4/27/2023 0 Comments Jmol b dna![]() However, the relative importance of both stabilizing interactions as well as how they interfere with each other is largely unknown. It is known that the stability of the double helical structure of B-DNA is supplied by the hydrogen bonds as proposed by Watson and Crick 3 and by the stacking interactions. In the present work, we wish to gain more insight in the stability of the structure of B-DNA with high-level quantum chemical computations. 2 It was shown how π–π stacking plays a less pronounced role for the selectivity, but it is important for the overall stability of the aggregate of incoming nucleotide and the template-primer complex. We showed that the intrinsic affinity of the template-primer complex to select the correct natural DNA base derives from the concerted action of hydrogen-bonding patterns, (de)solvation effects, twist angle and π–π stacking interactions. 2 This study consisted of the first high-level quantum chemical study on DNA replication covering not only the formation of DNA base pairs but also π–π stacking interactions in a model system consisting of four DNA bases. 1,2 Recently, we revealed the importance of π–π stacking as well solvent effects for the immensely high fidelity with which DNA replication occurs. Introduction Stacking interactions play a central role in determining the structure and stability of DNA, as follows from various computational studies. 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. The electronic mechanism behind this preference for a twisted arrangement depends on the base pairs involved. This holds especially for stacked AT pairs but also for other stacked base pairs, including GC. ![]() 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. Furthermore, we have analyzed the functionality of the twist-angle on the stability of the structure. 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. 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. We have computationally investigated the structure and stability of B-DNA.
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