Imino proton exchange and base-pair kinetics in the AMP-RNA aptamer complex

Journal of Molecular Biology
S NoninD J Patel

Abstract

We report on the dynamics of base-pair opening in the ATP-binding asymmetric internal loop and flanking base-pairs of the AMP-RNA aptamer complex by monitoring the exchange characteristics of the extremely well resolved imino protons in the NMR spectrum of the complex. The kinetics of imino proton exchange as a function of basic pH or added ammonia catalyst are used to measure the apparent base-pair dissociation constants and lifetimes of Watson-Crick and mismatched base-pairs, as well as the solvent accessibility of the unpaired imino protons in the complex. The exchange characteristics of the imino protons identify the existence of four additional hydrogen bonds stabilizing the conformation of the asymmetric ATP-binding internal loop that were not detected by NOEs and coupling constants alone, but are readily accommodated in the previously reported solution structure of the AMP-RNA aptamer complex published from our laboratory. The hydrogen exchange kinetics of the non-Watson-Crick pairs in the asymmetric internal loop of the AMP-RNA aptamer complex have been characterized and yield apparent dissociation constants (alphaKd) that range from 10(-2) to 10(-7). Surprisingly, three of these alphaKd values are amongst the lowest me...Continue Reading

References

May 22, 1990·Biochemistry·M KochoyanM Guéron
Feb 1, 1985·Journal of Biomolecular Structure & Dynamics·J L LeroyM Guérón
Jun 11, 1995·Nucleic Acids Research·J G MoeI M Russu
Jul 14, 1995·Journal of Molecular Biology·F H Allain, G Varani
Aug 5, 1993·Nature·M Sassanfar, J W Szostak
Feb 15, 1996·Nucleic Acids Research·S NoninM Gueron

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Citations

Nov 1, 2011·Nature Methods·Jameson R BotheHashim M Al-Hashimi
Sep 5, 2007·Nucleic Acids Research·Isabelle LebarsJean-Jacques Toulmé
Aug 20, 2003·Biopolymers·Coby B CarlsonPeter A Beal
Oct 26, 2005·Chembiochem : a European Journal of Chemical Biology·Barry D GoochPeter A Beal
Apr 19, 2019·Chembiochem : a European Journal of Chemical Biology·Maja MarušičKatja Petzold
Nov 22, 2002·The Journal of Biological Chemistry·Dan Shu, Peixuan Guo
Aug 25, 2020·Medical Devices & Sensors·Subhashish Dolai, Massood Tabib-Azar
May 10, 2017·Journal of Biomolecular NMR·Zachary R ChurcherPhilip E Johnson
Jul 27, 2001·Biochemistry·K Snoussi, J L Leroy
Sep 8, 2011·Accounts of Chemical Research·Jörg RinnenthalHarald Schwalbe
Sep 4, 2020·Biophysical Journal·Zachary R ChurcherPhilip E Johnson
Mar 26, 2008·Chemical Reviews·Jason R Thomas, Paul J Hergenrother
Aug 26, 2004·Journal of the American Chemical Society·Barry D Gooch, Peter A Beal

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