Nuclear magnetic resonance structural studies of intramolecular purine · purine · pyrimidine DNA triplexes in solution. Base triple pairing alignments and strand direction

Recently, P.A. Beal and P.B. Dervan, expanding on earlier observations by others, have established the formation of purine · purine · pyrimidine triple helices stabilized by G · GC, A · AT and T · AT base triples where the purine-rich third strand was positioned in the major groove of the Watson-Crick duplex and anti-parallel to its purine strand. The present nuclear magnetic resonance (n.m.r.) study characterizes the base triple pairing alignments and strand direction in a 31-mer deoxyoligonucleotide that intramolecularly folds to generate a 7-mer ( R Y -)_n · (R+)_n(Y -)_n triplex with the strands linked by two T₅ loops and stabilized by potential T · AT and G · GC base triples. (R and Y stand for purine and pyrimidine, respectively, while the signs establish the strand direction.) This intramolecular triplex gives well-resolved exchangeable and non-exchangeable proton spectra with Li⁺ as counterion in aqueous solution. These studies establish that the T1 to C7 pyrimidine and the G8 to A14 purine strands are anti-parallel to each other and align through Watson-Crick A · T and G · C pair formation. The T15 to G21 purine-rich third strand is positioned in the major groove of this duplex and pairs through Hoogsteen alignment with the purine strand to generate T · AT and G · GC triples. Several lines of evidence establish that the thymidine and guanosine bases in the T15 to G21 purine-rich third strand adopt anti glycosidic torsion angles under conditions where this strand is aligned anti-parallel to the G8 to A14 purine strand. We have also recorded imino proton n.m.r. spectra for an (R -)_n · (R+)_n(Y -)_n triplex stabilized by G · GC and A · AT triples through intramolecular folding of a related 31-mer deoxyoligonucleotide with Li⁺ as counterion. The intramolecular purine · purine · pyrimidine triplexes containing unprotonated G · GC, A · AT and T · AT triples are stable at basic pH in contrast to pyrimidine · purine · pyrimidine triplexes containing protonated C⁺ · GC and T · AT triples, which are only stable at acidic pH.