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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 six base pair parameters; twist, roll, tilt, rise, shift and slide. DNA base pairs are shown by rectangular solids (top). Schematic view of the adjacent base pairs, and the covalent bonds along the backbones, which are simply modeled by two springs (bottom). The half of the length and width of of the base pairs are shown by l and w, respectively, and b equals to the rise of undeformed DNA. At each base pair, we consider a localized Cartesian coordinate system xyz.
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Figure 1: The six base pair parameters; twist, roll, tilt, rise, shift and slide. DNA base pairs are shown by rectangular solids (top). Schematic view of the adjacent base pairs, and the covalent bonds along the backbones, which are simply modeled by two springs (bottom). The half of the length and width of of the base pairs are shown by l and w, respectively, and b equals to the rise of undeformed DNA. At each base pair, we consider a localized Cartesian coordinate system xyz.

Mentions: The base pairs are considered as rectangular solids of half length and width of l = 1 nm and w = 1/3 nm (11). As a result of deformation and changes in the base pair parameters values, the lengths of two strands of DNA can change. These changes result in the elastic energy of deformed covalent bonds between the monomers of each strand. DNA is an anisotropic chiral molecule, so the changes in the length of the two strands can differ. The covalent bonds between the bases of each strand are modeled by springs of stiffness of about kc≃104 pN/nm (12). These springs connect the middle of the width of one base pair to that of the adjacent base pair. At each base pair, we can affix a localized Cartesian coordinate system, so that its x and y axes lie along the width and length of the rectangular solid, respectively (Figure 1). The orientation of these localized coordinates can change from one base pair to the other and we have:(1)where α = 1,2,3 labels the three axes of the localized coordinates, n is a dimensionless parameter, which labels the base pair, δ is the z component of the displacement vector between the middle of the adjacent base pairs and shows the rate of the change in the orientation of the adjacent rectangular solids, and can be written in terms of the angular base pair parameters; roll, R, tilt, T and twist, θ, as:(2)Figure 1.


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 six base pair parameters; twist, roll, tilt, rise, shift and slide. DNA base pairs are shown by rectangular solids (top). Schematic view of the adjacent base pairs, and the covalent bonds along the backbones, which are simply modeled by two springs (bottom). The half of the length and width of of the base pairs are shown by l and w, respectively, and b equals to the rise of undeformed DNA. At each base pair, we consider a localized Cartesian coordinate system xyz.
© Copyright Policy - creative-commons
Related In: Results  -  Collection

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

Figure 1: The six base pair parameters; twist, roll, tilt, rise, shift and slide. DNA base pairs are shown by rectangular solids (top). Schematic view of the adjacent base pairs, and the covalent bonds along the backbones, which are simply modeled by two springs (bottom). The half of the length and width of of the base pairs are shown by l and w, respectively, and b equals to the rise of undeformed DNA. At each base pair, we consider a localized Cartesian coordinate system xyz.
Mentions: The base pairs are considered as rectangular solids of half length and width of l = 1 nm and w = 1/3 nm (11). As a result of deformation and changes in the base pair parameters values, the lengths of two strands of DNA can change. These changes result in the elastic energy of deformed covalent bonds between the monomers of each strand. DNA is an anisotropic chiral molecule, so the changes in the length of the two strands can differ. The covalent bonds between the bases of each strand are modeled by springs of stiffness of about kc≃104 pN/nm (12). These springs connect the middle of the width of one base pair to that of the adjacent base pair. At each base pair, we can affix a localized Cartesian coordinate system, so that its x and y axes lie along the width and length of the rectangular solid, respectively (Figure 1). The orientation of these localized coordinates can change from one base pair to the other and we have:(1)where α = 1,2,3 labels the three axes of the localized coordinates, n is a dimensionless parameter, which labels the base pair, δ is the z component of the displacement vector between the middle of the adjacent base pairs and shows the rate of the change in the orientation of the adjacent rectangular solids, and can be written in terms of the angular base pair parameters; roll, R, tilt, T and twist, θ, as:(2)Figure 1.

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