SAXS studies of ionnucleic acid interactions

Annual Review of Biophysics

Volumn 40, Issue 1, 2011, Pages 225-242

  Pollack, Lois ^a  

^a Cornell University   (United States)

Author keywords

ASAXS; condensed counterions; DNA; electrostatic interactions; RNA

Indexed keywords

DNA; ION; NUCLEIC ACID; RNA; SODIUM ION; STRONTIUM;

ANISOTROPY; ARTICLE; ATOM; CHEMICAL INTERACTION; CHEMICAL STRUCTURE; CONFORMATIONAL TRANSITION; DNA HELIX; MOLECULAR SIZE; PRIORITY JOURNAL; X RAY CRYSTALLOGRAPHY; BINDING SITE; CHEMISTRY; METHODOLOGY; REVIEW; SMALL ANGLE SCATTERING; ULTRASTRUCTURE; X RAY DIFFRACTION;

BINDING SITES; IONS; NUCLEIC ACIDS; SCATTERING, SMALL ANGLE; X-RAY DIFFRACTION;

EID: 79955846859     PISSN: 1936122X     EISSN: None     Source Type: Book Series    
DOI: 10.1146/annurev-biophys-042910-155349     Document Type: Article

References (103)

1. Anderson CF, Record MT. 1990. Ion distributions around DNA and other cylindrical polyions- theoretical descriptions and physical implications. Annu. Rev. Biophys. Biophys. Chem. 19:423-65 (Pubitemid 20205631)
2. Andresen K, Das R, Park HY, Smith H, Kwok LW, et al. 2004. Spatial distribution of competing ions around DNA in solution. Phys. Rev. Lett. 93:248103
3. Andresen K, Qiu X, Pabit SA, Lamb JS, Park HY, et al. 2008. Mono- and trivalent ions around DNA: a small-angle scattering study of competition and interactions. Biophys. J. 95:287-95
4. Bai Y, Das R, Millett IS, Herschlag D, Doniach S. 2005. Probing counterion modulated repulsion and attraction between nucleic acid duplexes in solution. Proc. Natl. Acad. Sci. USA 102:1035-40 (Pubitemid 40170721)
5. Bai Y, Greenfeld M, Travers KJ, Chu VB, Lipfert J, et al. 2007. Quantitative and comprehensive decomposition of the ion atmosphere around nucleic acids. J. Am. Chem. Soc. 129:14981-88 (Pubitemid 350230720)
6. Baird NJ, Gong HP, Zaheer SS, Freed KF, Pan T, Sosnick TR. 2010. Extended structures in RNA folding intermediates are due to non-native interactions rather than electrostatic repulsion. J. Mol. Biol. 397:1298-306
7. Baird NJ, Westhof E, Qin H, Pan T, Sosnick TR. 2005. Structure of a folding intermediate reveals the interplay between core and peripheral elements in RNA folding. J. Mol. Biol. 352:712-22 (Pubitemid 41225480)
8. Baker NA, Sept D, Joseph S, Holst MJ, McCammon JA. 2001. Electrostatics of nanosystems: application to microtubules and the ribosome. Proc. Natl. Acad. Sci. USA 98:10037-41 (Pubitemid 32802969)
9. Barone G, Sayers Z, Svergun D, Koch MHJ. 1999. A synchrotron radiation X-ray scattering study of aqueous solutions of native DNA. J. Synch. Rad. 6:1031-34 (Pubitemid 129489139)
10. Bendedouch D, Chen SH. 1983. Structure and interparticle interactions of bovine serum-albumin in solution studied by small-angle neutron-scattering. J. Phys. Chem. 87:1473-77
11. Bloomfield VA. 1997. DNA condensation by multivalent cations. Biopolymers 44:269-82
12. Bocquet L, Trizac E, Aubouy M. 2002. Effective charge saturation in colloidal suspensions. J. Chem. Phys. 117:8138-52 (Pubitemid 35355077)
13. Bonetta L. 2009. RNA-based therapeutics: Ready for delivery? Cell 136:581-84
14. + with helical B-DNA probed by Co-59 and Na-23 NMR. Biochemistry 26:7724-31
15. Braunlin WH, Xu QW. 1992. Hexaamminecobalt (III) binding environments on double-helical DNA. Biopolymers 32:1703-11
16. Caliskan G, Hyeon C, Perez-Salas U, Briber RM, Woodson SA, Thirumalai D. 2005. Persistence length changes dramatically as RNA folds. Phys. Rev. Lett. 95:268303
17. Cantor CR, Schimmel PR. 1980. Biophysical Chemistry Part II: Techniques for the Study of Biological Structure and Function. New York: Freeman
