Targeting duplex DNA with chimeric α,β-triplex-forming oligonucleotides

Abstract

Triplex-directed DNA recognition is strictly limited by polypurine sequences. In an attempt to address this problem with synthetic biology tools, we designed a panel of short chimeric α,β-triplex-forming oligonucleotides (TFOs) and studied their interaction with fluorescently labelled duplex hairpins using various techniques. The hybridization of hairpin with an array of chimeric probes suggests that recognition of double-stranded DNA follows complicated rules combining reversed Hoogsteen and non-canonical homologous hydrogen bonding. In the presence of magnesium ions, chimeric TFOs are able to form highly stable α,β-triplexes, as indicated by native gel-electrophoresis, on-array thermal denaturation and fluorescence-quenching experiments. CD spectra of chimeric triplexes exhibited features typically observed for anti-parallel purine triplexes with a GA or GT third strand. The high potential of chimeric α,β-TFOs in targeting double-stranded DNA was demonstrated in the EcoRI endonuclease protection assay. In this paper, we report, for the first time, the recognition of base pair inversions in a duplex by chimeric TFOs containing α-thymidine and α-deoxyguanosine.

Molecular Engineering of Guanine-Rich Sequences: Z-DNA, DNA Triplexes, and G-Quadruplexes

“…347 A few nucleobase analogues have been developed in line with this strategy and summarized in recent reviews, 345,348 but none have been explored further in molecular and cell biology applications. A very recent paper has proved that the affinity of such α,β-chimeric TFOs was greatly underestimated in the past, 349 thus showing a perspective in exploitation of this strategy in the future. The main obstacle here is that a shift in the position of a nucleobase, depending on the strand targeted, can disrupt stacking interactions between nucleobases, which destabilizes triplex formation.…”

Anomeric DNA quadruplexes

“…19 We have shown recently that this mimetic ability may be exploited for the recognition of base pair inversions in triplex DNA. 32 In antiparallel GQs, syn guanines play a role of reversed strand mimetics. In this way, α guanosines can presumably replace selected core nucleotides.…”

Synthesis of 2′‐deoxy‐4‐aminopyridinylpseudocytidine Derivatives for Incorporation Into Triplex Forming Oligonucleotides

“…The presence of this limitation has been a hindrance to the development of triplex DNA technology. In spite of the number of many studies for antiparallel type (Kolganova et al., ; Sasaki and Taniguchi et al., ; Taniguchi & Sasaki, ; Taniguchi, Nakamura, Senko, Nagatsugi, & Sasaki, .) and parallel type (Hari, Akabane, & Obika, ; Ohkubo et al., ; Semenyuk et al., ) triplex formations, there are no general compounds for the formation of the stable triplex DNA with a high selectivity.…”