Protonation-dependent base flipping in the catalytic triad of a small RNA

Zhaoxi Sun, Xiaohui Wang, John Z.H. Zhang

Research output: Contribution to journalArticlepeer-review


Protonation dependent base flipping in RNA has never been studied theoretically. In this work we studied protonation-dependent behavior of the base flipping in the catalytic triad of a single-stranded RNA which was previously characterized by NMR experiment. Molecular dynamics simulation reveals that the GA mismatch in this region accounts for this behavior. Free energy profiles show that the stable point for flipping dihedral shifts about 35° and the free energy barrier along the flipping pathway is elevated upon protonation. The orientation of Guanine from syn to anti conformation is coupled with protonation-dependent base flipping and G-HA+ base pair is formed under acidic condition.

Original languageEnglish (US)
Pages (from-to)239-244
Number of pages6
JournalChemical Physics Letters
StatePublished - 2017

ASJC Scopus subject areas

  • General Physics and Astronomy
  • Physical and Theoretical Chemistry


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