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Nucleic Acids Research 2005 33(18):5771-5780; doi:10.1093/nar/gki865
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Published online 11 October 2005

© The Author 2005. Published by Oxford University Press. All rights reserved
The online version of this article has been published under an open access model. Users are entitled to use, reproduce, disseminate, or display the open access version of this article for non-commercial purposes provided that: the original authorship is properly and fully attributed; the Journal and Oxford University Press are attributed as the original place of publication with the correct citation details given; if an article is subsequently reproduced or disseminated not in its entirety but only in part or as a derivative work this must be clearly indicated. For commercial re-use, please contact journals.permissions{at}oxfordjournals.org

Article

Chemical synthesis and thermodynamic characterization of oxanine-containing oligodeoxynucleotides

Seung Pil Pack1,2, Mitsuru Nonogawa2,3, Tsutomu Kodaki2,3 and Keisuke Makino1,2,3,*

1International Innovation Center, Kyoto University Yoshida-honmachi, Sakyo-ku, Kyoto 606-8501, Japan 2CREST, JST (Japanese Science and Technology), Kyoto University Gokasho, Uji 611-0011, Japan 3Institute of Advanced Energy, Kyoto University Gokasho, Uji 611-0011, Japan

*To whom correspondence should be addressed. Tel: +81 774 38 3517; Fax: +81 774 38 3524; Email: kmak{at}iae.kyoto-u.ac.jp

Received August 11, 2005. Revised September 8, 2005. Accepted September 8, 2005.

Oxanine (Oxa, O), one of the major damaged bases from guanine generated by NO- or HNO2-induced nitrosative deamination, has been considered as a mutagen-potent lesion. For exploring more detailed properties of Oxa, large-scale preparation of Oxa-containing oligodeoxynucleotide (Oxa-ODN) with the desired base sequence is a prerequisite. In the present study, we have developed a chemical synthesis procedure of Oxa-ODNs and characterized thermodynamic properties of Oxa in DNA strands. First, 2'-deoxynucleoside of Oxa (dOxo) obtained from 2'-deoxyguanosine by HNO2-nitrosation was subjected to 5'-O-selective tritylation to give 5'-O-(4,4'-dimethoxytrityl)-dOxo (DMT-dOxo) with a maximum yield of 70%. Subsequently, DMT-dOxo was treated with conventional phosphoramidation, which resulted in DMT-dOxo-amidite monomer with a maximum yield of 72.5%. The amidite obtained was used for synthesizing Oxa-ODNs: the coupling yields for Oxa incorporation were over 93%. The prepared Oxa-ODNs were employed for analyzing the thermodynamic properties of DNA duplexes containing base-matches of O:N [N; C (cytosine), T (thymine), G (guanine) or A (adenine)]. Melting temperatures (Tm) and thermodynamic stability () were found to be lower by 6.83~13.41°C and 2.643~6.047 kcal mol–1, respectively, compared with those of oligodeoxynucleotides, which had the same base sequence except that O:N was replaced by G:C (wild type). It has also been found that Oxa-pairing with cytosine shows relatively high stability in DNA duplex compared with other base combinations. The orders of were O:C > O:T > O:A > O:G. The chemical synthesis procedure and thermodynamic characteristics of Oxa-ODNs established here will be helpful for elucidating the biological significance of Oxa in relation to genotoxic and repair mechanisms.


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S. P. Pack, N. K. Kamisetty, M. Nonogawa, K. C. Devarayapalli, K. Ohtani, K. Yamada, Y. Yoshida, T. Kodaki, and K. Makino
Direct immobilization of DNA oligomers onto the amine-functionalized glass surface for DNA microarray fabrication through the activation-free reaction of oxanine
Nucleic Acids Res., September 27, 2007; 35(17): e110 - e110.
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