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Nucleic Acids Research Advance Access published online on December 6, 2006
Nucleic Acids Research, doi:10.1093/nar/gkl948
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© 2006 The Author(s)
This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/2.0/uk/) which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.

Chemistry

The chemical stability of abasic RNA compared to abasic DNA

Pascal A. Küpfer and Christian J. Leumann*

Department of Chemistry and Biochemistry, University of Bern Freiestrasse 3, CH-3012 Bern, Switzerland

*To whom correspondence should be addressed. Tel: +41 31 631 4355; Fax: +41 31 631 3422; Email: leumann{at}ioc.unibe.ch

Received September 11, 2006. Revised October 20, 2006. Accepted October 20, 2006.

We describe the synthesis of an abasic RNA phosphoramidite carrying a photocleavable 1-(2-nitrophenyl)ethyl (NPE) group at the anomeric center and a triisopropylsilyloxymethyl (TOM) group as 2'-O-protecting group together with the analogous DNA and the 2'-OMe RNA abasic building blocks. These units were incorporated into RNA-, 2'-OMe-RNA- and DNA for the purpose of studying their chemical stabilities towards backbone cleavage in a comparative way. Stability measurements were performed under basic conditions (0.1 M NaOH) and in the presence of aniline (pH 4.6) at 37°C. The kinetics and mechanisms of strand cleavage were followed by High pressure liquid chromotography and ESI-MS. Under basic conditions, strand cleavage at abasic RNA sites can occur via ß,{delta}-elimination and 2',3'-cyclophosphate formation. We found that ß,{delta}-elimination was 154-fold slower compared to the same mechanism in abasic DNA. Overall strand cleavage of abasic RNA (including cyclophosphate formation) was still 16.8 times slower compared to abasic DNA. In the presence of aniline at pH 4.6, where only ß,{delta}-elimination contributes to strand cleavage, a 15-fold reduced cleavage rate at the RNA abasic site was observed. Thus abasic RNA is significantly more stable than abasic DNA. The higher stability of abasic RNA is discussed in the context of its potential biological role.


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