Faculty Publications

Title

Examining the effects of netropsin on the curvature of DNA a-tracts using electrophoresis

Document Type

Article

Keywords

A-tract curvature, DNA shape, Electrophoresis, Netropsin

Journal/Book/Conference Title

Molecules

Volume

26

Issue

19

Abstract

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.

Department

Department of Chemistry and Biochemistry

Original Publication Date

10-1-2021

DOI of published version

10.3390/molecules26195871

Repository

UNI ScholarWorks, Rod Library, University of Northern Iowa

Language

en

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