Hydration sites in purine·purine·pyrimidine and pyrimidine·purine·pyrimidine DNA triplexes in aqueous solution  Ishwar Radhakrishnan, Dinshaw J Patel  Structure  Volume 2, Issue 5, Pages 395-405 (May 1994) DOI: 10.1016/S0969-2126(00)00041-1

Figure 1 (a) Oligonucleotide sequence and numbering scheme for the R·RY DNA triplex. The crosses (x) denote Watson–Crick interactions while dots (•) signify Hoogsteen interactions. (b) A schematic depiction of the pairing alignments of G·GC and T·AT triples in the triplex. The polarities of the strands are shown along with the groove nomenclature used in the text. Structure 1994 2, 395-405DOI: (10.1016/S0969-2126(00)00041-1)

Figure 1 (a) Oligonucleotide sequence and numbering scheme for the R·RY DNA triplex. The crosses (x) denote Watson–Crick interactions while dots (•) signify Hoogsteen interactions. (b) A schematic depiction of the pairing alignments of G·GC and T·AT triples in the triplex. The polarities of the strands are shown along with the groove nomenclature used in the text. Structure 1994 2, 395-405DOI: (10.1016/S0969-2126(00)00041-1)

Figure 2 (a) Oligonucleotide sequence and numbering scheme for the Y·RY DNA triplex. The crosses (x) denote Watson–Crick interactions while dots (•) signify Hoogsteen interactions. N 3-protonated cytosine residues are indicated (+). (b) A schematic depiction of the pairing alignments of C +·GC and T·AT triples in the triplex. The polarities of the strands are shown along with the groove nomenclature used in the text. Structure 1994 2, 395-405DOI: (10.1016/S0969-2126(00)00041-1)

Figure 2 (a) Oligonucleotide sequence and numbering scheme for the Y·RY DNA triplex. The crosses (x) denote Watson–Crick interactions while dots (•) signify Hoogsteen interactions. N 3-protonated cytosine residues are indicated (+). (b) A schematic depiction of the pairing alignments of C +·GC and T·AT triples in the triplex. The polarities of the strands are shown along with the groove nomenclature used in the text. Structure 1994 2, 395-405DOI: (10.1016/S0969-2126(00)00041-1)

Figure 3 Expanded plots (6 to 15 ppm) of the cross sections taken along ω 2at the ω 1resonance frequency of water in the ROESY (top) and NOESY (center) spectra of the R·RY DNA triplex recorded at −4° C. These spectra are plotted in absolute intensity mode. The one-dimensional reference spectrum is shown at the bottom. The water-suppression sequences produce a sinusoidal excitation profile of the form sin[0.19(δ −5)] where δ is the chemical shift in ppm and the argument of the sine function is given in radians. Some of the more rapidly-exchanging proton resonances are labeled in the NOESY spectrum. The dots (•) denote signals belonging to a minor conformer. Structure 1994 2, 395-405DOI: (10.1016/S0969-2126(00)00041-1)

Figure 4 Expanded plots (6.3 to 8.2 ppm) of the same cross sections shown in Figure 3. The ROESY (top) and NOESY (center) spectra are plotted in absolute intensity mode. The one- dimensional reference spectrum is shown at the bottom. The interactions between DNA protons and water are labeled at the top of the figure. The crosses (x) denote NOEs involving H3′ protons that resonate near the water chemical shift. Structure 1994 2, 395-405DOI: (10.1016/S0969-2126(00)00041-1)

Figure 5 The methyl proton region (1 to 2 ppm) of the ω 1cross sections taken at the water frequency in the ROESY (top) and NOESY (center) spectra of the R·RY DNA triplex recorded at (a) −4° C and (b) 15° C. The spectra are plotted in the absolute intensity mode. The corresponding one- dimensional reference spectra are shown at the bottom. The interactions between methyl protons and water are labeled at the top of the figure. The asterisk (∗) denotes an impurity in the sample. The crosses (x) denote NOEs involving H3′ protons that resonate near the water chemical shift. Structure 1994 2, 395-405DOI: (10.1016/S0969-2126(00)00041-1)

