A Universal Base in a Specific Role: Tuning up a Thrombin Aptamer with 5-Nitroindole

In this study we describe new modified analogs of the thrombin binding aptamer (TBA) containing 5-nitroindole residues. It has been shown that all modified TBAs form an anti-parallel G-quadruplex structure and retain the ability to inhibit thrombin. The most advanced TBA variant (TBA-N8) has a subst...

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Main Authors:	Tsvetkov, Vladimir B., Varizhuk, Anna M., Pozmogova, Galina E., Smirnov, Igor P., Kolganova, Natalia A., Timofeev, Edward N.
Format:	Online
Language:	English
Published:	Nature Publishing Group 2015
Online Access:	https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4648099/

id	pubmed-4648099
recordtype	oai_dc
spelling	pubmed-46480992015-11-23 A Universal Base in a Specific Role: Tuning up a Thrombin Aptamer with 5-Nitroindole Tsvetkov, Vladimir B. Varizhuk, Anna M. Pozmogova, Galina E. Smirnov, Igor P. Kolganova, Natalia A. Timofeev, Edward N. Article In this study we describe new modified analogs of the thrombin binding aptamer (TBA) containing 5-nitroindole residues. It has been shown that all modified TBAs form an anti-parallel G-quadruplex structure and retain the ability to inhibit thrombin. The most advanced TBA variant (TBA-N8) has a substantially increased clotting time and two-fold lower IC50 value compared to the unmodified prototype. Molecular modelling studies suggest that the improved anticoagulant properties of TBA-N8 result from changes in the binding mode of the analog. A modified central loop in TBA-N8 is presumed to participate in the binding of the target protein. Studies of FAM labelled TBA and TBA-N8 showed an improved binding affinity of the modified aptamer and provided evidence of a direct interaction between the modified central loop and thrombin. Our findings have implications for the design of new aptamers with improved binding affinities. Nature Publishing Group 2015-11-17 /pmc/articles/PMC4648099/ http://dx.doi.org/10.1038/srep16337 Text en Copyright © 2015, Macmillan Publishers Limited http://creativecommons.org/licenses/by/4.0/ This work is licensed under a Creative Commons Attribution 4.0 International License. The images or other third party material in this article are included in the article’s Creative Commons license, unless indicated otherwise in the credit line; if the material is not included under the Creative Commons license, users will need to obtain permission from the license holder to reproduce the material. To view a copy of this license, visit http://creativecommons.org/licenses/by/4.0/
repository_type	Open Access Journal
institution_category	Foreign Institution
institution	US National Center for Biotechnology Information
building	NCBI PubMed
collection	Online Access
language	English
format	Online
author	Tsvetkov, Vladimir B. Varizhuk, Anna M. Pozmogova, Galina E. Smirnov, Igor P. Kolganova, Natalia A. Timofeev, Edward N.
spellingShingle	Tsvetkov, Vladimir B. Varizhuk, Anna M. Pozmogova, Galina E. Smirnov, Igor P. Kolganova, Natalia A. Timofeev, Edward N. A Universal Base in a Specific Role: Tuning up a Thrombin Aptamer with 5-Nitroindole
author_facet	Tsvetkov, Vladimir B. Varizhuk, Anna M. Pozmogova, Galina E. Smirnov, Igor P. Kolganova, Natalia A. Timofeev, Edward N.
author_sort	Tsvetkov, Vladimir B.
title	A Universal Base in a Specific Role: Tuning up a Thrombin Aptamer with 5-Nitroindole
title_short	A Universal Base in a Specific Role: Tuning up a Thrombin Aptamer with 5-Nitroindole
title_full	A Universal Base in a Specific Role: Tuning up a Thrombin Aptamer with 5-Nitroindole
title_fullStr	A Universal Base in a Specific Role: Tuning up a Thrombin Aptamer with 5-Nitroindole
title_full_unstemmed	A Universal Base in a Specific Role: Tuning up a Thrombin Aptamer with 5-Nitroindole
title_sort	universal base in a specific role: tuning up a thrombin aptamer with 5-nitroindole
description	In this study we describe new modified analogs of the thrombin binding aptamer (TBA) containing 5-nitroindole residues. It has been shown that all modified TBAs form an anti-parallel G-quadruplex structure and retain the ability to inhibit thrombin. The most advanced TBA variant (TBA-N8) has a substantially increased clotting time and two-fold lower IC50 value compared to the unmodified prototype. Molecular modelling studies suggest that the improved anticoagulant properties of TBA-N8 result from changes in the binding mode of the analog. A modified central loop in TBA-N8 is presumed to participate in the binding of the target protein. Studies of FAM labelled TBA and TBA-N8 showed an improved binding affinity of the modified aptamer and provided evidence of a direct interaction between the modified central loop and thrombin. Our findings have implications for the design of new aptamers with improved binding affinities.
publisher	Nature Publishing Group
publishDate	2015
url	https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4648099/
_version_	1613502347403591680

A Universal Base in a Specific Role: Tuning up a Thrombin Aptamer with 5-Nitroindole

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