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Geometrical correlations in the nucleosomal DNA conformation and the role of the covalent bonds rigidity.

Ghorbani M, Mohammad-Rafiee F - Nucleic Acids Res. (2010)

Bottom Line: We develop a simple elastic model to study the conformation of DNA in the nucleosome core particle.We show that because of the rigidity of the covalent bonds in the sugar-phosphate backbones, the base pair parameters are highly correlated, especially, strong twist-roll-slide correlation in the conformation of the nucleosomal DNA is vividly observed in the calculated results.This simple model succeeds to account for the detailed features of the structure of the nucleosomal DNA, particularly, its more important base pair parameters, roll and slide, in good agreement with the experimental results.

View Article: PubMed Central - PubMed

Affiliation: Department of Physics, Institute for Advanced Studies in Basic Sciences, Zanjan 45137-66731, Iran.

ABSTRACT
We develop a simple elastic model to study the conformation of DNA in the nucleosome core particle. In this model, the changes in the energy of the covalent bonds that connect the base pairs of each strand of the DNA double helix, as well as the lateral displacements and the rotation of adjacent base pairs are considered. We show that because of the rigidity of the covalent bonds in the sugar-phosphate backbones, the base pair parameters are highly correlated, especially, strong twist-roll-slide correlation in the conformation of the nucleosomal DNA is vividly observed in the calculated results. This simple model succeeds to account for the detailed features of the structure of the nucleosomal DNA, particularly, its more important base pair parameters, roll and slide, in good agreement with the experimental results.

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Related in: MedlinePlus

The calculated and the experimentally observed roll, tilt, shift and slide. The filled circles correspond to the experimental data taken from Reference (7), and the hollow squares show the calculated results using A1 = 75 nm, A2 = 37 nm,  and G = 25 nm. In the calculation process, the twist angles are directly read off from the experimental data of Richmond and Davey. We can see a strong coupling between twist, roll and slide. The negative values of the roll and positive values of the slide are in good agreement with the experimental results.
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Figure 2: The calculated and the experimentally observed roll, tilt, shift and slide. The filled circles correspond to the experimental data taken from Reference (7), and the hollow squares show the calculated results using A1 = 75 nm, A2 = 37 nm, and G = 25 nm. In the calculation process, the twist angles are directly read off from the experimental data of Richmond and Davey. We can see a strong coupling between twist, roll and slide. The negative values of the roll and positive values of the slide are in good agreement with the experimental results.

Mentions: After minimizing the energy of the Equation (8), with considering the wrapping constraint, Equation (15) and reading off the twist values from the experimental data of Richmond and Davey, the calculated values of the roll (R), tilt (T), shift (S), Slide (D) and rise are found. We have shown the results in Figures 2 and 3. As one can see, the calculated values of the base pair parameters are significantly correlated with the experimental results of Reference (7), especially, for the roll and slide.Figure 2.


Geometrical correlations in the nucleosomal DNA conformation and the role of the covalent bonds rigidity.

Ghorbani M, Mohammad-Rafiee F - Nucleic Acids Res. (2010)

The calculated and the experimentally observed roll, tilt, shift and slide. The filled circles correspond to the experimental data taken from Reference (7), and the hollow squares show the calculated results using A1 = 75 nm, A2 = 37 nm,  and G = 25 nm. In the calculation process, the twist angles are directly read off from the experimental data of Richmond and Davey. We can see a strong coupling between twist, roll and slide. The negative values of the roll and positive values of the slide are in good agreement with the experimental results.
© Copyright Policy - creative-commons
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC3045607&req=5

Figure 2: The calculated and the experimentally observed roll, tilt, shift and slide. The filled circles correspond to the experimental data taken from Reference (7), and the hollow squares show the calculated results using A1 = 75 nm, A2 = 37 nm, and G = 25 nm. In the calculation process, the twist angles are directly read off from the experimental data of Richmond and Davey. We can see a strong coupling between twist, roll and slide. The negative values of the roll and positive values of the slide are in good agreement with the experimental results.
Mentions: After minimizing the energy of the Equation (8), with considering the wrapping constraint, Equation (15) and reading off the twist values from the experimental data of Richmond and Davey, the calculated values of the roll (R), tilt (T), shift (S), Slide (D) and rise are found. We have shown the results in Figures 2 and 3. As one can see, the calculated values of the base pair parameters are significantly correlated with the experimental results of Reference (7), especially, for the roll and slide.Figure 2.

Bottom Line: We develop a simple elastic model to study the conformation of DNA in the nucleosome core particle.We show that because of the rigidity of the covalent bonds in the sugar-phosphate backbones, the base pair parameters are highly correlated, especially, strong twist-roll-slide correlation in the conformation of the nucleosomal DNA is vividly observed in the calculated results.This simple model succeeds to account for the detailed features of the structure of the nucleosomal DNA, particularly, its more important base pair parameters, roll and slide, in good agreement with the experimental results.

View Article: PubMed Central - PubMed

Affiliation: Department of Physics, Institute for Advanced Studies in Basic Sciences, Zanjan 45137-66731, Iran.

ABSTRACT
We develop a simple elastic model to study the conformation of DNA in the nucleosome core particle. In this model, the changes in the energy of the covalent bonds that connect the base pairs of each strand of the DNA double helix, as well as the lateral displacements and the rotation of adjacent base pairs are considered. We show that because of the rigidity of the covalent bonds in the sugar-phosphate backbones, the base pair parameters are highly correlated, especially, strong twist-roll-slide correlation in the conformation of the nucleosomal DNA is vividly observed in the calculated results. This simple model succeeds to account for the detailed features of the structure of the nucleosomal DNA, particularly, its more important base pair parameters, roll and slide, in good agreement with the experimental results.

Show MeSH
Related in: MedlinePlus