Action at a distance along a DNA.

A number of ways are known by which an event at one location on a DNA molecule can affect an event at a distant location on the same molecule. Three classes of mechanisms are described for such distal actions: tracking or translocation of a protein along a DNA, the association of two proteins bound at separate sites to form a DNA loop in between, and distal interactions that are affected by the topology of the DNA. The basic characteristics of each type of mechanism are discussed in terms of the known physicochemical properties of DNA. The various modes of action at a distance are often interrelated. Examples include the formation of positively and negatively supercoiled DNA loops by tracking and the strong effects of DNA topology on looping.

[1]  J. Wang,et al.  On the probability of ring closure of lambda DNA. , 1966, Journal of molecular biology.

[2]  J. Wang,et al.  Interaction between DNA and an Escherichia coli protein omega. , 1971, Journal of molecular biology.

[3]  S. Linn,et al.  Uncoupling of the recBC ATPase from DNase by DNA crosslinked with psoralen. , 1972, Proceedings of the National Academy of Sciences of the United States of America.

[4]  Replication of colicin E1 plasmid DNA in cell extracts. , 1974, Proceedings of the National Academy of Sciences of the United States of America.

[5]  H. Smith,et al.  Action of ATP-dependent DNase from Hemophilus influenzae on cross-linked DNA molecules. , 1976, The Journal of biological chemistry.

[6]  P. Williamson,et al.  Transcription of histone-covered T7 DNA by Escherichia coli RNA polymerase. , 1978, Biochemistry.

[7]  J. Wang,et al.  Micrococcus luteus DNA gyrase: active components and a model for its supercoiling of DNA. , 1978, Proceedings of the National Academy of Sciences of the United States of America.

[8]  B. Endlich,et al.  Electron microscopic studies of the mechanism of action of the restriction endonuclease of Escherichia coli B. , 1979, Journal of molecular biology.

[9]  P. Chambon,et al.  Transcription of in vitro assembled chromatin by Escherichia coli RNA polymerase. , 1979, Journal of molecular biology.

[10]  J. Wang,et al.  Helical repeat of DNA in solution. , 1979, Proceedings of the National Academy of Sciences of the United States of America.

[11]  F. Stahl.  Special sites in generalized recombination. , 1979, Annual review of genetics.

[12]  A. Klug,et al.  Helical periodicity of DNA determined by enzyme digestion , 1980, Nature.

[13]  D. Parker,et al.  The vestibular apparatus. , 1980, Scientific American.

[14]  N. Cozzarelli.  DNA gyrase and the supercoiling of DNA. , 1980, Science.

[15]  T. Itoh,et al.  Formation of an RNA primer for initiation of replication of ColE1 DNA by ribonuclease H. , 1980, Proceedings of the National Academy of Sciences of the United States of America.

[16]  R. Yuan,et al.  DNA translocation by the restriction enzyme from E. coli K , 1980, Cell.

[17]  Gerald R. Smith,et al.  Unwinding and rewinding of DNA by the RecBC enzyme , 1980, Cell.

[18]  L. J. Peck,et al.  Sequence dependence of the helical repeat of DNA in solution , 1981, Nature.

[19]  Z. Kam,et al.  Dependence of laser light scattering of DNA on NaCl concentration , 1981, Biopolymers.

[20]  A. Klug,et al.  Sequence-dependent helical periodicity of DNA , 1981, Nature.

[21]  P. Hagerman,et al.  Investigation of the flexibility of DNA using transient electric birefringence , 1981, Biopolymers.

[22]  R. J. Robbins,et al.  Torsion and bending of nucleic acids studied by subnanosecond time-resolved fluorescence depolarization of intercalated dyes , 1982 .

[23]  M. Chamberlin,et al.  Studies of in vitro transcription by calf thymus RNA polymerase II using a novel duplex DNA template. , 1982, The Journal of biological chemistry.

[24]  J. Sonnenbichler,et al.  Oligonucleosomes as a model system for chromatin transcription. Transcription with Escherichia coli DNA-dependent RNA polymerase. , 1982, Journal of molecular biology.

[25]  B. Alberts,et al.  Properties of the T4 bacteriophage DNA replication apparatus: The T4 dda DNA helicase is required to pass a bound RNA polymerase molecule , 1983, Cell.

[26]  R. L. Baldwin,et al.  Energetics of DNA twisting. I. Relation between twist and cyclization probability. , 1983, Journal of molecular biology.

[27]  J. Legrange,et al.  Dependence of DNA helix flexibility on base composition , 1983, Nature.

[28]  S. Adhya,et al.  A control element within a structural gene: The gal operon of Escherichia coli , 1983, Cell.

[29]  Hen-Ming Wu,et al.  The locus of sequence-directed and protein-induced DNA bending , 1984, Nature.

[30]  S. Adhya,et al.  Demonstration of two operator elements in gal: in vitro repressor binding studies. , 1984, Proceedings of the National Academy of Sciences of the United States of America.

[31]  J. Shimada,et al.  DNA-topoisomer analysis on the basis of the helical wormlike chain. , 1984, Biopolymers.

[32]  T. Dunn,et al.  An operator at -280 base pairs that is required for repression of araBAD operon promoter: addition of DNA helical turns between the operator and promoter cyclically hinders repression. , 1984, Proceedings of the National Academy of Sciences of the United States of America.

