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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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Related in: MedlinePlus

The twist (A and E), rise (B and F), twist–rise (C and G) and helical phase (D and H) correlations within DNA-cry (A–D) and DNA-nmr (E–H) at base pair steps separated by i intervening base pairs (i = 0 for correlations at the same step, i = 1 for adjoining steps, etc.).
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Figure 3: The twist (A and E), rise (B and F), twist–rise (C and G) and helical phase (D and H) correlations within DNA-cry (A–D) and DNA-nmr (E–H) at base pair steps separated by i intervening base pairs (i = 0 for correlations at the same step, i = 1 for adjoining steps, etc.).

Mentions: Using the DNA-cry and -nmr models, we calculated the pair correlation functions 〈 x/y〉 ≡ 〈(x − 〈x 〉) (y − 〈 y〉)〉, for the twist (<Ωl /Ωl+i >, rise (g20<hl/hl+i >), twist-rise (g0<Ωl/hl+i>), and helical phase step (<δΦl/δΦl+i> where δΦl ≡ Φl − Φl−1) as outlined in the ‘Methods’ section. Here the indices l and i indicate the number of the base pair step in the DNA construct. We used three different sets of Ωi and hi (see ‘Methods’ section): (i) based on the standard local reference frame implemented in NDB, to which we refer to as a local z/3DNA set; (ii) based on the global helical axis for each oligonucleotide and Freehelix reference frame, to which we refer to as a global z/Freehelix set and (iii) based on the local Freehelix reference frame, to which we refer to as a local z/Freehelix set. All three sets produced similar pair correlation functions (Figure 3).Figure 3.


Helical coherence of DNA in crystals and solution.

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

The twist (A and E), rise (B and F), twist–rise (C and G) and helical phase (D and H) correlations within DNA-cry (A–D) and DNA-nmr (E–H) at base pair steps separated by i intervening base pairs (i = 0 for correlations at the same step, i = 1 for adjoining steps, etc.).
© Copyright Policy - creative-commons
Related In: Results  -  Collection

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

Figure 3: The twist (A and E), rise (B and F), twist–rise (C and G) and helical phase (D and H) correlations within DNA-cry (A–D) and DNA-nmr (E–H) at base pair steps separated by i intervening base pairs (i = 0 for correlations at the same step, i = 1 for adjoining steps, etc.).
Mentions: Using the DNA-cry and -nmr models, we calculated the pair correlation functions 〈 x/y〉 ≡ 〈(x − 〈x 〉) (y − 〈 y〉)〉, for the twist (<Ωl /Ωl+i >, rise (g20<hl/hl+i >), twist-rise (g0<Ωl/hl+i>), and helical phase step (<δΦl/δΦl+i> where δΦl ≡ Φl − Φl−1) as outlined in the ‘Methods’ section. Here the indices l and i indicate the number of the base pair step in the DNA construct. We used three different sets of Ωi and hi (see ‘Methods’ section): (i) based on the standard local reference frame implemented in NDB, to which we refer to as a local z/3DNA set; (ii) based on the global helical axis for each oligonucleotide and Freehelix reference frame, to which we refer to as a global z/Freehelix set and (iii) based on the local Freehelix reference frame, to which we refer to as a local z/Freehelix set. All three sets produced similar pair correlation functions (Figure 3).Figure 3.

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