A Single 2′-Hydroxyl Group Converts B-DNA to A-DNA : Crystal Structure of the DNA-RNA Chimeric Decamer Duplex d(CCGGC)r(G)d(CCGG) with a Novel Intermolecular G·C Base-paired Quadruplet

Abstract

We have found that the introduction of a single 2′-hydroxyl group on the sugar-phosphate backbone of the B-DNA decamer d(CCGGCGCCGG) transforms it to A-DNA. Thus, for the first time the X-ray structures of the same sequence have been observed in both the A and B-DNA conformations, permitting a comparison. Crystals of the DNA-RNA chimeric decamer d(CCGGC)r(G)d(CCGG) belong to the orthorhombic space group P 2 12 12 1 with unit cell dimensions a = 25·63 Å, b = 45·24 Å and c = 47·99 Å, and one decamer duplex in the asymmetric unit. The structure was solved by a rigid body search using the coordinates of the isomorphous structure d(CCCGGCCGGG) and refined to an R value of 0·136 using 2753 unique reflections at 1·9 Å resolution. The final model contains 406 nucleotide atoms and 61 water molecules. The chimeric duplex exhibits typical A-DNA geometry, with all the sugars in the C (3′)- endo puckering and the base-pairs inclined and displaced from the helix axis. The 2′-hydroxyl groups on rG6 and rG16 protrude into the minor groove surface and form different types of hydrogen bonds; that on strand 1 forms an intermolecular hydrogen bond with the furanose ring O (4′) of a symmetry-related C1 residue, while that on strand 2 is involved in two water bridges. Crystal packing forces the G4·C17 base-pair in the top half of the duplex to slide significantly into the minor groove compared to the corresponding C7·G14 base-pair in the bottom half, resulting in these base-pairs exhibiting different base stacking and intermolecular interactions. The base G4 of the G4·C17 base-pair forms an unorthodox base "triple", G4 *(G10·C11), hydrogen-bonding through its minor groove sites N (2) and N (3) to the minor groove atoms N (2) and O (2) of both bases of the G10·C11 base-pair of a symmetry-related molecule. The base G10 of this triple in turn forms a second similar unorthodox base triple, G10 *(G3 *C18), with the adjacent base-pair G3·C18 of the duplex, thus G10 is involved in a double triple. On the other hand, in the bottom half of the duplex, the C7·G14 base pair is involved only in a single similar unorthodox base triple with G20, (C7·G14) *G20, while the adjacent base-pair rG6·C15 is involved in a novel quadruple with C1·G20, (rG6·C15) * (C1·G20), where the latter base-pairs are hydrogen-bonded to each other via the minor groove sites G(N (2))…C(O (2)). The double base triple and quadruple are features observed for the first time.