tet repressor-tet operator contacts probed by operator DNA-modification interference studies. , 1988, Journal of molecular biology.

[194]  M. Lipsett.  COMPLEX FORMATION BETWEEN POLYCYTIDYLIC ACID AND GUANINE OLIGONUCLEOTIDES. , 1964, The Journal of biological chemistry.

[195]  E. Ohtsuka,et al.  Structure- and sequence-specificity of ozone degradation of supercoiled plasmid DNA. , 1986, Nucleic acids research.

[196]  W. Gilbert,et al.  Formation of parallel four-stranded complexes by guanine-rich motifs in DNA and its implications for meiosis , 1988, Nature.

[197]  P. Doty,et al.  STRAND SEPARATION AND SPECIFIC RECOMBINATION IN DEOXYRIBONUCLEIC ACIDS: PHYSICAL CHEMICAL STUDIES. , 1960, Proceedings of the National Academy of Sciences of the United States of America.

[198]  E. Paleček,et al.  Probing of DNA structure with osmium tetroxide. Effect of ligands. , 1989, Biophysical chemistry.

[199]  M. Behe.  The DNA sequence of the human beta-globin region is strongly biased in favor of long strings of contiguous purine or pyrimidine residues. , 1987, Biochemistry.

[200]  J. Greve,et al.  Studying single living cells and chromosomes by confocal Raman microspectroscopy , 1990, Nature.

[201]  R. Wells,et al.  B-Z DNA junctions contain few, if any, nonpaired bases at physiological superhelical densities. , 1985, Journal of Biological Chemistry.

[202]  R. Wells,et al.  Multiple non-B-DNA conformations of polypurine.polypyrimidine sequences in plasmids. , 1990, Biochemistry.

[203]  Y. Kohwi,et al.  Torsional stress stabilizes extended base unpairing in suppressor sites flanking immunoglobulin heavy chain enhancer. , 1990, Biochemistry.

[204]  D. Patel,et al.  NMR studies of DNA (R+)n.(Y-)n.(Y+)n triple helices in solution: imino and amino proton markers of T.A.T and C.G.C+ base-triple formation. , 1989, Biochemistry.

[205]  E. Taillandier,et al.  Right- and left-handed helixes of poly[d(A-T)].poly[d(A-T)] investigated by infrared spectroscopy. , 1986, Biochemistry.

[206]  A. C. Felici,et al.  Molecular structure of DNA by scanning tunneling microscopy. , 1989, Science.

[207]  D. Kowalski,et al.  Altered DNA conformations detected by mung bean nuclease occur in promoter and terminator regions of supercoiled pBR322 DNA. , 1985, Nucleic acids research.

[208]  K. Klenin,et al.  Computer simulation of DNA supercoiling. , 1991, Journal of molecular biology.

[209]  J. Chaires,et al.  A premelting conformational transition in poly(dA)-Poly(dT) coupled to daunomycin binding. , 1989, Biochemistry.

[210]  J. Klysik,et al.  Dam methyltransferase sites located within the loop region of the oligopurine-oligopyrimidine sequences capable of forming H-DNA are undermethylated in vivo. , 1990, Nucleic acids research.

[211]  J. Van De Sande,et al.  Length-dependent formation of parallel-stranded DNA in alternating AT segments. , 1990, Biochemistry.

[212]  J. Marmur,et al.  STRAND SEPARATION AND SPECIFIC RECOMBINATION IN DEOXYRIBONUCLEIC ACIDS: BIOLOGICAL STUDIES. , 1960, Proceedings of the National Academy of Sciences of the United States of America.

[213]  J. Feigon,et al.  Formation of a stable triplex from a single DNA strand. , 1990 .

[214]  W. Guschlbauer,et al.  Physicochemical properties of nucleosides 3. Gel formation by 8‐bromoguanosine , 1969, FEBS letters.

[215]  Aaron Klug,et al.  Telomeric DNA dimerizes by formation of guanine tetrads between hairpin loops , 1989, Nature.

[216]  M. Beltrame,et al.  Specific recognition of cruciform DNA by nuclear protein HMG1. , 1989, Science.

[217]  T. Jovin,et al.  Energetics of the B-Z DNA Transition , 1987 .

[218]  P. Serwer,et al.  Atypical sieving of open circular DNA during pulsed field agarose gel electrophoresis. , 1989, Biochemistry.

[219]  J. Van De Sande,et al.  Parallel stranded DNA. , 1988, Science.

[220]  D. Lilley.  In vivo consequences of plasmid topology , 1981, Nature.

[221]  J. Barton,et al.  Metals and DNA: molecular left-handed complements , 1986, Science.

[222]  J. A. Subirana,et al.  The complex of poly(dG).poly(dC) with arginine: stabilization of the B form and transition to multistranded structures. , 1987, Journal of biomolecular structure & dynamics.

[223]  J. Wang,et al.  On the sequence determinants and flexibility of the kinetoplast DNA fragment with abnormal gel electrophoretic mobilities. , 1985, Journal of molecular biology.

[224]  P. Chambon,et al.  Folding of the DNA double helix in chromatin-like structures from simian virus 40. , 1975, Proceedings of the National Academy of Sciences of the United States of America.

[225]  H R Drew,et al.  Structure of a B-DNA dodecamer: conformation and dynamics. , 1981, Proceedings of the National Academy of Sciences of the United States of America.

[226]  L. Lerman,et al.  Sequence-determined DNA separations. , 1984, Annual review of biophysics and bioengineering.

[227]  S. Mirkin,et al.  An unusual DMA structure detected in a telomeric sequence under superhelical stress and at low pH , 1989, Nature.

[228]  D. Lilley.  The kinetic properties of cruciform extrusion are determined by DNA base-sequence. , 1985, Nucleic acids research.

[229]  W. Gilbert,et al.  Sequencing end-labeled DNA with base-specific chemical cleavages. , 1980, Methods in enzymology.

[230]  A. Nordheim,et al.  Diethyl pyrocarbonate: a chemical probe for DNA cruciforms. , 1986, Nucleic acids research.

[231]  R. Umek,et al.  The ease of DNA unwinding as a determinant of initiation at yeast replication origins , 1988, Cell.

[232]  D. Schwartz,et al.  Separation of yeast chromosome-sized DNAs by pulsed field gradient gel electrophoresis , 1984, Cell.

[233]  W. Lutz,et al.  Sensitivity of DNA and nucleotides to oxidation by permanganate and hydrogen peroxide. , 1987, Archives of toxicology. Supplement. = Archiv fur Toxikologie. Supplement.

[234]  Leroy F. Liu,et al.  Transcription generates positively and negatively supercoiled domains in the template , 1988, Cell.

[235]  R Nussinov,et al.  Sequence signals in eukaryotic upstream regions. , 1986, Biochimica et biophysica acta.

[236]  W. Hunter,et al.  Oligonucleotide structure: a decade of results from single crystal X-ray diffraction studies , 1989, Quarterly Reviews of Biophysics.

[237]  D. Lilley,et al.  Highly selective chemical modification of cruciform loops by diethyl pyrocarbonate. , 1986, Nucleic acids research.

[238]  C. Calladine,et al.  1 New Approaches to DNA in the Crystal and in Solution , 1990 .

[239]  J. Boyle,et al.  Immunoassay of carcinogen-modified DNA. , 1984, Progress in nucleic acid research and molecular biology.

[240]  E. Paleček.  Oscillographic polarography of deoxyribonucleic acid degradation products. , 1961, Biochimica et biophysica acta.

[241]  A Klug,et al.  Sequence-dependent variation in the conformation of DNA. , 1981, Journal of molecular biology.

[242]  B. Wold,et al.  Inhibition of DNA binding proteins by oligonucleotide-directed triple helix formation. , 1989, Science.

[243]  B. Frantz,et al.  The MerR heavy metal receptor mediates positive activation in a topologically novel transcription complex , 1989, Cell.

[244]  J. Dahlberg,et al.  Topology and formation of triple-stranded H-DNA. , 1989, Science.

[245]  A. M. Poverenny,et al.  Immunochemical approaches to DNA structure investigation--I. Immunochemical identification of the product of cytosine modification with bisulphite and O-methylhydroxylamine mixture. , 1979, Molecular immunology.

[246]  D. Lilley,et al.  The Extrusion of Cruciform Structures in Supercoiled DNA — Kinetics and Mechanisms , 1987 .

[247]  C. Marck,et al.  Poly(dG).poly(dC) at neutral and alkaline pH: the formation of triple stranded poly(dG).poly(dG).poly(dC). , 1978, Nucleic acids research.

[248]  D. Pulleyblank,et al.  Facile transition of poly[d(TG)·d(CA)] into a left-handed helix in physiological conditions , 1983, Nature.

