161D

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

Summary for 161D

• Entry DOI: 10.2210/pdb161d/pdb
• Descriptor: DNA/RNA (5'-D(*CP*CP*GP*GP*CP*)-R(*GP*)-D(*CP*CP*GP*G)-3') (2 entities in total)
• Functional Keywords: a-dna/rna, double helix, dna-rna hybrid
• Total number of polymer chains: 2
• Total formula weight: 6125.96

Authors

Ban, C.,Ramakrishnan, B.,Sundaralingam, M. (deposition date: 1994-02-10, release date: 1994-05-18, Last modification date: 2024-02-07)

Primary citation

Ban, C.,Ramakrishnan, B.,Sundaralingam, M.
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.
J.Mol.Biol., 236:275-285, 1994

PubMed 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 P2(1)2(1)2(1) with unit cell dimensions a = 25.63 A, b = 45.24 A and c = 47.99 A, 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 A 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-G17 base-pair in the top half of the duplex to slide significantly into the minor groove compared to the corresponding G7-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-G17 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)).(ABSTRACT TRUNCATED AT 400 WORDS)

PubMed: 7508984
DOI: 10.1006/jmbi.1994.1134

Experimental method

X-RAY DIFFRACTION (1.9 Å)