18. Chacon P, Diaz JF, Moran F, Andreu JM. 2000. Reconstruction of protein form with X-ray solution scattering and a genetic algorithm. J. Mol. Biol. 299:1289-302
19. Chang SL, Chen SH, Rill RL, Lin JS. 1990. Measurements of monovalent and divalent counterion distributions around persistence length DNA fragments in solution. J. Phys. Chem. 94:8025-28
20. Chauhan S, Caliskan G, Briber RM, Perez-Salas U, Rangan P, et al. 2005. RNA tertiary interactions mediate native collapse of a bacterial group I ribozyme. J. Mol. Biol. 353:1199-209 (Pubitemid 41503283)
21. Chen LL, Hodgson KO, Doniach S. 1996. A lysozyme folding intermediate revealed by solution X-ray scattering. J. Mol. Biol. 261:658-71 (Pubitemid 26300800)
22. Chen SH, Sheu EY, Kalus J, Hoffmann H. 1988. Small-angle neutron-scattering investigation of correlations in charged macromolecular and supramolecular solutions. J. Appl. Crystallogr. 21:751-69
23. Chen SJ. 2008. RNA folding: conformational statistics, folding kinetics, and ion electrostatics. Annu. Rev. Biophys. 37:197-214
24. Chin K, Sharp KA, Honig B, Pyle AM. 1999. Calculating the electrostatic properties of RNA provides new insights into molecular interactions and function. Nat. Struct. Biol. 6:1055-61 (Pubitemid 29519601)
25. Das R, Kwok LW, Millett IS, Bai Y, Mills TT, et al. 2003. The fastest global events in RNA folding: electrostatic relaxation and tertiary collapse of the Tetrahymena ribozyme. J. Mol. Biol. 332:311-19 (Pubitemid 37013501)
26. Das R, Mills TT, Kwok LW, Maskel GS, Millett IS, et al. 2003. The counterion distribution around DNA probed by solution X-ray scattering. Phys. Rev. Lett. 90:188103
27. Doniach S, Lipfert J. 2009. Use of small angle X-ray scattering to characterize conformational states of functional RNAs. Methods Enzymol. 469:237-51
28. Draper DE. 2008. RNA folding: thermodynamic and molecular descriptions of the roles of ions. Biophys. J. 95:5489-95
29. Draper DE, Grilley D, Soto AM. 2005. Ions and RNA folding. Annu. Rev. Biophys. Biomol. Struct. 34:221-43 (Pubitemid 40847724)
30. Eliezer D, Chiba K, Tsuruta H, Doniach S, Hodgson KO, Kihara H. 1993. Evidence of an associative intermediate on the myoglobin refolding pathway. Biophys. J. 65:912-17 (Pubitemid 23263902)
31. Fang X, Littrell K, Yang XJ, Henderson SJ, Siefert S, et al. 2000. Mg2+-dependent compaction and folding ofyeast tRNA- and the catalytic domain of the B. subtilis RNase P RNA determined by small-angle X-ray scattering. Biochemistry 39:11107-13
32. Fang XW, Golden BL, Littrell K, Shelton V, Thiyagarajan P, et al. 2001. The thermodynamic origin of the stability of a thermophilic ribozyme. Proc. Natl. Acad. Sci. USA 98:4355-60 (Pubitemid 32294981)
33. Fang XW, Thiyagarajan P, Sosnick TR, Pan T. 2002. The rate-limiting step in the folding of a large ribozyme without kinetic traps. Proc. Natl. Acad. Sci. USA 99:8518-23 (Pubitemid 34693594)
34. Fang XW, Yang XJ, Littrell K, Niranjanakumari S, Thiyagarajan P, et al. 2001. The Bacillus subtilis RNase P holoenzyme contains two RNase P RNA and two RNase P protein subunits. RNA 7:233-41 (Pubitemid 33590506)
35. Glatter O. 1982. Small Angle X-ray Scattering. London: Academic
36. 2+-RNA interaction free energies and their relationship to the folding of RNA tertiary structures. Proc. Natl. Acad. Sci. USA 103:14003-8 (Pubitemid 44452970)
37. Guinier A, Fournet G. 1955. Small-Angle Scattering of X-Rays. New York: Wiley
38. Hayter JB, Penfold J. 1981. An analytic structure factor for macroion solutions. Mol. Phys. 42:109-18
