TY - JOUR
T1 - Altered Mechanisms for Acid-Catalyzed RNA Cleavage and Isomerization Reactions Models
AU - Xu, Yuqing
AU - Harris, Michael E.
AU - York, Darrin M.
AU - Wong, Kin Yiu
N1 - Computing resources were provided by Inspur TS10K High Performance Computing Cluster at Ludong University. The authors are grateful for financial support provided by the National Institutes of Health (GM62248 to D.M.Y. and GM127100 to M.E.H.).
Publisher Copyright:
© 2023 American Chemical Society.
PY - 2023/2/28
Y1 - 2023/2/28
N2 - RNA strand cleavage by 2′-O-transphosphorylation is catalyzed not only by numerous nucleolytic RNA enzymes (ribozymes) but also by hydroxide or hydronium ions. In experiments, both cleavage of the 5′-linked nucleoside and isomerization between 3′,5′- and 2′,5′-phosphodiesters occur under acidic conditions, while only the cleavage reaction is observed under basic conditions. An ab initio path-integral approach for simulating kinetic isotope effects is used to reveal the reaction mechanisms for RNA cleavage and isomerization reactions under acidic conditions. Moreover, the proposed mechanisms can also be combined through the experimental pH-rate profiles.
AB - RNA strand cleavage by 2′-O-transphosphorylation is catalyzed not only by numerous nucleolytic RNA enzymes (ribozymes) but also by hydroxide or hydronium ions. In experiments, both cleavage of the 5′-linked nucleoside and isomerization between 3′,5′- and 2′,5′-phosphodiesters occur under acidic conditions, while only the cleavage reaction is observed under basic conditions. An ab initio path-integral approach for simulating kinetic isotope effects is used to reveal the reaction mechanisms for RNA cleavage and isomerization reactions under acidic conditions. Moreover, the proposed mechanisms can also be combined through the experimental pH-rate profiles.
UR - http://www.scopus.com/inward/record.url?scp=85147889038&partnerID=8YFLogxK
UR - https://pubs.acs.org/doi/10.1021/acs.jctc.2c01277
U2 - 10.1021/acs.jctc.2c01277
DO - 10.1021/acs.jctc.2c01277
M3 - Journal article
C2 - 36753428
AN - SCOPUS:85147889038
SN - 1549-9618
VL - 19
SP - 1322
EP - 1332
JO - Journal of Chemical Theory and Computation
JF - Journal of Chemical Theory and Computation
IS - 4
ER -
