Stringent Nucleotide Recognition by the Ribosome at the Middle Codon Position

Wei Liu; Dongwon Shin; Martin Ng; Karissa Y Sanbonmatsu; Yitzhak Tor; Barry S Cooperman

doi:10.3390/molecules22091427

Stringent Nucleotide Recognition by the Ribosome at the Middle Codon Position

Molecules. 2017 Aug 29;22(9):1427. doi: 10.3390/molecules22091427.

Authors

Wei Liu¹, Dongwon Shin², Martin Ng³, Karissa Y Sanbonmatsu⁴, Yitzhak Tor⁵, Barry S Cooperman⁶

Affiliations

¹ Department of Chemistry, University of Pennsylvania, Philadelphia, PA 19104, USA. weiliu@sas.upenn.edu.
² Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, CA 92093, USA. dshin@trilinkbiotech.com.
³ Department of Chemistry, University of Pennsylvania, Philadelphia, PA 19104, USA. martinng@sas.upenn.edu.
⁴ Theoretical Biology and Biophysics Group, Los Alamos National Laboratory, Los Alamos, NM 87545, USA. kys@lanl.gov.
⁵ Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, CA 92093, USA. ytor@ucsd.edu.
⁶ Department of Chemistry, University of Pennsylvania, Philadelphia, PA 19104, USA. cooprman@pobox.upenn.edu.

Abstract

Accurate translation of the genetic code depends on mRNA:tRNA codon:anticodon base pairing. Here we exploit an emissive, isosteric adenosine surrogate that allows direct measurement of the kinetics of codon:anticodon University of California base formation during protein synthesis. Our results suggest that codon:anticodon base pairing is subject to tighter constraints at the middle position than at the 5'- and 3'-positions, and further suggest a sequential mechanism of formation of the three base pairs in the codon:anticodon helix.

Keywords: atomic mutagenesis; fluorescent mRNA; kinetic mechanism; mRNA:tRNA base pairing; steric constraint.

MeSH terms

Base Pairing
Genetic Code
Kinetics
Models, Molecular
Nucleotides / genetics*
RNA, Messenger / genetics
RNA, Transfer / genetics
Ribosomes / genetics*

Substances

Nucleotides
RNA, Messenger
RNA, Transfer

Abstract

MeSH terms

Substances

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