2v3l: Difference between revisions
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|PDB= 2v3l |SIZE=350|CAPTION= <scene name='initialview01'>2v3l</scene> | |PDB= 2v3l |SIZE=350|CAPTION= <scene name='initialview01'>2v3l</scene> | ||
|SITE= | |SITE= | ||
|LIGAND= <scene name='pdbligand=R6G:RHODAMINE 6G'>R6G</scene> | |LIGAND= <scene name='pdbligand=DA:2'-DEOXYADENOSINE-5'-MONOPHOSPHATE'>DA</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=R6G:RHODAMINE+6G'>R6G</scene> | ||
|ACTIVITY= | |ACTIVITY= | ||
|GENE= | |GENE= | ||
|DOMAIN= | |||
|RELATEDENTRY= | |||
|RESOURCES=<span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2v3l FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2v3l OCA], [http://www.ebi.ac.uk/pdbsum/2v3l PDBsum], [http://www.rcsb.org/pdb/explore.do?structureId=2v3l RCSB]</span> | |||
}} | }} | ||
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[[Category: Verdier, L.]] | [[Category: Verdier, L.]] | ||
[[Category: Volkmer, A.]] | [[Category: Volkmer, A.]] | ||
[[Category: dna]] | [[Category: dna]] | ||
[[Category: nucleic acid]] | [[Category: nucleic acid]] | ||
''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on | ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Mon Mar 31 05:08:10 2008'' | ||
Revision as of 05:08, 31 March 2008
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| Ligands: | , , , , | ||||||
| Resources: | FirstGlance, OCA, PDBsum, RCSB | ||||||
| Coordinates: | save as pdb, mmCIF, xml | ||||||
ORIENTATIONAL AND DYNAMICAL HETEROGENEITY OF RHODAMINE 6G TERMINALLY ATTACHED TO A DNA HELIX
OverviewOverview
The comparison of Forster resonance energy transfer (FRET) efficiencies between two fluorophores covalently attached to a single protein or DNA molecule is an elegant approach for deducing information about their structural and dynamical heterogeneity. For a more detailed structural interpretation of single-molecule FRET assays, information about the positions as well as the dynamics of the dye labels attached to the biomolecule is important. In this work, Rhodamine 6G (2-[3'-(ethylamino)-6'-(ethylimino)-2',7'-dimethyl-6'H-xanthen-9'-yl]-benz oic acid) bound to the 5'-end of a 20 base pair long DNA duplex is investigated by both single-molecule multiparameter fluorescence detection (MFD) experiments and NMR spectroscopy. Rhodamine 6G is commonly employed in nucleic acid research as a FRET dye. MFD experiments directly reveal the equilibrium of the dye bound to DNA between three heterogeneous environments, which are characterized by distinct fluorescence lifetime and intensity distributions as a result of different guanine-dye excited-state electron transfer interactions. Sub-ensemble fluorescence autocorrelation analysis shows the highly dynamic character of the dye-DNA interactions ranging from nano- to milliseconds and species-specific triplet relaxation times. Two-dimensional NMR spectroscopy corroborates this information by the determination of the detailed geometric structures of the dye-nucleobase complex and their assignment to each population observed in the single-molecule fluorescence experiments. From both methods, a consistent and detailed molecular description of the structural and dynamical heterogeneity is obtained.
About this StructureAbout this Structure
2V3L is a Single protein structure of sequence from [1]. Full crystallographic information is available from OCA.
ReferenceReference
Orientational and dynamical heterogeneity of rhodamine 6G terminally attached to a DNA helix revealed by NMR and single-molecule fluorescence spectroscopy., Neubauer H, Gaiko N, Berger S, Schaffer J, Eggeling C, Tuma J, Verdier L, Seidel CA, Griesinger C, Volkmer A, J Am Chem Soc. 2007 Oct 24;129(42):12746-55. Epub 2007 Sep 27. PMID:17900110
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