Ionic strength-dependent persistence lengths of single-stranded RNA and DNA

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

Volumn 109, Issue 3, 2012, Pages 799-804

  Chen, Huimin ^a   Meisburger, Steve P ^a   Pabit, Suzette A ^a   Sutton, Julie L ^a   Webb, Watt W ^a   Pollack, Lois ^a  

^a Cornell University   (United States)

Author keywords

Ion nucleic acid interactions; Single molecule FRET; Small angle X ray scattering; Worm like chain

Indexed keywords

COUNTERION; SINGLE STRANDED DNA; SINGLE STRANDED RNA; THYMIDINE PHOSPHATE; URIDINE PHOSPHATE;

ARTICLE; BASE PAIRING; CHEMICAL ENVIRONMENT; CONFORMATION; DNA BINDING; DYNAMICS; FLUORESCENCE RESONANCE ENERGY TRANSFER; IN VIVO STUDY; IONIC STRENGTH; MOLECULAR INTERACTION; NUCLEIC ACID STRUCTURE; PRIORITY JOURNAL; PROTEIN FOLDING; RNA FOLDING;

DNA, SINGLE-STRANDED; FLUORESCENCE RESONANCE ENERGY TRANSFER; IONS; MAGNESIUM CHLORIDE; MODELS, MOLECULAR; OSMOLAR CONCENTRATION; PLIABILITY; RNA; SCATTERING, SMALL ANGLE; SODIUM CHLORIDE; X-RAY DIFFRACTION;

EID: 84863012080     PISSN: 00278424     EISSN: 10916490     Source Type: Journal    
DOI: 10.1073/pnas.1119057109     Document Type: Article

References (50)