39. Heller WT, Abusamhadneh E, Finley N, Rosevear PR, Trewhella J. 2002. The solution structure of a cardiac troponin C-troponin I-troponin T complex shows a somewhat compact troponin C interacting with an extended troponin I-troponin T component. Biochemistry 41:15654-63 (Pubitemid 36062470)
40. Herschlag D, ed. 2009. Methods in Enzymology, Vol. 469: Biophysical, Chemical, and Functional Probes of RNA Structure, Interactions and Folding, Pt. B. San Diego, CA: Elsevier/Academic
41. Kilburn D, Roh JH, Guo L, Briber RM, Woodson SA. 2010. Molecular crowding stabilizes folded RNA structure by the excluded volume effect. J. Am. Chem. Soc. 132:8690-96
42. Kirmizialtin S, Elber R. 2010. Computational exploration of mobile ion distributions around RNA duplex. J. Phys. Chem. B 114:8207-20
43. Koch MHJ, Sayers Z, Sicre P, Svergun D. 1995. A synchrotron-radiation electric-field X-ray solution scattering study of DNA at very-low ionic-strength. Macromolecules 28:4904-7
44. Koculi E, Hyeon C, Thirumalai D, Woodson SA. 2007. Charge density of divalent metal cations determines RNA stability. J. Am. Chem. Soc. 129:2676-82 (Pubitemid 46364076)
45. Koculi E, Lee NK, Thirumalai D, Woodson SA. 2004. Folding of the Tetrahymena ribozyme by polyamines: importance of counterion valence and size. J. Mol. Biol. 341:27-36 (Pubitemid 39090632)
46. Koculi E, Thirumalai D, Woodson SA. 2006. Counterion charge density determines the position and plasticity of RNA folding transition states. J. Mol. Biol. 359:446-54
47. Kornyshev AA, Lee DJ, Leikin S, Wynveen A. 2007. Structure and interactions of biological helices. Rev. Mod. Phys. 79:943-96 (Pubitemid 47364615)
48. 2+ ionstopolyadenylate, polyuridylate, and their complexes.Biopolymers 10:2459-90
49. Kwok LW, Shcherbakova I, Lamb JS, Park HY, Andresen K, et al. 2006. Concordant exploration of the kinetics of RNA folding from global and local perspectives. J. Mol. Biol. 355:282-93 (Pubitemid 41774131)
50. Lake JA, Beeman WW. 1967. Yeast transfer RNA-a small-angle X-ray study. Science 156:1371-73
51. Lamb JS, Kwok L, Qiu X, Andresen K, Park H, Pollack L. 2008. Reconstructing three dimensional shape envelopes from time resolved small angle X-ray scattering data. J. Appl. Crystallogr. 41:1046-52
52. Li L, Pabit SS, Lamb JS, Park HY, Pollack L. 2008. Closing the lid on DNA end-to-end stacking interactions. Appl. Phys. Lett. 92:223901
53. Lipfert J, Doniach S. 2007. Small-angle X-ray scattering from RNA, proteins, and protein complexes. Annu. Rev. Biophys. Biomol. Struct. 36:307-27 (Pubitemid 46998121)
54. Liu J, Declais AC, Lilley DMJ. 2004. Electrostatic interactions and the folding of the four-way DNA junction: analysis by selective methyl phosphonate substitution. J. Mol. Biol. 343:851-64 (Pubitemid 39345948)
55. Liu Y, Chen WR, Chen SH. 2005. Cluster formation in two-Yukawa fluids. J. Chem. Phys. 122:44507
56. Liu Y, Fratini E, Baglioni P, Chen WR, Chen SH. 2005. Effective long-range attraction between protein molecules in solutions studied by small angle neutron scattering. Phys. Rev. Lett. 95:118102
57. Lohman TM, Dehaseth PL, Record MT. 1980. Pentalysine-deoxyribonucleic acid interactions: a model for the general effects of ion concentrations on the interactions of proteins with nucleic-acids. Biochemistry 19:3522-30
58. Luzzati V, Masson F, Nicolaieff A. 1961. Structure of deoxyribonucleic acid in solution. Study by the diffusion of X-rays at small angles. J. Mol. Biol. 3:185-201 (In French)
59. Manning GS. 1969. Limiting laws and counterion condensation in polyelectrolyte solutions. I. Colligative properties. J. Chem. Phys. 51:924-33
60. 2 in the B, A, and wrinkled D conformations. Biopolymers 32:1491-501
