Sequence-dependent elasticity and electrostatics of single-stranded DNA: Signatures of base-stacking

Biophysical Journal

Volumn 106, Issue 3, 2014, Pages 659-666

  McIntosh, Dustin B ^a   Duggan, Gina ^a   Gouil, Quentin ^b   Saleh, Omar A ^a  

^a UNIVERSITY OF CALIFORNIA   (United States)

^b ECOLE NORMALE SUPÉRIEURE   (France)

Author keywords

[No Author keywords available]

Indexed keywords

DEOXYADENOSINE PHOSPHATE HOMOPOLYMER; POLYADENYLIC ACID; SINGLE STRANDED DNA;

ARTICLE; CHEMISTRY; ELASTICITY; NUCLEOTIDE SEQUENCE; STATIC ELECTRICITY;

BASE SEQUENCE; DNA, SINGLE-STRANDED; ELASTICITY; POLY A; STATIC ELECTRICITY;

EID: 84893497493     PISSN: 00063495     EISSN: 15420086     Source Type: Journal    
DOI: 10.1016/j.bpj.2013.12.018     Document Type: Article

References (39)

1. S. Kojima, E.L. Sher-Chen, and C.B. Green Circadian control of mRNA polyadenylation dynamics regulates rhythmic protein expression Genes Dev. 26 2012 2724 2736
2. S. Uehara, and N. Shimada K. Sakurai 3′ Poly(dA)-tailed thrombin DNA aptamer to increase DNase-resistance and clotting inhibitory activity Bull. Chem. Soc. Jpn. 81 2008 1485 1491
3. D.L. Theobald, R.M. Mitton-Fry, and D.S. Wuttke Nucleic acid recognition by OB-fold proteins Annu. Rev. Biophys. Biomol. Struct. 32 2003 115 133
4. T. Liedl, and B. Högberg W.M. Shih Self-assembly of three-dimensional prestressed tensegrity structures from DNA Nat. Nanotechnol. 5 2010 520 524
5. V.A. Bloomfield, D.M. Crothers, and I. Tinoco Nucleic Acids: Structures, Properties, and Functions 2000 University Science Books Mill Valley, CA
6. Y. Seol, and G.M. Skinner A. Halperin Stretching of homopolymeric RNA reveals single-stranded helices and base-stacking Phys. Rev. Lett. 98 2007 158103
7. J.B. Mills, E. Vacano, and P.J. Hagerman Flexibility of single-stranded DNA: use of gapped duplex helices to determine the persistence lengths of poly(dT) and poly(dA) J. Mol. Biol. 285 1999 245 257
8. O.A. Saleh, and D.B. McIntosh N. Ribeck Nonlinear low-force elasticity of single-stranded DNA molecules Phys. Rev. Lett. 102 2009 068301 068304
9. D.B. McIntosh, N. Ribeck, and O.A. Saleh Detailed scaling analysis of low-force polyelectrolyte elasticity Phys. Rev. E Stat. Nonlin. Soft Matter Phys. 80 2009 041803
10. R.R. Netz Strongly stretched semiflexible extensible polyelectrolytes and DNA Macromolecules 34 2001 7522 7529
11. G.S. Manning The persistence length of DNA is reached from the persistence length of its null isomer through an internal electrostatic stretching force Biophys. J. 91 2006 3607 3616
12. C.E. Wickersham, D.H.S. Kerr, and E.A. Lipman Synthesis of extended nanoscale optical encoders Bioconjug. Chem. 21 2010 2234 2238
13. C. Brockman, S.J. Kim, and C.M. Schroeder Direct observation of single flexible polymers using single stranded DNA Soft Matter 7 2011 8005 8012
14. N. Ribeck, and O.A. Saleh Multiplexed single-molecule measurements with magnetic tweezers Rev. Sci. Instrum. 79 2008 094301 094306
15. G. Neuert, and C. Albrecht H. Gaub Dynamic force spectroscopy of the digoxigenin-antibody complex FEBS Lett. 580 2006 505 509
16. P. Pincus Excluded volume effects and stretched polymer-chains Macromolecules 9 1976 386 388
17. H. Eisenberg, and G. Felsenfeld Studies of the temperature-dependent conformation and phase separation of polyriboadenylic acid solutions at neutral pH J. Mol. Biol. 30 1967 17 37
