PMID: 9547282Jun 20, 1998Paper

Exploratory studies on azole carboxamides as nucleobase analogs: thermal denaturation studies on oligodeoxyribonucleotide duplexes containing pyrrole-3-carboxamide

Nucleic Acids Research
P ZhangD E Bergstrom

Abstract

In order to study base pairing properties of the amide group in DNA duplexes, a nucleoside analog, 1-(2'-deoxy-beta-D-ribofuranosyl)pyrrole-3-carboxamide, was synthesized by a new route from the ester, methyl 1-(2'-deoxy-3',5'-di-O-p -toluoyl-beta-D-erythro-pentofuranosyl)pyrrole-3-carboxylate, obtained from the coupling reaction between 1-chloro-2-deoxy-3,5-di-O -toluoyl-d-erythropentofuranose and methyl pyrrole-3-carboxylate by treatment with dimethylaluminum amide. 1-(2'-Deoxy-beta-D-ribofuranosyl)pyrrole-3-carboxamide was incorporated into a series of oligodeoxyribonucleotides by solid-phase phosphoramidite technology. The corresponding oligodeoxyribonucleotides with 3-nitropyrrole in the same position in the sequence were synthesized for UV comparison of helix-coil transitions. The thermal melting studies indicate that pyrrole-3-carboxamide, which could conceptually adopt either a dA-like or a dI-like hydrogen bond conformation, pairs with significantly higher affinity to T than to dC. Pyrrole-3-carboxamide further resembles dA in the relative order of its base pairing preferences (T >dG >dA >dC). Theoretical calculations on the model compound N-methylpyrrole-3-carboxamide using density functional theory show little differ...Continue Reading

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Citations

Oct 10, 2002·Bioorganic & Medicinal Chemistry Letters·Scott M UlrichKevan M Shokat
Jan 25, 2012·Physical Chemistry Chemical Physics : PCCP·Lesley R Rutledge, Stacey D Wetmore
Apr 2, 1999·Nucleic Acids Research·J P DayF Barany
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Jun 19, 2001·Nucleic Acids Research·D Loakes
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Apr 23, 2008·Current Protocols in Nucleic Acid Chemistry·Weidong WuV Jo Davisson
Feb 6, 2002·Chembiochem : a European Journal of Chemical Biology·H AsanumaM Komiyama

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