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

Physical Review E - Statistical, Nonlinear, and Soft Matter Physics

Volumn 86, Issue 2, 2012, Pages

  Sim, Adelene Y L ^a   Lipfert, Jan ^b   Herschlag, Daniel ^a   Doniach, Sebastian ^a  

^a STANFORD UNIVERSITY   (United States)

^b DELFT UNIVERSITY OF TECHNOLOGY   (Netherlands)

Author keywords

[No Author keywords available]

Indexed keywords

BASE-STACKING; BIOLOGICAL PROCESS; EXTERNAL FORCE; MOLECULAR FLEXIBILITY; PERSISTENCE LENGTH; RADIUS OF GYRATION; SALT DEPENDENCE; SINGLE-STRANDED DNA; SMALL ANGLE X-RAY SCATTERING;

DNA; IONIC STRENGTH;

X RAY SCATTERING;

EID: 84864597023     PISSN: 15393755     EISSN: 15502376     Source Type: Journal    
DOI: 10.1103/PhysRevE.86.021901     Document Type: Article

References (50)

1. M. Zuker, Curr. Opin. Struct. Biol. COSBEF 0959-440X 10.1016/S0959- 440X(00)00088-9 10, 303 (2000). (Pubitemid 30333099)
2. R. Das, J. Karanicolas, and D. Baker, Nat. Methods 1548-7091 10.1038/nmeth.1433 7, 291 (2010).
3. Z. J. Tan and S. J. Chen, Biophys. J. BIOJAU 0006-3495 10.1016/j.bpj.2011.05.050 101, 176 (2011).
4. P. Brion and E. Westhof, Annu. Rev. Biophys. Biomol. Struct. ABBSE4 1056-8700 10.1146/annurev.biophys.26.1.113 26, 113 (1997). (Pubitemid 27255369)
5. V. B. Chu, J. Lipfert, Y. Bai, V. S. Pande, S. Doniach, and D. Herschlag, RNA 1355-8382 10.1261/rna.1747509 15, 2195 (2009).
6. J. E. Croy and D. S. Wuttke, Trends Biochem. Sci. TBSCDB 0968-0004 10.1016/j.tibs.2006.07.004 31, 516 (2006). (Pubitemid 44279982)
7. D. P. Martin, P. Biagini, P. Lefeuvre, M. Golden, P. Roumagnac, and A. Varsani, Viruses 10.3390/v3091699 3, 1699 (2011).
8. P. W. Rothemund, Nature 0028-0836 10.1038/nature04586 440, 297 (2006).
9. N. C. Seeman, Annu. Rev. Biochem. ARBOAW 0066-4154 10.1146/annurev- biochem-060308-102244 79, 65 (2010).
10. D.-N. Kim F. Kilchherr, H. Dietz, and M. Bathe, Nucleic Acids Res. 0305-1048 10.1093/nar/gkr1173 40, 2862 (2012).
11. S. B. Smith, Y. Cui, and C. Bustamante, Science SCIEAS 0036-8075 10.1126/science.271.5250.795 271, 795 (1996).
12. Y. Seol, G. M. Skinner, and K. Visscher, Phys. Rev. Lett. PRLTAO 0031-9007 10.1103/PhysRevLett.93.118102 93, 118102 (2004).
13. O. A. Saleh, D. B. McIntosh, P. Pincus, and N. Ribeck, Phys. Rev. Lett. PRLTAO 0031-9007 10.1103/PhysRevLett.102.068301 102, 068301 (2009).
14. B. Tinland, A. Pluen, J. Sturm, and G. Weill, Macromolecules MAMOBX 0024-9297 10.1021/ma970381+ 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 PNASA6 0027-8424 10.1073/pnas.1119057109 109, 799 (2012).
16. S. Doose, H. Barsch, and M. Sauer, Biophys. J. BIOJAU 0006-3495 10.1529/biophysj.107.107342 93, 1224 (2007). (Pubitemid 47330902)
17. N. L. Goddard, G. Bonnet, O. Krichevsky, and A. Libchaber, Phys. Rev. Lett. PRLTAO 0031-9007 10.1103/PhysRevLett.85.2400 85, 2400 (2000).
18. J. B. Mills, E. Vacano, and P. J. Hagerman, J. Mol. Biol. JMOBAK 0022-2836 10.1006/jmbi.1998.2287 285, 245 (1999). (Pubitemid 29034041)
19. M. C. Murphy, I. Rasnik, W. Cheng, T. M. Lohman, and T. Ha, Biophys. J. BIOJAU 0006-3495 10.1016/S0006-3495(04)74308-8 86, 2530 (2004).