[249]  S. Diekmann.  DNA methylation can enhance or induce DNA curvature. , 1987, The EMBO journal.

[250]  B. Johnston,et al.  The S1-sensitive form of d(C-T)n.d(A-G)n: chemical evidence for a three-stranded structure in plasmids. , 1988, Science.

[251]  H. Mizusawa,et al.  Unwinding of double-stranded DNA helix by dehydration. , 1981, Proceedings of the National Academy of Sciences of the United States of America.

[252]  Z. Wang,et al.  B----A transitions within a 5 S ribosomal RNA gene are highly sequence-specific. , 1989, The Journal of biological chemistry.

[253]  E. Major,et al.  Unusual DNA structure in the regulatory region of the human papovavirus JC virus , 1988, Journal of virology.

[254]  S. Diekmann,et al.  The influence of exocyclic substituents of purine bases on DNA curvature. , 1987, Proceedings of the National Academy of Sciences of the United States of America.

[255]  V. P. Chuprina.  Anomalous structure and properties of poly (dA).poly(dT). Computer simulation of the polynucleotide structure with the spine of hydration in the minor groove , 1987, Nucleic Acids Res..

[256]  T. Beerman,et al.  Further analysis of the altered secondary structure of superhelical DNA. Sensitivity to methylmercuric hydroxide a chemical probe for unpaired bases. , 1973, Journal of molecular biology.

[257]  Yolk proteins from nematodes, chickens, and frogs bind strongly and preferentially to left-handed Z-DNA. , 1988, The Journal of biological chemistry.

[258]  R. Shafer,et al.  Structural analysis of the (dA)10.2(dT)10 triple helix. , 1990, Proceedings of the National Academy of Sciences of the United States of America.

[259]  J. Portugal.  Footprinting analysis of sequence-specific DNA-drug interactions. , 1989, Chemico-biological interactions.

[260]  D. Lilley,et al.  Single base mismatches in DNA. Long- and short-range structure probed by analysis of axis trajectory and local chemical reactivity. , 1989, Journal of molecular biology.

[261]  M. M. Garner,et al.  A gel electrophoresis method for quantifying the binding of proteins to specific DNA regions: application to components of the Escherichia coli lactose operon regulatory system , 1981, Nucleic Acids Res..

[262]  H. Blöcker,et al.  Crystal structure analysis of an A-DNA fragment at 1.8 A resolution: d(GCCCGGGC). , 1987, Nucleic acids research.

[263]  T. Thomas,et al.  A left-handed (Z) conformation of poly(dA-dC).poly(dG-dT) induced by polyamines. , 1986, Nucleic acids research.

[264]  D. Lilley.  Structural perturbation in supercoiled DNA: hypersensitivity to modification by a single-strand-selective chemical reagent conferred by inverted repeat sequences. , 1983, Nucleic acids research.

[265]  A. A. Chernyi,et al.  Parallel stranded DNA with AT base pairing , 1989, FEBS letters.

[266]  H. Buc,et al.  Fine mapping of DNA single-stranded regions using base-specific chemical probes: study of an open complex formed between RNA polymerase and the lac UV5 promoter. , 1989, Biochemistry.

[267]  Lawley Pd.  Effects of Some Chemical Mutagens and Carcinogens on Nucleic Acids , 1966 .

[268]  N. Pattabiraman.  Can the double helix be parallel? , 1986, Biopolymers.

[269]  D. Wemmer,et al.  Duplex-hairpin transitions in DNA: NMR studies on CGCGTATACGCG. , 1985, Nucleic acids research.

[270]  A. Nordheim,et al.  DNA supercoiling changes the spacing requirement of two lac operators for DNA loop formation with lac repressor. , 1988, The EMBO journal.

[271]  K. Rippe,et al.  Parallel-stranded duplex DNA. , 1988, Methods in enzymology.

[272]  Dipankar Sen,et al.  A sodium-potassium switch in the formation of four-stranded G4-DNA , 1990, Nature.

[273]  B. Stollar,et al.  Dependence of Z-DNA antibody binding to polytene chromosomes on acid fixation and DNA torsional strain , 1983, Nature.

[274]  G. Cohen,et al.  X-ray fiber diffraction and model-building study of polyguanylic acid and polyinosinic acid. , 1975, Journal of molecular biology.

[275]  H R Drew,et al.  Influence of the sequence-dependent flexure of DNA on transcription in E. coli. , 1989, Nucleic acids research.

[276]  G. Church,et al.  Genomic sequencing. , 1993, Methods in molecular biology.

[277]  M. Frank-Kamenetskii,et al.  Evidence of cruciform structures in superhelical DNA provided by two‐dimensional gel electrophoresis , 1983, FEBS letters.

[278]  M. Leng,et al.  Conformation of DNA modified at a d(GG) or a d(AG) site by the antitumor drug cis-diamminedichloroplatinum(II). , 1989, Biochemistry.

[279]  J. Šponar,et al.  Flexibility of A.T pairs in left-handed DNA helices. , 1990, Journal of biomolecular structure & dynamics.

[280]  T. Jovin,et al.  Immunological detection of left‐handed Z DNA in isolated polytene chromosomes. Effects of ionic strength, pH, temperature and topological stress. , 1984, The EMBO journal.

[281]  E. Hamori,et al.  Generation of left-handed Z-DNA in solution and visualization in polytene chromosomes by immunofluorescence. , 1983, Cold Spring Harbor symposia on quantitative biology.

[282]  T. Steitz,et al.  Crystal lattice packing is important in determining the bend of a DNA dodecamer containing an adenine tract. , 1989, Proceedings of the National Academy of Sciences of the United States of America.

[283]  A. Rich,et al.  Crystal structure of Z-DNA without an alternating purine-pyrimidine sequence. , 1985, Proceedings of the National Academy of Sciences of the United States of America.

[284]  M. Ellison,et al.  In vivo assessment of the Z-DNA-forming potential of d(CA.GT)n and d(CG.GC)n sequences cloned into SV40 minichromosomes. , 1989, Journal of molecular biology.

[285]  C. Wu,et al.  Promoter search by Escherichia coli RNA polymerase on a circular DNA template. , 1987, The Journal of biological chemistry.

[286]  E. Paleček,et al.  Salt-induced conformational changes of poly(dA-dT). , 1980, Nucleic acids research.

[287]  T. Jovin.  Parallel-Stranded DNA with trans-Crick-Watson Base Pairs , 1991 .

[288]  M. Frank-Kamenetskii.  The turn of the quadruplex? , 1989, Nature.

[289]  W. Bauer,et al.  Structure and reactions of closed duplex DNA. , 1978, Annual review of biophysics and bioengineering.

[290]  P. Chan,et al.  Identification of a long stretch of homopurine.homopyrimidine sequence in a cluster of retroposons in the human genome. , 1990, Journal of molecular biology.

[291]  W. Gilbert,et al.  Chemical probes for higher-order structure in RNA. , 1980, Proceedings of the National Academy of Sciences of the United States of America.

[292]  A. Rich,et al.  Z-DNA-binding proteins in Escherichia coli purification, generation of monoclonal antibodies and gene isolation. , 1988, Journal of molecular biology.

[293]  D. Lilley,et al.  The inverted repeat as a recognizable structural feature in supercoiled DNA molecules. , 1980, Proceedings of the National Academy of Sciences of the United States of America.

[294]  S. Diekmann,et al.  DNA curvature in native and modified EcoRI recognition sites and possible influence upon the endonuclease cleavage reaction. , 1988, Journal of molecular biology.

[295]  W. Chang,et al.  Intracellular oxidative cleavage of DNA in Escherichia coli by the copper-1,10-phenanthroline complex. , 1989, Free radical research communications.

[296]  E. Paleček,et al.  Osmium tetroxide recognized structural distortions at junctions between right- and left-handed DNA in a bacterial cell. , 1987, General physiology and biophysics.

[297]  E. Taillandier,et al.  Raman spectroscopy of Z-form poly[d(A-T)].poly[d(A-T)]. , 1988, Biochemistry.

[298]  S. Brahmachari,et al.  Supercoil-induced unusual DNA structures as transcriptional block. , 1990, Nucleic acids research.

[299]  V. P. Chuprina,et al.  Electrophoretic behavior of d(GGAAAAAAGG)n, d(CCAAAAAACC)n, and (CCAAAAAAGG)n and implications for a DNA bending model. , 1990, Nucleic acids research.

[300]  D. Lilley.  DNA: Sequence, Structure and Supercoiling , 1984 .

[301]  E. Paleček,et al.  Determination of nanogram quantities of osmium-labeled nucleic acids by stripping (inverse) voltammetry. , 1983, Analytical biochemistry.

