pH-independent recognition of the dG center dot dC base pair in triplex DNA: 9-Deazaguanine N-7-(2 `-deoxyribonucleoside) and halogenated derivatives replacing protonated dC

Abstract

Triplex-forming oligonucleotides (TFOs) containing 9-deazaguanine N-7-(2'-deoxyribonucleoside) 1a and halogenated derivatives 1b,c were synthesized employing solid-phase oligonucleotide synthesis. For that purpose, the phosphoramidite building blocks 5a-c and 8a-c were synthesized. Multiple incorporations of la-c in place of dC were performed within TFOs, which involved the sequence of five consecutive 1a-c(.)dG(.)dC triplets as well as of three alternating 1a-c(.)dG(.)dC and dT(.)dA(.)dT triplets. These TFOs were designed to bind in a parallel orientation to the target duplex. Triplex forming properties of these oligonucleotides containing la-c in the presence of Na+ and Mg2+ were studied by UV/melting-curve analysis and confirmed by circular-dichroism (CD) spectroscopy. The oligonucleotides containing la in the place of dC formed stable triplexes at physiological pH in the case of sequence of five consecutive 1a(.)dG(.)dC triplets as well as three alternating 1a-c(.)dG(.)dC and dT(.)dA(.)dT triplets. The replacement of la by 9-halogenated derivatives 1b,c further enhanced the stability of DNA triplexes. Nucleosides 1a-c also stabilized duplex DNA.