Specificity of the three-stranded complex formation between double-stranded DNA and single-stranded RNA containing repeating nucleotide sequences

Three-stranded nucleic acid complexes have been shown to be formed from double-stranded DNA and single-stranded RNA polymers with restricted base sequences. Complex formation takes place only when the DNA contains all purine bases in one strand and all pyrimidine bases in the other strand and the RNA must be a polypyrimidine polymer. Hence, poly (dA)·(dT) forms a three-stranded complex with poly U, and poly d(T-C)·d(G-A)† forms a three-stranded complex with poly (U-C) in acidic solutions. No other RNA's including the random co-polymer poly (U,C) interact with poly d(T-C)·dG-A) to give a stoichiometric three-stranded structure. Under no condition is a complex detected between poly d(T-G)·d(C-A) or poly d(A-T)·d(A-T) and any polyribonucleotide. The three-stranded poly d(T-C)·d(G-A)·(U-CH+) was characterized by cesium sulfate buoyant density studies, by continuous variations study, by ultraviolet spectral properties and by optical density-temperature profiles. Addition of poly (U-C) to poly d(T-C)·d(G-A) and addition of poly U to poly (dA)·(dT), prior to the addition of Escherichia coli RNA polymerase, effectively reduced the transcription rate of both strands of these DNA's. Other combinations of RNA's with DNA's showed essentially no inhibition; all of these RNA-DNA mixtures were also found to be inert as regards triplex formation. Possible biological roles of the triplexes are discussed.