[302]  C. L. Jackson,et al.  The human apolipoprotein C-II gene sequence contains a novel chromosome 19-specific minisatellite in its third intron. , 1987, Journal of Biological Chemistry.

[303]  Alfred Nordheim,et al.  THE CHEMISTRY AND BIOLOGY OF LEFT-HANDED Z-DNA , 1984 .

[304]  M. Bianchi,et al.  Interaction of a protein from rat liver nuclei with cruciform DNA. , 1988, The EMBO journal.

[305]  H. Hamada,et al.  Characterization of genomic poly(dT-dG).poly(dC-dA) sequences: structure, organization, and conformation , 1984, Molecular and cellular biology.

[306]  Jacques H. van Boom,et al.  Molecular structure of a left-handed double helical DNA fragment at atomic resolution , 1979, Nature.

[307]  J. K. Walker,et al.  DNA secondary structures: helices, wrinkles, and junctions. , 1983, Cold Spring Harbor symposia on quantitative biology.

[308]  Wang Jc,et al.  DNA topoisomerases: nature's solution to the topological ramifications of the double-helix structure of DNA. , 1985 .

[309]  G. Chu.  Pulsed field electrophoresis in contour‐clamped homogeneous electric fields for the resolution of DNA by size or topology , 1989, Electrophoresis.

[310]  James C. Wang,et al.  Use of light for footprinting DNA in vivo , 1984, Nature.

[311]  P. Hagerman.  Pyrimidine 5-methyl groups influence the magnitude of DNA curvature. , 1990, Biochemistry.

[312]  Alfred Nordheim,et al.  Antibodies to left-handed Z-DNA bind to interband regions of Drosophila polytene chromosomes , 1981, Nature.

[313]  R. D. Campbell,et al.  Chemical reactivity of matched cytosine and thymine bases near mismatched and unmatched bases in a heteroduplex between DNA strands with multiple differences. , 1989, Nucleic acids research.

[314]  S. Arnott,et al.  Structures for the polynucleotide complexes poly(dA) with poly (dT) and poly(dT) with poly(dA) with poly (dT). , 1974, Journal of molecular biology.

[315]  M. Guéron,et al.  Evidence from base-pair kinetics for two types of adenine tract structures in solution: their relation to DNA curvature. , 1988, Biochemistry.

[316]  G. Steger,et al.  Analysis of RNA structures by temperature-gradient gel electrophoresis: viroid replication and processing. , 1988, Gene.

[317]  M. Linial,et al.  A unique endonuclease from Crithidia fasciculata which recognizes a bend in the DNA helix. Specificity of the cleavage reaction. , 1988, The Journal of biological chemistry.

[318]  A. Worcel,et al.  On the structure of the folded chromosome of Escherichia coli. , 1972, Journal of molecular biology.

[319]  T. Ando.  A nuclease specific for heat-denatured DNA in isolated from a product of Aspergillus oryzae. , 1966, Biochimica et biophysica acta.

[320]  G. Zon,et al.  Comparative inhibition of chloramphenicol acetyltransferase gene expression by antisense oligonucleotide analogues having alkyl phosphotriester, methylphosphonate and phosphorothioate linkages. , 1987, Nucleic acids research.

[321]  D. Pulleyblank,et al.  Transition of a cloned d(AT)n-d(AT)n tract to a cruciform in vivo. , 1985, Nucleic acids research.

[322]  D. Lilley,et al.  Helix stability and the mechanism of cruciform extrusion in supercoiled DNA molecules. , 1988, Nucleic acids research.

[323]  A. Gunasekera,et al.  Conversion of a helix-turn-helix motif sequence-specific DNA binding protein into a site-specific DNA cleavage agent. , 1990, Proceedings of the National Academy of Sciences of the United States of America.

[324]  D. Lilley,et al.  Base methylation and local DNA helix stability. Effect on the kinetics of cruciform extrusion. , 1989, Journal of molecular biology.

[325]  R. Umek,et al.  Yeast regulatory sequences preferentially adopt a non-B conformation in supercoiled DNA. , 1987, Nucleic acids research.

[326]  D. Lilley,et al.  The contrasting structures of mismatched DNA sequences containing looped-out bases (bulges) and multiple mismatches (bubbles). , 1989, Nucleic acids research.

[327]  J. Langowski,et al.  Dynamics of superhelical DNA studied by photon correlation spectroscopy. , 1986, Biophysical chemistry.

[328]  J. Gralla,et al.  High-resolution analysis of lac transcription complexes inside cells. , 1986, Biochemistry.

[329]  B. Hingerty,et al.  AAF linked to the guanine amino group: a B-Z junction. , 1983, Nucleic acids research.

[330]  J. S. Lee,et al.  Complexes formed by (pyrimidine)n . (purine)n DNAs on lowering the pH are three-stranded. , 1979, Nucleic acids research.

[331]  J. Platt.  POSSIBLE SEPARATION OF INTERTWINED NUCLEIC ACID CHAINS BY TRANSFER-TWIST. , 1955, Proceedings of the National Academy of Sciences of the United States of America.

[332]  J. Francois,et al.  Sequence-targeted cleavage of single- and double-stranded DNA by oligothymidylates covalently linked to 1,10-phenanthroline. , 1989, The Journal of biological chemistry.

[333]  J. S. Lee,et al.  Triplex DNA in plasmids and chromosomes. , 1989, Gene.

[334]  R. Wells,et al.  Tetracycline promoter mutations decrease non-B DNA structural transitions, negative linking differences and deletions in recombinant plasmids in Escherichia coli. , 1989, Journal of molecular biology.

[335]  R. C. Hammond,et al.  New findings in methane-utilizing bacteria highlight their importance in the biosphere and their commercial potential , 1980, Nature.

[336]  D. Lilley,et al.  The three‐way DNA junction is a Y‐shaped molecule in which there is no helix‐helix stacking. , 1990, The EMBO journal.

[337]  S. West,et al.  Specific binding of cruciform DNA structures by a protein from human extracts. , 1988, Nucleic acids research.

[338]  J. Griffith,et al.  Visualization of the bent helix in kinetoplast DNA by electron microscopy , 1986, Cell.

[339]  A. Rich,et al.  A bifurcated hydrogen-bonded conformation in the d(A.T) base pairs of the DNA dodecamer d(CGCAAATTTGCG) and its complex with distamycin. , 1987, Proceedings of the National Academy of Sciences of the United States of America.

[340]  J. S. Lee,et al.  A monoclonal antibody to triplex DNA binds to eucaryotic chromosomes. , 1987, Nucleic acids research.

[341]  D. Santi,et al.  Migration properties of circular DNAs using orthogonal‐field‐alternation gel electrophoresis , 1989, Electrophoresis.

[342]  F. Jelen,et al.  Polarography of circular DNAs , 1981 .

[343]  R. Sederoff,et al.  Distribution of polypyrimidine . polypurine segments in DNA from diverse organisms. , 1979, European journal of biochemistry.

[344]  B. Singer,et al.  Chloroacetaldehyde-treated ribo- and deoxyribopolynucleotides. 2. Errors in transcription by different polymerases resulting from ethenocytosine and its hydrated intermediate. , 1982, Biochemistry.

[345]  J E Hearst,et al.  Psoralens as photoactive probes of nucleic acid structure and function: organic chemistry, photochemistry, and biochemistry. , 1985, Annual review of biochemistry.

[346]  R. Sarma,et al.  Effect of the methyl group on DNA bending and curvature: structure of d(GA4U4C)2 in solution. , 1990, Biochemistry.

[347]  E. Trifonov,et al.  The pitch of chromatin DNA is reflected in its nucleotide sequence. , 1980, Proceedings of the National Academy of Sciences of the United States of America.

[348]  J. Dixon,et al.  Z-DNA in the rat somatostatin gene. , 1985, The Journal of biological chemistry.

[349]  D. Lilley,et al.  The stereochemistry of a four-way DNA junction: a theoretical study. , 1990, Nucleic acids research.

[350]  W. Saenger.  Structure and dynamics of water surrounding biomolecules. , 1987, Annual review of biophysics and biophysical chemistry.

[351]  H. Krause,et al.  Supercoiling and integration host factor change the DNA conformation and alter the flow of convergent transcription in phage Mu. , 1989, The Journal of biological chemistry.

[352]  James H. White,et al.  The helical repeat of nucleosome-wrapped DNA , 1989, Cell.

[353]  L. J. Peck,et al.  DNA supercoiling and its effects on DNA structure and function. , 1983, Cold Spring Harbor symposia on quantitative biology.

[354]  J. Van De Sande,et al.  Relative stability of parallel- and antiparallel-stranded duplex DNA. , 1988, Biochemistry.

