UNIT 5.9 Synthesis of Building Blocks and Oligonucleotides with {G}O6-Alkyl-O6{G} Cross-Links

  1. Christopher J. Wilds,
  2. Jason D. M. Booth,
  3. Anne M. Noronha

Published Online: 1 MAR 2011

DOI: 10.1002/0471142700.nc0509s44

Current Protocols in Nucleic Acid Chemistry

Current Protocols in Nucleic Acid Chemistry

How to Cite

Wilds, C. J., Booth, J. D. M. and Noronha, A. M. 2011. Synthesis of Building Blocks and Oligonucleotides with {G}O6-Alkyl-O6{G} Cross-Links. Current Protocols in Nucleic Acid Chemistry. 44:5.9:5.9.1–5.9.19.

Author Information

  1. Concordia University, Montreal, Quebec, Canada

Publication History

  1. Published Online: 1 MAR 2011
  2. Published Print: MAR 2011


This unit describes two methods for preparing oligonucleotides containing an O6-2′-deoxyguanosine-alkyl-O6-2′-deoxyguanosine interstrand cross-link by a solid-phase synthesis approach. Depending on the desired orientation of the cross-link in the DNA duplex, either a bis- or a mono-phosphoramidite synthesis strategy can be employed. Both procedures require the preparation of a protected 2′-deoxyguanosine-containing dimer where the two nucleosides are attached at the O6-atoms by an alkyl linker. This linker is introduced as a protected diol using two successive Mitsunobu reactions to produce a cross-linked amidite that is incorporated into an oligonucleotide via solid-phase synthesis. The use of a protected diol lends versatility to this method, as cross-links of variable chain length may be prepared. The bis-phosphoramidite approach is a direct method to preparing the cross-linked duplex, whereas the mono-phosphoramidite strategy requires additional manipulation of the solid support to prepare cross-linked oligonucleotides. Once all synthetic steps are completed, these oligonucleotides can then be removed from the solid support and deprotected, and then purified via ion-exchange HPLC to produce sufficient quantities of substrates that can be used in DNA repair studies. Curr. Protoc. Nucleic Acid Chem. 44:5.9.1-5.9.19. © 2011 by John Wiley & Sons, Inc.


  • interstrand cross-link;
  • phosphoramidite;
  • oligonucleotide synthesis;
  • chemical synthesis;
  • solid-phase synthesis;
  • DNA repair