Solution structure of a pyrimidine·purine·pyrimidine DNA triplex containing T·AT, C+ ·GC and G·TA triples  Ishwar Radhakrishnan, Dinshaw J Patel  Structure  Volume 2, Issue 1, Pages 17-32 (January 1994) DOI: 10.1016/S0969-2126(00)00005-8

Figure 1 Sequence, numbering scheme and the two-dimensional folding topology of the intramolecular Y·RY DNA triplex. Residues numbered 1–7, 8–14 and 15–21 comprise the first, second and third strand segments, respectively. Dots indicate Hoogsteen interactions, crosses (x) represent Watson–Crick base pairing. Protonation of cytosines is indicated by (+). Structure 1994 2, 17-32DOI: (10.1016/S0969-2126(00)00005-8)

Figure 2 A schematic depiction of (a) the inter-residue sequential NOEs, and (b) long range NOEs observed between various proton pairs in the Y·RY triplex. Only resolved cross peaks in the two-dimensional and three-dimensional data sets have been included. Structure 1994 2, 17-32DOI: (10.1016/S0969-2126(00)00005-8)

Figure 2 A schematic depiction of (a) the inter-residue sequential NOEs, and (b) long range NOEs observed between various proton pairs in the Y·RY triplex. Only resolved cross peaks in the two-dimensional and three-dimensional data sets have been included. Structure 1994 2, 17-32DOI: (10.1016/S0969-2126(00)00005-8)

Figure 3 Plots comparing the distances calculated from the three-dimensional NOESY-TOCSY data set with the distances calculated from NOE build-ups. The values obtained from NOE build-ups are plotted against: (a) those from the ω3=H1′ planes using the H2′ –H2″ cross peak as the reference, and (b) those from the ω3=H5 planes using the H5–H6 cross peak as the reference. Structure 1994 2, 17-32DOI: (10.1016/S0969-2126(00)00005-8)

Figure 3 Plots comparing the distances calculated from the three-dimensional NOESY-TOCSY data set with the distances calculated from NOE build-ups. The values obtained from NOE build-ups are plotted against: (a) those from the ω3=H1′ planes using the H2′ –H2″ cross peak as the reference, and (b) those from the ω3=H5 planes using the H5–H6 cross peak as the reference. Structure 1994 2, 17-32DOI: (10.1016/S0969-2126(00)00005-8)

Figure 4 (a) Distribution of distance restraints: restraints calculated from NOE-buildups in D2O (■), inter-proton restraints from the NOESY spectrum in H2O (◩), restraints calculated from the three-dimensional NOESY-TOCSY spectrum in D2O (▨), hydrogen bonding distance restraints (◨) and ‘repulsive’ restraints between selected proton pairs (□). Inter-residue restraints were counted as 0.5 restraint for each residue of a pair. (b) Distribution of inter-residue (◩ ) and intra-residue ( ■) distance restraints derived from NMR data. Inter-residue restraints counted as in (a). (c) Atomic rms deviations shown by residue, after least squares fitting the 13 structures relative to the representative structure RM. The circles indicate the average value, the bars denote extreme values. Structure 1994 2, 17-32DOI: (10.1016/S0969-2126(00)00005-8)

Figure 4 (a) Distribution of distance restraints: restraints calculated from NOE-buildups in D2O (■), inter-proton restraints from the NOESY spectrum in H2O (◩), restraints calculated from the three-dimensional NOESY-TOCSY spectrum in D2O (▨), hydrogen bonding distance restraints (◨) and ‘repulsive’ restraints between selected proton pairs (□). Inter-residue restraints were counted as 0.5 restraint for each residue of a pair. (b) Distribution of inter-residue (◩ ) and intra-residue ( ■) distance restraints derived from NMR data. Inter-residue restraints counted as in (a). (c) Atomic rms deviations shown by residue, after least squares fitting the 13 structures relative to the representative structure RM. The circles indicate the average value, the bars denote extreme values. Structure 1994 2, 17-32DOI: (10.1016/S0969-2126(00)00005-8)

Figure 4 (a) Distribution of distance restraints: restraints calculated from NOE-buildups in D2O (■), inter-proton restraints from the NOESY spectrum in H2O (◩), restraints calculated from the three-dimensional NOESY-TOCSY spectrum in D2O (▨), hydrogen bonding distance restraints (◨) and ‘repulsive’ restraints between selected proton pairs (□). Inter-residue restraints were counted as 0.5 restraint for each residue of a pair. (b) Distribution of inter-residue (◩ ) and intra-residue ( ■) distance restraints derived from NMR data. Inter-residue restraints counted as in (a). (c) Atomic rms deviations shown by residue, after least squares fitting the 13 structures relative to the representative structure RM. The circles indicate the average value, the bars denote extreme values. Structure 1994 2, 17-32DOI: (10.1016/S0969-2126(00)00005-8)

Figure 5 Stereo views of the 14 structures from the final stages of the two refinements which were subsequently considered for structure analysis. The structures have been superimposed over the representative structure RM. The first strand is colored cyan, the second strand yellow, and the third strand, magenta. In these views, the 5′-end of the first strand is located on top while those of the second and third strands are located on the bottom. Structure 1994 2, 17-32DOI: (10.1016/S0969-2126(00)00005-8)

Figure 6 Helicoidal parameters for the duplex and third strand segments in the 14 structures. Variation in (a) axial rise, (b) helical twist, (c)x-displacement and (d)y-displacement values for the duplex segment. Variation in (e)axial rise and (f)helical twist values for the third strand. All parameters are relative to an optimized global helical axis calculated separately for each segment. The filled circles correspond to average values over the 14 structures and the bars denote standard deviations. Structure 1994 2, 17-32DOI: (10.1016/S0969-2126(00)00005-8)

