Chemical Reagents for Investigating the Major Groove of DNA

Steven E. Rokita1

1 University of Maryland, College Park, Maryland
Publication Name:  Current Protocols in Nucleic Acid Chemistry
Unit Number:  Unit 6.6
DOI:  10.1002/0471142700.nc0606s05
Online Posting Date:  August, 2001
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Chemical modification provides an inexpensive and rapid method for characterizing the structure of DNA and its association with drugs and proteins. Numerous conformationā€specific probes are available, but most investigations rely on only the most common and readily available of these. The major groove of DNA is typically characterized by reaction with dimethyl sulfate, diethyl pyrocarbonate, potassium permanganate, osmium tetroxide, and, quite recently, bromide with monoperoxysulfate. This commentary discusses the specificity of these reagents and their applications in protection, interference, and missing contact experiments.

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Table of Contents

  • General Considerations for Data Analysis
  • Experimental Procedures Supported by Chemical Modification
  • Individual Characteristics of Reagents Commonly Used to Probe the Major Groove of DNA
  • Applying Chemical Reagents to Probe the Major Groove of DNA
  • Literature Cited
  • Figures
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Literature Cited

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