18. D.N. Holcomb, and I. Tinoco Conformation of polyriboadenylic acid: pH and temperature dependence Biopolymers 3 1965 121 133
19. M.J. Stevens, D.B. McIntosh, and O.A. Saleh Simulations of stretching a strong, flexible polyelectrolyte Macromolecules 45 2012 5757 5765
20. N.M. Toan, and D. Thirumalai On the origin of the unusual behavior in the stretching of single-stranded DNA J. Chem. Phys. 136 2012 235103
21. J.F. Marko, and E.D. Siggia Stretching DNA Macromolecules 28 1995 8759 8770
22. A. Buhot, and A. Halperin Effects of stacking on the configurations and elasticity of single-stranded nucleic acids Phys. Rev. E Stat. Nonlin. Soft Matter Phys. 70 2004 020902
23. B.M. Lansdorp, and O.A. Saleh Power spectrum and Allan variance methods for calibrating single-molecule video-tracking instruments Rev. Sci. Instrum. 83 2012 025115
24. A. Dittmore, and D.B. McIntosh O.A. Saleh Single-molecule elasticity measurements of the onset of excluded volume in poly(ethylene glycol) Phys. Rev. Lett. 107 2011 148301
25. N.L. Goddard, and G. Bonnet A. Libchaber Sequence dependent rigidity of single stranded DNA Phys. Rev. Lett. 85 2000 2400 2403
26. M. Rief, H. Clausen-Schaumann, and H.E. Gaub Sequence-dependent mechanics of single DNA molecules Nat. Struct. Biol. 6 1999 346 349
27. X. Zhang, and H. Chen J. Yan Revealing the competition between peeled ssDNA, melting bubbles, and S-DNA during DNA overstretching by single-molecule calorimetry Proc. Nat. Acad. Sci. USA. 110 2013 3865 3870
28. G.S. Manning Limiting laws and counterion condensation in polyelectrolyte solutions. I. Colligative properties J. Chem. Phys. 51 1969 924 933
29. Y. Burak, and R.R. Netz Charge regulation of interacting weak polyelectrolytes J. Phys. Chem. B 108 2004 4840 4849
30. N. Schwierz, D. Horinek, and R.R. Netz Anionic and cationic Hofmeister effects on hydrophobic and hydrophilic surfaces Langmuir 29 2013 2602 2614
31. S.B. Smith, Y.J. Cui, and C. Bustamante Overstretching B-DNA: the elastic response of individual double-stranded and single-stranded DNA molecules Science 271 1996 795 799
32. V.V. Filimonov, and P.L. Privalov Thermodynamics of base interaction in (A)n and (A.U)n J. Mol. Biol. 122 1978 465 470
33. S.M. Freier, and K.O. Hill D.H. Turner Solvent effects on the kinetics and thermodynamics of stacking in poly(cytidylic acid) Biochemistry 20 1981 1419 1426
34. J. Suurkuusk, and J. Alvarez R. Biltonen Calorimetric determination of the heat capacity changes associated with the conformational transitions of polyriboadenylic acid and polyribouridylic acid Biopolymers 16 1977 2641 2652
35. D. Poland, J.N. Vournakis, and H.A. Scheraga Cooperative interactions in single-strand oligomers of adenylic acid Biopolymers 4 1966 223 235
36. J. Applequist, and V. Damie Thermodynamics of the one-stranded helix-coil equilibrium in polyadenylic acid J. Am. Chem. Soc. 88 1966 3895 3900
37. M. Leng, and G. Felsenfeld A study of polyadenylic acid at neutral pH J. Mol. Biol. 15 1966 455 466
38. J.T. Powell, E.G. Richards, and W.B. Gratzer The nature of stacking equilibria in polynucleotides Biopolymers 11 1972 235 250
39. A. Savelyev, C.K. Materese, and G.A. Papoian Is DNA's rigidity dominated by electrostatic or nonelectrostatic interactions? J. Am. Chem. Soc. 133 2011 19290 19293