[355]  T M Jovin,et al.  Salt-induced co-operative conformational change of a synthetic DNA: equilibrium and kinetic studies with poly (dG-dC). , 1972, Journal of molecular biology.

[356]  P. Hagerman,et al.  Gel electrophoretic analysis of the geometry of a DNA four-way junction. , 1987, Journal of molecular biology.

[357]  C. Giovannangeli,et al.  Sequence-specific artificial photo-induced endonucleases based on triple helix-forming oligonucleotides , 1990, Nature.

[358]  N. Seeman,et al.  NMR analysis of DNA junctions: imino proton NMR studies of individual arms and intact junction. , 1985, Biochemistry.

[359]  A. Rich,et al.  Identification of homologous pairing and strand-exchange activity from a human tumor cell line based on Z-DNA affinity chromatography. , 1988, Proceedings of the National Academy of Sciences of the United States of America.

[360]  E. Paleček,et al.  Osmium tetroxide, N,N,N',N'‐tetramethylethylendiamine A new probe of DNA structure in the cell , 1990, FEBS letters.

[361]  T. Hsieh,et al.  Thermodynamic properties of superhelical DNAs. , 1975, Biochemistry.

[362]  F. Wu,et al.  Chemical modification of Escherichia coli RNA polymerase by diethyl pyrocarbonate: evidence of histidine requirement for enzyme activity and intrinsic zinc binding. , 1986, Biochemistry.

[363]  W. Fitch,et al.  Evolutionary selection for perfect hairpin structures in viral DNAs , 1982, Nature.

[364]  A. Rich,et al.  Z-DNA forms without an alternating purine-pyrimidine sequence in solution. , 1985, Science.

[365]  R. Sinden,et al.  Cruciform transitions in DNA. , 1984, The Journal of biological chemistry.

[366]  T. Tullius,et al.  Physical studies of protein-DNA complexes by footprinting. , 1989, Annual review of biophysics and biophysical chemistry.

[367]  D. Thiele,et al.  The structures of polyinosinic acid , 1973, Biophysik.

[368]  P. Dervan,et al.  Sequence-specific cleavage of double helical DNA by triple helix formation. , 1987, Science.

[369]  R. Wells,et al.  Further studies on telestability in DNA. The synthesis and characterization of the duplex block polymers d(C20A10) - d(T10G20) and d(C20A15) - d(T15G20). , 1975, The Journal of biological chemistry.

[370]  K. Drlica,et al.  DNA supercoiling and prokaryotic transcription , 1989, Cell.

[371]  Supercoil‐stabilized left‐handed DNA in the plasmid (dA‐dT)16 insert formed in the presence of Ni2+ , 1989, FEBS letters.

[372]  C. C. Hardin,et al.  Conformational analysis of d(C3G3), a B-family duplex in solution. , 1989, Biochemistry.

[373]  J. T. Yang,et al.  Optical activity of 5'-guanylic acid gel. , 1965, Biochemical and biophysical research communications.

[374]  V. Sasisekharan,et al.  Interaction of synthetic analogues of distamycin and netropsin with nucleic acids. Does curvature of ligand play a role in distamycin-DNA interactions? , 1988, Biochemistry.

[375]  R. Wells,et al.  The role of sequence in the stabilization of left-handed DNA helices in vitro and in vivo. , 1988, Biochimica et biophysica acta.

[376]  R. Wells,et al.  Intramolecular DNA triplexes in supercoiled plasmids. I. Effect of loop size on formation and stability. , 1989, The Journal of biological chemistry.

[377]  N R Cozzarelli,et al.  Structure of plectonemically supercoiled DNA. , 1990, Journal of molecular biology.

[378]  Alfred Nordheim,et al.  Negatively supercoiled plasmids contain left-handed Z-DNA segments as detected by specific antibody binding , 1982, Cell.

[379]  T. Cech,et al.  Monovalent cation-induced structure of telomeric DNA: The G-quartet model , 1989, Cell.

[380]  D. Lilley.  Hairpin-loops in supercoiled DNA , 1982 .

[381]  Characteristics of Z-DNA helices formed by imperfect (purine-pyrimidine) sequences in plasmids. , 1988, The Journal of biological chemistry.

[382]  J. Axelrod,et al.  An improved method for photofootprinting yeast genes in vivo using Taq polymerase. , 1989, Nucleic acids research.

[383]  W. Krzyzosiak,et al.  The reaction of adenine and cytosine residues in tRNA with chloroacetaldehyde. , 1981, Nucleic acids research.

[384]  R. Wells,et al.  Intramolecular DNA triplexes in supercoiled plasmids. II. Effect of base composition and noncentral interruptions on formation and stability. , 1989, The Journal of biological chemistry.

[385]  M. Leng,et al.  Distortions induced in double-stranded oligonucleotides by the binding of cis- or trans-diammine-dichloroplatinum(II) to the d(GTG) sequence. , 1990, Nucleic acids research.

[386]  T. Pinnavaia,et al.  Letter: Self-assembled 5'-guanosine monophosphate. Nuclear magnetic resonance evidence for a regular, ordered structure and slow chemical exchange. , 1975, Journal of the American Chemical Society.

[387]  V. Anshelevich,et al.  Statistical mechanics of supercoils and the torsional stiffness of the DNA double helix , 1979, Nature.

[388]  R. Sheardy.  Preliminary spectroscopic characterization of a synthetic DNA oligomer containing a B-Z junction at high salt. , 1988, Nucleic acids research.

[389]  A. Courey,et al.  Cruciform formation in a negatively supercoiled DNA may be kinetically forbidden under physiological conditions , 1983, Cell.

[390]  L. J. Peck,et al.  Transcriptional block caused by a negative supercoiling induced structural change in an alternating CG sequence , 1985, Cell.

[391]  R. Wells,et al.  Effect of length, supercoiling, and pH on intramolecular triplex formation. Multiple conformers at pur.pyr mirror repeats. , 1990, The Journal of biological chemistry.

[392]  S. Diekmann.  The migration anomaly of DNA fragments in polyacrylamide gels allows the detection of small sequence‐specific DNA structure variations , 1989, Electrophoresis.

[393]  J. Brahms,et al.  Structural changes in positively and negatively supercoiled DNA. , 1989, European journal of biochemistry.

[394]  R. Wells,et al.  Cytosine methylation enhances Z-DNA formation in vivo , 1990, Journal of bacteriology.

[395]  D. Lilley,et al.  The anomalous gel migration of a stable cruciform: temperature and salt dependence, and some comparisons with curved DNA. , 1987, Nucleic acids research.

[396]  B. Müller-Hill,et al.  Insertion of d(pCpG)n.d(pCpG)n into the lacZ gene of Escherichia coli inhibits expression of beta-galactosidase in vivo. , 1988, Journal of molecular biology.

[397]  S. Harvey,et al.  Molecular mechanics model of supercoiled DNA. , 1989, Journal of molecular biology.

[398]  D. Davies,et al.  Helix formation by guanylic acid. , 1962, Proceedings of the National Academy of Sciences of the United States of America.

[399]  T. Cech.  G-strings at chromosome ends , 1988, Nature.

[400]  M. Rougée,et al.  Interactions of the dimethyldiazaperopyrenium dication with nucleic acids. 2. Binding to double-stranded polynucleotides. , 1989, Biochemistry.

[401]  W. Bauer,et al.  The interaction of closed circular DNA with intercalative dyes. I. The superhelix density of SV40 DNA in the presence and absence of dye. , 1970, Journal of molecular biology.

[402]  Y. Nishimura,et al.  Raman spectrum of a closed-circular DNA. , 1985, Biopolymers.

[403]  D. Lilley,et al.  The structure of the holliday junction, and its resolution , 1988, Cell.

[404]  M. Linial,et al.  The sequence-directed bent structure in kinetoplast DNA is recognized by an enzyme from Crithidia fasciculata. , 1987, The Journal of biological chemistry.

[405]  L. Kedes,et al.  Human homologs of TU transposon sequences: polypurine/polypyrimidine sequence elements that can alter DNA conformation in vitro and in vivo , 1986, Molecular and cellular biology.

[406]  S. Pochet,et al.  IR and UV studies on stability and conformations of short DNA duplexes containing a no-base residue: coexistence of B and Z conformations. , 1988, Journal of biomolecular structure & dynamics.

[407]  M. Gellert,et al.  Cruciform structures in palindromic DNA are favored by DNA supercoiling. , 1982, Journal of molecular biology.

[408]  F. Pohl.  Hysteretic behaviour of a Z-DNA-antibody complex. , 1987, Biophysical Chemistry.

