EurekaMag.com logo
+ Translate

Single molecule FRET data analysis procedures for FRET efficiency determination: probing the conformations of nucleic acid structures


, : Single molecule FRET data analysis procedures for FRET efficiency determination: probing the conformations of nucleic acid structures. Methods 64(1): 36-42

Single molecule FRET microscopy is an attractive technique for studying structural dynamics and conformational diversity of nucleic acid structures. Some of its strengths are that it can follow structural changes on a fast time scale and identify conformation distributions arising from dynamic or static population heterogeneity. Here, we give a description of the experiment and data analysis procedures of this method and detail what parameters are needed for FRET efficiency calculation. Using single molecule FRET data obtained on G-quadruplex DNA structures that exhibit large conformation diversity, we illustrate that the shape of the FRET distribution changes depending on what parameters are included in the data analysis procedure.

(PDF same-day service: $19.90)

Accession: 036846686

PMID: 23583888

DOI: 10.1016/j.ymeth.2013.04.001

Submit PDF Full Text: Here


Submit PDF Full Text

No spam - Every submission is manually reviewed

Due to poor quality, we do not accept files from Researchgate

Submitted PDF Full Texts will always be free for everyone
(We only charge for PDFs that we need to acquire)

Select a PDF file:
Close
Close

Related references

König, S.L.B.; Hadzic, Mélodie.; Fiorini, E.; Börner, R.; Kowerko, D.; Blanckenhorn, W.U.; Sigel, R.K.O., 2014: BOBA FRET: bootstrap-based analysis of single-molecule FRET data. Time-binned single-molecule Förster resonance energy transfer (smFRET) experiments with surface-tethered nucleic acids or proteins permit to follow folding and catalysis of single molecules in real-time. Due to the intrinsically low signal-to-noi...

Hohng, S.; Lee, S.; Lee, J.; Jo, M.Hyun., 2014: Maximizing information content of single-molecule FRET experiments: multi-color FRET and FRET combined with force or torque. Since its first demonstration about twenty years ago, single-molecule fluorescence resonance energy transfer (FRET) has undergone remarkable technical advances. In this tutorial review, we will discuss two technical advances that increase the info...

Hirata, E.; Kiyokawa, E., 2016: Future Perspective of Single-Molecule FRET Biosensors and Intravital FRET Microscopy. Förster (or fluorescence) resonance energy transfer (FRET) is a nonradiative energy transfer process between two fluorophores located in close proximity to each other. To date, a variety of biosensors based on the principle of FRET have been deve...

Long, X.; Parks, J.W.; Stone, M.D., 2016: Integrated magnetic tweezers and single-molecule FRET for investigating the mechanical properties of nucleic acid. Many enzymes promote structural changes in their nucleic acid substrates via application of piconewton forces over nanometer length scales. Magnetic tweezers (MT) is a single molecule force spectroscopy method widely used for studying the energeti...

Sambrook, J.; Russell, D.W., 2006: Probing Protein Interactions Using GFP and FRET * Stage 2: Cell Preparation for FLIM-FRET Analysis. Csh Protocols 2006(1): -

He, Y.; Lu, M.; Cao, J.; Lu, H.Peter., 2012: Manipulating protein conformations by single-molecule AFM-FRET nanoscopy. Combining atomic force microscopy and fluorescence resonance energy transfer spectroscopy (AFM-FRET), we have developed a single-molecule AFM-FRET nanoscopy approach capable of effectively pinpointing and mechanically manipulating a targeted dye-l...

Edel, J.B.; Eid, J.S.; Meller, A., 2007: Accurate single molecule FRET efficiency determination for surface immobilized DNA using maximum likelihood calculated lifetimes. Single molecule fluorescent lifetime trajectories of surface immobilized double-stranded DNA coupled with a tetramethylrhodmaine and Cy5 FRET pair were directly measured using time-tagged single-photon counting and scanning confocal microscopy. A...

Goodson, K.A.; Wang, Z.; Haeusler, A.R.; Kahn, J.D.; English, D.S., 2013: LacI-DNA-IPTG loops: equilibria among conformations by single-molecule FRET. The E. coli Lac repressor (LacI) tetramer binds simultaneously to a promoter-proximal DNA binding site (operator) and an auxiliary operator, resulting in a DNA loop, which increases repression efficiency. Induction of the lac operon by allolactose...

Reif, M.M.; Oostenbrink, C., 2015: Molecular dynamics simulation of configurational ensembles compatible with experimental FRET efficiency data through a restraint on instantaneous FRET efficiencies. Förster resonance energy transfer (FRET) measurements are widely used to investigate (bio)molecular interactions or/and association. FRET efficiencies, the primary data obtained from this method, give, in combination with the common assumption of...

Vieweger, M.; Holmstrom, E.D.; Nesbitt, D.J., 2016: Single-Molecule FRET Reveals Three Conformations for the TLS Domain of Brome Mosaic Virus Genome. Metabolite-dependent conformational switching in RNA riboswitches is now widely accepted as a critical regulatory mechanism for gene expression in bacterial systems. More recently, similar gene regulation mechanisms have been found to be important...