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Functional binding of hexanucleotides to 3C protease of hepatitis A virus

Oligonucleotides as short as 6 nt in length have been shown to bind specifically and tightly to proteins and affect their biological function. Yet, sparse structural data are available for corresponding complexes. Employing a recently developed hexanucleotide array, we identified hexadeoxyribonucleo...

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Autores principales: Blaum, Bärbel S., Wünsche, Winfried, Benie, Andrew J., Kusov, Yuri, Peters, Hannelore, Gauss-Müller, Verena, Peters, Thomas, Sczakiel, Georg
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Oxford University Press 2012
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3326307/
https://www.ncbi.nlm.nih.gov/pubmed/22156376
http://dx.doi.org/10.1093/nar/gkr1152
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author Blaum, Bärbel S.
Wünsche, Winfried
Benie, Andrew J.
Kusov, Yuri
Peters, Hannelore
Gauss-Müller, Verena
Peters, Thomas
Sczakiel, Georg
author_facet Blaum, Bärbel S.
Wünsche, Winfried
Benie, Andrew J.
Kusov, Yuri
Peters, Hannelore
Gauss-Müller, Verena
Peters, Thomas
Sczakiel, Georg
author_sort Blaum, Bärbel S.
collection PubMed
description Oligonucleotides as short as 6 nt in length have been shown to bind specifically and tightly to proteins and affect their biological function. Yet, sparse structural data are available for corresponding complexes. Employing a recently developed hexanucleotide array, we identified hexadeoxyribonucleotides that bind specifically to the 3C protease of hepatitis A virus (HAV 3C(pro)). Inhibition assays in vitro identified the hexanucleotide 5′-GGGGGT-3′ (G(5)T) as a 3C(pro) protease inhibitor. Using (1)H NMR spectroscopy, G(5)T was found to form a G-quadruplex, which might be considered as a minimal aptamer. With the help of (1)H, (15)N-HSQC experiments the binding site for G(5)T was located to the C-terminal β-barrel of HAV 3C(pro). Importantly, the highly conserved KFRDI motif, which has previously been identified as putative viral RNA binding site, is not part of the G(5)T-binding site, nor does G(5)T interfere with the binding of viral RNA. Our findings demonstrate that sequence-specific nucleic acid–protein interactions occur with oligonucleotides as small as hexanucleotides and suggest that these compounds may be of pharmaceutical relevance.
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spelling pubmed-33263072012-04-16 Functional binding of hexanucleotides to 3C protease of hepatitis A virus Blaum, Bärbel S. Wünsche, Winfried Benie, Andrew J. Kusov, Yuri Peters, Hannelore Gauss-Müller, Verena Peters, Thomas Sczakiel, Georg Nucleic Acids Res Molecular Biology Oligonucleotides as short as 6 nt in length have been shown to bind specifically and tightly to proteins and affect their biological function. Yet, sparse structural data are available for corresponding complexes. Employing a recently developed hexanucleotide array, we identified hexadeoxyribonucleotides that bind specifically to the 3C protease of hepatitis A virus (HAV 3C(pro)). Inhibition assays in vitro identified the hexanucleotide 5′-GGGGGT-3′ (G(5)T) as a 3C(pro) protease inhibitor. Using (1)H NMR spectroscopy, G(5)T was found to form a G-quadruplex, which might be considered as a minimal aptamer. With the help of (1)H, (15)N-HSQC experiments the binding site for G(5)T was located to the C-terminal β-barrel of HAV 3C(pro). Importantly, the highly conserved KFRDI motif, which has previously been identified as putative viral RNA binding site, is not part of the G(5)T-binding site, nor does G(5)T interfere with the binding of viral RNA. Our findings demonstrate that sequence-specific nucleic acid–protein interactions occur with oligonucleotides as small as hexanucleotides and suggest that these compounds may be of pharmaceutical relevance. Oxford University Press 2012-04 2011-12-10 /pmc/articles/PMC3326307/ /pubmed/22156376 http://dx.doi.org/10.1093/nar/gkr1152 Text en © The Author(s) 2011. Published by Oxford University Press. http://creativecommons.org/licenses/by-nc/3.0 This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/3.0), which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.
spellingShingle Molecular Biology
Blaum, Bärbel S.
Wünsche, Winfried
Benie, Andrew J.
Kusov, Yuri
Peters, Hannelore
Gauss-Müller, Verena
Peters, Thomas
Sczakiel, Georg
Functional binding of hexanucleotides to 3C protease of hepatitis A virus
title Functional binding of hexanucleotides to 3C protease of hepatitis A virus
title_full Functional binding of hexanucleotides to 3C protease of hepatitis A virus
title_fullStr Functional binding of hexanucleotides to 3C protease of hepatitis A virus
title_full_unstemmed Functional binding of hexanucleotides to 3C protease of hepatitis A virus
title_short Functional binding of hexanucleotides to 3C protease of hepatitis A virus
title_sort functional binding of hexanucleotides to 3c protease of hepatitis a virus
topic Molecular Biology
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3326307/
https://www.ncbi.nlm.nih.gov/pubmed/22156376
http://dx.doi.org/10.1093/nar/gkr1152
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