Volume 2, Issue 6, Pages 483-494 (June 1994) Crystal and molecular structure of r(CGCGAAUUAGCG): an RNA duplex containing two G(anti)· A(anti) base pairs  Gordon A Leonard, Katherine E McAuley-Hecht, Susanne Ebel, David M Lough, Tom Brown, William N Hunter  Structure  Volume 2, Issue 6, Pages 483-494 (June 1994) DOI: 10.1016/S0969-2126(00)00049-6

Figure 1 Four base-pairing arrangements for GA base pairs. (a) The G (anti)· A (anti) conformation. (b) G(anti)· A(syn). (c) The protonated G (syn)· AH+ (anti). (d) The G· A N7-amino, amino-N3 base pair. Possible hydrogen bonding interactions have been omitted. Structure 1994 2, 483-494DOI: (10.1016/S0969-2126(00)00049-6)

Figure 2 The electron density map (2F o− F c, α calc; green chicken wire) for the G4· A21 base pair in the r(CGCGAAUUAGCG) duplex with the final refined model. The contour level is set at approximately one rms deviation from the mean value observed in the unit cell. The bases are depicted as sticks coloured as follows; carbon yellow, oxygen red and nitrogen blue, with key functional groups labelled. Structure 1994 2, 483-494DOI: (10.1016/S0969-2126(00)00049-6)

Figure 3 A CPK representation in stereo of the RNA duplex. Base atoms are red, the sugar–phosphate atoms are black with the exception of the O2′ hydroxyl which is coloured green. The selected view has the minor groove at the bottom of the diagram, the major groove at the top. (Figure 3, Figure 5, Figure 7, Figure 8 and Figure 9 were obtained using MOLSCRIPT [53]). Structure 1994 2, 483-494DOI: (10.1016/S0969-2126(00)00049-6)

Figure 4 The arrangement of r(CGCGAA- UUAGCG) duplexes in the unit cell. (a) The duplexes viewed approximately parallel to their helix axes to show the cross-section of the cell perpendicular to the c-axis. For clarity, only the sugar– phosphate backbone atoms are shown. Note that the arrangement closely mimics a C-centred motif and that the central helix interacts with four others in this plane. (b) A stereoview illustrating how the helices are aligned along the c- axis to form a continuous tube of RNA. Structure 1994 2, 483-494DOI: (10.1016/S0969-2126(00)00049-6)

Figure 4 The arrangement of r(CGCGAA- UUAGCG) duplexes in the unit cell. (a) The duplexes viewed approximately parallel to their helix axes to show the cross-section of the cell perpendicular to the c-axis. For clarity, only the sugar– phosphate backbone atoms are shown. Note that the arrangement closely mimics a C-centred motif and that the central helix interacts with four others in this plane. (b) A stereoview illustrating how the helices are aligned along the c- axis to form a continuous tube of RNA. Structure 1994 2, 483-494DOI: (10.1016/S0969-2126(00)00049-6)

Figure 5 Stereoview to show one of the O2′ to O2′ hydrogen bonds that help to stabilize the crystal lattice. In black is the trinucleotide r(UAG), residues 8, 9 and 10 of the asymmetric unit. In red, r(GCG) residues 14, 15 and 16 of a symmetry related duplex (1− x, 1/2+y, − z). The dashed green line indicates the hydrogen bond formed between O2′ A(9) and O2′ C(15). Structure 1994 2, 483-494DOI: (10.1016/S0969-2126(00)00049-6)

Figure 6 A representation of the reverse three-centre hydrogen bonding scheme that may help to stabilize the G· A base pairs in the structure of r(CGCGAAUUAGCG). (a) The G (anti)· A (anti) bases. The lone pair on N1 of the adenine is depicted as a lobe, the guanine proton that could interact with this lone pair is circled. (b) The definitions of geometrical parameters tabulated in Table 2 which are useful to analyze three-centre hydrogen bonding possibilities. Parameters r1 and r2 are distances, α , θ 1 and θ 2 are angles. Structure 1994 2, 483-494DOI: (10.1016/S0969-2126(00)00049-6)

Figure 7 A stereo ball-and-stick representation of the r(AAUU) 2 middle section of the RNA duplex. This view highlights the large propeller twist of the A6· U19 and A18· U7 base pairs and the major groove, cross-strand three-centre hydrogen bonds (green dashed lines) that could form as a result of this. Atoms are coloured as follows; phosphorous yellow, oxygen red, nitrogen blue, carbon white. Structure 1994 2, 483-494DOI: (10.1016/S0969-2126(00)00049-6)

Figure 8 Two views of the duplex (ball-and-stick model, red for base atoms, black for sugar–phosphate backbone atoms) with associated solvent positions depicted as cyan spheres. (a) Side view perpendicular to the duplex axis. (b) View down the helix axis. Structure 1994 2, 483-494DOI: (10.1016/S0969-2126(00)00049-6)

Figure 9 Four specific examples of O2′ hydroxyl hydration. The colour scheme is; phosphorous yellow, oxygen red, nitrogen blue, carbon white, solvent molecules cyan spheres. Hydrogen bonds are green dashed lines. (a) The link between O2′ U(8) to the O2 mediated by HOH89. (b)O2′ G(16) to N3 through HOH40. (c) The link from O2′ C(11) through HOH52 to the O3′. (d) HOH35 interacts with O2′ A(21), N3A(21) and O4′ G(22). Structure 1994 2, 483-494DOI: (10.1016/S0969-2126(00)00049-6)