61. Moghaddam S, Caliskan G, Chauhan S, Hyeon C, Briber RM, et al. 2009. Metal ion dependence of cooperative collapse transitions in RNA. J. Mol. Biol. 393:753-64
62. Nakata M, Zanchetta G, Chapman BD, Jones CD, Cross JO, et al. 2007. End-to-end stacking and liquid crystal condensation of 6- to 20-base pair DNA duplexes. Science 318:1276-79 (Pubitemid 350172887)
63. Nossal R, Glinka CJ, Chen SH. 1986. SANS studies of concentrated protein solutions. I. Bovine serum-albumin. Biopolymers 25:1157-75
64. Pabit SA, Finkelstein KD, Pollack L. 2009. Using anomalous small angle X-ray scattering to probe the ion atmosphere around nucleic acids. Methods Enzymol. 469:391-410
65. Pabit SA, Meisburger SP, Li L, Blose JM, Jones CD, Pollack L. 2010. Counting ions around DNA with anomalous small angle X-ray scattering. J. Am. Chem. Soc. 132:16334-36
66. Pabit SA, Qiu XY, Lamb JS, Li L, Meisburger SP, Pollack L. 2009. Both helix topology and counterion distribution contribute to the more effective charge screening in dsRNA compared with dsDNA. Nucleic Acids Res. 37:3887-96
67. Pelta J, Livolant F, Sikorav JL. 1996. DNA aggregation induced by polyamines and cobalthexamine. J. Biol. Chem. 271:5656-62 (Pubitemid 26083901)
68. Perez-Salas UA, Rangan P, Krueger S, Briber RM, Thirumalai D, Woodson SA. 2004. Compaction of a bacterial group I ribozyme coincides with the assembly of core helices. Biochemistry 43:1746-53 (Pubitemid 38200581)
69. Plum GE, Bloomfield VA. 1988. Equilibrium dialysis study of binding of hexammine cobalt(III) to DNA. Biopolymers 27:1045-51
70. Pollack L, Doniach S. 2009. Time-resolved X-ray scattering and RNA folding. Methods Enzymol. 469:253-68
71. Putnam CD, Hammel M, Hura GL, Tainer JA. 2007. X-ray solution scattering (SAXS) combined with crystallography and computation: defining accurate macromolecular structures, conformations and assemblies in solution. Q. Rev. Biophys. 40:191-285 (Pubitemid 350261954)
72. Qiu XY, Andresen K, Kwok LW, Lamb JS, Park HY, Pollack L. 2007. Inter-DNA attraction mediated by divalent counterions. Phys. Rev. Lett. 99:038104
73. Qiu XY, Andresen K, Lamb JS, Kwok LW, Pollack L. 2008. Abrupt transition from a free, repulsive to a condensed, attractive DNA phase, induced by multivalent polyamine cations. Phys. Rev. Lett. 101:228101
74. Qiu XY, Kwok LW, Park HY, Lamb JS, Andresen K, Pollack L. 2006. Measuring inter-DNA potentials in solution. Phys. Rev. Lett. 96:138101
75. Rambo RP, Tainer JA. Bridging the solution divide: comprehensive structural analyses of dynamic RNA, DNA, and protein assemblies by small-angle X-ray scattering. Curr. Opin. Struct. Biol. 20:128-37
76. Raspaud E, Durand D, Livolant F. 2005. Interhelical spacing in liquid crystalline spermine and spermidine-DNA precipitates. Biophys. J. 88:392-403 (Pubitemid 40070685)
77. Rau DC, Parsegian VA. 1992. Direct measurement of the intermolecular forces between counterion-condensed DNA double helices: evidence for long-range attractive hydration forces. Biophys. J. 61:246-59
78. Roh JH, Guo L, Kilburn JD, Briber RM, Irving T, Woodson SA. 2010. Multistage collapse of a bacterial ribozyme observed by time-resolved small-angle X-ray scattering. J. Am. Chem. Soc. 132:10148-54
79. Romer R, Hach R. 1975. Transfer-RNA conformation and magnesium binding: study of yeast phenylalanine-specific transfer-RNA by a fluorescent indicator and differential melting curves. Eur. J. Biochem. 55:271-84
80. Rouzina I, Bloomfield VA. 1996. Competitive electrostatic binding of charged ligands to polyelectrolytes: planar and cylindrical geometries. J. Phys. Chem. 100:4292-304 (Pubitemid 126793371)
