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Examining the Effects of Netropsin on the Curvature of DNA A-Tracts Using Electrophoresis

A-tracts are sequences of repeated adenine bases that, under the proper conditions, are capable of mediating DNA curvature. A-tracts occur naturally in the regulatory regions of many organisms, yet their biological functions are not fully understood. Orienting multiple A-tracts together constructive...

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Detalles Bibliográficos
Autores principales: Miller, Jillian, Peters, Justin P.
Formato: Online Artículo Texto
Lenguaje:English
Publicado: MDPI 2021
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8510488/
https://www.ncbi.nlm.nih.gov/pubmed/34641414
http://dx.doi.org/10.3390/molecules26195871
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author Miller, Jillian
Peters, Justin P.
author_facet Miller, Jillian
Peters, Justin P.
author_sort Miller, Jillian
collection PubMed
description A-tracts are sequences of repeated adenine bases that, under the proper conditions, are capable of mediating DNA curvature. A-tracts occur naturally in the regulatory regions of many organisms, yet their biological functions are not fully understood. Orienting multiple A-tracts together constructively or destructively in a phase has the potential to create different shapes in the DNA helix axis. One means of detecting these molecular shape differences is from altered DNA mobilities measured using electrophoresis. The small molecule netropsin binds the minor groove of DNA, particularly at AT-rich sequences including A-tracts. Here, we systematically test the hypothesis that netropsin binding eliminates the curvature of A-tracts by measuring the electrophoretic mobilities of seven 98-base pair DNA samples containing different numbers and arrangements of centrally located A-tracts under varying conditions with netropsin. We find that netropsin binding eliminates the mobility difference between the DNA fragments with different A-tract arrangements in a concentration-dependent manner. This work provides evidence for the straightening of A-tracts upon netropsin binding and illustrates an artificial approach to re-sculpt DNA shape.
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spelling pubmed-85104882021-10-13 Examining the Effects of Netropsin on the Curvature of DNA A-Tracts Using Electrophoresis Miller, Jillian Peters, Justin P. Molecules Article A-tracts are sequences of repeated adenine bases that, under the proper conditions, are capable of mediating DNA curvature. A-tracts occur naturally in the regulatory regions of many organisms, yet their biological functions are not fully understood. Orienting multiple A-tracts together constructively or destructively in a phase has the potential to create different shapes in the DNA helix axis. One means of detecting these molecular shape differences is from altered DNA mobilities measured using electrophoresis. The small molecule netropsin binds the minor groove of DNA, particularly at AT-rich sequences including A-tracts. Here, we systematically test the hypothesis that netropsin binding eliminates the curvature of A-tracts by measuring the electrophoretic mobilities of seven 98-base pair DNA samples containing different numbers and arrangements of centrally located A-tracts under varying conditions with netropsin. We find that netropsin binding eliminates the mobility difference between the DNA fragments with different A-tract arrangements in a concentration-dependent manner. This work provides evidence for the straightening of A-tracts upon netropsin binding and illustrates an artificial approach to re-sculpt DNA shape. MDPI 2021-09-28 /pmc/articles/PMC8510488/ /pubmed/34641414 http://dx.doi.org/10.3390/molecules26195871 Text en © 2021 by the authors. https://creativecommons.org/licenses/by/4.0/Licensee MDPI, Basel, Switzerland. This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution (CC BY) license (https://creativecommons.org/licenses/by/4.0/).
spellingShingle Article
Miller, Jillian
Peters, Justin P.
Examining the Effects of Netropsin on the Curvature of DNA A-Tracts Using Electrophoresis
title Examining the Effects of Netropsin on the Curvature of DNA A-Tracts Using Electrophoresis
title_full Examining the Effects of Netropsin on the Curvature of DNA A-Tracts Using Electrophoresis
title_fullStr Examining the Effects of Netropsin on the Curvature of DNA A-Tracts Using Electrophoresis
title_full_unstemmed Examining the Effects of Netropsin on the Curvature of DNA A-Tracts Using Electrophoresis
title_short Examining the Effects of Netropsin on the Curvature of DNA A-Tracts Using Electrophoresis
title_sort examining the effects of netropsin on the curvature of dna a-tracts using electrophoresis
topic Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8510488/
https://www.ncbi.nlm.nih.gov/pubmed/34641414
http://dx.doi.org/10.3390/molecules26195871
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