Binding to the DNA Minor Groove by Heterocyclic Dications: From AT‐Specific Monomers to GC Recognition with Dimers

Rupesh Nanjunda1, W. David Wilson1

1 Department of Chemistry, Georgia State University, Atlanta, Georgia
Publication Name:  Current Protocols in Nucleic Acid Chemistry
Unit Number:  Unit 8.8
DOI:  10.1002/0471142700.nc0808s51
Online Posting Date:  December, 2012
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Abstract

Compounds that bind in the DNA minor groove have provided critical information on DNA molecular recognition, have found extensive uses in biotechnology, and are providing clinically useful drugs against diseases as diverse as cancer and sleeping sickness. This review focuses on the development of clinically useful heterocyclic diamidine minor groove binders. These compounds have shown us that the classical model for minor groove binding in AT DNA sequences must be expanded in several ways: compounds with nonstandard shapes can bind strongly to the groove, water can be directly incorporated into the minor groove complex in an interfacial interaction, and the compounds can form cooperative stacked dimers to recognize GC and mixed AT/GC base pair sequences. Curr. Protoc. Nucleic Acid Chem. 51:8.8.1‐8.8.20. © 2012 by John Wiley & Sons, Inc.

Keywords: DNA minor groove; heterocyclic amidines; DNA complex structures; surface plasmon resonance; stacked minor groove dimers

     
 
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Table of Contents

  • Introduction
  • DNA Groove Shape and Chemistry
  • Classical‐AT‐Specific Minor Groove Binders
  • Variations on the Classical Minor Groove Model
  • Extension to GC Base Pair Recognition
  • Conclusion and Prospects
  • Acknowledgments
  • Literature Cited
  • Figures
     
 
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Literature Cited

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