Triplex Formation of an Oligonucleotide Containing 2′‐O‐methylpseudoisocytidine with Single and Double Stranded Nucleic Acids at Neutral pH

An oligonucleotide analog containing 2′-O-methylpseudoisocytidine (P) and 2′-O-methyluridine (X) in an alternated homopyrimidine sequence (P-X-)7P-T can form triplexes with d-A-(G-A-)7G single strand and [d-A-(G-A-)7G]:[d-C-(T-C-)7T] duplex in neutral conditions. An UV mixing titration showed an end point of two units of (P-X-)7P-T to one unit of d-A-(G-A-)7G. This indicates that a [(P-X-)7P-T]·[d-A-(G-A-)7G]·[(P-X-)7P-T] is formed. The [(P-X-)7P-T]·[d-A-(G-A-)7G]·[(P-X-)7P-T] triplex is stable in a 0.1 M NaCl solution at neutral pH. However, the formation of triplex with [(P-X-)7P-T] and a duplex [d-A-(G-A-)7G]·[d-C-(T-C-)7T] can be accomplished in solution also containing 5 mM MgCl2. CD spectra of both triplexes showed large negative bands at wavelength 210–230 nm. Both triplexes can be detected by native gel electrophoresis. The thermal dissociation/association results indicate that this triplex dissociates to the single strands directly without going through a stable duplex intermediate.