Structural and Energetic Features of Base–Base Stacking Contacts in RNA

Authors

Zakir Ali, Computational Biochemistry Laboratory, Department of Chemistry and Centre for Advanced Studies in Chemistry, Panjab University, Chandigarh
Ambika Goyal, Computational Biochemistry Laboratory, Department of Chemistry and Centre for Advanced Studies in Chemistry, Panjab University, Chandigarh
Ayush Jhunjhunwala, Center for Computational Natural Sciences and Bioinformatics, International Institute of Information Technology, Hyderabad, Gachibowli, Hyderabad, Telangana
Abhijit Mitra, Center for Computational Natural Sciences and Bioinformatics, International Institute of Information Technology, Hyderabad, Gachibowli, Hyderabad, Telangana
John F. Trant, Department of Chemistry and Biochemistry, University of Windsor, 401 Sunset Avenue, Windsor, OntarioN9B 3P4, Canada Binary Star Research Services, LaSalle, Ontario N9J 3X8, CanadaFollow
Purshotam Sharma, Computational Biochemistry Laboratory, Department of Chemistry and Centre for Advanced Studies in Chemistry, Panjab University, Chandigarh160014, India Department of Chemistry and Biochemistry, University of Windsor, 401 Sunset Avenue, Windsor, Ontario N9B 3P4, CanadaFollow

Author ORCID Identifier

https://orcid.org/0000-0001-9597-4737 : Zakir Ali

https://orcid.org/0000-0002-6876-4838 : Abhijit Mitra

https://orcid.org/0000-0002-5164-9833 : Purshotam Sharma

https://orcid.org/0000-0002-4780-4968 : John F. Trant

Document Type

Article

Publication Date

1-12-2023

Publication Title

Journal of Chemical Information and Modeling

Volume

2023

Issue

63

First Page

655

Keywords

Chemical structure, Crystal structure, Genetics, Interaction energies, Mathematical methods

Last Page

669

Abstract

Nucleobase π–π stacking is one of the crucial organizing interactions within three-dimensional (3D) RNA architectures. Characterizing the structural variability of these contacts in RNA crystal structures will help delineate their subtleties and their role in determining function. This analysis of different stacking geometries found in RNA X-ray crystal structures is the largest such survey to date; coupled with quantum-mechanical calculations on typical representatives of each possible stacking arrangement, we determined the distribution of stacking interaction energies. A total of 1,735,481 stacking contacts, spanning 359 of the 384 theoretically possible distinct stacking geometries, were identified. Our analysis reveals preferential occurrences of specific consecutive stacking arrangements in certain regions of RNA architectures. Quantum chemical calculations suggest that 88 of the 359 contacts possess intrinsically stable stacking geometries, whereas the remaining stacks require the RNA backbone or surrounding macromolecular environment to force their formation and maintain their stability. Our systematic analysis of π–π stacks in RNA highlights trends in the occurrence and localization of these noncovalent interactions and may help better understand the structural intricacies of functional RNA-based molecular architectures.

DOI

https://doi.org/10.1021/acs.jcim.2c01116

ISSN

1549-9596

Recommended Citation

Ali, Zakir; Goyal, Ambika; Jhunjhunwala, Ayush; Mitra, Abhijit; Trant, John F.; and Sharma, Purshotam. (2023). Structural and Energetic Features of Base–Base Stacking Contacts in RNA. Journal of Chemical Information and Modeling, 2023 (63), 655-669.
https://scholar.uwindsor.ca/chemistrybiochemistrypub/344