Flexibility of RNA

Annual Review of Biophysics and Biomolecular Structure

Volumn 26, Issue , 1997, Pages 139-156

  Hagerman, Paul J ^a  

^a UNIVERSITY OF COLORADO   (United States)

Author keywords

Molecular evolution; Ribozymes; RNA structure; Transcription; Translation

Indexed keywords

DOUBLE STRANDED RNA; MAGNESIUM ION; RIBOSOME RNA; RIBOZYME; TRANSFER RNA;

HYDRODYNAMICS; INTRON; PRIORITY JOURNAL; PROTEIN SECONDARY STRUCTURE; PROTEIN TERTIARY STRUCTURE; REVIEW; RNA CONFORMATION; RNA TRANSCRIPTION; RNA TRANSLATION; TETRAHYMENA;

BASE SEQUENCE; MOLECULAR SEQUENCE DATA; NUCLEIC ACID CONFORMATION; RNA; RNA, DOUBLE-STRANDED;

EID: 0030992351     PISSN: 10568700     EISSN: None     Source Type: Book Series    
DOI: 10.1146/annurev.biophys.26.1.139     Document Type: Review

References (65)

1. Bednar J, Furrer P, Katritch V, Stasiak AZ, Dubochet J, et al. 1995. Determination of DNA persistence length by cryoelectron microscopy. Separation of the static and dynamic contributions to the apparent persistence length of DNA. J. Mol. Biol. 254:579-94
2. Bhattacharyya A, Murchie AIH, Lilley DMJ. 1990. RNA bulges and the helical periodicity of double-stranded RNA. Nature 343:484-87
3. Biebricher CK, Diekmann S, Luce R. 1982. Structural analysis of self-replicating RNA synthesized by Qβ replicase. J. Mol. Biol. 154:629-48
4. Branch AD, Benenfield BJ, Robertson HD. 1985. Ultraviolet light-induced crosslinking reveals a unique region of local tertiary structure in potato spindle tuber viroid and HeLa 5S RNA. Proc. Natl. Acad. Sci. USA 82:6590-94
5. Charney E. 1988. Electric linear dichroism and birefringence of biological polyelectrolytes. Q. Rev. Biophys. 21:1-60
6. Crothers DM, Haran TE, Nadeau JG. 1990. Intrinsically bent DNA. J. Biol. Chem. 265:7093-96
7. Delihas N, Anderson J, Singhal RP. 1984. Structure, function and evolution of 5S ribosomal RNAs. Prog. Nucleic Acids Res. 31:161-90
8. Edmondson SP, Gray DM. 1984. Analysis of the electrophoretic properties of double-stranded DNA and RNA in agarose gels at a finite voltage gradient. Biopolymers 23:2725-42
9. Flory PJ. 1973. Moments of the end-to-end vector of a chain molecule, its persistence and distribution. Proc. Natl. Acad. Sci. USA 70:1819-23
10. Flory PJ. 1969. Appendix G. The Porod-Kratky chain. In Statistical Mechanics of Chain Molecules, pp. 401-3. New York: Wylie (Interscience).
11. Fox GE. 1985. The structure and evolution of archaebacterial ribosomal RNA. In Bacteria, ed. C Woese, R Wolfe, 8:257-310. New York: Academic
12. Fredericq E, Houssier C. 1973. Electric Dichroism and Electric Birefringence. Oxford: Clarendon. 219 pp.
13. Friederich MW, Gast F-U, Vacano E, Hagerman PJ. 1995. Determination of the angle between the anticodon and aminoacyl acceptor stems of yeast phenylalanyl tRNA in solution. Proc. Natl. Acad. Sci. USA 92:4803-7
14. Gast F-U, Hagerman PJ. 1991. Electrophoretic and hydrodynamic properties of duplex ribonucleic acid molecules transcribed in vitro: evidence that A tracts do not induce curvature in RNA. Biochemistry 30:4268-77
15. Gohlke C, Murchie AIH, Lilley DMJ, Clegg RM. 1994. Kinking of DNA and RNA helices by bulged nucleotides observed by fluorescence resonance energy transfer. Proc. Natl. Acad. Sci. USA 91:11660-64
16. Gorin AA, Zhurkin VB, Olson WK. 1995. B-DNA twisting correlates with base-pair morphology. J. Mol. Biol. 247:34-48
17. Hagerman PJ. 1988. Flexibility of DNA. Annu. Rev. Biophys. Biophys. Chem. 17:265-86
18. Hagerman PJ. 1990. Sequence directed curvature of DNA. Annu. Rev. Biochem. 59:755-81
19. Hagerman PJ. 1992. Straightening out the bends in curved DNA. Biochim. Biophys. Acta 1131:125-32
20. Hagerman PJ. 1996. 'Sometimes a great motion': the application of transient electric birefringence to the study of macromolecular structure. Curr. Opin. Struct. Bio. 6:643-649
21. Hagerman PJ, Amiri KMA. 1996. Hammering away at RNA global structure. Curr. Opin. Struct. Biol. 6:317-21
22. Hagerman PJ, Ramadevi VA. 1990. Application of the method of phage T4 DNA ligase-catalyzed ring-closure to the study of DNA structure: I. Computational analysis. J. Mol. Biol. 212:351-62
23. Hingerty B, Brown RS, Jack A. 1978. Further refinement of the structure of yeast tRNA(Phe). J. Mol. Biol. 124:523-34
24. Holbrook SR, Sussman JL, Warrant RW, Kim S-H. 1978. Crystal structure of yeast phenylalanine transfer RNA. II. Structural features and functional implications. J. Mol. Biol. 123:631-60
25. Kapahnke R, Rappold W, Desselberger U, Riesner D. 1986. The stiffness of dsRNA: hydrodynamic studies on fluorescence-labelled RNA segments of bovine rotavirus. Nucleic Acids Res. 14:3215-28
