Issue 26, 2014

B-DNA structure and stability: the role of hydrogen bonding, π–π stacking interactions, twist-angle, and solvation

Abstract

We have computationally investigated the structure and stability of B-DNA. To this end, we have analyzed the bonding in a series of 47 stacks consisting of two base pairs, in which the base pairs cover the full range of natural Watson–Crick pairs, mismatched pairs, and artificial DNA base pairs. Our analyses provide detailed insight into the role and relative importance of the various types of interactions, such as, hydrogen bonding, π–π stacking interactions, and solvation/desolvation. Furthermore, we have analyzed the functionality of the twist-angle on the stability of the structure. Interestingly, we can show that all stacked base pairs benefit from a stabilization by 6 to 12 kcal mol−1 if stacked base pairs are twisted from 0° to 36°, that is, if they are mutually rotated from a congruent superposition to the mutually twisted stacking configuration that occurs in B-DNA. This holds especially for stacked AT pairs but also for other stacked base pairs, including GC. The electronic mechanism behind this preference for a twisted arrangement depends on the base pairs involved. We also show that so-called “diagonal interactions” (or cross terms) in the stacked base pairs are crucial for understanding the stability of B-DNA, in particular, in GC-rich sequences.

Graphical abstract: B-DNA structure and stability: the role of hydrogen bonding, π–π stacking interactions, twist-angle, and solvation

Supplementary files

Article information

Article type
Paper
Submitted
24 פבר 2014
Accepted
20 מאי 2014
First published
20 מאי 2014
This article is Open Access
Creative Commons BY-NC license

Org. Biomol. Chem., 2014,12, 4691-4700

Author version available

B-DNA structure and stability: the role of hydrogen bonding, π–π stacking interactions, twist-angle, and solvation

J. Poater, M. Swart, F. M. Bickelhaupt and C. Fonseca Guerra, Org. Biomol. Chem., 2014, 12, 4691 DOI: 10.1039/C4OB00427B

This article is licensed under a Creative Commons Attribution-NonCommercial 3.0 Unported Licence. You can use material from this article in other publications, without requesting further permission from the RSC, provided that the correct acknowledgement is given and it is not used for commercial purposes.

To request permission to reproduce material from this article in a commercial publication, please go to the Copyright Clearance Center request page.

If you are an author contributing to an RSC publication, you do not need to request permission provided correct acknowledgement is given.

If you are the author of this article, you do not need to request permission to reproduce figures and diagrams provided correct acknowledgement is given. If you want to reproduce the whole article in a third-party commercial publication (excluding your thesis/dissertation for which permission is not required) please go to the Copyright Clearance Center request page.

Read more about how to correctly acknowledge RSC content.

Social activity

Spotlight

Advertisements