The synthesis and stability of oligodeoxyribonucleotides containing the deoxyadenosine mimic 1-(2'-deoxy-beta-D-ribofuranosyl)imidazole-4-carboxamide.
Oligodeoxyribonucleotides containing the nucleoside analog 1-(2'-deoxy-beta-D-ribofuranosyl) imidazole-4-carboxamide (1) were synthesized by solid phase phosphoramidite technology. Nucleoside 1, which contains a reactive exocyclic amide moiety, was incorporated into synthetic oligodeoxyribonucleotides with the use of a benzoyl protecting group. The corresponding oligodeoxyribonucleotides with dI or dA in the same position in the sequence were synthesized for UV comparison of helix-coil transitions. The thermal melting studies indicate that 1, which could conceptually adopt either a dA- or a dI-like hydrogen bond configuration, pairs with significantly higher affinity to T than to dC. Nucleoside 1 further resembles dA in the relative order of its base pairing preferences (T >dG >dA >dC), but may be less discriminating than dA in its bias for base pairing with T over dG.
Johnson
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WT
Department of Medicinal Chemistry and Molecular Pharmacology, Purdue University, West Lafayette, IN 47907, USA.
Zhang
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P
Bergstrom
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DE
D000620:Aminoimidazole Carboxamide / Q000031:analogs & derivatives* / Q000737:chemistry; D003839:Deoxyadenosines / Q000737:chemistry*; D003853:Deoxyribonucleosides / Q000737:chemistry*; D008958:Models, Molecular; D009691:Nucleic Acid Denaturation; D009838:Oligodeoxyribonucleotides / Q000737:chemistry*
D003839:Deoxyadenosines; D003853:Deoxyribonucleosides; D009838:Oligodeoxyribonucleotides; D000620:Aminoimidazole Carboxamide; C066662:5-amino-1-(2'-deoxy-beta-D-ribofuranosyl)imidazole-4-carboxamide