Issue 1, 2008
From the journal:

Organic & Biomolecular Chemistry

Synthetic nucleic acid secondary structures containing the four stereoisomers of 1,4-bis(thymine-1-yl)butane-2,3-diol†

Mikkel S. Christensen,ab   Andrew D. Bondb  and  Poul Nielsen*ab  

* Corresponding authors

a Nucleic Acid Center, University of Southern Denmark, Odense M, Denmark

b Department of Physics and Chemistry, University of Southern Denmark, Odense M, Denmark
E-mail: pon@ifk.sdu.dk
Fax: +45 66158780
Tel: +45 65502565

Abstract

The four stereoisomers of the double-headed acyclic nucleoside 1,4-bis(thymine-1-yl)butane-2,3-diol were incorporated in the central position of four 13-mer oligonucleotides. The phosphoramidite building blocks were synthesized in four or six steps from either D- or L-2,3-O-isopropylidenethreitol. Two epimeric and fully deprotected double-headed nucleosides were analyzed by X-ray crystallography. The incorporation into oligonucleotides was hampered by steric hindrance and formation of a cyclic phosphate. The use of pyridinium chloride as the activator and a kinetic analysis based on 31P NMR of the coupling and detritylation processes led to improved yields of the oligonucleotides. In comparison with the (S)-GNA monomer, one of the four stereoisomers was found to show a similar destabilization of a DNA duplex, indicating that the additional base can be introduced without a thermal penalty. Another stereoisomer was found to induce a thermal stabilization of a DNA:RNA three-way junction. Thus, the stereochemistry of this acyclic double-headed nucleoside motif is important, indicating potential for the design of artificial nucleic acid secondary structures.

Graphical abstract: Synthetic nucleic acid secondary structures containing the four stereoisomers of 1,4-bis(thymine-1-yl)butane-2,3-diol

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Article information

DOI
https://doi.org/10.1039/B713888A
Article type
Paper
Submitted
10 Sep 2007
Accepted
17 Oct 2007
First published
07 Nov 2007

Org. Biomol. Chem., 2008,6, 81-91

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Synthetic nucleic acid secondary structures containing the four stereoisomers of 1,4-bis(thymine-1-yl)butane-2,3-diol

M. S. Christensen, A. D. Bond and P. Nielsen, Org. Biomol. Chem., 2008, 6, 81 DOI: 10.1039/B713888A

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