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Helical coherence of DNA in crystals and solution.

Wynveen A, Lee DJ, Kornyshev AA, Leikin S - Nucleic Acids Res. (2008)

Bottom Line: We find, e.g. that the solution structure of synthetic oligomers is characterized by 100-200 A coherence length, which is similar to approximately 150 A coherence length of natural, salmon-sperm DNA.Packing of oligomers in crystals dramatically alters their helical coherence.The coherence length increases to 800-1200 A, consistent with its theoretically predicted role in interactions between DNA at close separations.

View Article: PubMed Central - PubMed

Affiliation: Institut für Theoretische Physik II: Weiche Materie, Heinrich-Heine-Universität Düsseldorf, Universitätsstrasse 1, D-40225 Düsseldorf, Germany. awynveen@googlemail.com

ABSTRACT
The twist, rise, slide, shift, tilt and roll between adjoining base pairs in DNA depend on the identity of the bases. The resulting dependence of the double helix conformation on the nucleotide sequence is important for DNA recognition by proteins, packaging and maintenance of genetic material, and other interactions involving DNA. This dependence, however, is obscured by poorly understood variations in the stacking geometry of the same adjoining base pairs within different sequence contexts. In this article, we approach the problem of sequence-dependent DNA conformation by statistical analysis of X-ray and NMR structures of DNA oligomers. We evaluate the corresponding helical coherence length--a cumulative parameter quantifying sequence-dependent deviations from the ideal double helix geometry. We find, e.g. that the solution structure of synthetic oligomers is characterized by 100-200 A coherence length, which is similar to approximately 150 A coherence length of natural, salmon-sperm DNA. Packing of oligomers in crystals dramatically alters their helical coherence. The coherence length increases to 800-1200 A, consistent with its theoretically predicted role in interactions between DNA at close separations.

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Relative accuracy of Equation (5) at different length scales (shown for local z/3DNA but similar for all models). The dashed line is the prediction from Equation (5).
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Figure 4: Relative accuracy of Equation (5) at different length scales (shown for local z/3DNA but similar for all models). The dashed line is the prediction from Equation (5).

Mentions: As expected, by direct averaging we found linear accumulation of mean-square deviations in the helical phase from that of an ideal helix [Equation (5)]. Figure 4 shows that Equation (5) becomes accurate in both DNA-cry and DNA-nmr at length scales larger than ∼50 Å. This accumulation results in the loss of correlations between azimuthal orientations of the base pairs with increasing separation between them along the molecule, which is described by the intrinsic helical coherence length λ(0)c (Figure 1B).Figure 4.


Helical coherence of DNA in crystals and solution.

Wynveen A, Lee DJ, Kornyshev AA, Leikin S - Nucleic Acids Res. (2008)

Relative accuracy of Equation (5) at different length scales (shown for local z/3DNA but similar for all models). The dashed line is the prediction from Equation (5).
© Copyright Policy - creative-commons
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC2553576&req=5

Figure 4: Relative accuracy of Equation (5) at different length scales (shown for local z/3DNA but similar for all models). The dashed line is the prediction from Equation (5).
Mentions: As expected, by direct averaging we found linear accumulation of mean-square deviations in the helical phase from that of an ideal helix [Equation (5)]. Figure 4 shows that Equation (5) becomes accurate in both DNA-cry and DNA-nmr at length scales larger than ∼50 Å. This accumulation results in the loss of correlations between azimuthal orientations of the base pairs with increasing separation between them along the molecule, which is described by the intrinsic helical coherence length λ(0)c (Figure 1B).Figure 4.

Bottom Line: We find, e.g. that the solution structure of synthetic oligomers is characterized by 100-200 A coherence length, which is similar to approximately 150 A coherence length of natural, salmon-sperm DNA.Packing of oligomers in crystals dramatically alters their helical coherence.The coherence length increases to 800-1200 A, consistent with its theoretically predicted role in interactions between DNA at close separations.

View Article: PubMed Central - PubMed

Affiliation: Institut für Theoretische Physik II: Weiche Materie, Heinrich-Heine-Universität Düsseldorf, Universitätsstrasse 1, D-40225 Düsseldorf, Germany. awynveen@googlemail.com

ABSTRACT
The twist, rise, slide, shift, tilt and roll between adjoining base pairs in DNA depend on the identity of the bases. The resulting dependence of the double helix conformation on the nucleotide sequence is important for DNA recognition by proteins, packaging and maintenance of genetic material, and other interactions involving DNA. This dependence, however, is obscured by poorly understood variations in the stacking geometry of the same adjoining base pairs within different sequence contexts. In this article, we approach the problem of sequence-dependent DNA conformation by statistical analysis of X-ray and NMR structures of DNA oligomers. We evaluate the corresponding helical coherence length--a cumulative parameter quantifying sequence-dependent deviations from the ideal double helix geometry. We find, e.g. that the solution structure of synthetic oligomers is characterized by 100-200 A coherence length, which is similar to approximately 150 A coherence length of natural, salmon-sperm DNA. Packing of oligomers in crystals dramatically alters their helical coherence. The coherence length increases to 800-1200 A, consistent with its theoretically predicted role in interactions between DNA at close separations.

Show MeSH
Related in: MedlinePlus