PROBING THE STRUCTURE OF A PUTATIVE INTERMEDIATE IN HOMOLOGOUS RECOMBINATION - THE 3RD STRAND IN THE PARALLEL DNA TRIPLEX IS IN CONTACT WITH THE MAJOR GROOVE OF THE DUPLEX

A three-stranded DNA that is a putative intermediate of homologous rec ombination is a novel DNA tripler, R-form DNA. In R-form DNA the third strand includes both purines and pyrimidines and is parallel to the i dentical strand of the duplex. To test and refine our previously propo sed R-form base triplets we have used two approaches: (1) dimethyl sul fate protection of R-form DNA; and (2) thermal dissociation of R-form DNAs in which the duplex strands were substituted in a strand-specific manner with either 7-deaza-guanine or 7-deaza-adenine. Together, the footprinting and isosteric substitution results demonstrate that the t hird strand in R-form DNA is in contact with the purines in the N-7 po sition in the major groove of the Watson-Crick duplex in three ((GC):G , (AT):A and (TA):T) out of the four possible triplets. Furthermore, t hese results suggest that the N-7 positions of the duplex play a signi ficant role in stabilizing the DNA-DNA contacts during the homology re cognition process.