Linear free energy relationships in RNA transesterification: theoretical models to aid experimental interpretations.

ABSTRACT: RNA cleavage transesterification is of fundamental reaction in biology that is catalyzed by both protein and RNA enzymes. In this work, a series of RNA transesterification model reactions with a wide range of leaving groups are investigated with density-functional calculations in an aqueous solvation environment in order to study linear free energy relationships (LFERs) and their connection to transition state structure and bonding. Overall, results obtained from the polarizable continuum solvation model with UAKS radii produce the best linear correlations and closest overall agreement with experimental results. Reactions with a poor leaving group are predicted to proceed via a stepwise mechanism with a late transition state that is rate controlling. As leaving group becomes more acidic an

SUBMITTER: Huang M 

PROVIDER: S-EPMC4366550 | biostudies-literature | 2014 Aug

REPOSITORIES: biostudies-literature