DNA structure: cations in charge?

Recent X-ray diffraction, NMR spectroscopy and molecular mechanics results suggest that monovalent cations selectively partition into the minor groove of AT-tracts in DNA. These observations are consistent with DNA deformation by electrostatic collapse around areas of uneven cation density. This model predicts the occurrence of known DNA deformations, such as AT-tract bending and changes in the minor-groove width.

[1]  Jennifer A. Doudna,et al.  A specific monovalent metal ion integral to the AA platform of the RNA tetraloop receptor , 1998, Nature Structural Biology.

[2]  A Klug,et al.  A crystallographic study of metal-binding to yeast phenylalanine transfer RNA. , 1977, Journal of molecular biology.

[3]  I. Brukner,et al.  Physiological concentration of magnesium ions induces a strong macroscopic curvature in GGGCCC-containing DNA. , 1994, Journal of molecular biology.

[4]  J. Feigon,et al.  Localization of Divalent Metal Ions in the Minor Groove of DNA A-Tracts , 1997 .

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

[6]  A. Rich,et al.  Interactions between an anthracycline antibiotic and DNA: molecular structure of daunomycin complexed to d(CpGpTpApCpG) at 1.2-A resolution. , 1987, Biochemistry.

[7]  T. Richmond,et al.  Crystal structure of the nucleosome core particle at 2.8 Å resolution , 1997, Nature.

[8]  L. Nordenskiöld,et al.  23Na NMR relaxation study of the effects of conformation and base composition on the interactions of counterions with double-helical DNA. , 1984, Biochemistry.

[9]  T. Tullius,et al.  The unusual conformation adopted by the adenine tracts in kinetoplast DNA , 1987, Cell.

[10]  L. Malinina,et al.  The structure of the most studied DNA fragment changes under the influence of ions: a new packing of d(CGCGAATTCGCG) , 1998, FEBS letters.

[11]  L. J. Maher,et al.  DNA bending by asymmetric phosphate neutralization. , 1994, Science.

[12]  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.

[13]  J. Bond,et al.  Importance of coulombic end effects on cation accumulation near oligoelectrolyte B-DNA: a demonstration using 23Na NMR. , 1995, Biophysical journal.

[14]  M Feig,et al.  Structural equilibrium of DNA represented with different force fields. , 1998, Biophysical journal.

[15]  J. Moe,et al.  Proton exchange and base-pair opening kinetics in 5'-d(CGCGAATTCGCG)-3' and related dodecamers. , 1990, Nucleic acids research.

[16]  R. Lavery,et al.  The dependence of the surface electrostatic potential of B-DNA on environmental factors. , 1985, Journal of biomolecular structure & dynamics.

[17]  D. Crothers,et al.  DNA bend direction by phase sensitive detection , 1987, Nature.

[18]  L. Nordenskiöld,et al.  A reexamination of 25Mg2+ NMR in DNA solution: site heterogeneity and cation competition effects. , 1991, Biopolymers.

[19]  Martin Egli,et al.  The Dickerson-Drew B-DNA Dodecamer Revisited-At Atomic Resolution , 1998 .

[20]  M Guéron,et al.  Determination of the residence time of water molecules hydrating B'- DNA and B-DNA, by one-dimensional zero-enhancement nuclear Overhauser effect spectroscopy. , 1999, Journal of molecular biology.

[21]  L. J. Maher,et al.  Electrostatic effects in DNA bending by GCN4 mutants. , 1998, Biochemistry.

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

[23]  A. Rich,et al.  An estimate of the extent of folding of nucleosomal DNA by laterally asymmetric neutralization of phosphate groups. , 1989, Journal of biomolecular structure & dynamics.

[24]  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.

[25]  H. Hashimoto,et al.  Regioselective effect of zwitterionic DNA substitutions on DNA alkylation: evidence for a strong side chain orientational preference. , 1997, Biochemistry.

[26]  T. Tullius,et al.  How the structure of an adenine tract depends on sequence context: a new model for the structure of TnAn DNA sequences. , 1993, Biochemistry.

[27]  A. Rich,et al.  Asymmetric lateral distribution of unshielded phosphate groups in nucleosomal DNA and its role in DNA bending. , 1979, Proceedings of the National Academy of Sciences of the United States of America.

[28]  L. Williams,et al.  Divalent cations stabilize unstacked conformations of DNA and RNA by interacting with base pi systems. , 1998, Biochemistry.

