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Dynamical ensemble of the active state and transition state mimic for the RNA-cleaving 8-17 DNAzyme in solution.

Abstract

We perform molecular dynamics simulations, based on recent crystallographic data, on the 8-17 DNAzyme at four states along the reaction pathway to determine the dynamical ensemble for the active state and transition state mimic in solution. A striking finding is the diverse roles played by Na+ and Pb2+ ions in the electrostatically strained active site that impact all four fundamental catalytic strategies, and share commonality with some features recently inferred for naturally occurring hammerhead and pistol ribozymes. The active site Pb2+ ion helps to stabilize in-line nucleophilic attack, provides direct electrostatic transition state stabilization, and facilitates leaving group departure. A conserved guanine residue is positioned to act as the general base, and is assisted by a bridging Na+ ion that tunes the pKa and facilitates in-line fitness. The present work provides insight into how DNA molecules are able to solve the RNA-cleavage problem, and establishes functional relationships between the mechanism of these engineered DNA enzymes with their naturally evolved RNA counterparts. This adds valuable information to our growing body of knowledge on general mechanisms of phosphoryl transfer reactions catalyzed by RNA, proteins and DNA.

Authors+Show Affiliations

Laboratory for Biomolecular Simulation Research, Institute for Quantitative Biomedicine, and Department of Chemistry and Chemical Biology, Rutgers University, Piscataway, NJ 08854, USA.Laboratory for Biomolecular Simulation Research, Institute for Quantitative Biomedicine, and Department of Chemistry and Chemical Biology, Rutgers University, Piscataway, NJ 08854, USA.

Pub Type(s)

Journal Article

Language

eng

PubMed ID

31511899

Citation

Ekesan, Şölen, and Darrin M. York. "Dynamical Ensemble of the Active State and Transition State Mimic for the RNA-cleaving 8-17 DNAzyme in Solution." Nucleic Acids Research, 2019.
Ekesan Ş, York DM. Dynamical ensemble of the active state and transition state mimic for the RNA-cleaving 8-17 DNAzyme in solution. Nucleic Acids Res. 2019.
Ekesan, Ş., & York, D. M. (2019). Dynamical ensemble of the active state and transition state mimic for the RNA-cleaving 8-17 DNAzyme in solution. Nucleic Acids Research, doi:10.1093/nar/gkz773.
Ekesan Ş, York DM. Dynamical Ensemble of the Active State and Transition State Mimic for the RNA-cleaving 8-17 DNAzyme in Solution. Nucleic Acids Res. 2019 Sep 12; PubMed PMID: 31511899.
* Article titles in AMA citation format should be in sentence-case
TY - JOUR T1 - Dynamical ensemble of the active state and transition state mimic for the RNA-cleaving 8-17 DNAzyme in solution. AU - Ekesan,Şölen, AU - York,Darrin M, Y1 - 2019/09/12/ PY - 2019/09/03/accepted PY - 2019/08/20/revised PY - 2019/06/25/received PY - 2019/9/13/entrez JF - Nucleic acids research JO - Nucleic Acids Res. N2 - We perform molecular dynamics simulations, based on recent crystallographic data, on the 8-17 DNAzyme at four states along the reaction pathway to determine the dynamical ensemble for the active state and transition state mimic in solution. A striking finding is the diverse roles played by Na+ and Pb2+ ions in the electrostatically strained active site that impact all four fundamental catalytic strategies, and share commonality with some features recently inferred for naturally occurring hammerhead and pistol ribozymes. The active site Pb2+ ion helps to stabilize in-line nucleophilic attack, provides direct electrostatic transition state stabilization, and facilitates leaving group departure. A conserved guanine residue is positioned to act as the general base, and is assisted by a bridging Na+ ion that tunes the pKa and facilitates in-line fitness. The present work provides insight into how DNA molecules are able to solve the RNA-cleavage problem, and establishes functional relationships between the mechanism of these engineered DNA enzymes with their naturally evolved RNA counterparts. This adds valuable information to our growing body of knowledge on general mechanisms of phosphoryl transfer reactions catalyzed by RNA, proteins and DNA. SN - 1362-4962 UR - https://www.unboundmedicine.com/medline/citation/31511899/Dynamical_ensemble_of_the_active_state_and_transition_state_mimic_for_the_RNA-cleaving_8-17_DNAzyme_in_solution L2 - https://academic.oup.com/nar/article-lookup/doi/10.1093/nar/gkz773 DB - PRIME DP - Unbound Medicine ER -