Unravelling the structural plasticity of stretched DNA under torsional constraint

Nature Communications

Volumn 7, Issue , 2016, Pages

  King, Graeme A ^a   Peterman, Erwin J G ^a   Wuite, Gijs J L ^a  

^a VU UNIVERSITY AMSTERDAM   (Netherlands)

Author keywords

[No Author keywords available]

Indexed keywords

DOUBLE STRANDED DNA; DNA;

DNA; FLUORESCENCE; GENOME; MELTING; METABOLISM; PROTEIN;

ARTICLE; AT RICH SEQUENCE; BASE PAIRING; BINDING AFFINITY; DNA STRUCTURE; FLUORESCENCE MICROSCOPE; FLUORESCENCE MICROSCOPY; GENOME; IN VIVO STUDY; IONIC STRENGTH; MELTING POINT; MOLECULAR STABILITY; OPTICAL TWEEZERS; PHENOTYPIC PLASTICITY; PROTEIN DNA INTERACTION; CHEMISTRY; CONFORMATION; DNA DENATURATION; GENETICS; MECHANICAL TORSION; MOLECULAR MODEL; NUCLEOTIDE SEQUENCE; OSMOLARITY; THERMODYNAMICS;

BASE PAIRING; BASE SEQUENCE; DNA; MICROSCOPY, FLUORESCENCE; MODELS, MOLECULAR; NUCLEIC ACID CONFORMATION; NUCLEIC ACID DENATURATION; OPTICAL TWEEZERS; OSMOLAR CONCENTRATION; THERMODYNAMICS; TORSION, MECHANICAL;

EID: 84973352099     PISSN: None     EISSN: 20411723     Source Type: Journal    
DOI: 10.1038/ncomms11810     Document Type: Article

References (33)

