We have designed parallel stranded AT DNA structures constrained to parallel polarity by terminal hemiprotonated CC+ """"""""clamps"""""""". The helices have reverse Watson-Crick pairing. These constructs were used to characterize and calibrate the same helical sequences without the terminal CC+ pairs. The data also show that CC+ helices can be constrained to duplexes rather than the four stranded structures recently shown for unconstrained acid oligo dC. We have obtained the first crystals of DNA triple helices and observed fiber type X-ray diffraction patterns. Molecular models were constructed and compared with Fourier transforms calculated from the diffraction patterns. Very good agreement with the experimental data was obtained for the two kinds of observed B form structures, one with 12 and one with 13 residues per turn. The DNA restriction sequence d-GGTACGCGTACC and its 6,7 IA mispair analog form duplex helices in equilibrium with monomer hairpins. We proposed that the hairpins had two-base loops, not previously demonstrated. We have now shown by NMR spectroscopy the loop size is two rather than four and have determined other aspects of the structures of helix and duplex. Dr. V. Sasisekharan has developed a new method of modeling polysaccharide structures. This approach has led to several stereochemically satisfactory structures of glycosaminoglycans which agree with experimental data. Previous structures had not agreed with experiment and had non-allowed short contacts.
