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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 relative changes in the length of the covalent bonds between the adjacent base pairs of the two strands of DNA,  (filled circles) and  (hollow squares).
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Figure 5: The relative changes in the length of the covalent bonds between the adjacent base pairs of the two strands of DNA, (filled circles) and (hollow squares).

Mentions: Using Equations (3)–(5) and the proper relations for the changes in the length of the covalent bonds between the adjacent base pairs of the two strands of DNA, one can determine the overall stretching of each strand of the nucleosomal DNA. The relative changes in the length of the covalent bonds between the adjacent base pairs of the two strands of DNA are shown in Figure 5. We see that the mentioned relative changes are less than for most of the base pair steps. As is expected, because of the rigidity of the covalent bonds, the arc length of the backbones does not vary significantly during the deformation. We note that, since DNA is an anisotropic molecule, the changes in the length of the springs of the two strands are not necessarily the same. In few base pairs, the length of the spring of one strand extends while the length of the spring of the other one decreases. In the base pair steps that the relative changes in the length of the springs are >10%, the relative changes in the twist are also large, which could be a consequence of DNA–protein interactions and sequence effects.Figure 5.


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 relative changes in the length of the covalent bonds between the adjacent base pairs of the two strands of DNA,  (filled circles) and  (hollow squares).
© Copyright Policy - creative-commons
Related In: Results  -  Collection

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

Figure 5: The relative changes in the length of the covalent bonds between the adjacent base pairs of the two strands of DNA, (filled circles) and (hollow squares).
Mentions: Using Equations (3)–(5) and the proper relations for the changes in the length of the covalent bonds between the adjacent base pairs of the two strands of DNA, one can determine the overall stretching of each strand of the nucleosomal DNA. The relative changes in the length of the covalent bonds between the adjacent base pairs of the two strands of DNA are shown in Figure 5. We see that the mentioned relative changes are less than for most of the base pair steps. As is expected, because of the rigidity of the covalent bonds, the arc length of the backbones does not vary significantly during the deformation. We note that, since DNA is an anisotropic molecule, the changes in the length of the springs of the two strands are not necessarily the same. In few base pairs, the length of the spring of one strand extends while the length of the spring of the other one decreases. In the base pair steps that the relative changes in the length of the springs are >10%, the relative changes in the twist are also large, which could be a consequence of DNA–protein interactions and sequence effects.Figure 5.

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