Article

New Base Pairing Motifs. The Synthesis and Thermal Stability of Oligodeoxynucleotides Containing Imidazopyridopyrimidine Nucleosides with the Ability to Form Four Hydrogen Bonds

Contribution from the Graduate School of Pharmaceutical Sciences, Hokkaido University, Kita-12, Nishi-6, Kita-ku, Sapporo 060-0812, Japan
J. Am. Chem. Soc., 2003, 125 (33), pp 9970–9982
DOI: 10.1021/ja0347686
Publication Date (Web): July 24, 2003
Copyright © 2003 American Chemical Society

Abstract

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The synthesis and thermal stability of oligodeoxynucleotides (ODNs) containing imidazo[5‘,4‘:4,5]pyrido[2,3-d]pyrimidine nucleosides 14 (NN, OO, NO, and ON, respectively) with the aim of developing two sets of new base pairing motifs consisting of four hydrogen bonds (H-bonds) is described. The proposed four tricyclic nucleosides 14 were synthesized through the Stille coupling reaction of a 5-iodoimidazole nucleoside with an appropriate 5-stannylpyrimidine derivative, followed by an intramolecular cyclization. These nucleosides were incorporated into ODNs to investigate the H-bonding ability. When one molecule of the tricyclic nucleosides was incorporated into the center of each ODN (ODN I and II, each 17mer), no apparent specificity of base pairing was observed, and all duplexes were less stable than the duplexes containing natural G:C and A:T pairs. On the other hand, when three molecules of the tricyclic nucleosides were consecutively incorporated into the center of each ODN (ODN III and IV, each 17mer), thermal and thermodynamic stabilization of the duplexes due to the specific base pairings was observed. The melting temperature (Tm) of the duplex containing the NO:ON pairs showed the highest Tm of 84.0 °C, which was 18.2 and 23.5 °C higher than that of the duplexes containing G:C and A:T pairs, respectively. This result implies that NO and ON form base pairs with four H-bonds when they are incorporated into ODNs. The duplex containing NO:ON pairs was markedly stabilized by the assistance of the stacking ability of the imidazopyridopyrimidine bases. Thus, we developed a thermally stable new base pairing motif, which should be useful for the stabilization and regulation of a variety of DNA structures.

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Received 20 February 2003
Published online 24 July 2003
Published in print 1 August 2003
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