Structural Mapping of the Base Stacks Containing Post-transcriptionally Modified Bases in RNA

Authors

Zakir Ali, Computational Biochemistry Laboratory, Department of Chemistry and Centre for Advanced Studies in Chemistry, Panjab University, Chandigarh
Sarabjeet Kaur, Computational Biochemistry Laboratory, Department of Chemistry and Centre for Advanced Studies in Chemistry, Panjab University, Chandigarh 160014, India Surface Chemistry and Catalysis: Characterisation and Application Team (COK-KAT), Leuven (Arenberg) Celestijnenlaan 200f─Box 2461, 3001 Leuven, Belgium
Teagan Kukhta, Department of Chemistry and Biochemistry, University of Windsor, 401 Sunset Avenue, Windsor, Ontario N9B 3P4, Canada
Abd Al-Aziz A Abu-Saleh, Department of Chemistry and Biochemistry, University of Windsor, 401 Sunset Avenue, Windsor, Ontario N9B 3P4, Canada Binary Star Research Services, LaSalle, Ontario N9J 3X8, Canada
Ayush Jhunjhunwala, Center for Computational Natural Sciences and Bioinformatics, International Institute of Information Technology (IIIT-H), Gachibowli, Hyderabad, Telangana
Abhijit Mitra, Center for Computational Natural Sciences and Bioinformatics, International Institute of Information Technology (IIIT-H), Gachibowli, Hyderabad, Telangana
John F. Trant, Department of Chemistry and Biochemistry, University of Windsor, 401 Sunset Avenue, Windsor, Ontario N9B 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, Chandigarh 160014, 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/0000-0003-1234-4161 : Sarabjeet Kaur

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

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

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

Document Type

Article

Publication Date

6-27-2023

Publication Title

The Journal of Physical Chemistry B

Volume

2023

Issue

127

First Page

6049

Keywords

Crystal structure, Genetics Interaction energies, Mathematical methods, Modification

Last Page

6060

Abstract

Post-transcriptionally modified bases play vital roles in many biochemical processes involving RNA. Analysis of the non-covalent interactions associated with these bases in RNA is crucial for providing a more complete understanding of the RNA structure and function; however, the characterization of these interactions remains understudied. To address this limitation, we present a comprehensive analysis of base stacks involving all crystallographic occurrences of the most biologically relevant modified bases in a large dataset of high-resolution RNA crystal structures. This is accompanied by a geometrical classification of the stacking contacts using our established tools. Coupled with quantum chemical calculations and an analysis of the specific structural context of these stacks, this provides a map of the stacking conformations available to modified bases in RNA. Overall, our analysis is expected to facilitate structural research on altered RNA bases.

DOI

10.1021/acs.jpcb.3c02268

ISSN

1520-6106

Recommended Citation

Ali, Zakir; Kaur, Sarabjeet; Kukhta, Teagan; Abu-Saleh, Abd Al-Aziz A; Jhunjhunwala, Ayush; Mitra, Abhijit; Trant, John F.; and Sharma, Purshotam. (2023). Structural Mapping of the Base Stacks Containing Post-transcriptionally Modified Bases in RNA. The Journal of Physical Chemistry B, 2023 (127), 6049-6060.
https://scholar.uwindsor.ca/chemistrybiochemistrypub/330