Unnatural Nucleosides with Unusual Base Pairing Properties

Donald E. Bergstrom1

1 Purdue University, West Lafayette, Indiana
Publication Name:  Current Protocols in Nucleic Acid Chemistry
Unit Number:  Unit 1.4
DOI:  10.1002/0471142700.nc0104s37
Online Posting Date:  June, 2009
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Synthetic modified nucleosides designed to pair in unusual ways with natural nucleobases have many potential applications in biology and biotechnology. This overview lays the foundation for future protocol units on synthesis and application of unnatural bases, with particular emphasis on unnatural base analogs that mimic natural bases in size, shape, and biochemical processing. Topics covered include base pairs with alternative H‐bonding schemes, dimensionally expanded base pairs, hydrophobic base pairs, metal‐ligated bases, degenerate bases, universal nucleosides, and triplex constituents. Curr. Protoc. Nucleic Acid Chem. 37:1.4.1‐1.4.32. © 2009 by John Wiley & Sons, Inc.

Keywords: nucleoside; mimetic; nonpolar; degenerate; universal

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Table of Contents

  • Introduction
  • Base Pairs with Alternative Hydrogen‐Bonding Patterns
  • Expanded Base Pairs
  • Non‐Hydrogen‐Bonding Base Pairs
  • Base Pairs Combining Non‐Hydrogen‐Bonding and Hydrogen‐Bonding Regions for RNA Transcription
  • Stacking Base Pairs
  • Mimics for Probing DNA Damage
  • Metal‐Mediated Association of Ligand Nucleobase Mimics
  • Covalent Base Pair Analogs
  • Degenerate Bases
  • Universal Nucleosides
  • Triplex Constituents
  • Modifying Natural Bases to Tune Pairing Affinity
  • Base Pair Recognition
  • Conclusion
  • Literature Cited
  • Figures
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Literature Cited

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