Examining the effects of netropsin on the curvature of DNA a-tracts using electrophoresis
A-tract curvature, DNA shape, Electrophoresis, Netropsin
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 of Chemistry and Biochemistry
Original Publication Date
DOI of published version
UNI ScholarWorks, Rod Library, University of Northern Iowa
Miller, Jillian and Peters, Justin P., "Examining the effects of netropsin on the curvature of DNA a-tracts using electrophoresis" (2021). Faculty Publications. 22.