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

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 difference in the preference for a syntau versus anti conformation about the bond from pyrrole C3 to the amide carbonyl. The amide groups in both the minimized antitau and syntau conformations are twisted out of the plane of the pyrrole ring by 6-14 degrees. This twist may be one source of destabilization when the amide group is placed in the helix. Another contribution to the difference in stability between the base pairs of pyrrole-3-carboxamide with T and pyrrole-3-carboxamide with C may be the presence of a hydrogen bond in the former involving an acidic proton (N3-H of T).

Triple helix formation: Binding avidity of acridine-conjugated AG motif third strands containing natural, modified and surrogate bases opposed to pyrimidine interruptions in a polypurine target

“…The parameters for the A@A:T and M@T:A triads are virtually identical if the 3-nitropyrrole occupies a position in which the hydrophobic C5 methyl is in van der Waals contact with the C4-H and NO 2 group of the nitropyrrole. Recent results indicated that 3-nitropyrrole greatly prefers to pair opposite itself rather than a hydrogen bonding base (51), and hydrogen bonding studies by NMR showed that 3-nitropyrrole exhibits virtually no hydrogen bonding association with the natural bases. As discussed in the Results section, models show that if A, C or G was placed opposite 3-nitropyrrole in the triad, there would have to be a significant shift in base position to achieve van der Waals contact.…”

Unnatural Nucleosides with Unusual Base Pairing Properties

“…1.4.25), which was originally designed as a universal nucleobase, pairs with almost equal affinity to each of the natural bases. However, a 12-mer duplex with nitropyrrole opposite itself is significantly more stable than the same duplex with nitropyrrole opposite each of the natural bases (Bergstrom et al, 1995;Zhang et al, 1998). The significance of the hydrophobic substituent (nitro) in mediating this effect is clear when one com-pares pyrrole-3-carboxamide, which in duplex DNA yields far more stable duplexes when paired opposite each of the natural bases than when paired opposite itself.…”

Unnatural Nucleosides with Unusual Base Pairing Properties

“…3-Nitropyrrole deoxyribonucleoside (S.26; Fig. 1.4.8), which was originally designed as a universal nucleobase, pairs with almost equal affinity to each of the natural bases, but a 12-mer duplex with nitropyrrole opposite itself is significantly more stable than the same duplex with nitropyrrole opposite each of the natural bases (Bergstrom et al, 1995;Zhang et al, 1998). The significance of the hydrophobic substituent (nitro) in mediating this effect is clear when one compares pyrrole-3-carboxamide, which in duplex DNA yields far more stable duplexes when paired opposite each of the natural bases than when paired opposite itself.…”

“…Modeling studies with azole carboxamides paired with the four natural bases in a B‐DNA duplex show that two important parameters of base‐pair geometry are maintained: the C1′ to C1′ distances are in the range of 10.8 to 11.0 Å, and λ 1 and λ 2 are ∼50°. Models of azole carboxamide base pairs with a natural base pair yield C1′ to C1′ distances that fall within 0.2 Å and λ 1 and λ 2 within 3° of the natural base pairs (Bergstrom et al, ; Johnson et al, ; Zhang et al, ). 1,2,4‐Triazole‐3‐carboxamide deoxyribonucleoside illustrates the difficulty of predicting both structural and biochemical behavior of nucleoside analogs.…”