2V3L: Orientational And Dynamical Heterogeneity Of Rhodamine 6g Terminally Attached To A Dna Helix

Citation:
Abstract
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]-benzoic 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.
PDB ID: 2V3LDownload
MMDB ID: 59758
PDB Deposition Date: 2007/6/18
Updated in MMDB: 2007/11
Experimental Method:
solution nmr
Source Organism:
Biological Unit for 2V3L: dimeric; determined by author
Molecular Components in 2V3L
Label Count Molecule
Nucleotides(2 molecules)
1
5'-d(*gp*ap*ap*tp*gp*gp*cp*gp*ap*ap *tp*gp*gp*cp*gp*cp*tp*tp*tp*g)-3'
Molecule annotation
1
5'-d(*cp*ap*ap*ap*gp*cp*gp*cp*cp*ap *tp*tp*cp*gp*cp*cp*ap*tp*tp*c)-3'
Molecule annotation
Chemical (1 molecule)
1
1
* Click molecule labels to explore molecular sequence information.

Citing MMDB
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