1. Mandal M, Breaker RR (2004) Gene regulation by riboswitches. Nat Rev Mol Cell Biol 5:451-463. (Pubitemid 38745495)
2. Murray LJW, Arendall WB, Richardson DC, Richardson JS (2003) RNA backbone is rotameric. Proc Natl Acad Sci USA 100:13904-13909. (Pubitemid 37499164)
3. Schlatterer JC, et al. (2008) Hinge stiffness is a barrier to RNA folding. J Mol Biol 379:859-870.
4. Draper DE (2004) A guide to ions and RNA structure. RNA 10:335-343. (Pubitemid 38240993)
5. Tinoco I, Jr, Bustamante C (1999) How RNA folds. J Mol Biol 293:271-281.
6. Cole PE, Crothers DM, Yang SK (1972) Conformational changes of transfer ribonucleic acid - equilibrium phase diagrams. Biochemistry 11:4358-4368.
7. Pyle AM (1993) Ribozymes - a distinct class of metalloenzymes. Science 261:709-714.
8. Cate JH, et al. (1996) Crystal structure of a group I ribozyme domain: Principles of RNA packing. Science 273:1678-1685. (Pubitemid 26317777)
9. Draper DE (2008) RNA folding: Thermodynamic and molecular descriptions of the roles of ions. Biophys J 95:5489-5495.
10. Woodson SA (2005) Metal ions and RNA folding: A highly charged topic with a dynamic future. Curr Opin Chem Biol 9:104-109.
11. Pabit SA, et al. (2009) Both helix topology and counterion distribution contribute to the more effective charge screening in dsRNA compared with dsDNA. Nucleic Acids Res 37:3887-3896.
12. Kirmizialtin S, Elber R (2010) Computational exploration of mobile ion distributions around RNA duplex. J Phys Chem B 114:8207-0220.
13. Bai Y, et al. (2008) Critical assessment of nucleic acid electrostatics via experimental and computational investigation of an unfolded state ensemble. J Am Chem Soc 130:12334-12341.
14. Tan ZJ, Chen SJ (2011) Salt contribution to RNA tertiary structure folding stability. Biophys J 101:176-187.
15. Wong GCL, and Pollack L (2010) Electrostatics of strongly charged biological polymers: Ion-mediated interactions and self-organization in nucleic acids and proteins. Annu Rev Phys Chem 61:171-189.
16. Chen AA, Draper DE, Pappu RV (2009) Molecular simulation studies of monovalent counterion-mediated interactions in a model RNA kissing loop. J Mol Biol 390:805-819.
17. Doose S, Barsch H, Sauer M (2007) Polymer properties of polythymine as revealed by translational diffusion. Biophys J 93:1224-1234. (Pubitemid 47330902)
18. Laurence TA, Kong XX, Jager M,Weiss S (2005) Probing structural heterogeneities and fluctuations of nucleic acids and denatured proteins. Proc Natl Acad Sci USA 102:17348-17353. (Pubitemid 41740869)
19. Murphy MC, Rasnik I, Cheng W, Lohman TM, Ha TJ (2004) Probing single-stranded DNA conformational flexibility using fluorescence spectroscopy. Biophys J 86:2530-2537. (Pubitemid 38524439)
20. Dressinges MN, et al. (2002) Stretching single stranded DNA, a model polyelectrolyte. Phys Rev Lett 89:248102.
21. McIntosh DB, Saleh OA (2011) Salt species-dependent electrostatic effects on ssDNA elasticity. Macromolecules 44:2328-2333.
22. Seol Y, Skinner GM, Visscher K (2004) Elastic properties of a single-stranded charged homopolymeric ribonucleotide. Phys Rev Lett 93:118102.
23. Seol Y, Skinner GM, Visscher K, Buhot A, Halperin A (2007) Stretching of homopolymeric RNA reveals single-stranded helices and base-stacking. Phys Rev Lett 98:158103.
24. Plaxco KW, Millett IS, Segel DJ, Doniach S, Baker D (1999) Chain collapse can occur concomitantly with the rate-limiting step in protein folding. Nat Struct Biol 6:554-556. (Pubitemid 29252835)
25. Jacob J, Krantz B, Dothager RS, Thiyagarajan P, Sosnick TR (2004) Early collapse is not an obligate step in protein folding. J Mol Biol 338:369-382. (Pubitemid 38447092)
26. Merchant KA, Best RB, Louis JM, Gopich IV, Eaton WA (2007) Characterizing the unfolded states of proteins using single-molecule FRET spectroscopy and molecular simulations. Proc Natl Acad Sci USA 104:1528-1533. (Pubitemid 46214624)
27. Kratky O, Porod G (1949) Röntgenuntersuchung aufgelöster Fadenmoleküle (X-ray investigation of dissolved chain molecules). Recueil des Travaux Chimiques des Pays-Bas 68:1106-1122 (German).
28. Thirumalai D, Ha BY (1998) Theoretical and Mathematical Models in Polymer Research: Modern Methods in Polymer Research and Technology, ed AY Grosberg (Academic Press, Boston), pp 1-36.
29. Pedersen JS, Schurtenberger P (1996) Scattering functions of semiflexible polymers with and without excluded volume effects. Macromolecules 29:7602-7612.
30. Odijk T (1977) Polyelectrolytes near the rod limit. J Polym Sci B Polym Phys 15:477-483.
31. Skolnick J, Fixman M (1977) Electrostatic persistence length of a wormlike polyelectrolyte. Macromolecules 10:944-948.
32. Ha BY, Thirumalai D (1995) Electrostatic persistence length of a polyelectrolyte chain. Macromolecules 28:577-581.
33. Muthukumar M (2004) Theory of counter-ion condensation on flexible polyelectrolytes: Adsorption mechanism. J Chem Phys 120:9343-9350.
34. Qiu X, et al. (2007) Inter-DNA attraction mediated by divalent counterions. Phys Rev Lett 99:038104.
35. Kim J, Doose S, Neuweiler H, Sauer M (2006) The initial step of DNA hairpin folding: a kinetic analysis using fluorescence correlation spectroscopy. Nucleic Acids Res 34:2516-2527. (Pubitemid 43985616)
36. Haynes WM (2011) CRC Handbook of Chemistry and Physics (CRC Press, Boca Raton, FL), 92nd Ed.
37. Olson WK, Flory PJ (1972) Spatial configurations of polynucleotide chains. I. Steric interactions in polyribonucleotides: A virtual bond model. Biopolymers 11:1-23.
38. Cheng DM, Dhingra MM, Sarman RH (1978) Spatial configuration of deoxyribotrinucleoside diphosphates in aqueous solution. Nucleic Acids Res 5:4399-4416.
39. Lee CH, Ezra FS, Kondo NS, Sarma RH, Danyluk SS (1976) Conformational properties of dinucleoside monophosphates in solution - dipurines and dipyrimidines. Biochemistry 15:3627-3638.
40. Young PR, Kallenbach NR (1978) Secondary structure in polyuridylic acid - non-classical hydrogen-bonding and the function of the ribose 2′-hydroxyl group. J Mol Biol 126:467-479.
41. Tinland B, Pluen A, Sturm J, Weill B (1997) Persistence length of single-stranded DNA. Macromolecules 30:5763-5765. (Pubitemid 127592220)
42. Mills JB, Vacano E, Hagerman PJ (1999) Flexibility of single-stranded DNA: Use of gapped duplex helices to determine the persistence lengths of poly(dT) and poly (dA). J Mol Biol 285:245-257. (Pubitemid 29034041)
43. Netz RR, Orland H (1999) Field theory for charged fluids and colloids. Europhys Lett 45:726-732.
44. Manghi M, Netz RR (2004) Variational theory for a single polyelectrolyte chain revisited. Eur Phys J E Soft Matter 14:67-77. (Pubitemid 40877397)
45. Saleh OA, McIntosh DB, Pincus P, Ribeck N (2009) Nonlinear low-force elasticity of single- stranded DNA molecules. Phys Rev Lett 102:68301.
46. Müller-Späth S, et al. (2010) Charge interactions can dominate the dimensions of intrinsically disordered proteins. Proc Natl Acad Sci USA 107:14609-14614.
47. Mao AH, Crick SL, Vitalis A, Chicoine CL, Pappu RV (2010) Net charge per residue modulates conformational ensembles of intrinsically disordered proteins. Proc Natl Acad Sci USA 107:8183-8188.
48. Stryer L, Haugland RP (1967) Energy transfer: A spectroscopic ruler. Proc Natl Acad Sci USA 58:719-726.
49. Tate MW, et al. (1995) A large-format high-resolution area X-ray detector based on a fiber-optically bonded charge-coupled device (CCD). J Appl Crystallogr 28:196-205.
50. Press WH, Teukolsky SA, Vetterling WT, Flannery BP (2007) Numerical Recipes 3rd Edition: The Art of Scientific Computing (Cambridge Univ Press, New York).