2v3l

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ORIENTATIONAL AND DYNAMICAL HETEROGENEITY OF RHODAMINE 6G TERMINALLY ATTACHED TO A DNA HELIX

Overview

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 Structure

2V3L is a Single protein structure of sequence from [1] with as ligand. Full crystallographic information is available from OCA.

Reference

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 Sep 27;. PMID:17900110

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