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Abstract

Guanine (G)-rich DNA sequences can adopt four-stranded quadruplex conformations that may play a role in the regulation of genetic processes. To explore the possibility of targeted molecular recognition of DNA sequences with short G-rich peptide nucleic acids (PNA) and to assess the strand arrangement in such complexes, we used PNA and DNA with the Oxytricha nova telomeric sequence d(G₄T₄G₄) as a model. PNA probes were complexed with DNA targets in the following forms: single-stranded oligonucleotides, a loop of DNA in a hairpin conformation, and as supercoiled plasmid with the (G₄T₄G₄)/(C₄A₄C₄) insert. Gel-shift mobility assays demonstrated formation of stable hybrid complexes between the homologous G₄T₄G₄ PNA and DNA with multiple modes of binding. Chemical and enzymatic probing revealed sequence-specific and G-quadruplex dependent binding of G₄T₄G₄ PNA to dsDNA. Spectroscopic and electrophoretic analysis of the complex formed between PNA and the synthetic DNA hairpin containing the G₄T₄G₄ loop showed that the stoichiometry of a prevailing complex is three PNA strands per one DNA strand. We speculate how this new PNA–DNA complex architecture can help to design more selective, quadruplex-specific PNA probes.

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G-Quadruplex Formation Between G-Rich PNA and Homologous Sequences in Oligonucleotides and Supercoiled Plasmid DNA

Abstract

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Supplementary Material