PMID: 11345440May 10, 2001Paper

Evaluation of methylphosphonates as analogs for detecting phosphate contacts in RNA-protein complexes

RNA
D Dertinger, O C Uhlenbeck

Abstract

The well-studied interaction between the MS2 coat protein and its cognate hairpin was used to test the utility of the methylphosphonate linkage as a phosphate analog. A nitrocellulose filter binding assay was used to measure the change in binding affinity upon introduction of a single methylphosphonate stereoisomer at 13 different positions in the RNA hairpin. Comparing these data to the available crystal structure of the complex shows that all phosphates that are in proximity to the protein show a weaker binding affinity when substituted with a phosphorothioate and control positions show no change. However, in two cases, a methylphosphonate isomer either increased or decreased the binding affinity where no interaction can be detected in the crystal structure. It is possible that methylphosphonate substitutions at these positions affect the structure or flexibility of the hairpin. The utility of the methylphosphonate substitution is compared to phosphate ethylation and phosphorothioate substitution experiments previously performed on the same system.

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Citations

Apr 23, 2003·Journal of Molecular Biology·Hatim T AllawiVictor I Lyamichev
Dec 22, 2012·Biochemistry·Carly A ShanahanScott A Strobel
Nov 1, 2012·Journal of the American Chemical Society·Jaeyoung PaiInjae Shin
Mar 4, 2008·Nucleic Acids Research·Songon AnKarin Musier-Forsyth
Jan 16, 2016·Journal of the American Chemical Society·Jaeyoung PaiInjae Shin
Apr 3, 2016·Methods : a Companion to Methods in Enzymology·Sara Flür, Ronald Micura
Dec 29, 2005·Journal of Molecular Biology·Dagmar Hobson, Olke C Uhlenbeck
May 6, 2015·Proceedings of the National Academy of Sciences of the United States of America·Miriam KochNorbert Polacek

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