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Explaining the striking difference in twist-stretch coupling between DNA and RNA: A comparative molecular dynamics analysis.

Liebl K, Drsata T, Lankas F, Lipfert J, Zacharias M - Nucleic Acids Res. (2015)

Bottom Line: Similar results are also found in simulations that include an external torque to induce over- or unwinding of DNA and RNA.Overwinding of RNA results in more compact conformations with a narrower major groove and consequently reduced helical extension.Overwinding of DNA decreases the size of the minor groove and the resulting positive base pair inclination leads to a slender and more extended helical structure.

View Article: PubMed Central - PubMed

Affiliation: Physik-Department T38, Technische Universität München, James-Franck-Strasse, D-85748 Garching, Germany.

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Coupling of helical rise and helical twist variation in unrestraint simulations of dsDNA and dsRNA. The plots were generated from a total of ∼100 000 regularly spaced snapshots (every 10 ps) taken during ∼1 μs unrestraint MD simulations. Recorded helical twist and rise of the 10 central base pair steps were analyzed as the mean helical rise and helical twist within intervals of 0.2°. Error bars for twist and rise were obtained as standard errors of the mean in each interval. The slope of the correlation was extracted from a linear fit to the data for a range of ±1.5° with respect to the average twist (over the entire range of twist values, indicated as dotted line). The slope was 0.032 Å·deg−1 in case of DNA and −0.037 Å·deg−1 in case of RNA.
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Figure 3: Coupling of helical rise and helical twist variation in unrestraint simulations of dsDNA and dsRNA. The plots were generated from a total of ∼100 000 regularly spaced snapshots (every 10 ps) taken during ∼1 μs unrestraint MD simulations. Recorded helical twist and rise of the 10 central base pair steps were analyzed as the mean helical rise and helical twist within intervals of 0.2°. Error bars for twist and rise were obtained as standard errors of the mean in each interval. The slope of the correlation was extracted from a linear fit to the data for a range of ±1.5° with respect to the average twist (over the entire range of twist values, indicated as dotted line). The slope was 0.032 Å·deg−1 in case of DNA and −0.037 Å·deg−1 in case of RNA.

Mentions: The conformational fluctuations observed during unrestrained MD simulations of the duplexes include correlated motions of important helical degrees of freedom. In the present study we are especially interested in the twist-stretch coupling of DNA and RNA as recent single molecule experiments indicated the opposite behavior for DNA and RNA (27). The twist-stretch coupling can be directly extracted from a correlation plot of the helical rise and helical twist (Figure 3). On the length scale of the present duplex oligonucleotides (10 base pair steps) effects due to bending are negligible. The extraction of a mean helical rise on short intervals of the sampled twist (dots in Figure 3) indicates a linear stretch/twist correlation over a range of twist fluctuations for both DNA and RNA. This is compatible with a near harmonic elastic response of the duplex molecules (see also paragraph on stiffness analysis, below). The correlation allows the extraction of the twist-stretch coupling constant (slope) which gives a value of 0.032 Ådeg−1 for DNA and −0.037 Ådeg−1 for RNA. This qualitatively different behavior of an opposite sign was also observed experimentally and the coupling constants are in quite good agreement with recent torque tweezer experiments on larger duplexes yielding 0.014 ± 0.003 Ådeg−1 for DNA and −0.024 ± 0.001 Ådeg−1 for RNA (27), respectively (see also Supplementary Information Table S1).


Explaining the striking difference in twist-stretch coupling between DNA and RNA: A comparative molecular dynamics analysis.

Liebl K, Drsata T, Lankas F, Lipfert J, Zacharias M - Nucleic Acids Res. (2015)

Coupling of helical rise and helical twist variation in unrestraint simulations of dsDNA and dsRNA. The plots were generated from a total of ∼100 000 regularly spaced snapshots (every 10 ps) taken during ∼1 μs unrestraint MD simulations. Recorded helical twist and rise of the 10 central base pair steps were analyzed as the mean helical rise and helical twist within intervals of 0.2°. Error bars for twist and rise were obtained as standard errors of the mean in each interval. The slope of the correlation was extracted from a linear fit to the data for a range of ±1.5° with respect to the average twist (over the entire range of twist values, indicated as dotted line). The slope was 0.032 Å·deg−1 in case of DNA and −0.037 Å·deg−1 in case of RNA.
© Copyright Policy - creative-commons
Related In: Results  -  Collection

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Figure 3: Coupling of helical rise and helical twist variation in unrestraint simulations of dsDNA and dsRNA. The plots were generated from a total of ∼100 000 regularly spaced snapshots (every 10 ps) taken during ∼1 μs unrestraint MD simulations. Recorded helical twist and rise of the 10 central base pair steps were analyzed as the mean helical rise and helical twist within intervals of 0.2°. Error bars for twist and rise were obtained as standard errors of the mean in each interval. The slope of the correlation was extracted from a linear fit to the data for a range of ±1.5° with respect to the average twist (over the entire range of twist values, indicated as dotted line). The slope was 0.032 Å·deg−1 in case of DNA and −0.037 Å·deg−1 in case of RNA.
Mentions: The conformational fluctuations observed during unrestrained MD simulations of the duplexes include correlated motions of important helical degrees of freedom. In the present study we are especially interested in the twist-stretch coupling of DNA and RNA as recent single molecule experiments indicated the opposite behavior for DNA and RNA (27). The twist-stretch coupling can be directly extracted from a correlation plot of the helical rise and helical twist (Figure 3). On the length scale of the present duplex oligonucleotides (10 base pair steps) effects due to bending are negligible. The extraction of a mean helical rise on short intervals of the sampled twist (dots in Figure 3) indicates a linear stretch/twist correlation over a range of twist fluctuations for both DNA and RNA. This is compatible with a near harmonic elastic response of the duplex molecules (see also paragraph on stiffness analysis, below). The correlation allows the extraction of the twist-stretch coupling constant (slope) which gives a value of 0.032 Ådeg−1 for DNA and −0.037 Ådeg−1 for RNA. This qualitatively different behavior of an opposite sign was also observed experimentally and the coupling constants are in quite good agreement with recent torque tweezer experiments on larger duplexes yielding 0.014 ± 0.003 Ådeg−1 for DNA and −0.024 ± 0.001 Ådeg−1 for RNA (27), respectively (see also Supplementary Information Table S1).

Bottom Line: Similar results are also found in simulations that include an external torque to induce over- or unwinding of DNA and RNA.Overwinding of RNA results in more compact conformations with a narrower major groove and consequently reduced helical extension.Overwinding of DNA decreases the size of the minor groove and the resulting positive base pair inclination leads to a slender and more extended helical structure.

View Article: PubMed Central - PubMed

Affiliation: Physik-Department T38, Technische Universität München, James-Franck-Strasse, D-85748 Garching, Germany.

Show MeSH
Related in: MedlinePlus