1. Milstein, J. N. & Meiners, J. C. On the role of DNA biomechanics in the regulation of gene expression. J. R. Soc. Interface 8, 1673-1681 (2011).
2. Rief, M., Clausen-Schaumann, H. & Gaub, H. E. Sequence-dependent mechanics of single DNA molecules. Nat. Struct. Biol. 6, 346-349 (1999).
3. Sheinin, M. Y., Forth, S., Marko, J. F. & Wang, M. D. Underwound DNA under tension: structure, elasticity, and sequence-dependent behaviors. Phys. Rev. Lett. 107, 108102-108106 (2011).
4. Bosaeus, N. et al. Tension induces a base-paired overstretched DNA conformation. Proc. Natl Acad. Sci. USA 109, 15179-15184 (2012).
5. Zhang, X. et al. Revealing the competition between peeled ssDNA, melting bubbles, and S-DNA during DNA overstretching by single-molecule calorimetry. Proc. Natl Acad. Sci. USA 110, 3865-3870 (2013).
6. King, G. A. et al. Revealing the competition between peeled ssDNA, melting bubbles, and S-DNA during DNA overstretching using fluorescence microscopy. Proc. Natl Acad. Sci. USA 110, 3859-3864 (2013).
7. Forth, S., Sheinin, M. Y., Inman, J. & Wang, M. D. Torque measurement at the single-molecule level. Annu. Rev. Biophys. 42, 583-604 (2013).
8. Meng, H., Bosman, J., van der Heijden, T. & van Noort, J. Coexistence of twisted, plectonemic, and melted DNA in small topological domains. Biophys. J. 106, 1174-1181 (2014).
9. Heller, I., Hoekstra, T. P., King, G. A., Peterman, E. J. G. & Wuite, G. J. L. Optical tweezers analysis of DNA-protein complexes. Chem. Rev. 114, 3087-3119 (2014).
10. Vlijm, R., Mashaghi, A., Bernard, S., Modesti, M. & Dekker, C. Experimental phase diagram of negatively supercoiled DNA measured by magnetic tweezers and fluorescence. Nanoscale 7, 3205-3216 (2015).
11. Sitters, G. et al. Acoustic force spectroscopy. Nat. Methods 12, 47-50 (2015).
12. Gore, J. et al. DNA overwinds when stretched. Nature 442, 836-839 (2006).
13. Gross, P. et al. Quantifying how DNA stretches, melts and changes twist under tension. Nat. Phys. 7, 731-736 (2011).
14. Cluzel, P. et al. DNA: an extensible molecule. Science 271, 792-794 (1996).
15. Smith, S. B., Cui, Y. & Bustamante, C. Overstretching B-DNA: the elastic response of individual double-stranded and single-stranded DNA molecules. Science 271, 795-799 (1996).
16. Léger, J. F. et al. Structural transitions of a twisted and stretched DNA molecule. Phys. Rev. Lett. 83, 1066-1069 (1999).
17. van Mameren, J. et al. Unraveling the structure of DNA during overstretching by using multicolor, single-molecule fluorescence imaging. Proc. Natl Acad. Sci. USA 106, 18231-18236 (2009).
18. Paik, D. H. & Perkins, T. T. Overstretching DNA at 65 pN does not require peeling from free ends or nicks. J. Am. Chem. Soc. 133, 3219-3221 (2011).
19. Strzelecki, J., Peplowski, L., Lenartowski, R., Nowak, W. & Balter, A. Mechanical transition in a highly stretched and torsionally constrained DNA. Phys. Rev. E 89, 020701-020705 (2014).
20. Sarkar, A., Léger, J. F., Chatenay, D. & Marko, J. F. Structural transitions in DNA driven by external force and torque. Phys. Rev. E 63, 051903-051912 (2001).
21. Marko, J. F. & Neukirch, S. Global force-torque phase diagram for the DNA double-helix: structural transitions, triple points, and collapsed plectonemes. Phys. Rev. E 88, 062722-062739 (2013).
22. Allemand, J. F., Bensimon, D., Lavery, R. & Croquette, V. Stretched and overwound DNA forms a pauling-like structure with exposed bases. Proc. Natl Acad. Sci. USA 95, 14152-14157 (1998).
23. Wereszczynski, J. & Andricioaei, I. On structural transitions, thermodynamic equilibrium, and the phase diagram of DNA and RNA duplexes under torque and tension. Proc. Natl Acad. Sci. USA 103, 16200-16205 (2006).
24. Schlick, T., Li, B. & Olson, W. K. The influence of salt on the structure and energetics of supercoiled DNA. Biophys. J. 67, 2146-2166 (1994).
25. Cocco, S., Yan, J., Léger, J. F., Chatenay, D. & Marko, J. F. Overstretching and force-driven strand separation of double-helix DNA. Phys. Rev. E 70, 011910 (2004).
26. Fu, H., Chen, H., Marko, J. F. & Yan, J. Two distinct overstretched DNA states. Nucleic Acids Res. 38, 5594-5600 (2010).
27. Fu, H. et al. Transition dynamics and selection of the distinct S-DNA and strand unpeeling modes of double helix overstretching. Nucleic Acids Res. 39, 3473-3481 (2011).
28. Zhang, X., Chen, H., Fu, H., Doyle, P. S. & Yan, J. Two distinct overstretched DNA structures revealed by single-molecule thermodynamics measurements. Proc. Natl Acad. Sci. USA 109, 8103-8108 (2012).
29. Bongini, L., Melli, L., Lombardi, V. & Bianco, P. Transient kinetics measured with force steps discriminate between double-stranded DNA elongation and melting and define the reaction energetics. Nucleic Acids Res. 42, 3436-3449 (2014).
30. De Vlaminck, I. et al. Torsional regulation of hRPA-induced unwinding of double-stranded DNA. Nucleic Acids Res. 38, 4133-4142 (2010).
31. van Mameren, J. et al. Counting RAD51 proteins disassembling from nucleoprotein filaments under tension. Nature 457, 745-748 (2009).
32. Gross, P., Farge, G., Peterman, E. J. G. & Wuite, G. J. L. Combining optical tweezers, single-molecule fluorescence microscopy, and microfluidics for studies of DNA-protein interactions. Methods Enzymol. 475, 427-453 (2010).
33. Modesti, M. Fluorescent labeling of proteins. Methods Mol. Biol. 783, 101-120 (2011).