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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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Intrinsic helical coherence length λ(0)c and its components, as described by Equations (8–11).
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Figure 5: Intrinsic helical coherence length λ(0)c and its components, as described by Equations (8–11).

Mentions: All three sets of Ωi and hi produced close values of λ(0)c (Figure 5). These values are consistent with the expected role of the calculation based on the local z/3DNA set as an upper bound approximation and the calculation based on the global z/Freehelix set as the lower bound approximation. Thus, we estimate 800 < λ(0)c < 1200 Å in DNA-cry and 100 < λ(0)c < 200 Å in DNA-nmr. The intrinsic helical coherence length of DNA appears to be 6–8 times smaller in solution than in crystals. The nearest neighbor anti-correlations in the local pitch within DNA-cry reduce the accumulation of the helical phase distortion, thereby increasing the helical coherence length. The positive correlations within DNA-nmr have an opposite effect, they decrease the helical coherence.Figure 5.


Helical coherence of DNA in crystals and solution.

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

Intrinsic helical coherence length λ(0)c and its components, as described by Equations (8–11).
© Copyright Policy - creative-commons
Related In: Results  -  Collection

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

Figure 5: Intrinsic helical coherence length λ(0)c and its components, as described by Equations (8–11).
Mentions: All three sets of Ωi and hi produced close values of λ(0)c (Figure 5). These values are consistent with the expected role of the calculation based on the local z/3DNA set as an upper bound approximation and the calculation based on the global z/Freehelix set as the lower bound approximation. Thus, we estimate 800 < λ(0)c < 1200 Å in DNA-cry and 100 < λ(0)c < 200 Å in DNA-nmr. The intrinsic helical coherence length of DNA appears to be 6–8 times smaller in solution than in crystals. The nearest neighbor anti-correlations in the local pitch within DNA-cry reduce the accumulation of the helical phase distortion, thereby increasing the helical coherence length. The positive correlations within DNA-nmr have an opposite effect, they decrease the helical coherence.Figure 5.

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