Antiparallel, intramolecular triplex DNA stimulates homologous recombination in human cells.

The DNA motif 5'-AAGGGAGAAXGGGTATAGGGYAAGAGGGAA-3' (named XY32) is an H-palindrome and has been shown to undergo a superhelix-induced, pH-dependent structural transition to H-form (pyrimidine purineo pyrimidine triplex) DNA when X = Y = A (AA32) or X = Y = G (GG32), but when X = A and Y = G (AG32) or X = G and Y = A (GA32), the transition is much more difficult [Mirkin, S. (1987) Nature (London) 330, 495-497]. Furthermore, AA32, GG32, and GA32 triplexes have the proper sequence structure to potentially form pyrimidineopurineopurine (*H-form) triplexes, but AG32 does not [Beal, P. A. & Dervan, P. B. (1992) Nucleic Acids Res. 20, 2773-2776]. Using an in vivo plasmid-plasmid recombination assay system in cultured human cells, we have found that AA32, GA32, and GG32 stimulate homologous recombination between plasmids 3- to 5-fold when both recombination substrates contain these triplex-forming sequences, whereas AG32, which differs from the others by only 1 or 2 bp, does not significantly affect the frequency of recombination. Double-strand breaks, which destroy supercoiling, nullify the stimulation. Therefore, stimulation of homologous recombination between plasmids containing these sequences correlates with their triplex-forming potential. Crosses in which the triplex-forming sequence is inserted into only one substrate exhibit an intermediate stimulation, suggesting that the inserts are acting alone as intramolecular triplexes.