1d97
From Proteopedia
| Line 1: | Line 1: | ||
[[Image:1d97.gif|left|200px]] | [[Image:1d97.gif|left|200px]] | ||
| - | + | <!-- | |
| - | + | The line below this paragraph, containing "STRUCTURE_1d97", creates the "Structure Box" on the page. | |
| - | + | You may change the PDB parameter (which sets the PDB file loaded into the applet) | |
| - | + | or the SCENE parameter (which sets the initial scene displayed when the page is loaded), | |
| - | | | + | or leave the SCENE parameter empty for the default display. |
| - | | | + | --> |
| - | + | {{STRUCTURE_1d97| PDB=1d97 | SCENE= }} | |
| - | + | ||
| - | + | ||
| - | }} | + | |
'''CHIRAL PHOSPHOROTHIOATE ANALOGUES OF B-DNA: THE CRYSTAL STRUCTURE OF RP-D(GP(S) CPGP(S)CPGP(S)C)''' | '''CHIRAL PHOSPHOROTHIOATE ANALOGUES OF B-DNA: THE CRYSTAL STRUCTURE OF RP-D(GP(S) CPGP(S)CPGP(S)C)''' | ||
| Line 19: | Line 16: | ||
==About this Structure== | ==About this Structure== | ||
| - | + | Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1D97 OCA]. | |
==Reference== | ==Reference== | ||
Chiral phosphorothioate analogues of B-DNA. The crystal structure of Rp-d[Gp(S)CpGp(S)CpGp(S)C]., Cruse WB, Salisbury SA, Brown T, Cosstick R, Eckstein F, Kennard O, J Mol Biol. 1986 Dec 20;192(4):891-905. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/3108513 3108513] | Chiral phosphorothioate analogues of B-DNA. The crystal structure of Rp-d[Gp(S)CpGp(S)CpGp(S)C]., Cruse WB, Salisbury SA, Brown T, Cosstick R, Eckstein F, Kennard O, J Mol Biol. 1986 Dec 20;192(4):891-905. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/3108513 3108513] | ||
| - | [[Category: Protein complex]] | ||
[[Category: Brown, T.]] | [[Category: Brown, T.]] | ||
[[Category: Cosstick, R.]] | [[Category: Cosstick, R.]] | ||
| Line 30: | Line 26: | ||
[[Category: Kennard, O.]] | [[Category: Kennard, O.]] | ||
[[Category: Salisbury, S A.]] | [[Category: Salisbury, S A.]] | ||
| - | [[Category: | + | [[Category: B-dna]] |
| - | [[Category: | + | [[Category: Double helix]] |
| - | [[Category: | + | [[Category: Modified]] |
| - | + | ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Fri May 2 13:35:24 2008'' | |
| - | ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on | + | |
Revision as of 10:35, 2 May 2008
CHIRAL PHOSPHOROTHIOATE ANALOGUES OF B-DNA: THE CRYSTAL STRUCTURE OF RP-D(GP(S) CPGP(S)CPGP(S)C)
Overview
The compound Rp-d[Gp(S)CpGp(S)CpGp(S)C], an analogue of the deoxyoligomer d(G-C)3, crystallizes in space group P2(1)2(1)2(1) with a = 34.90 A, b = 39.15 A and c = 20.64 A. The structure, which is not isomorphous with any previously determined deoxyoligonucleotide, was refined to an R factor of 14.5% at a resolution of 2.17 A, with 72 solvent molecules located. The two strands of the asymmetric unit form a right-handed double helix, which is a new example of a B-DNA conformation and brings to light an important and overlooked component of flexibility of the double helix. This flexibility is manifest in the alternation of the backbone conformation between two states, defined by the adjacent torsion angles epsilon and zeta, trans . gauche-(BI) and gauche-. trans (BII). BI is characteristic of classical of B-DNA and has an average C(1') to C(1') separation of 4.5 A. The corresponding separation for BII is 5.3 A. Each state is associated with a distinct phosphate orientation where the plane of the PO2 (or POS) group is alternately near horizontal or vertical with respect to the helix axis. The BI and BII conformations are out of phase on the two strands. As a consequence, on one strand purine-pyrimidine stacking is better than pyrimidine-purine, while the converse holds for the other strand. At each base-pair step, good and bad stacking alternate across the helix axis. The pattern of alternation is regular in the context of a fundamental dinucleotide repeat. Re-examination of the B-DNA dodecamer d(C-G-C-G-A-A-T-T-C-G-C-G) shows that the C-G-C-G regions contain the BI and BII conformations, and the associated dual phosphate orientation and asymmetric base stacking. Different mechanisms are used in the two structures to avoid clashes between guanine residues on opposite strands, a combination of lateral slide, tilt and helical twist in the present structure, and base roll, tilt and longitudinal slide (Calladine rules) in the dodecamer. The flexibility of the phosphate orientations demonstrated in this structure is important, since it offers a structural basis for protein-nucleic acid recognition.
About this Structure
Full crystallographic information is available from OCA.
Reference
Chiral phosphorothioate analogues of B-DNA. The crystal structure of Rp-d[Gp(S)CpGp(S)CpGp(S)C]., Cruse WB, Salisbury SA, Brown T, Cosstick R, Eckstein F, Kennard O, J Mol Biol. 1986 Dec 20;192(4):891-905. PMID:3108513 Page seeded by OCA on Fri May 2 13:35:24 2008
