1k1r
From Proteopedia
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|PDB= 1k1r |SIZE=350|CAPTION= <scene name='initialview01'>1k1r</scene> | |PDB= 1k1r |SIZE=350|CAPTION= <scene name='initialview01'>1k1r</scene> | ||
|SITE= | |SITE= | ||
| - | |LIGAND= | + | |LIGAND= <scene name='pdbligand=CMR:2'-DEOXY-CYTIDINE-5'-RP-MONOMETHYLPHOSPHONATE'>CMR</scene>, <scene name='pdbligand=DC:2'-DEOXYCYTIDINE-5'-MONOPHOSPHATE'>DC</scene>, <scene name='pdbligand=DG:2'-DEOXYGUANOSINE-5'-MONOPHOSPHATE'>DG</scene>, <scene name='pdbligand=DT:THYMIDINE-5'-MONOPHOSPHATE'>DT</scene>, <scene name='pdbligand=RMP:2'-DEOXY-ADENOSINE-5'-RP-MONOMETHYLPHOSPHONATE'>RMP</scene> |
|ACTIVITY= | |ACTIVITY= | ||
|GENE= | |GENE= | ||
| + | |DOMAIN= | ||
| + | |RELATEDENTRY=[[1k1h|1k1h]] | ||
| + | |RESOURCES=<span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1k1r FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1k1r OCA], [http://www.ebi.ac.uk/pdbsum/1k1r PDBsum], [http://www.rcsb.org/pdb/explore.do?structureId=1k1r RCSB]</span> | ||
}} | }} | ||
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[[Category: modified dna]] | [[Category: modified dna]] | ||
| - | ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on | + | ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Sun Mar 30 21:42:05 2008'' |
Revision as of 18:42, 30 March 2008
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| Ligands: | , , , , | ||||||
| Related: | 1k1h
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| Resources: | FirstGlance, OCA, PDBsum, RCSB | ||||||
| Coordinates: | save as pdb, mmCIF, xml | ||||||
HETERODUPLEX OF CHIRALLY PURE R-METHYLPHOSPHONATE/DNA DUPLEX
Overview
Methyl phosphonate oligonucleotides have been used as antisense and antigene agents. Substitution of a methyl group for oxygen in the phosphate ester backbone introduces a new chiral center. Significant differences in physical properties and hybridization abilities are observed between the R(p) and S(p) diastereomers. Chirally pure methylphosphonate deoxyribooligonucleotides were synthesized, and the solution structures of duplexes formed between a single strand heptanucleotide methylphosphonate, d(Cp(Me)Cp(Me)Ap(Me)Ap(Me)Ap(Me)Cp(Me)A), hybridized to a complementary octanucleotide, d(TpGpTpTpTpGpGpC), were studied by NMR spectroscopy. Stereochemistry at the methylphosphonate center for the heptanucleotide was either RpRpRpRpRpRp (R(p) stereoisomer) or RpRpRpSpRpRp (S(p) stereoisomer, although only one of the six methylphosphonate centers has the S(p) stereochemistry). The results show that the methylphosphonate strands in the heteroduplexes exhibit increased dynamics relative to the DNA strand. Substitution of one chiral center from R(p) to S(p) has a profound effect on the hybridization ability of the methylphosphonate strand. Sugars in the phosphodiester strand exhibit C(2)(') endo sugar puckering while the sugars in the methyl phosphonate strand exhibit an intermediate C(4)(') endo puckering. Bases are well stacked on each other throughout the duplex. The hybridization of the methylphosphonate strand does not perturb the structure of the complementary DNA strand in the hetero duplexes. The sugar residue 5' to the S(p) chiral center shows A-form sugar puckering, with a C(3)(')-endo conformation. Minor groove width in the R(p) stereoisomer is considerably wider, particularly at the R(p) vs S(p) site and is attributed to either steric interactions across the minor groove or poorer metal ion coordination within the minor groove.
About this Structure
1K1R is a Protein complex structure of sequences from [1]. Full crystallographic information is available from OCA.
Reference
Structure of hybrid backbone methylphosphonate DNA heteroduplexes: effect of R and S stereochemistry., Thiviyanathan V, Vyazovkina KV, Gozansky EK, Bichenchova E, Abramova TV, Luxon BA, Lebedev AV, Gorenstein DG, Biochemistry. 2002 Jan 22;41(3):827-38. PMID:11790104
Page seeded by OCA on Sun Mar 30 21:42:05 2008
