UNIT 4.52 Convenient and Efficient Approach to the Permanent or Reversible Conjugation of RNA and DNA Sequences with Functional Groups

  1. Jacek Cieślak,
  2. Cristina Ausín,
  3. Andrzej Grajkowski,
  4. Serge L. Beaucage

Published Online: 1 SEP 2012

DOI: 10.1002/0471142700.nc0452s50

Current Protocols in Nucleic Acid Chemistry

Current Protocols in Nucleic Acid Chemistry

How to Cite

Cieślak, J., Ausín, C., Grajkowski, A. and Beaucage, S. L. 2012. Convenient and Efficient Approach to the Permanent or Reversible Conjugation of RNA and DNA Sequences with Functional Groups. Current Protocols in Nucleic Acid Chemistry. 50:4.52:4.52.1–4.52.36.

Author Information

  1. Food and Drug Administration, Bethesda, Maryland

Publication History

  1. Published Online: 1 SEP 2012


The conversion of 3′,5′-disilylated 2′-O-(methylthiomethyl)ribonucleosides to 2′-O-(phthalimidooxymethyl)ribonucleosides is achieved in yields of 66% to 94%. Desilylation and dephtalimidation of these ribonucleosides by treatment with NH4F in MeOH produce 2′-O-aminooxymethylated ribonucleosides, which are efficient in producing stable and yet reversible 2′-conjugates upon reaction with 1-pyrenecarboxaldehyde. Exposure of 2′-pyrenylated ribonucleosides to 0.5 M tetra-n-butylammonium fluoride (TBAF) in THF or DMSO results in the cleavage of their iminoether functions to give the native ribonucleosides along with an innocuous nitrile side product. Conversely, the reaction of 2′-O-(aminooxymethyl)uridine with 5-cholesten-3-one leads to a permanent uridine 2′-conjugate, which is left unreacted when treated with TBAF. The versatility and uniqueness of 2′-O-(aminooxymethyl)ribonucleosides is demonstrated by the single or double incorporation of a reversible pyrenylated uridine 2′-conjugate into an RNA sequence. Furthermore, the conjugation of 2′-O-(aminooxymethyl)ribonucleosides with various aldehydes, including those generated from their acetals, is also presented. The preparation of 5′-O-(aminooxymethyl)thymidine is also achieved, albeit in modest yields, from the conversion of 5′-O-methylthiomethyl-3′-O-(levulinyl)thymidine to 5′-O-phthalimidooxymethyl-3′-O-(levuliny)lthymidine followed by hydrazinolysis of both 5′-phthalimido and 3′-levulinyl groups. Pyrenylation of the 5′-O-(aminooxymethyl)deoxyribonucleoside also provides a reversible 5′-conjugate that is sensitive to TBAF, thereby further demonstrating the usefulness of 5′-O-(aminooxymethyl)deoxyribonucleosides for permanent or reversible modification of DNA sequences. Curr. Protoc. Nucleic Acid Chem. 50:4.52.1-4.52.36. © 2012 by John Wiley & Sons, Inc.


  • 2′-O-(aminooxymethyl)ribonucleosides;
  • 5′-O-(aminooxymethyl)deoxyribonucleosides;
  • permanent or reversible conjugation;
  • modification of DNA or RNA sequences;
  • ribonucleoside 2′-conjugates;
  • deoxyribonucleoside 5′-conjugates