81. Rouzina I, Bloomfield VA. 1996. Influence of ligand spatial organization on competitive electrostatic binding to DNA. J. Phys. Chem. 100:4305-13 (Pubitemid 126793372)
82. Rouzina I, Bloomfield VA. 1997. Competitive electrostatic binding of charged ligands to polyelec-trolytes: practical approach using the nonlinear Poisson-Boltzmann equation. Biophys. Chem. 64:139-55 (Pubitemid 27148664)
83. Russell R, Millett IS, Doniach S, Herschlag D. 2000. Small angle X-ray scattering reveals a compact intermediate in RNA folding. Nat. Struct. Biol. 7:367-70 (Pubitemid 30249997)
84. Russell R, Millettt IS, Tate MW, Kwok LW, Nakatani B, et al. 2002. Rapid compaction during RNA folding. Proc. Natl. Acad. Sci. USA 99:4266-71 (Pubitemid 34285975)
85. Saenger W. 1984. Principles of Nucleic Acid Structure. New York: Springer-Verlag
86. Schlatterer JC, Kwok LW, Lamb JS, Park HY, Andresen K, et al. 2008. Hinge bending: a barrier to RNA folding. J. Mol. Biol. 379:859-70
87. Semisotnov GV, Kihara H, Kotova NV, Kimura K, Amemiya Y, et al. 1996. Protein globularization during folding. A study by synchrotron small-angle X-ray scattering. J. Mol. Biol. 262:559-74 (Pubitemid 26341174)
88. Sharp PA. 2009. The centrality of RNA. Cell 136:577-80
89. Shukla A, Mylonas E, Di Cola E, Finet S, Timmins P, et al. 2008. Absence of equilibrium cluster phase in concentrated lysozyme solutions. Proc. Natl. Acad. Sci. USA 105:5075-80 (Pubitemid 351738512)
90. Skibinska L, Gapinski J, Liu H, Patkowski A, Fischer EW, Pecora R. 1999. Effect of electrostatic interactions on the structure and dynamics of a model polyelectrolyte. II. Intermolecular correlations. J. Chem. Phys. 110:1794-800 (Pubitemid 129614712)
91. Stuhrmann HB. 1981. Anomalous small-angle scattering. Q. Rev. Biophys. 14:433-62
92. Svergun DI. 1999. Restoring low resolution structure of biological macromolecules from solution scattering using simulated annealing. Biophys. J. 76:2879-86 (Pubitemid 29269438)
93. Svergun DI, Koch MHJ. 2003. Small-angle scattering studies of biological macromolecules in solution. Rep. Prog. Phys. 66:1735-82 (Pubitemid 37365734)
94. Takamoto K, DasR, He Q, DoniachS, Brenowitz M,et al. 2004. Principles of RNA compaction: insights from the equilibrium folding pathway of the P4-P6 RNA domain in monovalent cations. J. Mol. Biol. 343:1195-206 (Pubitemid 39387820)
95. Timasheff S, Witz J, Luzzati V. 1961. Structure of high molecular weight ribonucleic acid in solution: a small-angle X-ray scattering study. Biophys. J. 1:525-37
96. Walther D, Cohen FE, Doniach S. 2000. Reconstruction of low-resolution three-dimensional density maps from one-dimensional small-angle X-ray solution scattering data for biomolecules. J. Appl. Crystallogr. 33:350-63 (Pubitemid 32142140)
97. Wang LX, Bloomfield VA. 1991. Small-angle X-ray-scattering of semidilute rodlike DNA solutions: polyelectrolyte behavior. Macromolecules 24:5791-95
98. Wensel TG, Meares CF, Vlachy V, Matthew JB. 1986. Distribution of ions around DNA, probed by energy transfer. Proc. Natl. Acad. Sci. USA 83:3267-71 (Pubitemid 16043018)
99. Weyerich B, Daguanno B, Canessa E, Klein R. 1990. Structure and dynamics of suspensions of charged rod-like particles. Faraday Dis. 90:245-59
100. 6. J. Mol. Biol. 144:431-53
101. Wong GC, Pollack L. 2010. Electrostatics of strongly charged biological polymers: ion-mediated interactions and self-organization in nucleic acids and proteins. Annu. Rev. Phys. Chem. 61:171-89
102. Woodson SA. 2005. Metal ions and RNA folding: a highly charged topic with a dynamic future. Curr. Opin. Chem. Biol. 9:104-9 (Pubitemid 40462481)
103. Woodson SA. 2010. Compact intermediates in RNA folding. Annu. Rev. Biophys. 39:61-77