[33]  J. Wang,et al.  Torsional rigidity of DNA and length dependence of the free energy of DNA supercoiling. , 1984, Journal of molecular biology.

[34]  H. Masukata,et al.  Effects of point mutations on formation and structure of the RNA primer for ColE1 DNA replication , 1984, Cell.

[35]  H. Weintraub.  Assembly and propagation of repressed and derepressed chromosomal states , 1985, Cell.

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

[37]  H. Echols,et al.  Specialized nucleoprotein structures at the origin of replication of bacteriophage lambda: complexes with lambda O protein and with lambda O, lambda P, and Escherichia coli DnaB proteins. , 1985, Proceedings of the National Academy of Sciences of the United States of America.

[38]  H. Vosberg.  DNA topoisomerases: enzymes that control DNA conformation. , 1985, Current topics in microbiology and immunology.

[39]  J. Wang,et al.  Bacterial DNA topoisomerase I can relax positively supercoiled DNA containing a single-stranded loop. , 1985, Journal of molecular biology.

[40]  D. Schultz,et al.  RecBC enzyme nicking at chi sites during DNA unwinding: Location and orientation-dependence of the cutting , 1985, Cell.

[41]  J. Tomizawa.  Control of cole1 plasmid replication: Initial interaction of RNA I and the primer transcript is reversible , 1985, Cell.

[42]  H. Echols,et al.  Multiple DNA-protein interactions governing high-precision DNA transactions. , 1986, Science.

[43]  D. Sherratt,et al.  Structural and catalytic properties of specific complexes between Tn3 resolvase and the recombination site res. , 1986, Biochemical Society transactions.

[44]  K. Mizuuchi,et al.  Role of DNA topology in Mu transposition: Mechanism of sensing the relative orientation of two DNA segments , 1986, Cell.

[45]  M. Ptashne,et al.  Cooperative binding of λ repressors to sites separated by integral turns of the DNA helix , 1986, Cell.

[46]  T. Baker,et al.  Extensive unwinding of the plasmid template during staged enzymatic initiation of DNA replication from the origin of the Escherichia coli chromosome , 1986, Cell.

[47]  M. Vigneron,et al.  Requirement of stereospecific alignments for initiation from the simian virus 40 early promoter , 1986, Nature.

[48]  H. Echols,et al.  Specialized nucleoprotein structures at the origin of replication of bacteriophage lambda: localized unwinding of duplex DNA by a six-protein reaction. , 1986, Proceedings of the National Academy of Sciences of the United States of America.

[49]  A. Hinnen,et al.  Removal of positioned nucleosomes from the yeast PHO5 promoter upon PHO5 induction releases additional upstream activating DNA elements. , 1986, The EMBO journal.

[50]  H. Masukata,et al.  Control of primer formation for ColE1 plasmid replication: Conformational change of the primer transcript , 1986, Cell.

[51]  E N Trifonov,et al.  Curved DNA: design, synthesis, and circularization. , 1986, Proceedings of the National Academy of Sciences of the United States of America.

[52]  Mark Ptashne,et al.  DNA loops induced by cooperative binding of λ repressor , 1986, Nature.

[53]  H. Eisenberg.  She walked in the very best circles , 1986 .

[54]  K. Martin,et al.  The DNA loop model for ara repression: AraC protein occupies the proposed loop sites in vivo and repression-negative mutations lie in these same sites. , 1986, Proceedings of the National Academy of Sciences of the United States of America.

[55]  M. Yaniv,et al.  Structure of transcriptionally active chromatin. , 1986, CRC critical reviews in biochemistry.

[56]  Mark Ptashne,et al.  Gene regulation by proteins acting nearby and at a distance , 1986, Nature.

[57]  R. Kornberg,et al.  Nucleosomes inhibit the initiation of transcription but allow chain elongation with the displacement of histones , 1987, Cell.

[58]  F. Dean,et al.  Simian virus 40 (SV40) DNA replication: SV40 large T antigen unwinds DNA containing the SV40 origin of replication. , 1987, Proceedings of the National Academy of Sciences of the United States of America.

[59]  J. Wang,et al.  Supercoiling of the DNA template during transcription. , 1987, Proceedings of the National Academy of Sciences of the United States of America.

[60]  M. Gellert,et al.  Communication between segments of DNA during site-specific recombination , 1987, Nature.

[61]  J. Wang.  Recent studies of DNA topoisomerases. , 1987, Biochimica et biophysica acta.

[62]  F. Dean,et al.  Unwinding of duplex DNA from the SV40 origin of replication by T antigen. , 1987, Science.

[63]  J. Li,et al.  Initiation of simian virus 40 DNA replication in vitro: large-tumor-antigen- and origin-dependent unwinding of the template. , 1987, Proceedings of the National Academy of Sciences of the United States of America.

[64]  T. Baker,et al.  Helicase action of dnaB protein during replication from the Escherichia coli chromosomal origin in vitro. , 1987, The Journal of biological chemistry.

[65]  M. Simon,et al.  Spatial relationship of the Fis binding sites for Hin recombinational enhancer activity , 1987, Nature.

[66]  N. Cozzarelli,et al.  Gin-mediated DNA inversion: product structure and the mechanism of strand exchange. , 1988, Proceedings of the National Academy of Sciences of the United States of America.