The binding site of a specific aminoglycoside binding RNA molecule

Biochemistry
J ChoR R Rando

Abstract

A small (40 nucleotides) stem-loop derivative (J6f1) of a specific aminoglycoside-binding RNA aptamer, containing a 3 nt and a 1 nt bulge, has previously been shown to stoichiometrically bind tobramycin with a dissociation constant of approximately 5 nM [Hamasaki, K., Killian, J., Cho, J. and Rando, R. R. (1997) Biochemistry 36, 1367-1371]. This construct can strongly discriminate among similar aminoglycosides with respect to binding. A combination of chemical interference studies, chemical modification studies, and mutational studies are performed to define the aminoglycoside binding site of J6f1. Recognition of the aminoglycoside by J6f1 involves contacts with nucleotide bases, rather than with the phosphate backbone. The binding site 1 comprised of part of the stem-loop region. The two bulges are also essential for high affinity and stoichiometric binding of tobramycin. These bulges are probably important for prying open the double helical region, thereby allowing the aminoglycoside access to the nucleotide bases.

References

Jan 1, 1991·Annual Review of Biochemistry·H F Noller

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Citations

May 20, 1999·Biopolymers·T Hermann, E Westhof
Jan 5, 2006·Applied Microbiology and Biotechnology·S Jana, J K Deb
Sep 15, 2000·Bioorganic & Medicinal Chemistry Letters·D P Arya, R L Coffee
Sep 6, 2012·ACS Chemical Biology·Matthew D DisneyJessica L Childs-Disney
Apr 25, 2000·Nucleic Acids Research·J Cho, R R Rando
Apr 11, 2000·Nucleic Acids Research·T KatoI Karube
May 19, 2004·Nucleic Acids Research·Dagmar KlostermeierJames R Williamson
Nov 18, 2000·Antimicrobial Agents and Chemotherapy·L P KotraS Mobashery
Feb 21, 2002·Proceedings of the National Academy of Sciences of the United States of America·Isabelle HarveyJerry Pelletier
Jun 19, 2004·Journal of Drug Targeting·Rohtash KumarJerry Pelletier
Apr 24, 2008·Tetrahedron·Seergazhi G Srivatsan, Yitzhak Tor
Jul 9, 2004·Chembiochem : a European Journal of Chemical Biology·Steven H L VerhelstJacques H van Boom
Jan 13, 2006·Chembiochem : a European Journal of Chemical Biology·Markus KaiserMarie-Paule Teulade-Fichou
Jun 25, 2014·Chemistry, an Asian Journal·Andreas A BastianAndreas Herrmann
May 31, 2018·Nucleic Acids Research·Jack O PhillipsAnastasia J Callaghan
Mar 6, 2012·Bioanalytical Reviews·Beate StrehlitzRegina Stoltenburg
Jul 26, 2008·Journal of the American Chemical Society·Matthew D DisneyJessica L Childs-Disney
Dec 3, 2021·Journal of Medicinal Chemistry·Xiao-Fei ChenZifeng Yang

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Aminoglycosides (ASM)

Aminoglycoside is a medicinal and bacteriologic category of traditional Gram-negative antibacterial medications that inhibit protein synthesis and contain as a portion of the molecule an amino-modified glycoside. Discover the latest research on aminoglycoside here.

Aminoglycosides

Aminoglycoside is a medicinal and bacteriologic category of traditional Gram-negative antibacterial medications that inhibit protein synthesis and contain as a portion of the molecule an amino-modified glycoside. Discover the latest research on aminoglycoside here.

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