PDBsum entry 117d

DNA

PDB id: 117d

Contents

DNA/RNA

Waters ×33

References listed in PDB file

Key reference

Title

Crystal and molecular structure of the alternating dodecamer d(gcgtacgtacgc) in the a-Dna form: comparison with the isomorphous non-Alternating dodecamer d(ccgtacgtacgg).

Authors

C.Bingman, S.Jain, G.Zon, M.Sundaralingam.

Ref.

Nucleic Acids Res, 1992, 20, 6637-6647.

PubMed id

1480485

Abstract

The crystal structure of the alternating dodecamer d(GCGTACGTACGC) (5'-GC) has been determined to a resolution of 2.55A using oscillation film data. The crystals belong to space group P6(1) 22, a = b = 46.2A, c = 71.5A with one strand in the asymmetric unit, and are isomorphous with a previously described non-alternating dodecamer, d(CCGTACGTACGG) (5'-CC). Refinement by X-PLOR/NUCLSQ gave a final R factor of 14.2% for 1089 observations. The molecule adopts the A-DNA form. The interchange of the terminal base pairs in the two dodecamers results in differences in the intermolecular contacts and may account for the differences in the bending. This dodecamer shows an axial deflection of 30 degrees, in the direction of the major groove compared to 20 degrees in 5'-CC and may be a consequence of additional contacts generated in 5'-GC by the interchange of end base pairs. The high helical axis deflection appreciably influences the local helical parameters. The molecule exhibits relatively high inclination angles, and has a narrow major groove. The helical parameters when described relative to the dyad-related hexamer halves of the molecule give more reasonable values. The crystal packing, local helical parameters, torsion angles, and hydration are described and also compared with the non-alternating 5'-CC dodecamer.

Secondary reference #1

Title

Crystal and molecular structure of the a-Dna dodecamer d(ccgtacgtacgg). Choice of fragment helical axis.

Authors

C.A.Bingman, G.Zon, M.Sundaralingam.

Ref.

J Mol Biol, 1992, 227, 738-756. [DOI no: 10.1016/0022-2836(92)90221-5]

PubMed id

1404387

Figure 4.
Figure 4. verall conformation of he dodecamer. (a) The helical axis is vertical and the dyad relating the 2 strands is n the plane of the age. (b) View down the dyad into the major groove. (c) View down the helical axis, showing the distinctive base-stacking pattern haracteristic of A-DNA with an alternating purine-pyrimidine sequence.

Figure 6.
Figure 6. Base-air tacking diagrams of individual dinucleotide seps in the dodecamer d(CCGTACGTACGG) viewed normal to the plane of the op base in strand 1. Te top base-pair is shown as filled bonds ad the bottom base-pair as open bonds. (a) The stacking patt'ern for t#he Pur-Pur and Pyr-Pyr step. (b), (d) and (f) The stacking for Pyr-Pur teps. (c) an (e) The stacking for the Pur-Pyr steps.

The above figures are reproduced from the cited reference with permission from Elsevier