Conformational dynamics of DNA hairpins at millisecond resolution obtained from analysis of single-molecule FRET histograms

Journal of Physical Chemistry B

Volumn 117, Issue 50, 2013, Pages 16105-16109

  Tsukanov, Roman ^a   Tomov, Toma E ^a   Berger, Yaron ^a   Liber, Miran ^a   Nir, Eyal ^a  

^a BEN GURION UNIVERSITY OF THE NEGEV   (Israel)

Author keywords

[No Author keywords available]

Indexed keywords

CONFORMATIONAL DYNAMICS; FOLDING REACTIONS; NEAREST NEIGHBOR METHOD; RESONANCE ENERGY TRANSFER; SINGLE-MOLECULE FRETS; TOTAL INTERNAL REFLECTIONS; TRANSITION STATE THEORIES; VALIDATION AND DEMONSTRATIONS;

DNA; DYNAMICS; ENERGY TRANSFER; GRAPHIC METHODS; MOLECULES; PROBABILITY DISTRIBUTIONS; REACTION RATES; REFRACTIVE INDEX;

BIOMOLECULES;

DNA;

ARTICLE; CHEMISTRY; CONFORMATION; FLUORESCENCE RESONANCE ENERGY TRANSFER; NUCLEOTIDE SEQUENCE;

BASE SEQUENCE; DNA; FLUORESCENCE RESONANCE ENERGY TRANSFER; NUCLEIC ACID CONFORMATION;

EID: 84890944332     PISSN: 15206106     EISSN: 15205207     Source Type: Journal    
DOI: 10.1021/jp411280n     Document Type: Article

References (21)

1. Sisamakis, E.; Valeri, A.; Kalinin, S.; Rothwell, P. J.; Seidel, C. A. M. Accurate Single-Molecule FRET Studies Using Multiparameter Fluorescence Detection Methods Enzymol. 2010, 475, 455
2. Kalinin, S.; Peulen, T.; Sindbert, S.; Rothwell, P. J.; Berger, S.; Restle, T.; Goody, R. S.; Gohlke, H.; Seidel, C. A. M. A Toolkit and Benchmark Study for FRET-Restrained High-Precision Structural Modeling Nat. Methods 2012, 9, 1218
3. Chung, H. S.; McHale, K.; Louis, J. M.; Eaton, W. A. Single-Molecule Fluorescence Experiments Determine Protein Folding Transition Path Times Science 2012, 335, 981
4. Schuler, B.; Hofmann, H. Single-Molecule Spectroscopy of Protein Folding Dynamics-Expanding Scope and Timescales Curr. Opin. Chem. Biol. 2013, 23, 36
5. Sabanayagam, C. R.; Eid, J. S.; Meller, A. High-Throughput Scanning Confocal Microscope for Single Molecule Analysis Appl. Phys. Lett. 2004, 84, 1216
6. Chung, H. S.; Gopich, I. V.; McHale, K.; Cellmer, T.; Louis, J. M.; Eaton, W. A. Extracting Rate Coefficients from Single-Molecule Photon Trajectories and FRET Efficiency Histograms for a Fast-Folding Protein J. Phys. Chem. A 2011, 115, 3642
7. Antonik, M.; Felekyan, S.; Gaiduk, A.; Seidel, C. A. M. Separating Structural Heterogeneities from Stochastic Variations in Fluorescence Resonance Energy Transfer Distributions Via Photon Distribution Analysis J. Phys. Chem. B 2006, 110, 6970
8. Nir, E.; Michalet, X.; Hamadani, K. M.; Laurence, T. A.; Neuhauser, D.; Kovchegov, Y.; Weiss, S. Shot-Noise Limited Single-Molecule FRET Histograms: Comparison between Theory and Experiments J. Phys. Chem. B 2006, 110, 22103
9. Kalinin, S.; Felekyan, S.; Valeri, A.; Seidel, C. A. M. Characterizing Multiple Molecular States in Single-Molecule Multiparameter Fluorescence Detection by Probability Distribution Analysis J. Phys. Chem. B 2008, 112, 8361
10. Santoso, Y.; Torella, J. P.; Kapanidis, A. N. Characterizing Single-Molecule FRET Dynamics with Probability Distribution Analysis ChemPhysChem 2010, 11, 2209
11. Kalinin, S.; Valeri, A.; Antonik, M.; Felekyan, S.; Seidel, C. A. Detection of Structural Dynamics by FRET: A Photon Distribution and Fluorescence Lifetime Analysis of Systems with Multiple States J. Phys. Chem. B 2010, 114, 7983
12. Torella, J. P.; Holden, S. J.; Santoso, Y.; Hohlbein, J.; Kapanidis, A. N. Identifying Molecular Dynamics in Single-Molecule FRET Experiments with Burst Variance Analysis Biophys. J. 2011, 100, 1568
13. Gopich, I. V.; Szabo, A. Decoding the Pattern of Photon Colors in Single-Molecule FRET J. Phys. Chem. B 2009, 113, 10965
14. Majumdar, D. S.; Smirnova, I.; Kasho, V.; Nir, E.; Kong, X.; Weiss, S.; Kaback, H. R. Single-Molecule FRET Reveals Sugar-Induced Conformational Dynamics in Lacy Proc. Natl. Acad. Sci. U. S. A. 2007, 104, 12640
15. Hohlbein, J.; Aigrain, L.; Craggs, T. D.; Bermek, O.; Potapova, O.; Shoolizadeh, P.; Grindley, N. D.; Joyce, C. M.; Kapanidis, A. N. Conformational Landscapes of DNA Polymerase I and Mutator Derivatives Establish Fidelity Checkpoints for Nucleotide Insertion Nat. Commun. 2013, 4, 2131
16. Tsukanov, R.; Tomov, T. E.; Masoud, R.; Drory, H.; Plavner, N.; Liber, M.; Nir, E. Detailed Study of DNA Hairpin Dynamics Using Single-Molecule Fluorescence Assisted by DNA Origami J. Phys. Chem. B 2013, 117, 11932
17. Tomov, T. E.; Tsukanov, R.; Masoud, R.; Liber, M.; Plavner, N.; Nir, E. Disentangling Subpopulations in Single-Molecule FRET and ALEX Experiments with Photon Distribution Analysis Biophys. J. 2012, 102, 1163
18. Gietl, A.; Holzmeister, P.; Grohmann, D.; Tinnefeld, P. DNA Origami as Biocompatible Surface to Match Single-Molecule and Ensemble Experiments Nucleic Acids Res. 2012, 40, e110
19. Kuznetsov, S. V.; Ren, C. C.; Woodson, S. A.; Ansari, A. Loop Dependence of the Stability and Dynamics of Nucleic Acid Hairpins Nucleic Acids Res. 2008, 36, 1098
20. SantaLucia, J. A Unified View of Polymer, Dumbbell, and Oligonucleotide DNA Nearest-Neighbor Thermodynamics Proc. Natl. Acad. Sci. U. S.A. 1998, 95, 1460
21. Pinheiro, A. V.; Han, D. R.; Shih, W. M.; Yan, H. Challenges and Opportunities for Structural DNA Nanotechnology Nat. Nanotechnol. 2011, 6, 763