BIMOLECULAR DNA TRIPLEXES - DUPLEX EXTENSIONS SHOW IMPLICATIONS FOR H-FORM DNA STABILITY

H-form DNA has recently been shown to be biologically relevant by its involvement in the process of homologous recombination [Kohwi, Y., and Panchenko, Y. (1993) Genes Dev. 7, 1766-1778]. A bimolecular DNA trip le-stranded structure (tripler) is central to the formation of H-form DNA. Understanding the formation and factors governing the stability o f such bimolecular triplexes is necessary to fully elucidate the struc ture/function relationship of I-I-form DNA. In this study, we extend k nown information on bimolecular triplexes by examining the effect of a variable CNC base triad (where N = A, C, T, or G) on a 10 base triad tripler that mimics the tripler motif in H-form DNA. We also examine t he effect that a duplex extension of four base pairs has on tripler st ability and selectivity for the base N. Results from thermal denaturat ion experiments indicate that the fully complementary tripler is more stable than its duplex counterpart (Delta T-m = 13 degrees C) and is r esistant to degradation by bovine spleen phosphodiesterase for at leas t 24 h at 10 degrees C. A single-base mismatch in the purine strand of the tripler structure is destabilizing (Delta T-m = similar to 20 deg rees C), and all structures containing a mismatch were readily degrade d by bovine spleen phosphodiesterase. An extension of four duplex base pairs onto the tripler structure affects the stability of the DNA com plex and may have implications relevant to H-form DNA.