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
The Journal of Physical Chemistry B
Crystal structure, Genetics Interaction energies, Mathematical methods, Modification
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.
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.
Available for download on Wednesday, September 11, 2024