UNIT 8.4 Chemistry of Minor Groove Binder–Oligonucleotide Conjugates

  1. Igor Kutyavin,
  2. Sergey Lokhov,
  3. Eugene Lukhtanov,
  4. Michael W. Reed

Published Online: 1 AUG 2003

DOI: 10.1002/0471142700.nc0804s13

Current Protocols in Nucleic Acid Chemistry

Current Protocols in Nucleic Acid Chemistry

How to Cite

Kutyavin, I., Lokhov, S., Lukhtanov, E. and Reed, M. W. 2003. Chemistry of Minor Groove Binder–Oligonucleotide Conjugates. Current Protocols in Nucleic Acid Chemistry. 13:8.4:8.4.1–8.4.21.

Author Information

  1. Epoch Biosciences, Bothell, Washington

Publication History

  1. Published Online: 1 AUG 2003
  2. Published Print: JUN 2003


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.