1l3m
From Proteopedia
| Line 4: | Line 4: | ||
|PDB= 1l3m |SIZE=350|CAPTION= <scene name='initialview01'>1l3m</scene> | |PDB= 1l3m |SIZE=350|CAPTION= <scene name='initialview01'>1l3m</scene> | ||
|SITE= | |SITE= | ||
| - | |LIGAND= | + | |LIGAND= <scene name='pdbligand=A2M:2'-O-METHYL-ADENOSINE-5'-MONOPHOSPHATE'>A2M</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> |
|ACTIVITY= | |ACTIVITY= | ||
|GENE= | |GENE= | ||
| + | |DOMAIN= | ||
| + | |RELATEDENTRY= | ||
| + | |RESOURCES=<span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1l3m FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1l3m OCA], [http://www.ebi.ac.uk/pdbsum/1l3m PDBsum], [http://www.rcsb.org/pdb/explore.do?structureId=1l3m RCSB]</span> | ||
}} | }} | ||
| Line 28: | Line 31: | ||
[[Category: Tsao, Y P.]] | [[Category: Tsao, Y P.]] | ||
[[Category: Wang, L Y.]] | [[Category: Wang, L Y.]] | ||
| - | [[Category: 2'o-methyl | + | [[Category: dna/rna hybrid,chimeric duplex,2'o-methyl]] |
| - | + | ||
| - | + | ||
| - | ''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 21:57:33 2008'' |
Revision as of 18:57, 30 March 2008
| |||||||
| Ligands: | , , , | ||||||
| Resources: | FirstGlance, OCA, PDBsum, RCSB | ||||||
| Coordinates: | save as pdb, mmCIF, xml | ||||||
The Solution Structure of [d(CGC)r(amamam)d(TTTGCG)]2
Overview
The solution structure and hydration of a DNA.RNA hybrid chimeric duplex [d(CGC)r(amamam)d(TTTGCG)]2 in which the RNA adenines were substituted by 2'-O-methylated riboadenines was determined using two-dimensional NMR, simulated annealing, and restrained molecular dynamics. Only DNA residue 7T in the 2'-OMe-RNA.DNA junction adopted an O4'-endo sugar conformation, while the other DNA residues including 3C in the DNA.2'-OMe-RNA junction, adopted C1'-exo or C2'-endo conformations. The observed NOE intensity of 2'-O-methyl group to H1' proton of 4am at the DNA.2'-OMe-RNA junction is much weaker than those of 5am and 6am. The 2'-O-methyl group of 4am was found to orient towards the minor groove in the trans domain while the 2'-O-methyl groups of 5am and 6am were found to be in the gauche (+) domain. In contrast to the long-lived water molecules found close to the RNA adenine H2 and H1' protons and the methyl group of 7T in the RNA-DNA junction of [d(CGC)r(aaa)d(TTTGCG)]2, there were no long-lived water molecules found in [d(CGC)r(amamam)d(TTTGCG)]2. This is probably due to the hydrophobic enviroment created by the 2'-O-methylated riboadenines in the minor groove or due to the wider minor groove width in the middle of the structure. In addition, the 2'-O-methylation of riboadenines in pure chimeric duplex increses its melting temperature from 48.5 degrees C to 51.9 degrees C. The characteristic structural features and hydration patterns of this chimeric duplex provide a molecular basis for further therapeutic applications of DNA.RNA hybrid and chimeric duplexes with 2'-modified RNA residues.
About this Structure
1L3M is a Protein complex structure of sequences from [1]. Full crystallographic information is available from OCA.
Reference
The solution structure of [d(CGC)r(amamam)d(TTTGCG)]2., Tsao YP, Wang LY, Hsu ST, Jain ML, Chou SH, Huang C, Cheng JW, J Biomol NMR. 2001 Nov;21(3):209-20. PMID:11775738
Page seeded by OCA on Sun Mar 30 21:57:33 2008
