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Tautomeric equilibria of nucleobases in the hachimoji expanded genetic alphabet

Eberlein, Lukas, Beierlein, Frank R., van Eikema Hommes, Nico J.R., Radadiya, Ashish ORCID:, Heil, Jochen, Benner, Steven A., Clark, Timothy, Kast, Stefan M. and Richards, Nigel G. J. ORCID: 2020. Tautomeric equilibria of nucleobases in the hachimoji expanded genetic alphabet. Journal of Chemical Theory and Computation 16 (4) , pp. 2766-2777. 10.1021/acs.jctc.9b01079

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Evolution has yielded biopolymers that are constructed from exactly four building blocks and are able to support Darwinian evolution. Synthetic biology aims to extend this alphabet, and we recently showed that 8-letter (hachimoji) DNA can support rule-based information encoding. One source of replicative error in non-natural DNA-like systems, however, is the occurrence of alternative tautomeric forms, which pair differently. Unfortunately, little is known about how structural modifications impact free-energy differences between tautomers of the non-natural nucleo¬bases used in the hachimoji expanded genetic alphabet. Determining experimental tautomer ratios is technically difficult and so strategies for improving hachimoji DNA replication efficiency will benefit from accurate computational predictions of equilibrium tautomeric ratios. We now report that high-level quantum-chemical calculations in aqueous solution by the embedded cluster reference interaction site model (EC-RISM), benchmarked against free energy molecular simulations for solvation thermodynamics, provide useful quantitative information on the tautomer ratios of both Watson-Crick and hachimoji nucleobases. In agreement with previous computational studies, all four Watson-Crick nucleobases adopt essentially only one tautomer in water. This is not the case, however, for non-natural nucleobases and their analogs. For example, although the enols of isoguanine and a series of related purines are not populated in water, these heterocycles possess N1-H and N3-H keto tautomers that are similar in energy thereby adversely impacting accurate nucleobase pairing. These robust computational strategies offer a firm basis for improving experimental measurements of tautomeric ratios, which are currently limited to studying molecules that exist only as two tautomers in solution.

Item Type: Article
Date Type: Publication
Status: Published
Schools: Chemistry
Advanced Research Computing @ Cardiff (ARCCA)
Publisher: American Chemical Society
ISSN: 1549-9626
Funders: BBSRC
Date of First Compliant Deposit: 13 March 2020
Date of Acceptance: 3 March 2020
Last Modified: 07 Nov 2023 01:40

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