%0 Journal Article %A Bei Liu %A Honglue Shi %A Atul Rangadurai %A Felix Nussbaumer %A Chia-Chieh Chu %A Kevin Andreas Erharter %A David A. Case %A Christoph Kreutz %A Hashim M. Al-Hashimi %T A quantitative model predicts how m6A reshapes the kinetic landscape of nucleic acid hybridization and conformational transitions %D 2020 %R 10.1101/2020.12.25.424401 %J bioRxiv %P 2020.12.25.424401 %X N6-methyladenosine (m6A) is a post-transcriptional modification that controls gene expression by recruiting proteins to RNA sites. The modification also slows biochemical processes through mechanisms that are not understood. Using NMR relaxation dispersion, we show that m6A pairs with uridine with the methylamino group in the anti conformation to form a Watson-Crick base pair that transiently exchanges on the millisecond timescale with a singly hydrogen-bonded low-populated (1%) mismatch-like conformation in which the methylamino group is syn. This ability to rapidly interchange between Watson-Crick or mismatch-like forms, combined with different syn:anti isomer preferences when paired (~1:100) versus unpaired (~10:1), explains how m6A robustly slows duplex annealing without affecting melting via two pathways in which isomerization occurs before or after duplex annealing. Our model quantitatively predicts how m6A reshapes the kinetic landscape of nucleic acid hybridization and conformational transitions, and provides an explanation for why the modification robustly slows diverse cellular processes.Competing Interest StatementH.M.A. is an advisor to and holds an ownership interest in Nymirum, an RNA-based drug discovery company. C.K. is an advisor to and holds an ownership interest in INNotope, a company providing RNA stable isotope labelling products. The remaining authors declare no competing interests. %U https://www.biorxiv.org/content/biorxiv/early/2020/12/26/2020.12.25.424401.full.pdf