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Enhancement of RNA/Ligand Association Kinetics via an Electrostatic Anchor

[Image: see text] The diverse biological processes mediated by RNA rest upon its recognition of various ligands, including small molecules and nucleic acids. Nevertheless, a recent literature survey suggests that RNA molecular recognition of these ligands is slow, with association rate constants ord...

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Autores principales: Sengupta, Raghuvir N., Herschlag, Daniel
Formato: Online Artículo Texto
Lenguaje:English
Publicado: American Chemical Society 2019
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6586055/
https://www.ncbi.nlm.nih.gov/pubmed/31117387
http://dx.doi.org/10.1021/acs.biochem.9b00231
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author Sengupta, Raghuvir N.
Herschlag, Daniel
author_facet Sengupta, Raghuvir N.
Herschlag, Daniel
author_sort Sengupta, Raghuvir N.
collection PubMed
description [Image: see text] The diverse biological processes mediated by RNA rest upon its recognition of various ligands, including small molecules and nucleic acids. Nevertheless, a recent literature survey suggests that RNA molecular recognition of these ligands is slow, with association rate constants orders of magnitude below the diffusional limit. Thus, we were prompted to consider strategies for increasing RNA association kinetics. Proteins can accelerate ligand association via electrostatic forces, and here, using the Tetrahymena group I ribozyme, we provide evidence that electrostatic forces can accelerate RNA/ligand association. This RNA enzyme (E) catalyzes cleavage of an oligonucleotide substrate (S) by an exogenous guanosine (G) cofactor. The G 2′- and 3′-OH groups interact with an active site metal ion, termed M(C), within E·S·G, and we perturbed each of these contacts via −NH(3)(+) substitution. New and prior data indicate that G(2′NH(3)(+)) and G(3′NH(3)(+)) bind as strongly as G, suggesting that the −NH(3)(+) substituents of these analogues avoid repulsive interactions with M(C) and make alternative interactions. Unexpectedly, removal of the adjacent −OH via −H substitution to give G(2′H,3′NH(3)(+)) and G(2′NH(3)(+)(,)3′H) enhanced binding, in stark contrast to the deleterious effect of these substitutions on G binding. Pulse–chase experiments indicate that the −NH(3)(+) moiety of G(2′H,3′NH(3)(+)) increases the rate of G association. These results suggest that the positively charged −NH(3)(+) group can act as a molecular “anchor” to increase the residence time of the encounter complex and thereby enhance productive binding. Electrostatic anchors may provide a broadly applicable strategy for the development of fast binding RNA ligands and RNA-targeted therapeutics.
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spelling pubmed-65860552020-05-22 Enhancement of RNA/Ligand Association Kinetics via an Electrostatic Anchor Sengupta, Raghuvir N. Herschlag, Daniel Biochemistry [Image: see text] The diverse biological processes mediated by RNA rest upon its recognition of various ligands, including small molecules and nucleic acids. Nevertheless, a recent literature survey suggests that RNA molecular recognition of these ligands is slow, with association rate constants orders of magnitude below the diffusional limit. Thus, we were prompted to consider strategies for increasing RNA association kinetics. Proteins can accelerate ligand association via electrostatic forces, and here, using the Tetrahymena group I ribozyme, we provide evidence that electrostatic forces can accelerate RNA/ligand association. This RNA enzyme (E) catalyzes cleavage of an oligonucleotide substrate (S) by an exogenous guanosine (G) cofactor. The G 2′- and 3′-OH groups interact with an active site metal ion, termed M(C), within E·S·G, and we perturbed each of these contacts via −NH(3)(+) substitution. New and prior data indicate that G(2′NH(3)(+)) and G(3′NH(3)(+)) bind as strongly as G, suggesting that the −NH(3)(+) substituents of these analogues avoid repulsive interactions with M(C) and make alternative interactions. Unexpectedly, removal of the adjacent −OH via −H substitution to give G(2′H,3′NH(3)(+)) and G(2′NH(3)(+)(,)3′H) enhanced binding, in stark contrast to the deleterious effect of these substitutions on G binding. Pulse–chase experiments indicate that the −NH(3)(+) moiety of G(2′H,3′NH(3)(+)) increases the rate of G association. These results suggest that the positively charged −NH(3)(+) group can act as a molecular “anchor” to increase the residence time of the encounter complex and thereby enhance productive binding. Electrostatic anchors may provide a broadly applicable strategy for the development of fast binding RNA ligands and RNA-targeted therapeutics. American Chemical Society 2019-05-22 2019-06-18 /pmc/articles/PMC6586055/ /pubmed/31117387 http://dx.doi.org/10.1021/acs.biochem.9b00231 Text en Copyright © 2019 American Chemical Society This is an open access article published under an ACS AuthorChoice License (http://pubs.acs.org/page/policy/authorchoice_termsofuse.html) , which permits copying and redistribution of the article or any adaptations for non-commercial purposes.
spellingShingle Sengupta, Raghuvir N.
Herschlag, Daniel
Enhancement of RNA/Ligand Association Kinetics via an Electrostatic Anchor
title Enhancement of RNA/Ligand Association Kinetics via an Electrostatic Anchor
title_full Enhancement of RNA/Ligand Association Kinetics via an Electrostatic Anchor
title_fullStr Enhancement of RNA/Ligand Association Kinetics via an Electrostatic Anchor
title_full_unstemmed Enhancement of RNA/Ligand Association Kinetics via an Electrostatic Anchor
title_short Enhancement of RNA/Ligand Association Kinetics via an Electrostatic Anchor
title_sort enhancement of rna/ligand association kinetics via an electrostatic anchor
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6586055/
https://www.ncbi.nlm.nih.gov/pubmed/31117387
http://dx.doi.org/10.1021/acs.biochem.9b00231
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