[409]  E. Paleček,et al.  Protonated triplex DNA in E. coli cells as detected by chemical probing , 1990, FEBS letters.

[410]  M. Wilkins.  Physical studies of the molecular structure of deoxyribose nucleic acid and nucleoprotein. , 1956, Cold Spring Harbor symposia on quantitative biology.

[411]  M. Schroeder.  Osmium tetraoxide cis hydroxylation of unsaturated substrates , 1980 .

[412]  A. Rich,et al.  (dC‐dA)n.(dG‐dT)n sequences have evolutionarily conserved chromosomal locations in Drosophila with implications for roles in chromosome structure and function. , 1987, The EMBO journal.

[413]  J. Campbell.  Eukaryotic DNA replication. , 1986, Annual review of biochemistry.

[414]  J. Torbet,et al.  Supercoiled DNA is interwound in liquid crystalline solutions. , 1989, The EMBO journal.

[415]  E. Paleček,et al.  Modification of ColE1 DNA with osmium tetroxide generates positively supercoiled molecules. , 1985, Journal of biomolecular structure & dynamics.

[416]  J. M. Gale,et al.  Photofootprint of nucleosome core DNA in intact chromatin having different structural states. , 1988, Journal of molecular biology.

[417]  R Balhorn,et al.  Direct observation of native DNA structures with the scanning tunneling microscope. , 1989, Science.

[418]  J. Barton,et al.  Tris(tetramethylphenanthroline)ruthenium(II): a chiral probe that cleaves A-DNA conformations. , 1988, Proceedings of the National Academy of Sciences of the United States of America.

[419]  R. Wells,et al.  Non-B right-handed DNA conformations of homopurine.homopyrimidine sequences in the murine immunoglobulin C alpha switch region. , 1988, The Journal of biological chemistry.

[420]  S. Diekmann,et al.  Definitions and nomenclature of nucleic acid structure parameters. , 1989, The EMBO journal.

[421]  F. Pohl,et al.  Searching for potential Z-DNA in genomic Escherichia coli DNA. , 1987, Journal of molecular biology.

[422]  E. Paleček,et al.  Osmium-induced alteration in DNA structure. , 1984, General physiology and biophysics.

[423]  S. Strobel,et al.  Site-specific cleavage of a yeast chromosome by oligonucleotide-directed triple-helix formation. , 1990, Science.

[424]  G. Manzini,et al.  Spectroscopic and calorimetric investigation on the DNA triplex formed by d(CTCTTCTTTCTTTTCTTTCTTCTC) and d(GAGAAGAAAGA) at acidic pH. , 1990, Nucleic acids research.

[425]  J. Langowski.  Salt effects on internal motions of superhelical and linear pUC8 DNA. Dynamic light scattering studies. , 1987, Biophysical chemistry.

[426]  D. Lilley,et al.  (A-T)n tracts embedded in random sequence DNA--formation of a structure which is chemically reactive and torsionally deformable. , 1986, Nucleic acids research.

[427]  R. D. Campbell,et al.  Reactivity of cytosine and thymine in single-base-pair mismatches with hydroxylamine and osmium tetroxide and its application to the study of mutations. , 1988, Proceedings of the National Academy of Sciences of the United States of America.

[428]  C. Benham,et al.  Environmental influences on DNA superhelicity. The effect of ionic strength on superhelix conformation in solution. , 1987, Journal of molecular biology.

[429]  A. Nordheim.  Z-DNA: Exploring the Biological Significance , 1987 .

[430]  E. Paleček,et al.  Electrochemical analysis of polynucleotides , 1981 .

[431]  R. Watson,et al.  The twisted circular form of polyoma viral DNA. , 1965, Proceedings of the National Academy of Sciences of the United States of America.

[432]  D. Lilley,et al.  Resolution of model Holliday junctions by yeast endonuclease: effect of DNA structure and sequence. , 1989, The EMBO journal.

[433]  P. Doty,et al.  The effect of temperature on the cross-linking of deoxyribonucleic acid strands by ultraviolet radiation , 1962 .

[434]  K. Rippe,et al.  Reactivity of parallel-stranded DNA to chemical modification reagents. , 1990, Biochemistry.

[435]  E. Paleček,et al.  Site-specific chemical modification of B-Z junctions in supercoiled DNA as detected by nuclease S1 digestion, inhibition of restriction cleavage and nucleotide sequencing. , 1988, Journal of biomolecular structure & dynamics.

[436]  U. Müller,et al.  Effect of in vitro transcription on cruciform stability. , 1990, Nucleic acids research.

[437]  J. W. Wiggins,et al.  Molecular microscopy of labeled polynucleotides: stability of osmium atoms. , 1977, Journal of molecular biology.

[438]  A. Rich,et al.  Isolation of Z-DNA binding proteins from SV40 minichromosomes: evidence for binding to the viral control region , 1985, Cell.

[439]  Richard E. Dickerson,et al.  Crystal structure analysis of a complete turn of B-DNA , 1980, Nature.

[440]  R. Wells,et al.  The chemistry and biology of unusual DNA structures adopted by oligopurine · oligopyrimidine sequences , 1988, FASEB journal : official publication of the Federation of American Societies for Experimental Biology.

[441]  G. Grigg,et al.  Diethylpyrocarbonate and permanganate provide evidence for an unusual DNA conformation induced by binding of the antitumour antibiotics bleomycin and phleomycin. , 1988, Nucleic acids research.

[442]  N. Seeman,et al.  Construction and analysis of monomobile DNA junctions. , 1988, Biochemistry.

[443]  D. Lilley,et al.  Thermodynamics of the ColE1 cruciform. Comparisons between probing and topological experiments using single topoisomers. , 1984, Journal of molecular biology.

[444]  J. Šponar,et al.  A Z-like form of poly(dA-dC).poly(dC-bT) in sotation? , 1982 .

[445]  M. Leng.  DNA bending induced by covalently bound drugs. Gel electrophoresis and chemical probe studies. , 1990, Biophysical chemistry.

[446]  J. Vinograd,et al.  THE CYCLIC HELIX AND CYCLIC COIL FORMS OF POLYOMA VIRAL DNA. , 1963, Proceedings of the National Academy of Sciences of the United States of America.

[447]  W. Gilbert,et al.  Contacts between Escherichia coli RNA polymerase and an early promoter of phage T7. , 1980, Proceedings of the National Academy of Sciences of the United States of America.

[448]  C. Alonso,et al.  Z-DNA in transcriptionally active chromosomes. , 1987, Proceedings of the National Academy of Sciences of the United States of America.

[449]  H. Vogel,et al.  Perturbation of DNA hairpins containing the EcoRI recognition site by hairpin loops of varying size and composition: physical (NMR and UV) and enzymatic (EcoRI) studies. , 1990, Nucleic acids research.

[450]  R. Sheardy,et al.  Temperature-dependent CD and NMR studies on a synthetic oligonucleotide containing a B-Z junction at high salt. , 1989, Biochemistry.

[451]  Francis Crick,et al.  The double helix: a personal view , 1974, Nature.

[452]  S. A. Salisbury,et al.  DNA double helical fragment at atomic resolution , 1978, Nature.

[453]  L. Simpson,et al.  Specific cleavage of kinetoplast minicircle DNA from Leishmania tarentolae by mung bean nuclease and identification of several additional minicircle sequence classes , 1986, Nucleic Acids Res..

[454]  B. Chernov,et al.  Parallel DNA: generation of a duplex between two Drosophila sequences in vitro , 1989, FEBS letters.

[455]  S. Elgin,et al.  Drosophila nuclear proteins bind to regions of alternating C and T residues in gene promoters. , 1989, Science.

[456]  R. Wells,et al.  Stabilization of Z DNA in vivo by localized supercoiling. , 1989, Science.

[457]  C. Hélène,et al.  Sequence-targeted chemical modifications of nucleic acids by complementary oligonucleotides covalently linked to porphyrins. , 1987, Nucleic acids research.

[458]  V. P. Kumarev,et al.  Energetics of the B-H transition in supercoiled DNA carrying d(CT)x.d(AG)x and d(C)n.d(G)n inserts. , 1989, Nucleic acids research.

[459]  J. Barton,et al.  Rh(DIP)3(3+): a shape-selective metal complex which targets cruciforms. , 1988, Nucleic acids research.

[460]  A. Rich,et al.  Raman spectra of single crystals of r(GCG)d(CGC) and d(CCCCGGGG) as models for A DNA, their structure transitions in aqueous solution, and comparison with double-helical poly(dG).poly(dC). , 1986, Biochemistry.

[461]  M. Frank-Kamenetskii.  Waves of DNA supercoiling , 1989, Nature.

