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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

(A) A typical diffraction pattern of hydrated DNA fibers (39) showing the layer lines. Imperfect vertical alignment results in broadening of these lines, but average tilt may be estimated from the width of the equatorial Bragg peak. (B) The helical coherence length extracted from experimental diffraction patterns taken from DNA fibers at different degrees of hydration (fiber density); open circles from data provided kindly by S. Zimmermann (16,38) and the filled square from the pattern shown in (A). The plotted values of λc were extracted by direct fitting of kz cross sections of n = ±5 peaks with Equation (13) without any corrections. The correction for the imperfect vertical alignment discussed in the text (‘Results’ section) increases estimated λc by 20–30% to 100–130 Å.
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Figure 6: (A) A typical diffraction pattern of hydrated DNA fibers (39) showing the layer lines. Imperfect vertical alignment results in broadening of these lines, but average tilt may be estimated from the width of the equatorial Bragg peak. (B) The helical coherence length extracted from experimental diffraction patterns taken from DNA fibers at different degrees of hydration (fiber density); open circles from data provided kindly by S. Zimmermann (16,38) and the filled square from the pattern shown in (A). The plotted values of λc were extracted by direct fitting of kz cross sections of n = ±5 peaks with Equation (13) without any corrections. The correction for the imperfect vertical alignment discussed in the text (‘Results’ section) increases estimated λc by 20–30% to 100–130 Å.

Mentions: A typical diffraction pattern from hydrated, oriented fibers of B-DNA is illustrated in Figure 6A by a reproduction of the classical Franklin and Gosling picture (39). The two strong peaks on the equator (n = 0 line) at are coherent scattering on DNA packed in a hexagonal array with the interaxial separation dint (intermolecular scattering). For a long time the diffraction peaks at n=±1, ±2, ±3 and ±5 lines were believed to be incoherent scattering on separate molecules (intramolecular scattering) (39,44). A recent study showed that intermolecular scattering may contribute to the latter peaks as well, but this contribution decreases exponentially with n2 and becomes small already at n= ±3 (38). While different interpretation of the n=±1, ±2, ±3 peaks may still be possible, it is clear that the n=±5 peaks in hydrated fibers should not be affected by intermolecular scattering.Figure 6.


Helical coherence of DNA in crystals and solution.

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

(A) A typical diffraction pattern of hydrated DNA fibers (39) showing the layer lines. Imperfect vertical alignment results in broadening of these lines, but average tilt may be estimated from the width of the equatorial Bragg peak. (B) The helical coherence length extracted from experimental diffraction patterns taken from DNA fibers at different degrees of hydration (fiber density); open circles from data provided kindly by S. Zimmermann (16,38) and the filled square from the pattern shown in (A). The plotted values of λc were extracted by direct fitting of kz cross sections of n = ±5 peaks with Equation (13) without any corrections. The correction for the imperfect vertical alignment discussed in the text (‘Results’ section) increases estimated λc by 20–30% to 100–130 Å.
© Copyright Policy - creative-commons
Related In: Results  -  Collection

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

Figure 6: (A) A typical diffraction pattern of hydrated DNA fibers (39) showing the layer lines. Imperfect vertical alignment results in broadening of these lines, but average tilt may be estimated from the width of the equatorial Bragg peak. (B) The helical coherence length extracted from experimental diffraction patterns taken from DNA fibers at different degrees of hydration (fiber density); open circles from data provided kindly by S. Zimmermann (16,38) and the filled square from the pattern shown in (A). The plotted values of λc were extracted by direct fitting of kz cross sections of n = ±5 peaks with Equation (13) without any corrections. The correction for the imperfect vertical alignment discussed in the text (‘Results’ section) increases estimated λc by 20–30% to 100–130 Å.
Mentions: A typical diffraction pattern from hydrated, oriented fibers of B-DNA is illustrated in Figure 6A by a reproduction of the classical Franklin and Gosling picture (39). The two strong peaks on the equator (n = 0 line) at are coherent scattering on DNA packed in a hexagonal array with the interaxial separation dint (intermolecular scattering). For a long time the diffraction peaks at n=±1, ±2, ±3 and ±5 lines were believed to be incoherent scattering on separate molecules (intramolecular scattering) (39,44). A recent study showed that intermolecular scattering may contribute to the latter peaks as well, but this contribution decreases exponentially with n2 and becomes small already at n= ±3 (38). While different interpretation of the n=±1, ±2, ±3 peaks may still be possible, it is clear that the n=±5 peaks in hydrated fibers should not be affected by intermolecular scattering.Figure 6.

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