Stacking of nucleic acid bases: optimization of the computational approach—the case of adenine dimers

Marek, Paulina H.; Szatyłowicz, Halina; Krygowski, Tadeusz M.

doi:10.1007/s11224-018-1253-7

Cited by 21 publications

(15 citation statements)

References 33 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…Further, two orientations either possess equal stability (isoenergetic) or up to 3.7 kcal mol −1 difference in their stacking interaction energies. In synchrony with previous quantum chemical calculations, 22,23,26 the substantial stability of both orientations for all four face orientations suggests that glycosidic orientation is a key parameter in distinguishing different stacks within each face combination. This in turn suggests that inclusion of the relative orientation of glycosidic bonds adds value toward a comprehensive annotation of stacked bases in RNA structural motifs.…”

Section: ■ Results and Discussionsupporting

confidence: 84%

On the Nature of Nucleobase Stacking in RNA: A Comprehensive Survey of Its Structural Variability and a Systematic Classification of Associated Interactions

Jhunjhunwala

Ali

Bhattacharya

et al. 2021

J. Chem. Inf. Model.

View full text Add to dashboard Cite

The astonishing diversity in folding patterns of RNA threedimensional (3D) structures is crafted by myriads of noncovalent contacts, of which base pairing and stacking are the most prominent. A systematic and comprehensive classification and annotation of these interactions is necessary for a molecular-level understanding of their roles. However, unlike in the case of base pairing, where a widely accepted nomenclature and classification scheme exists in the public domain, currently available classification schemes for base−base stacking need major enhancements to comprehensively capture the necessary features underlying the rich stacking diversity in RNA. Here, we extend the previous stacking classification based on nucleobase interacting faces by introducing a structurally intuitive geometry-cum topology-based scheme. Specifically, a stack is first classified in terms of the geometry described by the relative orientation of the glycosidic bonds, which generates eight basic stacking geometric families for heterodimeric stacks and six of those for homodimeric stacks. Further annotation in terms of the identity of the bases and the region of involvement of purines (five-membered, six-membered, or both rings) leads to the enumeration of 384 distinct RNA base stacks. Based on our classification scheme, we present an algorithm for automated identification of stacks in RNA crystal structures and analyze the stacking context in selected RNA structures. Overall, the work described here is expected to greatly facilitate the structure-based RNA research.

show abstract

Section: ■ Results and Discussionsupporting

confidence: 84%

On the Nature of Nucleobase Stacking in RNA: A Comprehensive Survey of Its Structural Variability and a Systematic Classification of Associated Interactions

Jhunjhunwala

Ali

Bhattacharya

et al. 2021

J. Chem. Inf. Model.

View full text Add to dashboard Cite

show abstract

“…For each studied system, optimization was carried out without any symmetry constraints (in the gas phase and in the solution) using the Gaussian09 program . According to the results of our previous research, the DFT-D method was used, namely, the B97D3 functional with Dunning’s aug-cc-pVDZ basis set . The choice of this computational level was due to its ability to characterize stacking interactions in adenine dimers; both energetic and geometric criteria were taken into account .…”

Section: Computational Detailsmentioning

confidence: 99%

Effect of the Solvent and Substituent on Tautomeric Preferences of Amine-Adenine Tautomers

et al. 2021

Self Cite

View full text Add to dashboard Cite

Adenine is one of the basic molecules of life; it is also an important building block in the synthesis of new pharmaceuticals, electrochemical (bio)sensors, or self-assembling molecular materials. Therefore, it is important to know the effects of the solvent and substituent on the electronic structure of adenine tautomers and their stability. The four most stable adenine amino tautomers (9H, 7H, 3H, and 1H), modified by substitution (C2– or C8−) of electron-withdrawing NO2 and electron-donating NH2 groups, are studied theoretically in the gas phase and in solvents of different polarities (1 ≤ ε < 109). Solvents have been modeled using the polarizable continuum model. Comparison of the stability of substituted adenine tautomers in various solvents shows that substitution can change tautomeric preferences with respect to the unsubstituted adenine. Moreover, C8 substitution results in slight energy differences between tautomers in polar solvents (<1 kcal/mol), which suggests that in aqueous solution, C8–X-substituted adenine systems may consist of a considerable amount of two tautomers9H and 7H for X = NH2 and 3H and 9H for X = NO2. Furthermore, solvation enhances the effect of the nitro group; however, the enhancement strongly depends on the proximity effects. This enhancement for the NO2 group with two repulsive N···ON contacts can be threefold higher than that for the NO2 with one attractive NH···ON contact. The proximity effects are even more significant for the NH2 group, as the solvation may increase or decrease its electron-donating ability, depending on the type of proximity.

show abstract

“…For all studied systems, optimization without any symmetry constraints was performed using the Gaussian 09 package. 38 According to the results of our previous research, 39 the DFT-D methods were used, that is functionals B97D3 (ref. 40) and uB97XD, 41 both with Dunning's aug-cc-pvdz basis set.…”

Section: Introductionmentioning

confidence: 99%

Substituent effects on the stability of the four most stable tautomers of adenine and purine

et al. 2019

Self Cite

View full text Add to dashboard Cite

show abstract

Stacking of nucleic acid bases: optimization of the computational approach—the case of adenine dimers

Cited by 21 publications

References 33 publications

On the Nature of Nucleobase Stacking in RNA: A Comprehensive Survey of Its Structural Variability and a Systematic Classification of Associated Interactions

On the Nature of Nucleobase Stacking in RNA: A Comprehensive Survey of Its Structural Variability and a Systematic Classification of Associated Interactions

Effect of the Solvent and Substituent on Tautomeric Preferences of Amine-Adenine Tautomers

Substituent effects on the stability of the four most stable tautomers of adenine and purine

Contact Info

Product

Resources

About