2V3L

Orientational and dynamical heterogeneity of Rhodamine 6G terminally attached to a DNA helix

Summary for 2V3L

• Entry DOI: 10.2210/pdb2v3l/pdb
• Descriptor: 5'-D(*GP*AP*AP*TP*GP*GP*CP*GP*AP*AP *TP*GP*GP*CP*GP*CP*TP*TP*TP*G)-3', 5'-D(*CP*AP*AP*AP*GP*CP*GP*CP*CP*AP *TP*TP*CP*GP*CP*CP*AP*TP*TP*C)-3', RHODAMINE 6G (3 entities in total)
• Functional Keywords: dna, nucleic acid
• Biological source: synthetic construct; More
• Total number of polymer chains: 2
• Total formula weight: 12828.64

Authors

Neubauer, H.,Gaiko, N.,Berger, S.,Schaffer, J.,Eggeling, C.,Tuma, J.,Verdier, L.,Seidel, C.A.M.,Griesinger, C.,Volkmer, A. (deposition date: 2007-06-18, release date: 2007-10-09, Last modification date: 2024-05-15)

Primary citation

Neubauer, H.,Gaiko, N.,Berger, S.,Schaffer, J.,Eggeling, C.,Tuma, J.,Verdier, L.,Seidel, C.A.,Griesinger, C.,Volkmer, A.
Orientational and Dynamical Heterogeneity of Rhodamine 6G Terminally Attached to a DNA Helix Revealed by NMR and Single-Molecule Fluorescence Spectroscopy.
J.Am.Chem.Soc., 129:12746-, 2007

PubMed Abstract: The comparison of Förster 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.

PubMed: 17900110
DOI: 10.1021/JA0722574

Experimental method

SOLUTION NMR