Figure 6 Helicoidal parameters for the duplex and third strand segments in the 14 structures. Variation in (a) axial rise, (b) helical twist, (c)x-displacement and (d)y-displacement values for the duplex segment. Variation in (e)axial rise and (f)helical twist values for the third strand. All parameters are relative to an optimized global helical axis calculated separately for each segment. The filled circles correspond to average values over the 14 structures and the bars denote standard deviations. Structure 1994 2, 17-32DOI: (10.1016/S0969-2126(00)00005-8)

Figure 6 Helicoidal parameters for the duplex and third strand segments in the 14 structures. Variation in (a) axial rise, (b) helical twist, (c)x-displacement and (d)y-displacement values for the duplex segment. Variation in (e)axial rise and (f)helical twist values for the third strand. All parameters are relative to an optimized global helical axis calculated separately for each segment. The filled circles correspond to average values over the 14 structures and the bars denote standard deviations. Structure 1994 2, 17-32DOI: (10.1016/S0969-2126(00)00005-8)

Figure 7 Orthogonal views perpendicular (left panels), and parallel (right panels) to the helix axis of the Y·RY triplex. (a)These views are shown in the ‘wireframe-and-ribbon’ representation using INSIGHT II (Biosym Technologies, Inc). The strands follow the coloring scheme in Figure 5. (b)Same views shown in the ‘boxes-and-ribbon’ representation using GRASP (A Nicholls, R Bharadwaj and B Honig, unpublished program). The green line traces the global helix axis of the Watson–Crick duplex segment. The first, second and third strands are colored red, blue and green, respectively. Structure 1994 2, 17-32DOI: (10.1016/S0969-2126(00)00005-8)

Figure 8 Stereo views of the central (T17-G18-T19)·(A10-T11-A12)·(T3-A4–T5) segment in the 14 structures. (a)These views are orthogonal to the helix axis with the major groove of the Watson–Crick duplex segment of the triplex in the foreground. G18, T11 and A4 constitute the G·TA triple. (b)These views are parallel to the helix axis. The strands in both views follow the coloring scheme in Figure 5. Structure 1994 2, 17-32DOI: (10.1016/S0969-2126(00)00005-8)

Figure 9 Pairing alignment of (a)T·AT, (b)C+·GC and (c)G·TA triples in the 14 structures. During structure calculations, no hydrogen-bonding distance restraints were imposed between amino protons of guanine and the O4atom of thymine in the G·TA triple; the resulting alignment being determined by the input NMR restraints. Structure 1994 2, 17-32DOI: (10.1016/S0969-2126(00)00005-8)

Figure 10 Stereo views of the (T17–G18–T19) segment in the Y·RY triplex. Views parallel to the helix axis are shown to emphasize the stacking pattern between bases in this segment and the large variations in helical twist. Structure 1994 2, 17-32DOI: (10.1016/S0969-2126(00)00005-8)

Figure 11 Average values (filled circles) and standard deviations (bars) calculated for (a)glycosidic torsion angle (χ) and (b)pseudo-rotation phase angle ( P) parameters for the various residues in the 14 structures. Structure 1994 2, 17-32DOI: (10.1016/S0969-2126(00)00005-8)

Figure 11 Average values (filled circles) and standard deviations (bars) calculated for (a)glycosidic torsion angle (χ) and (b)pseudo-rotation phase angle ( P) parameters for the various residues in the 14 structures. Structure 1994 2, 17-32DOI: (10.1016/S0969-2126(00)00005-8)

Figure 12 Stacking patterns at (a)(C2–T3)·(A12–G13), (b)(T3–A4)·(T11–A12), and (c)(A4–T5)·(A10–T11) base pair steps in the Watson–Crick duplex segment in the Y·RY triplex. Structure 1994 2, 17-32DOI: (10.1016/S0969-2126(00)00005-8)

Figure 12 Stacking patterns at (a)(C2–T3)·(A12–G13), (b)(T3–A4)·(T11–A12), and (c)(A4–T5)·(A10–T11) base pair steps in the Watson–Crick duplex segment in the Y·RY triplex. Structure 1994 2, 17-32DOI: (10.1016/S0969-2126(00)00005-8)

Figure 12 Stacking patterns at (a)(C2–T3)·(A12–G13), (b)(T3–A4)·(T11–A12), and (c)(A4–T5)·(A10–T11) base pair steps in the Watson–Crick duplex segment in the Y·RY triplex. Structure 1994 2, 17-32DOI: (10.1016/S0969-2126(00)00005-8)

Figure 13 Three views of the molecular surface differing by 120° rotations about the approximate helix axis of the Y·RY triplex. The molecular surface was calculated using GRASP assuming a probe radius of 1.4 å to represent a water molecule [88]. The views emphasize the dimensions and nature of (a)the Watson–Crick groove, (b)the Crick–Hoogsteen groove, and (c)the Watson–Hoogsteen groove. The most convex parts of the surface are colored green while the most concave and planar parts are colored gray and white, respectively. Colors are linearly interpolated for the intermediate values. Structure 1994 2, 17-32DOI: (10.1016/S0969-2126(00)00005-8)

Figure 14 Structure comparison between Y·RY (yellow) and R·RY (magenta) triplexes. Stereoviews of the two structures (a)parallel and (b)perpendicular to the helix axis are shown in the ‘wireframe-and-ribbon’ representation. The structures were overlaid by least squares fitting heavy atom coordinates of residues in the Watson–Crick duplex segment using INSIGHT II. Only bases in the Watson–Crick duplex segment are shown; all other atoms have been omitted for clarity. The arrows in (b) indicate third strand orientations. Structure 1994 2, 17-32DOI: (10.1016/S0969-2126(00)00005-8)