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Paper | Special issue | Vol 82, No. 1, 2010, pp.775-790
Published online, 16th July, 2010
DOI: 10.3987/COM-10-S(E)65
Screening the Structural Space of Bicyclo-DNA: Synthesis and Properties of Bicyclo-DNA Functionalized at C(6’)

Samuel Luisier and Christian J. Leumann*

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

Abstract

The synthesis of a novel bicyclo-thymidine nucleoside bearing an ester functionality at C(6’) (bcα-alk-nucleosides) is reported. This nucleoside was incorporated into oligodeoxynucleotides via solid phase phosphoramidite chemistry, and the ester moiety was post-synthetically converted to an amide or a carboxy group, or was left unchanged. Thermal melting data (Tm) with complementary DNA and RNA were collected and compared to natural DNA and to bc- and bcox-DNA. It was found that single incorporations of bcα-alk-nucleosides in DNA duplexes were destabilizing by 0.5 to 2.5 °C/mod, whereas two consecutive bcα-alk-residues were less destabilizing, and in some cases even stabilizing by 0.5 °C/mod. In duplexes with complementary RNA, isolated bcα-alk-residues destabilized the duplex by -1.0 to -4.0 °C/mod, depending on the chemical nature of the substituent, whereas two consecutive modifications were only destabilizing by 0.3-1.0 °C/mod. The pairing selectivity was similar to that of unmodified or bc-DNA.