[462]  D. Lilley,et al.  A dominant influence of flanking sequences on a local structural transition in DNA , 1986, Cell.

[463]  M. Beer,et al.  Determination of base sequence in nucleic acids with the electron microscope. V. The thymine-specific reactions of osmium tetroxide with deoxyribonucleic acid and its components. , 1966, Biochemistry.

[464]  M. Linial,et al.  A nicking enzyme from trypanosomatids which specifically affects the topological linking of duplex DNA circles. Purification and characterization. , 1986, The Journal of biological chemistry.

[465]  A M Gronenborn,et al.  Determination of three-dimensional structures of proteins and nucleic acids in solution by nuclear magnetic resonance spectroscopy. , 1989, Critical reviews in biochemistry and molecular biology.

[466]  James H. White.  Self-Linking and the Gauss Integral in Higher Dimensions , 1969 .

[467]  A. Kinniburgh.  A cis-acting transcription element of the c-myc gene can assume an H-DNA conformation. , 1989, Nucleic acids research.

[468]  P. V. von Hippel,et al.  Laser cross-linking of nucleic acids to proteins. Methodology and first applications to the phage T4 DNA replication system. , 1986, The Journal of biological chemistry.

[469]  T. Tullius,et al.  High-resolution footprints of the DNA-binding domain of Epstein-Barr virus nuclear antigen 1 , 1989, Molecular and cellular biology.

[470]  Robert D. Wells,et al.  Left-handed Z-DNA is induced by supercoiling in physiological ionic conditions , 1982, Nature.

[471]  J. Wang,et al.  DNA supercoiling in vivo. , 1988, Biophysical chemistry.

[472]  H. Manor,et al.  (dT-dC)n and (dG-dA)n tracts arrest single stranded DNA replication in vitro. , 1989, Nucleic acids research.

[473]  Y. Courtois,et al.  Protonated polynucleotide structures. 3. An optical rotatory dispersion study of the protonation of DNA. , 1968, European journal of biochemistry.

[474]  L. Bracco,et al.  Synthetic curved DNA sequences can act as transcriptional activators in Escherichia coli. , 1989, The EMBO journal.

[475]  Structural models for non‐helical DNA. , 1986, The EMBO journal.

[476]  N. Panayotatos,et al.  A native cruciform DNA structure probed in bacteria by recombinant T7 endonuclease. , 1987, The Journal of biological chemistry.

[477]  S. Stirdivant,et al.  Left-handed DNA in restriction fragments and a recombinant plasmid , 1981, Nature.

[478]  V. Vogt.  Purification and further properties of single-strand-specific nuclease from Aspergillus oryzae. , 1973, European journal of biochemistry.

[479]  R. Wells,et al.  Multiple DNA secondary structures in perfect inverted repeat inserts in plasmids. Right-handed B-DNA, cruciforms, and left-handed Z-DNA. , 1988, The Journal of biological chemistry.

[480]  D M Crothers,et al.  Intrinsically bent DNA. , 1990, The Journal of biological chemistry.

[481]  W. Gilbert,et al.  Detection in vivo of protein-DNA interactions within the lac operon of Escherichia coli , 1985, Nature.

[482]  A. Wani,et al.  Immunoassays for carbodiimide modified DNA-detection of unpairing transitions in supercoiled ColE1 DNA. , 1989, Nucleic acids research.

[483]  B. Dombroski,et al.  Iron(II) EDTA used to measure the helical twist along any DNA molecule. , 1985, Science.

[484]  Elaine A. Ostrander,et al.  High resolution psoralen mapping reveals an altered DNA helical structure in the SV40 regulatory region , 1988, Nucleic Acids Res..

[485]  M. Gellert,et al.  DNA gyrase and DNA supercoiling. , 1979, Cold Spring Harbor symposia on quantitative biology.

[486]  F. Della Seta,et al.  Structure of RNA polymerase II promoters. Coordinate conformational alteration of the upstream activator of the TATA- and RNA-initiation sequences under moderate torsional stress. , 1986, Journal of Biological Chemistry.

[487]  J. Barton,et al.  Metal Complexes Which Target DNA Sites: Coupling Recognition to Reactivity , 1988 .

[488]  R. Wells,et al.  Left-handed Z-DNA and intramolecular triplex formation at the site of an unequal sister chromatid exchange. , 1990, The Journal of biological chemistry.

[489]  D. Pulleyblank.  Non-Commensurate Polypurine/Polypyrimidine DNA Structures , 1988 .

[490]  E. Sage,et al.  Sequence context effects on 8-methoxypsoralen photobinding to defined DNA fragments. , 1987, Biochemistry.

[491]  D. Lilley,et al.  Facile cruciform formation by an (A-T)34 sequence from a Xenopus globin gene. , 1985, Journal of molecular biology.

[492]  E. Paleček,et al.  Polarographic behaviour of native and denatured deoxyribonucleic acids. , 1966, Journal of molecular biology.

[493]  S. Mirkin,et al.  Chemical probing of the homopurine·homopyrimidine tract in supercoiled DNA at single‐nucleotide resolution , 1988, FEBS letters.

[494]  V. Vlassov,et al.  Sequence-specific chemical modification of double-stranded DNA with alkylating oligodeoxyribonucleotide derivatives. , 1988, Gene.

[495]  W. Guschlbauer,et al.  Physico-chemical properties of nucleosides , 1971 .

[496]  T. Evans,et al.  Sequence-dependent S1 nuclease hypersensitivity of a heteronomous DNA duplex. , 1986, The Journal of biological chemistry.

[497]  E. I. Budowsky,et al.  Magnesium-dependent supercoiling-induced transition in (dG)n.(dC)n stretches and formation of a new G-structure by (dG)n strand. , 1989, Nucleic acids research.

[498]  B. Singer,et al.  Chloroacetaldehyde-treated ribo- and deoxyribopolynucleotides. 1. Reaction products. , 1982, Biochemistry.

[499]  Steven D. Goodman,et al.  Functional replacement of a protein-induced bend in a DNA recombination site , 1989, Nature.

[500]  H. Mark,et al.  Encyclopedia of polymer science and engineering , 1985 .

[501]  V. Trimble.  The shifting centre , 1988, Nature.

[502]  Transcription regulation in vitro by an E. coli promoter containing a DNA cruciform in the '-35' region. , 1989, Nucleic acids research.

[503]  M. Bustin,et al.  Hierarchy of binding sites for chromosomal proteins HMG 1 and 2 in supercoiled deoxyribonucleic acid. , 1985, Biochemistry.

[504]  R E Harrington,et al.  Sequence-dependent kinks induced in curved DNA. , 1990, Journal of biomolecular structure & dynamics.

[505]  S. Arnott,et al.  Models of triple-stranded polynucleotides with optimised stereochemistry. , 1976, Nucleic acids research.

[506]  G. Gilmore,et al.  Site of unequal sister chromatid exchange contains a potential Z-DNA-forming tract. , 1988, Proceedings of the National Academy of Sciences of the United States of America.

[507]  W. Guschlbauer,et al.  Polynucléotides protonés. VII. Transitions thermiques entre differents complexes de l'acide polyinosinique et de l'acide polycytidylique en milieu acide , 1969 .

[508]  R. Wells,et al.  Left-handed Z-DNA and genetic recombination. , 1989, Progress in nucleic acid research and molecular biology.

[509]  J. Michael Schurr,et al.  Change of conformation and internal dynamics of supercoiled DNA upon binding of Escherichia coli single-strand binding protein. , 1985, Biochemistry.

[510]  J. Miller,et al.  A molecular model for gene repression. , 1966, Proceedings of the National Academy of Sciences of the United States of America.

[511]  K. Rippe,et al.  Helix-coil transition of parallel-stranded DNA. Thermodynamics of hairpin and linear duplex oligonucleotides. , 1989, Biochemistry.

[512]  E. Paleček,et al.  Inhibition of restriction endonuclease cleavage due to site-specific chemical modification of the B-Z junction in supercoiled DNA. , 1987, General physiology and biophysics.

[513]  M. Yoshida,et al.  Nonhistone protein HMG1 removes the transcriptional block caused by left-handed Z-form segment in a supercoiled DNA. , 1988, Biochemical and biophysical research communications.

[514]  J. Cadet,et al.  Recent aspects of the photochemistry of nucleic acids and related model compounds. , 1985, Biochimie.

[515]  E. Paleček,et al.  Correlation between polarographic reducibility and circular dichroism of DNA at submelting temperatures. , 1972, Biochemical and Biophysical Research Communications - BBRC.

[516]  A. Wolffe,et al.  A protein-protein interaction is essential for stable complex formation on a 5 S RNA gene. , 1989, The Journal of biological chemistry.

