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Related Experiment Videos

RNA hydrolysis via an oxyphosphorane intermediate.

T Uchimaru1, J W Storer, K Tanabe

  • 1National Chemical Laboratory for Industry, Agency of Industrial Science & Technology, MITI, Tsukuba Science City, Japan.

Biochemical and Biophysical Research Communications
|September 30, 1992
PubMed
Summary
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Computational chemistry revealed key transition states and a dianionic intermediate in base-catalyzed RNA hydrolysis. These findings help interpret enzyme mechanisms in the absence of water.

Area of Science:

  • Biochemistry
  • Computational Chemistry
  • Molecular Biology

Background:

  • Base-catalyzed RNA hydrolysis is crucial for RNA function and degradation.
  • Understanding the reaction mechanism, including intermediates and transition states, is essential for enzyme studies.
  • Previous studies have investigated RNA hydrolysis using various computational and experimental methods.

Purpose of the Study:

  • To computationally investigate the mechanism of base-catalyzed RNA hydrolysis.
  • To identify and characterize key intermediates and transition states.
  • To correlate computational findings with experimental mutagenesis data for enzymes like Barnase and RNase T1.

Main Methods:

  • Ab initio calculations at the 3-21G* and STO-3G levels.
  • Modeling of a reaction scheme for base-catalyzed RNA hydrolysis.

Related Experiment Videos

  • Analysis of pentacoordinate dianionic intermediates and transition states.

    • Main Results:

    • A pentacoordinate dianionic intermediate (2a) and two transition states (TS1, TS2) were located.
    • The intermediate is unlikely to be kinetically significant due to shallow well depth.
    • The rate-limiting transition state (TS2) shows significant P-O(5') bond breaking, consistent across different computational levels.

    Conclusions:

    • Computational results provide insights into the gas-phase reaction mechanism of RNA hydrolysis.
    • The findings offer a qualitative interpretation of mutagenesis data for Barnase and RNase T1 in anhydrous active sites.
    • The study highlights the importance of computational modeling in understanding enzyme-catalyzed reactions.