Effect of Triazole-Modified Thymidines on DNA and RNA Duplex Stability

Abstract

Previous reports showed that consecutive incorporations of triazole-modified 2′-deoxyuridines stabilized DNA•DNA and DNA•RNA duplexes due to additional πstacking between triazole moieties. In this work, several triazole-modified thymidines (1−3) have been synthesized via Cu-catalyzed azide−alkyne cycloaddition reaction and incorporated into oligodeoxyribonucleotides (ODNs). Compounds 1−3 decreased the stability of DNA•DNA and DNA• RNA duplexes. Among these triazole-modified thymidines, 3 with a coumarin-modified triazole moiety showed the most destabilizing effect on ODN duplexes while 1 with an unsubstituted triazole moiety showed the least destabilizing effect. These data suggested that a bulky substituent at the 4 position of triazole ring further destabilizes DNA duplex possibly due to steric hindrance interfering Watson−Crick base pairing. The destabilizing effect per modified nucleoside is smaller for two or three consecutive incorporations than single incorporation. Density functional theory computation suggested the presence of π-stacking interactions among the modified triazole moieties at the C5-methyl group of thymine, which may slightly stabilize the DNA duplex. However, due to the noncoplanar conformation between the modified triazole groups and thymine moieties, the destabilizing effect caused by the steric hindrance is larger than the stabilizing effect arisen from π-stacking. Although the triazole moieties slightly alter the pK a values of thymidine, they did not affect the pH dependence of DNA duplex stability. Similar to native ODNs, the stability of the DNA duplexes containing 1−3 decreased in the following order: pH 7.0/ pH 8.0 > pH 6.0 > pH 9.0 > pH 5.0. Our study provides additional insights into and a novel guide for duplexes' thermal stability caused by base modifications.

Enzymatic Synthesis of Vancomycin-Modified DNA

“…vancomycin moiety led to a rather significant destabilization of the duplex (ΔTm = −3.9 °C) compared to that of the unmodified dsDNA (62.7 ± 0.3 °C compared to 66.6 ± 0.1 °C). This destabilization might be caused either by the presence of the bulky vancomycin moiety since other large moieties such as polyethylene glycol [56] induced similar decreases in Tm values, or by the thermal penalty imparted by the introduction of a single triazole-containing nucleotide [57][58][59]. Nonetheless, this UV-melting analysis indicates that the modification did not significantly interfere with duplex formation.…”