20. J. Lipfert, I. S. Millett, S. Seifert, and S. Doniach, Rev. Sci. Instrum. RSINAK 0034-6748 10.1063/1.2194484 77, 046108 (2006).
21. P. Calmettes, D. Durand, M. Desmadril, P. Minard, V. Receveur, and J. C. Smith, Biophys. Chem. 0301-4622 10.1016/0301-4622(94)00081-6 53, 105 (1994). (Pubitemid 24370345)
22. S. Doniach, Chem. Rev. CHREAY 0009-2665 10.1021/cr990071k 101, 1763 (2001). (Pubitemid 35377802)
23. J. Lipfert and S. Doniach, Annu. Rev. Biophys. Biomol. Struct. ABBSE4 1056-8700 10.1146/annurev.biophys.36.040306.132655 36, 307 (2007). (Pubitemid 46998121)
24. A. Guinier, Ann. Phys. 12, 161 (1939).
25. D. I. Svergun, J. Appl. Crystallogr. JACGAR 0021-8898 10.1107/S0021889892001663 25, 495 (1992). (Pubitemid 23564996)
26. See Supplemental Material at http://link.aps.org/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 PNASA6 0027-8424 10.1073/pnas.0404448102 102, 1035 (2005). (Pubitemid 40170721)
28. X. Qiu, L. W. Kwok, H. Y. Park, J. S. Lamb, K. Andresen, and L. Pollack, Phys. Rev. Lett. PRLTAO 0031-9007 10.1103/PhysRevLett.96.138101 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 PNASA6 0027-8424 10.1073/pnas.0409693102 102, 11698 (2005). (Pubitemid 41170789)
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 MAMOBX 0024-9297 10.1021/ma00110a021 28, 1859 (1995).
32. C. Bustamante, J. F. Marko, E. D. Siggia, and S. Smith, Science SCIEAS 0036-8075 10.1126/science.8079175 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 PNASA6 0027-8424 10.1073/pnas.0403643101 101, 12491 (2004). (Pubitemid 39122051)
35. D. C. Rapaport, J. Phys. A JPHAC5 0305-4470 1361-6447 10.1088/0305-4470/18/1/023 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 BICHAW 0006-2960 10.1021/bi048221v 43, 15996 (2004). (Pubitemid 40041013)
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. PRLTAO 0031-9007 10.1103/PhysRevLett.99.018302 99, 018302 (2007). (Pubitemid 47150515)
40. J. B. Hays, M. E. Magar, and B. H. Zimm, Biopolymers BIPMAA 0006-3525 10.1002/bip.1969.360080410 8, 531 (1969).
41. H. Benoit and P. Doty, J. Phys. Chem. 0022-3654 10.1021/j150510a025 57, 958 (1954).
42. T. A. Laurence, X. Kong, M. Jäger, and S. Weiss, Proc. Natl. Acad. Sci. USA PNASA6 0027-8424 10.1073/pnas.0508584102 102, 17348 (2005). (Pubitemid 41740869)
43. J. S. Pedersen and P. Schurtenberger, Macromolecules MAMOBX 0024-9297 10.1021/ma9607630 29, 7602 (1996).
44. S. V. Kuznetsov, Y. Shen, A. S. Benight, and A. Ansari, Biophys. J. BIOJAU 0006-3495 10.1016/S0006-3495(01)75927-9 81, 2864 (2001).
45. C. Rivetti, C. Walker, and C. Bustamante, J. Mol. Biol. JMOBAK 0022-2836 10.1006/jmbi.1998.1830 280, 41 (1998). (Pubitemid 28312805)
46. T. Odijk, J. Polym. Sci. 15, 447 (1977).
47. J. Skolnick and M. Fixman, Macromolecules MAMOBX 0024-9297 10.1021/ma60059a011 10, 944 (1977).
48. J. L. Barrat and J. F. Joanny, Europhys. Lett. EULEEJ 0295-5075 10.1209/0295-5075/24/5/003 24, 333 (1993).
49. J. L. Barrat and J. F. Joanny, Adv. Chem. Phys. 0065-2385 10.1002/9780470141533.ch1 94, 1 (1996).
50. B.-Y. Ha and D. Thirumalai, J. Chem. Phys. JCPSA6 0021-9606 10.1063/1.478656 110, 7533 (1999).