Chemistry of Minor Groove Binder–Oligonucleotide Conjugates

Igor Kutyavin1, Sergey Lokhov1, Eugene Lukhtanov1, Michael W. Reed1

1 Epoch Biosciences, Bothell, Washington
Publication Name:  Current Protocols in Nucleic Acid Chemistry
Unit Number:  Unit 8.4
DOI:  10.1002/0471142700.nc0804s13
Online Posting Date:  August, 2003
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Various types of minor groove binders have been attached to synthetic oligodeoxynucleotides, and the interactions of these conjugates (MB‐ODNs) with DNA are reviewed here. MB‐ODNs have enhanced DNA affinity and have improved the hybridization properties of sequence‐specific DNA probes. Short MB‐ODNs hybridize with ssDNA to give more stable DNA duplexes than unmodified ODNs with similar lengths. Mismatch discrimination of short MB‐ODNs is enhanced in comparison to longer unmodified ODNs. The stronger binding of MB‐ODNs allows for more stringent hybridization conditions to be used in DNA probe‐based assays. MB‐ODNs are especially useful in quantitative “real‐time” PCR assays since they bind efficiently during the high‐temperature primer extension cycle. The synthesis and biophysical chemistry of MB‐ODN conjugates are reviewed here. Four published structural classes of MB‐ODNs and their various dsDNA binding modes are discussed, and the well‐characterized DPI3‐type MB‐ODNs and their interactions with ssDNA target strands are described in detail.

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Table of Contents

  • DNA Binding Modes and Structure of MB‐ODN Conjugates
  • Synthesis and Hybridization of DPI3‐Type MB‐ODNs
  • Hybridization Properties of DPI3‐ODNs
  • Applications of DPI3‐ODNs in PCR Assays
  • Summary
  • Literature Cited
  • Figures
  • Tables
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Literature Cited

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