[29]  D. VanDerveer,et al.  Structure of the potassium form of CGCGAATTCGCG: DNA deformation by electrostatic collapse around inorganic cations. , 1998, Biochemistry.

[30]  D. Stigter An electrostatic model for the dielectric effects, the adsorption of multivalent ions, and the bending of B-DNA , 1998 .

[31]  L. J. Maher,et al.  Effects of neutralization pattern and stereochemistry on DNA bending by methylphosphonate substitutions. , 1997, Biochemistry.

[32]  I. Rouzina,et al.  DNA bending by small, mobile multivalent cations. , 1998, Biophysical journal.

[33]  R. Fahlman,et al.  Cation-regulated self-association of "synapsable" DNA duplexes. , 1998, Journal of molecular biology.

[34]  J. Feigon,et al.  Localization of ammonium ions in the minor groove of DNA duplexes in solution and the origin of DNA A-tract bending. , 1999, Journal of molecular biology.

[35]  Bhyravabhotla Jayaram,et al.  Intrusion of Counterions into the Spine of Hydration in the Minor Groove of B-DNA: Fractional Occupancy of Electronegative Pockets , 1997 .

[36]  L. I. Volkova,et al.  Structure of the B DNA cationic shell as revealed by an X-ray diffraction study of CsDNA. Sequence-specific cationic stabilization of B form DNA. , 1983, Journal of molecular biology.

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

[38]  R. Dickerson,et al.  Anisotropic thermal‐parameter refinement of the DNA dodecamer CGCGAATTCGCG by the segmented rigid‐body method , 1985 .

[39]  J. Feigon,et al.  Binding sites and dynamics of ammonium ions in a telomere repeat DNA quadruplex. , 1999, Journal of molecular biology.

[40]  G G Hu,et al.  The B-DNA dodecamer at high resolution reveals a spine of water on sodium. , 1998, Biochemistry.

[41]  R E Harrington,et al.  Bending and Torsional Flexibility of G/C-rich Sequences as Determined by Cyclization Assays (*) , 1995, The Journal of Biological Chemistry.

[42]  D. Beveridge,et al.  Molecular dynamics simulations of an oligonucleotide duplex with adenine tracts phased by a full helix turn. , 1998, Journal of molecular biology.

[43]  B. Gold,et al.  Control over the Localization of Positive Charge in DNA: The Effect on Duplex DNA and RNA Stability , 1998 .

[44]  B. DeDecker,et al.  The effects of salt on the TATA binding protein-DNA interaction from a hyperthermophilic archaeon. , 1998, Journal of molecular biology.

[45]  H. Merlitz,et al.  Salt effects on the structure and internal dynamics of superhelical DNAs studied by light scattering and Brownian dynamics. , 1997, Biophysical Journal.

[46]  C. Switzer,et al.  DNA bending by a phantom protein. , 1996, Chemistry & biology.

[47]  J. Feigon,et al.  Ammonium Ion as an NMR Probe for Monovalent Cation Coordination Sites of DNA Quadruplexes , 1998 .

[48]  C. Switzer,et al.  DNA bending by hexamethylene-tethered ammonium ions. , 1996, Proceedings of the National Academy of Sciences of the United States of America.

[49]  A. Klug,et al.  Crystallographic refinement of yeast phenylalanine transfer RNA at 2-5A resolution. , 1976, Journal of molecular biology.

[50]  A. Mildvan,et al.  Magnetic resonance studies of the conformation of enzyme-bound adenylyl(3' leads to 5')uridine and adenosine 5'-triphosphate on RNA polymerase from Esherichia coli. , 1977, Biochemistry.

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

[52]  N. Seeman,et al.  Double Helix at Atomic Resolution , 1973, Nature.

[53]  K. Marx,et al.  A gel electrophoresis study of the competitive effects of monovalent counterion on the extent of divalent counterions binding to DNA. , 1998, Biophysical journal.

[54]  R. Dickerson,et al.  DNA bending: the prevalence of kinkiness and the virtues of normality. , 1998, Nucleic acids research.

[55]  M. Record,et al.  Salt-nucleic acid interactions. , 1995, Annual review of physical chemistry.

[56]  D. Draper,et al.  RNA shows its metal , 1998, Nature Structural Biology.

[57]  M. Record,et al.  Sodium-23 nuclear magnetic resonance studies of cation-deoxyribonucleic acid interactions , 1983 .

[58]  J. Griffith,et al.  Cationic metals promote sequence-directed DNA bending. , 1987, Biochemistry.