Single-molecule FRET and linear dichroism studies of DNA breathing and helicase binding at replication fork junctions

Proceedings of the National Academy of Sciences of the United States of America

Volumn 110, Issue 43, 2013, Pages 17320-17325

  Phelps, Carey ^a   Lee, Wonbae ^a   Jose, Davis ^a   Von Hippel, Peter H ^a   Marcus, Andrew H ^a  

^a UNIVERSITY OF OREGON   (United States)

Author keywords

DNA helicase; Single molecule linear dichroism; SmFRET; T4 primosome helicase; Thermal fluctuations

Indexed keywords

DNA; DOUBLE STRANDED DNA; HELICASE;

ARTICLE; BACTERIOPHAGE T4; CHEMICAL ANALYSIS; DNA BREATHING; DNA REPLICATION; DNA SEQUENCE; ENERGY TRANSFER; ENZYME BINDING; FORSTER RESONANCE ENERGY TRANSFER; GENE EXPRESSION; GENE FUNCTION; LINEAR DICHROISM; PRIORITY JOURNAL; PROTEIN DNA INTERACTION; RELAXATION TIME;

DNA HELICASE; SINGLE-MOLECULE LINEAR DICHROISM; SMFRET; T4 PRIMOSOME HELICASE; THERMAL FLUCTUATIONS;

ALGORITHMS; BACTERIOPHAGE T4; CARBOCYANINES; DNA; DNA REPLICATION; DNA, SINGLE-STRANDED; DNA, VIRAL; FLUORESCENCE RESONANCE ENERGY TRANSFER; FLUORESCENT DYES; KINETICS; MODELS, GENETIC; MODELS, MOLECULAR; NUCLEIC ACID CONFORMATION; PROTEIN MULTIMERIZATION; VIRAL PROTEINS;

EID: 84886383360     PISSN: 00278424     EISSN: 10916490     Source Type: Journal    
DOI: 10.1073/pnas.1314862110     Document Type: Article

References (27)

1. Delagoutte E, von Hippel PH (2002) Helicase mechanisms and the coupling of helicases within macromolecular machines. Part I: Structures and properties of isolated helicases. Q Rev Biophys 35(4):431-478.
2. Choi CH, et al. (2004) DNA dynamically directs its own transcription initiation. Nucleic Acids Res 32(4):1584-1590.
3. Peyrard M, Cuesta-López S, James G (2009) Nonlinear analysis of the dynamics of DNA breathing. J Biol Phys 35(1):73-89.
4. McConnell B, von Hippel PH (1970) Hydrogen exchange as a probe of the dynamic structure of DNA. I. General acid-base catalysis. J Mol Biol 50(2):297-316.
5. Jose D, Weitzel SE, von Hippel PH (2012) Breathing fluctuations in position-specific DNA base pairs are involved in regulating helicase movement into the replication fork. Proc Natl Acad Sci USA 109(36):14428-14433.
6. Jose D, Datta K, Johnson NP, von Hippel PH (2009) Spectroscopic studies of positionspecific DNA "breathing" fluctuations at replication forks and primer-template junctions. Proc Natl Acad Sci USA 106(11):4231-4236.
7. Altan-Bonnet G, Libchaber A, Krichevsky O (2003) Bubble dynamics in doublestranded DNA. Phys Rev Lett 90(13):138101.
8. Nossal N (1994) Molecular Biology of Bacteriophage T4 (Am Soc Microbiol, Washington, DC), pp 43-53.
9. Alberts BM (1987) Prokaryotic DNA replication mechanisms. Philos Trans R Soc Lond B Biol Sci 317(1187):395-420.
10. Richardson RW, Nossal NG (1989) Characterization of the bacteriophage T4 gene 41 DNA helicase. J Biol Chem 264(8):4725-4731.
11. Dong F, Gogol EP, von Hippel PH (1995) The phage T4-coded DNA replication helicase (gp41) forms a hexamer upon activation by nucleoside triphosphate. J Biol Chem 270(13):7462-7473.
12. Dong F, von Hippel PH (1996) The ATP-activated hexameric helicase of bacteriophage T4 (gp41) forms a stable primosome with a single subunit of T4-coded primase (gp61). J Biol Chem 271(32):19625-19631.
13. Jose D, Weitzel SE, Jing D, von Hippel PH (2012) Assembly and subunit stoichiometry of the functional helicase-primase (primosome) complex of bacteriophage T4. Proc Natl Acad Sci USA 109(34):13596-13601.
14. Lee W, Jose D, Phelps C, Marcus AH, von Hippel PH (2013) A single-molecule view of the assembly pathway, subunit stoichiometry, and unwinding activity of the bacteriophage T4 primosome (helicase-primase) complex. Biochemistry 52(18):3157-3170.
15. Ha T, et al. (2002) Initiation and re-initiation of DNA unwinding by the Escherichia coli Rep helicase. Nature 419(6907):638-641.
16. Weston KD, Goldner LS (2001) Orientation imaging and reorientation dynamics of single dye molecules. J Phys Chem B 105:3453-3462.
17. Wei C-YJ, Lu CY, Kim YH, Vanden Bout DA (2007) Determining if a system is heterogeneous: The analysis of single molecule rotational correlation functions and their limitations. J Fluoresc 17(6):797-804.
18. Ha T, Laurence TA, Chemla DS, Weiss S (1999) Polarization spectroscopy of single fluorescent molecules. J Phys Chem B 103:6839-6850.
19. Beausang JF, Sun Y, Quinlan ME, Forkey JN, Goldman YE (2012) Orientation and rotational motions of single molecules by polarized total internal reflection fluorescence microscopy (polTIRFM). Cold Spring Harb Protoc, 10.1101/pdb.top069344.
20. Beausang JF, Shroder DY, Nelson PC, Goldman YE (2013) Tilting and wobble of myosin V by high-speed single-molecule polarized fluorescence microscopy. Biophys J 104(6): 1263-1273.
21. Thomsson D, Lin H, Scheblykin IG (2010) Correlation analysis of fluorescence intensity and fluorescence anisotropy fluctuations in single-molecule spectroscopy of conjugated polymers. ChemPhysChem 11(4):897-904.
22. Tubasum S, Cogdell RJ, Scheblykin IG, Pullerits T (2011) Excitation-emission polarization spectroscopy of single light harvesting complexes. J Phys Chem B 115(17):4963-4970.
23. Widom JR, et al. (2013) Electronic transition moments of 6-methyl isoxanthopterin - a fluorescent analogue of the nucleic acid base guanine. Nucleic Acids Res 41(2): 995-1004.
24. Nordén B, Rodger A, Dafforn T (2010) Linear Dichroism and Circular Dichroism: A Textbook on Polarized-Light Spectroscopy (RSC, Cambridge, UK).
25. Horowitz P, Hill W (1986) The Art of Electronics (Cambridge Univ Press, New York).
26. Chandler D (1987) Introduction to Modern Statistical Mechanics (Oxford Univ Press, New York).
27. Fink MC, Adair KV, Guenza MG, Marcus AH (2006) Translational diffusion of fluorescent proteins by molecular Fourier imaging correlation spectroscopy. Biophys J 91(9):3482-3498.