We have previously found that well-formed crystals of DNA triple helices unexpectedly exhibited fiber type X-ray diffraction patterns rather than a regular array of spots, usually seen with crystals (cf. Biopolymers, 39, 573-589, 1996). Two other approaches were then tried. We designed a palindromic triplex with a dyad axis at the center, but single crystals again gave only fiber-type diffraction. We next made a duplex-triplex construct, since crystals of double helices do diffract normally, hoping that the duplex would induce the triplex to be well-ordered laterally as well as axially. These crystals did in fact exhibit normal X-ray diffraction. We introduced Br atoms for MAD analysis, but the crystallographers were unable to solve the structure. We are now attempting to obtain crystals suitable for isomorphous heavy atom replacement. We have placed phosphorothioate linkages at discrete points in the backbone to bind mercury to the sulfur for use as heavy atoms in MIR. Good crystals of the phosphorothioate triplexes have been obtained but so far no mercury derivatives. We have previously shown that DNA sequences that are complementary for Hoogsteen pairing can form Hoogsteen duplexes in acid solution but that when the chains are shortened to dTGAGGAAAGAAGGT and dCTCCTTTCTTCC they form instead a triple helix at slightly acidic pH (cf. Nucleic Acids Research 23, 4116-4121, 1995). Our recent NMR study (cf. Biopolymers, 41, 773-784, 1997) found that the same sequences in neutral solution form antiparrallel duplexes with mispairs. Despite their complemantarity for parallel pairing, the oligomers form an ordered antiparallel duplex with five AT and four CG Watson-Crick base pairs and three mispairs: GT AC, and CT. The relative stability of different possible helical structures changes radically with slight changes in pH, and non-standard base pairs are formed to help stabilize complexes under unfavorable conditions.
