Nucleic Acids Research Advance Access originally published online on October 27, 2006
Nucleic Acids Research 2006 34(20):5987-6000; doi:10.1093/nar/gkl719
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Nucleic Acids Research, 2006, Vol. 34, No. 20 5987-6000
© 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 |
pH-Dependent mismatch discrimination of oligonucleotide duplexes containing 2'-deoxytubercidin and 2- or 7-substituted derivatives: protonated base pairs formed between 7-deazapurines and cytosine
1 Laboratorium für Organische und Bioorganische Chemie, Institut für Chemie, Universität Osnabrück Barbarastrasse 7, D-49069 Osnabrück, Germany 2 Laboratory of Bioorganic Chemistry and Chemical Biology, Center for Nanotechnology (CeNTech) Heisenbergstrasse 11, D-48149 Münster, Germany
*To whom correspondence should be addressed. Tel: +49 541 969 2791; Fax:+49 541 969 2370; Email: Frank.Seela{at}uni-osnabrueck.de
Received June 20, 2006. Revised September 18, 2006. Accepted September 18, 2006.
Oligonucleotides incorporating 2'-deoxytubercidin (1a), its 2-amino derivative 2a and related 2-, or 7-substituted analogs (1d, 2b–d, 3 and 4) are synthesized. For this purpose, a series of novel phosphoramidites are prepared and employed in solid-phase synthesis. Hybridization experiments performed with 12mer duplexes indicate that 7-halogenated nucleosides enhance the duplex stability both in antiparallel and parallel DNA, whereas 2-fluorinated 7-deaza-2'-deoxyadenosine residues destabilize the duplex structure. The 7-deazaadenine nucleosides 1a, 1d and their 2-amino derivatives 2a–d form stable base pairs with dT but also with dC and dG. The mispairing with dC is pH-dependent. Ambiguous base pairing is observed at pH 7 or under acid conditions, whereas base discrimination occurs in alkaline medium (pH 8.0). This results from protonated base pairs formed between 1a or 2a and dC under neutral or acid condition, which are destroyed in alkaline medium. It is underlined by the increased basicity of the pyrrolo[2,3-d]pyrimidine nucleosides over that of the parent purine compounds (pKa values: 1a = 5.30; 2a = 5.71; dA = 3.50).