The Study of Protein Folding and Dynamics by Determination of Intramolecular Distance Distributions and Their Fluctuations Using Ensemble and Single-Molecule FRET Measurements

ChemPhysChem ◽  
2005 ◽  
Vol 6 (5) ◽  
pp. 858-870 ◽  
Author(s):  
Elisha Haas
Keyword(s):  
Protein Folding ◽  
Single Molecule ◽  
Single Molecule Fret ◽  
Distance Distributions ◽  
Intramolecular Distance

Determination of the size of lipid rafts studied through single-molecule FRET simulations

2021 ◽  
Author(s):  
Pablo Luis Hernández-Adame ◽  
Ulises Meza ◽  
Aldo A. Rodríguez-Menchaca ◽  
Sergio Sánchez-Armass ◽  
Jaime Ruiz-García ◽  
...  
Keyword(s):  
Lipid Rafts ◽  
Single Molecule ◽  
Single Molecule Fret

scholarly journals High-Resolution Single-Molecule FRET via DNA eXchange (FRET X)

2020 ◽  
Author(s):  
Mike Filius ◽  
Sung Hyun Kim ◽  
Ivo Severins ◽  
Chirlmin Joo
Keyword(s):  
Structural Analysis ◽  
High Resolution ◽  
Single Molecule ◽  
Single Object ◽  
Single Molecule Fret ◽  
Dna Strands ◽  
Versatile Tool ◽  
Fret Efficiency ◽  
Fret Pair

ABSTRACTSingle-molecule FRET is a versatile tool to study nucleic acids and proteins at the nanometer scale. However, currently, only a couple of FRET pairs can be reliably measured on a single object. The limited number of available FRET pair fluorophores and complicated data analysis makes it challenging to apply single-molecule FRET for structural analysis of biomolecules. Currently, only a couple of FRET pairs can be reliably measured on a single object. Here we present an approach that allows for the determination of multiple distances between FRET pairs in a single object. We use programmable, transient binding between short DNA strands to resolve the FRET efficiency of multiple fluorophore pairs. By allowing only a single FRET pair to be formed at a time, we can determine the FRET efficiency and pair distance with sub-nanometer resolution. We determine the distance between other pairs by sequentially exchanging DNA strands. We name this multiplexing approach FRET X for FRET via DNA eXchange. We envision that our FRET X technology will be a tool for the high-resolution structural analysis of biomolecules and other nano-structures.

scholarly journals Multicolor single-molecule FRET to explore protein folding and binding

2010 ◽  
Vol 6 (9) ◽  
pp. 1540 ◽  
Author(s):  
Yann Gambin ◽  
Ashok A. Deniz
Keyword(s):  
Protein Folding ◽  
Single Molecule ◽  
Single Molecule Fret

scholarly journals Probing the kinetic and thermodynamic consequences of the tetraloop/tetraloop receptor monovalent ion-binding site in P4–P6 RNA by smFRET

2015 ◽  
Vol 43 (2) ◽  
pp. 172-178 ◽  
Author(s):  
Namita Bisaria ◽  
Daniel Herschlag
Keyword(s):  
Single Molecule ◽  
Specific Binding ◽  
Specific Interaction ◽  
Monovalent Cations ◽  
Folding Kinetics ◽  
Rna Molecules ◽  
Single Molecule Fret ◽  
Wide Range ◽  
Monovalent Ion

Structured RNA molecules play roles in central biological processes and understanding the basic forces and features that govern RNA folding kinetics and thermodynamics can help elucidate principles that underlie biological function. Here we investigate one such feature, the specific interaction of monovalent cations with a structured RNA, the P4–P6 domain of the Tetrahymena ribozyme. We employ single molecule FRET (smFRET) approaches as these allow determination of folding equilibrium and rate constants over a wide range of stabilities and thus allow direct comparisons without the need for extrapolation. These experiments provide additional evidence for specific binding of monovalent cations, Na+ and K+, to the RNA tetraloop–tetraloop receptor (TL–TLR) tertiary motif. These ions facilitate both folding and unfolding, consistent with an ability to help order the TLR for binding and further stabilize the tertiary contact subsequent to attainment of the folding transition state.

scholarly journals Three-Color Single-Molecule FRET and Fluorescence Lifetime Analysis of Fast Protein Folding

2019 ◽  
Vol 116 (3) ◽  
pp. 138a-139a
Author(s):  
Janghyun Yoo ◽  
John M. Louis ◽  
Irina V. Gopich ◽  
Hoi Sung Chung
Keyword(s):  
Protein Folding ◽  
Single Molecule ◽  
Fluorescence Lifetime ◽  
Single Molecule Fret ◽  
Lifetime Analysis
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