[517]  R. L. Baldwin,et al.  HELIX--RANDOM COIL TRANSITIONS IN DNA HOMOPOLYMER PAIRS. , 1964, Journal of molecular biology.

[518]  J. L. Crawford,et al.  The tetramer d(CpGpCpG) crystallizes as a left-handed double helix. , 1980, Proceedings of the National Academy of Sciences of the United States of America.

[519]  W. Bauer,et al.  Superhelical DNA with local substructures. A generalization of the topological constraint in terms of the intersection number and the ladder-like correspondence surface. , 1987, Journal of molecular biology.

[520]  M. Savino,et al.  Kinetic persistence of cruciform structures in reconstituted minichromosomes. , 1988, Biochimica et biophysica acta.

[521]  M Eisenstein,et al.  The structure and hydration of the A-DNA fragment d(GGGTACCC) at room temperature and low temperature. , 1990, Nucleic acids research.

[522]  H R Drew,et al.  Ordered water structure around a B-DNA dodecamer. A quantitative study. , 1983, Journal of molecular biology.

[523]  C. A. Thomas,et al.  The P22 bacteriophage DNA molecule. I. The mature form. , 1968, Journal of molecular biology.

[524]  U. Singh,et al.  On loop folding in nucleic acid hairpin-type structures. , 1986, Journal of biomolecular structure & dynamics.

[525]  D. M. Brown,et al.  Base-specific reactions useful for DNA sequencing: methylene blue--sensitized photooxidation of guanine and osmium tetraoxide modification of thymine. , 1978, Nucleic acids research.

[526]  Thomas M. Jovin,et al.  The Transition Between B-DNA and Z-DNA , 1987 .

[527]  R. Wells,et al.  The role of DNA sequence in the formation of Z-DNA versus cruciforms in plasmids. , 1988, The Journal of biological chemistry.

[528]  R. Wells,et al.  Reaction conditions affect the specificity of bromoacetaldehyde as a probe for DNA cruciforms and B-Z junctions. , 1987, Nucleic acids research.

[529]  J. S. Lee,et al.  Immunogenic duplex nucleic acids are nuclease resistant. , 1988, Journal of immunology.

[530]  H. Zachau,et al.  Simple DNA sequences and dispersed repetitive elements in the vicinity of mouse immunoglobulin K light chain genes. , 1983, Journal of molecular biology.

[531]  F. Jelen,et al.  442 — Polarography of circular DNAs☆ , 1981 .

[532]  D. Crothers,et al.  A computer graphics study of sequence-directed bending in DNA. , 1983, Journal of biomolecular structure & dynamics.

[533]  K. Rippe,et al.  The hydrogen-bonding structure in parallel-stranded duplex DNA is reverse Watson-Crick. , 1991, Biochemistry.

[534]  G. Georgiev,et al.  The suffix sequence is involved in processing the 3′ ends of different mRNAs in Drosophila melanogaster , 1986, The EMBO journal.

[535]  H. Vogel,et al.  Characterization of a parallel-stranded DNA hairpin. , 1989, Biochemistry.

[536]  N. Cozzarelli,et al.  Isolation and characterization of the Tn3 resolvase synaptic intermediate. , 1988, The EMBO journal.

[537]  D. Kowalski,et al.  Mung bean nuclease cleavage of a dA + dT-rich sequence or an inverted repeat sequence in supercoiled PM2 DNA depends on ionic environment. , 1984, Nucleic acids research.

[538]  Y. Kohwi,et al.  Unusual conformational effect exerted by Z-DNA upon its neighboring sequences. , 1987, Proceedings of the National Academy of Sciences of the United States of America.

[539]  E. Taillandier,et al.  Z form of poly d(A-C).poly d(G-T) in solution studied by Raman spectroscopy. , 1987, Nucleic acids research.

[540]  J. Jost,et al.  Genomic sequencing and in vivo footprinting. , 1989, Analytical biochemistry.

[541]  R. Wells,et al.  The segment inversion site of herpes simplex virus type 1 adopts a novel DNA structure. , 1987, The Journal of biological chemistry.

[542]  S. Mirkin,et al.  Structures of homopurine-homopyrimidine tract in superhelical DNA. , 1986, Journal of biomolecular structure & dynamics.

[543]  J. Gralla,et al.  KMnO4 as a probe for lac promoter DNA melting and mechanism in vivo. , 1989, The Journal of biological chemistry.

[544]  N. Leonard,et al.  Reaction of diethyl pyrocarbonate with nucleic acid components. Bases and nucleosides derived from guanine, cytosine, and uracil. , 1973, Journal of the American Chemical Society.

[545]  E. Blackburn.  The molecular structure of centromeres and telomeres. , 1984, Annual review of biochemistry.

[546]  R. Simpson,et al.  Cromatin and core particles formed from the inner histones and synthetic polydeoxyribonucleotides of defined sequence. , 1979, Nucleic acids research.

[547]  L. Shlyakhtenko,et al.  Early melting of supercoiled DNA. , 1988, Nucleic acids research.

[548]  D. Pulleyblank,et al.  The in-vivo occurrence of Z DNA. , 1983, Journal of biomolecular structure & dynamics.

[549]  C. C. Hardin,et al.  Telomeric DNA oligonucleotides form novel intramolecular structures containing guanine·guanine base pairs , 1987, Cell.

[550]  J. Wang,et al.  Influence of DNA sequence and supercoiling on the process of cruciform formation. , 1988, Journal of molecular biology.

[551]  Y. Kohwi.  Cationic metal-specific structures adopted by the poly(dG) region and the direct repeats in the chicken adult beta A globin gene promoter. , 1989, Nucleic acids research.

[552]  E. Paleček,et al.  Osmium tetroxide: a new probe for site-specific distortions in supercoiled DNAs. , 1984, Nucleic acids research.

[553]  V. Vlassov,et al.  Complementary-addressed (sequence-specific) modification of nucleic acids. , 1985, Progress in nucleic acid research and molecular biology.

[554]  D. Lilley,et al.  The tertiary structure of the four-way DNA junction affords protection against DNase I cleavage. , 1990, Nucleic acids research.

[555]  Chi‐hong B. Chen,et al.  Chemical nucleases: new reagents in molecular biology. , 1990, Annual review of biochemistry.

[556]  M. Leng.  Immunological detection of lesions in DNA. , 1985, Biochimie.

[557]  L. J. Peck,et al.  Flipping of cloned d(pCpG)n.d(pCpG)n DNA sequences from right- to left-handed helical structure by salt, Co(III), or negative supercoiling. , 1982, Proceedings of the National Academy of Sciences of the United States of America.

[558]  A. Rich,et al.  Nonrandom distribution of long mono- and dinucleotide repeats in Drosophila chromosomes: correlations with dosage compensation, heterochromatin, and recombination , 1989, Molecular and cellular biology.

[559]  D. Lilley,et al.  Influence of cation size and charge on the extrusion of a salt-dependent cruciform. , 1987, Journal of molecular biology.

[560]  L. Iacono-Connors,et al.  Altered DNA conformations in the gene regulatory region of torsionally-stressed SV40 DNA. , 1986, Nucleic acids research.

[561]  Effect of base composition at the center of inverted repeated DNA sequences on cruciform transitions in DNA. , 1988, The Journal of biological chemistry.

[562]  J. Pehrson.  Thymine dimer formation as a probe of the path of DNA in and between nucleosomes in intact chromatin. , 1989, Proceedings of the National Academy of Sciences of the United States of America.

[563]  C R Calladine,et al.  Mechanics of sequence-dependent stacking of bases in B-DNA. , 1982, Journal of molecular biology.

[564]  M. Bichara,et al.  Z-DNA-forming sequences are spontaneous deletion hot spots. , 1989, Proceedings of the National Academy of Sciences of the United States of America.

[565]  M. Zannis‐Hadjopoulos,et al.  The dynamic distribution and quantification of DNA cruciforms in eukaryotic nuclei. , 1990, Experimental cell research.

[566]  G. Brady,et al.  X-ray diffraction studies of circular superhelical DNA at 300–10,000-Å resolution , 1976, Nature.

[567]  S. Mirkin,et al.  Structure of (dG)n.(dC)n under superhelical stress and acid pH. , 1987, Journal of biomolecular structure & dynamics.

[568]  T. Prangé,et al.  Coexistence of A- and B-form DNA in a single crystal lattice , 1989, Nature.

[569]  M. Behe,et al.  An oligopurine sequence bias occurs in eukaryotic viruses. , 1988, Nucleic acids research.

[570]  J. Toulmé,et al.  Comparative inhibition of rabbit globin mRNA translation by modified antisense oligodeoxynucleotides. , 1989, Nucleic acids research.

