4-(2'-Pyridyl)imidazole as an artificial nucleobase in highly stabilizing Ag(I)-mediated base pairs.

Abstract

A new artificial nucleoside 2 comprising 4-(2'-pyridyl)imidazole as the nucleobase was devised and incorporated into a series of DNA oligonucleotide duplexes. The propensity of 2 to form metal-mediated homo and hetero base pairs was investigated in various 13mer and 26mer duplexes. The artificial nucleoside readily forms Ag(I)-mediated homo base pairs of the type 2-Ag(I)-2, in which the Ag(I) ion resides in a [2+2] coordination environment. In addition, the combination with the previously established imidazole nucleoside 1 leads to the formation of Ag(I)-mediated hetero base pairs (2-Ag(I)-1 and 1-Ag(I)-2) with a [2+1] coordination environment. With an increase in the melting temperature of ΔT m=21.8°C upon the formation of a Ag(I)-mediated base pair, the 2-Ag(I)-1 pair with the 13mer duplex is the most stabilizing Ag(I)-mediated base pair so far. Generally, the impact of the formation of a metal-mediated base pair on the properties of the DNA duplex was found to be significantly more prominent for shorter, intrinsically less stable duplexes.