Searching genomes for sequences with the potential to form intrastrand triple helices

The canonical double-helix form of DNA is thought to predominate both in di lute solution and in living cells. Sequence-dependent fluctuations in local DNA shape occur within the double helix. Besides these relatively modest v ariations in shape, more extreme and remarkable structures have been detect ed in which some bases become unpaired. Examples include unusual three-stra nded structures such as H-DNA. Certain RNA and DNA strands can also fold on to themselves to form intrastrand triplexes. Although they have been extens ively studied in vitro, it remains unknown whether nucleic acid triplexes p lay natural roles in cells. If natural nucleic acid triplexes were identifi ed in cells, much could be learned by examining the formation, stabilizatio n, and function of such structures. With these goals in mind, we adapted a pattern-recognition program to search genetic databases for a type of poten tial tripler structure whose presence in genomes has not been previously in vestigated. We term these sequences Potential Intrastrand Tripler (PIT) ele ments. The formation of an intrastrand tripler requires three consecutive s equence domains with appropriate symmetry along a single nucleic acid stran d. It is remarkable that we discovered multiple copies of sequence elements with the potential to form one particular class of intrastrand triplexes i n the fully sequenced genomes of several bacteria. We then focused on the c haracterization of the 25 copies of a particular similar to 37 nt PIT seque nce detected in Escherichia coli. Through biochemical studies, we demonstra te that an isolated DNA strand from this family of E. coli PIT elements for ms a stable intrastrand tripler at physiological temperature and pH in the presence of physiological concentrations of Mg2+ (C) 2000 Academic Press.