Figure 6 Expanded plots (6 to 15 ppm) of the cross sections taken along ω 2at the ω 1resonance frequency of water in the ROESY (top) and NOESY (center) spectra of the Y·RY DNA triplex recorded at −4° C. These spectra are plotted in absolute intensity mode. The one-dimensional reference spectrum is shown at the bottom. The water-suppression sequences produce a sinusoidal excitation profile of the form sin[0.19(δ − 5)]. Some of the more rapidly-exchanging proton resonances are labeled in the NOESY spectrum. Also labeled are the chemical shift ranges of the hydrogen bonded (denoted ‘NH 2b’) and non-hydrogen bonded (denoted ‘NH 2e’) protonated cytosine amino proton resonances. The dots (•) denote signals belonging to a minor conformer while the asterisks (∗) denote residual ammonium ion in the sample. Structure 1994 2, 395-405DOI: (10.1016/S0969-2126(00)00041-1)

Figure 7 Expanded plots (6.3 to 8.7 ppm) of the same cross sections shown in Figure 6. The ROESY (top) and NOESY (center) spectra are plotted in absolute intensity mode. The one- dimensional reference spectrum is shown at the bottom. The interactions between DNA protons and water are labeled at the top of the figure. The crosses (x) denote NOEs involving H3′ protons that resonate near the water chemical shift while the asterisks (∗) denote residual ammonium ion in the sample; dots (•) denote signals from a minor conformer. Structure 1994 2, 395-405DOI: (10.1016/S0969-2126(00)00041-1)

Figure 8 The methyl proton region (0.7 to 1.9 ppm) of the ω 1 cross sections taken at the water frequency in the ROESY (top) and NOESY (center) spectra of the Y·RY DNA triplex recorded at (a) −4° C and (b) 15° C. The corresponding one-dimensional reference spectra are shown at the bottom. The interactions between methyl protons and water are labeled at the top of the figure. The asterisk (∗) denotes an impurity in the sample. Structure 1994 2, 395-405DOI: (10.1016/S0969-2126(00)00041-1)

Figure 9 The base proton region (8.7 to 7.0 ppm) of the ω 1cross sections taken at the water frequency in the ROESY spectra recorded at −4° C for the Y·RY DNA triplex samples prepared with Na + (top) and Li + (bottom) as the counter ions. The interactions between the base protons and water are labeled at the top of the figure. The asterisks (∗) denote an impurity in the sample; dots (•) denote signals from a minor conformer. Structure 1994 2, 395-405DOI: (10.1016/S0969-2126(00)00041-1)

Figure 10 Views of the Crick–Hoogsteen groove in (a) the R·RY, and (b) the Y·RY DNA triplexes. The molecular surfaces mapped using a spherical probe of radius 1.4 å are shown in the views on the left. The most convex parts of the molecular surface are coded green while the most concave and planar parts are coded gray and white, respectively. Colors are linearly interpolated for the intermediate values. The views on the right are shown in the ‘boxes-and-ribbon’ representation with strands I, II and III colored red, blue and green, respectively. (Images were generated using the GRASP program [43] provided by Anthony Nicholls, Ranganathan Bharadwaj and Barry Honig). Structure 1994 2, 395-405DOI: (10.1016/S0969-2126(00)00041-1)

Figure 10 Views of the Crick–Hoogsteen groove in (a) the R·RY, and (b) the Y·RY DNA triplexes. The molecular surfaces mapped using a spherical probe of radius 1.4 å are shown in the views on the left. The most convex parts of the molecular surface are coded green while the most concave and planar parts are coded gray and white, respectively. Colors are linearly interpolated for the intermediate values. The views on the right are shown in the ‘boxes-and-ribbon’ representation with strands I, II and III colored red, blue and green, respectively. (Images were generated using the GRASP program [43] provided by Anthony Nicholls, Ranganathan Bharadwaj and Barry Honig). Structure 1994 2, 395-405DOI: (10.1016/S0969-2126(00)00041-1)