[571]  D. Lilley,et al.  The structure of cruciforms in supercoiled DNA: probing the single‐stranded character of nucleotide bases with bisulphite. , 1986, The EMBO journal.

[572]  E. Paleček,et al.  Antibodies to DNAs chemically modified with osmium structural probes. , 1989, General physiology and biophysics.

[573]  G. A. van der Marel,et al.  Hairpin formation in synthetic oligonucleotides. , 1985, Biochimie.

[574]  Chamberlin Mj.  Comparative properties of DNA, RNA, and hybrid homopolymer pairs. , 1965 .

[575]  M. Ellison,et al.  The obtention of simian virus 40 recombinants carrying d(CG.GC)n, d(CA.GT)n and d(CT.GA)n sequences. Stability of the inserted simple repeating sequences. , 1987, European journal of biochemistry.

[576]  J. Sutherland,et al.  Separation of chromosomal length DNA molecules: Pneumatic apparatus for rotating gels during electrophoresis , 1989, Electrophoresis.

[577]  B. Malcolm,et al.  Telomere G-strand structure and function analyzed by chemical protection, base analogue substitution, and utilization by telomerase in vitro. , 1990, Biochemistry.

[578]  E. Paleček,et al.  Electrochemical behaviour of biological macromolecules , 1986 .

[579]  A. Rich,et al.  Chemical probes of DNA conformation: detection of Z-DNA at nucleotide resolution , 1985, Cell.

[580]  D. Lilley,et al.  Superhelical torsion in cellular DNA responds directly to environmental and genetic factors. , 1990, Proceedings of the National Academy of Sciences of the United States of America.

[581]  N. Cozzarelli,et al.  4 Primer on the Topology and Geometry of DNA Supercoiling , 1990 .

[582]  S. Jayasena,et al.  Competitive nucleosome reconstitution of polydeoxynucleotides containing oligoguanosine tracts. , 1989, Journal of molecular biology.

[583]  N. Thuong,et al.  Oligo-[α]-Deoxyribonucleotides Covalently Linked to Intercalating Agents. A New Family of Sequence-Specific Nucleic Acid Reagents , 1988 .

[584]  D. Rhodes,et al.  Nucleosome cores reconstituted from poly (dA-dT) and the octamer of histones. , 1979, Nucleic acids research.

[585]  T. Kistenmacher,et al.  Conformational properties of the osmium tetraoxide bispyridine ester of 1-methylthymine and a comment on the linearity of the trans O=Os=O group. , 1976, Bioinorganic chemistry.

[586]  Stephen C. Harvey,et al.  DNA structural dynamics: longitudinal breathing as a possible mechanism for the B ⇄ Z transition , 1983 .

[587]  D. Lilley,et al.  A two-state conformational equilibrium for alternating (A-T)n sequences in negatively supercoiled DNA. , 1987, Journal of molecular biology.

[588]  D. Lilley,et al.  The supercoil‐stabilised cruciform of ColE1 is hyper‐reactive to osmium tetroxide. , 1984, The EMBO journal.

[589]  F. Della Seta,et al.  Structure of RNA polymerase II promoters. Conformational alterations and template properties of circularized Saccharomyces cerevisiae GAL1‐GAL10 divergent promoters. , 1986, The EMBO journal.

[590]  Johnf . Thompson,et al.  Phasing of protein-induced DNA bends in a recombination complex , 1989, Nature.

[591]  R. Wells,et al.  Thermodynamic parameters are sequence-dependent for the supercoil-induced B to Z transition in recombinant plasmids. , 1986, The Journal of biological chemistry.

[592]  L. Ehrenberg,et al.  Diethyl pyrocarbonate in nucleic acid research. , 1976, Progress in nucleic acid research and molecular biology.

[593]  F. B. Howard,et al.  Infrared demonstration of two- and three-strand helix formation between poly C and guanosine mononucleotides and oligonucleotides , 1964 .

[594]  Long range structural communication between sequences in supercoiled DNA. Sequence dependence of contextual influence on cruciform extrusion mechanism. , 1988, The Journal of biological chemistry.

[595]  E. Blackburn.  Telomeres: Do the ends justify the means? , 1984, Cell.

[596]  J C Wang,et al.  DNA Supercoiling and its Effects on the Structure of DNA , 1984, Journal of Cell Science.

[597]  S. Mirkin,et al.  Chemical probing of homopurine-homopyrimidine mirror repeats in supercoiled DNA , 1988, Nature.

[598]  A. Lipanov,et al.  Poly(dA)\ṁpoly(dT) is a B-type double helix with a distinctively narrow minor groove , 1987, Nature.

[599]  R. Wells,et al.  Left-handed DNA in vivo. , 1987, Science.

[600]  D Kowalski,et al.  The DNA unwinding element: a novel, cis‐acting component that facilitates opening of the Escherichia coli replication origin. , 1989, The EMBO journal.

[601]  J. Toulmé,et al.  Specific regulation of gene expression by antisense, sense and antigene nucleic acids. , 1990, Biochimica et biophysica acta.

[602]  C. A. Thomas,et al.  The P22 bacteriophage DNA molecule. II. Circular intracellular forms. , 1968, Journal of molecular biology.

[603]  M. Frank-Kamenetskii,et al.  Protection against UV-induced pyrimidine dimerization in DNA by triplex formation , 1990, Nature.

[604]  R. Sinden,et al.  Hyperreactivity of B-Z junctions to 4,5',8-trimethylpsoralen photobinding assayed by an exonuclease III/photoreversal mapping procedure. , 1989, Journal of molecular biology.

[605]  R. Wells,et al.  Influence of DNA sequence on the formation of non-B right-handed helices in oligopurine.oligopyrimidine inserts in plasmids. , 1988, The Journal of biological chemistry.

[606]  A. Furano,et al.  The structure of the guanine-rich polypurine:polypyrimidine sequence at the right end of the rat L1 (LINE) element. , 1989, The Journal of biological chemistry.

[607]  U. Heinemann.  A note on crystal packing and global helix structure in short A-DNA duplexes. , 1991, Journal of biomolecular structure & dynamics.

[608]  M Linial,et al.  Sequence-directed bent DNA helix is the specific binding site for Crithidia fasciculata nicking enzyme. , 1987, Proceedings of the National Academy of Sciences of the United States of America.

[609]  C. Marck,et al.  Protonated polynucleotides structures - 23. The acid-base hysteresis of poly(dG).poly(dC). , 1978, Nucleic Acids Research.

[610]  H. Vasmel.  Influence of supercoiling on DNA structure: Laser Raman spectroscopy of the plasmid pBR322 , 1985, Biopolymers.

[611]  Wolfram Saenger,et al.  Principles of Nucleic Acid Structure , 1983 .

[612]  E. I. Budowsky,et al.  Polynucleotide-protein cross-links induced by ultraviolet light and their use for structural investigation of nucleoproteins. , 1989, Progress in nucleic acid research and molecular biology.

[613]  Hen-Ming Wu,et al.  DNA bending at adenine · thymine tracts , 1986, Nature.

[614]  T. Jovin,et al.  Left-handed Z-DNA in bands of acid-fixed polytene chromosomes. , 1983, Proceedings of the National Academy of Sciences of the United States of America.

[615]  A. Bacolla,et al.  An unusually long poly(purine)-poly(pyrimidine) sequence is located upstream from the human thyroglobulin gene. , 1985, Nucleic acids research.

[616]  R. D. Wells,et al.  Site-specific inhibition of EcoRI restriction/modification enzymes by a DNA triple helix , 1990, Nucleic Acids Res..

[617]  E. Paleček,et al.  Properties of DNA modified with N-methyl-N-nitrosourea , 1977, Radiation and environmental biophysics.

[618]  W. Herr.  Diethyl pyrocarbonate: a chemical probe for secondary structure in negatively supercoiled DNA. , 1985, Proceedings of the National Academy of Sciences of the United States of America.

[619]  R. Wells,et al.  Specificity of the three-stranded complex formation between double-stranded DNA and single-stranded RNA containing repeating nucleotide sequences. , 1968, Journal of molecular biology.

[620]  E. Paleček.  Deoxyribonucleic acid conformational changes at temperatures below melting temperature. , 1968, Archives of biochemistry and biophysics.

[621]  N. Cozzarelli,et al.  Use of site-specific recombination as a probe of DNA structure and metabolism in vivo. , 1987, Journal of molecular biology.

[622]  D. Lilley.  Structural isomerization in DNA: the formation of cruciform structures in supercoiled DNA molecules , 1989 .

[623]  J. Wang,et al.  Variation of the average rotation angle of the DNA helix and the superhelical turns of covalently closed cyclic lambda DNA. , 1969, Journal of molecular biology.