26. Kebbekus P, Draper DE, Hagerman P. 1995. Persistence length of RNA. Biochemistry 34:4354-57
27. Kleinschmidt AK, Dunnebacke TH, Spendlove RS, Schaffer FL, Whitcomb RF. 1964. Electron microscopy of RNA from reovirus and wound tumor virus. J. Mol. Biol. 10:282-88
28. 2 bacteriophages. Biochim. Biophys. Acta 61:857-64
29. Lang D, Kleinschmidt AK, Zahn RK. 1964. Configuration and length distribution of DNA molecules in solution. Biochim. Biophys. Acta 88:142-54
30. Levene SD, Crothers DM. 1986. Ring closure probabilities for DNA fragments by Monte Carlo simulation. J. Mol. Biol. 189: 61-72
31. Levene SD, Crothers DM. 1986. Topological distributions and the torsional rigidity of DNA. A Monte Carlo study of DNA circles. J. Mol. Biol. 189:73-83
32. Livshits MA, Amosova OA, Lyubchenko YL. 1990. Flexibility difference between double-stranded RNA and DNA as revealed by gel electrophoresis. J. Biomol. Struct. Dyn. 7:1237-49
33. Michel F, Westhof E. 1990. Modeling of the three-dimensional architecture of group I catalytic introns based on comparative sequence analysis. J. Mol. Biol. 216:585-610
34. Nakamura TM, Wang Y-H, Zaug AJ, Griffith JD, Cech TR. 1995. Relative orientation of RNA helices in a group I ribozyme determined by helix extension electron microscopy. EMBO J. 14:4849-59
35. Olson WK, Babcock MS, Gorin A, Liu G, Marky NL, et al. 1995. Flexing and folding double helical DNA. Biophys. Chem. 55:7-29
36. Riordan FA, Bhattacharyya A, McAteer S, Lilley DM. 1992. Kinking of RNA helices by bulged bases, and the structure of the human immunodeficiency virus transactivator response element. J. Mol. Biol. 226:305-10
37. Roitman DB, Zimm BH. 1984. An elastic hinge model for dynamics of stiff chains. II. Transient electro-optical properties. J. Chem. Phys. 81:6348-55
38. 2 in solution from NMR and restrained molecular dynamics. Biochemistry 32:1612-23
39. Schellman JA. 1974. Flexibility of DNA. Biopolymers 13:217-26
40. Schellman JA. 1980. The flexibility of DNA. I. Thermal fluctuations. Biophys. Chem. 11:321-28
41. Schellman JA, Harvey SC. 1995. Static contributions to the persistence length of DNA and dynamic contributions to DNA curvature. Biophys. Chem. 55:95-114
42. Shen Z. 1994. Conformation of the conserved, three-helix junction of 5S ribosomal RNAs. PhD thesis. Univ. Colorado HSC, Denver
43. Shen LX, Cai Z, Tinoco I Jr. 1995. RNA structure at high resolution. FASEB J. 1023-33
44. Shen Z, Hagerman PJ. 1994. Conformation of the central, three-helix junction of the 5S ribosomal RNA of Sulfolobus acidocaldarius. J. Mol. Biol. 241:415-30
45. Shore D, Baldwin RL. 1983. Energetics of DNA twisting. I. Relation between twist and cyclization probability. J. Mol. Biol. 170:957-81
46. Shore D, Baldwin RL. 1983. Energetics of DNA twisting. II. Topoisomer analysis. J. Mol. Biol. 170:983-1007
47. Shore D, Langowski J, Baldwin RL. 1981. DNA flexibility studied by covalent closure of short fragments into circles. Proc. Natl. Acad. Sci. USA 78:4833-37
48. Song L, Schurr JM. 1990. Dynamic bending rigidity of DNA. Biopolymers 30:229-37
49. Stahl DA, Luehrsen KR, Woese CR, Pace NR. 1981. An unusual 5S rRNA, from Sulfolobus acidocaldarius, and its implications for a general 5S rRNA structure. Nucleic Acids Res. 9:6129-37
50. Sussman JL, Holbrook SR, Warrant RW, Church GM, Kim S-H. 1978. Crystal structure of yeast phenylalanine transfer RNA. I. Crystallographic refinement. J. Mol. Biol. 123:607-30
51. Tang RS, Draper DE. 1990. Bulge loops used to measure the helical twist of RNA in solution. Biochemistry 29:5232-37
52. Tang RS, Draper DE. 1994. On the use of phasing experiments to measure helical repeat and bulge loop-associated twist in RNA. Nucleic Acids Res. 22:835-41
53. Taylor WH, Hagerman PJ. 1990. Application of the method of T4 DNA ligase- catalyzed ring-closure to the study of DNA structure: II. NaCl-dependence of DNA flexibility and helical repeat. J. Mol. Biol. 212:363-76
54. Trifonov EN, Tan RK-Z, Harvey SC. 1987. In DNA Bending and Curvature, ed. WK Olson, MH Sarma, M Sundaralingam. Schenectady, NY: Adenine
55. Varani G, Wimberly B, Tinoco I Jr. 1989. Conformation and dynamics of an RNA internal loop. Biochemistry 28:7760-72
56. Wang Y-H, Howard MT, Griffith JD. 1991. Phased adenine tracts in double-stranded RNA do not induce sequence-directed bending. Biochemistry 30:5444-49
57. Wang Y-H, Barker P, Griffith J. 1992. Visualization of diagnostic heteroduplex DNAs from cystic fibrosis deletion heterozygotes provides an estimate of the kinking of DNA by bulge bases. J. Biol. Chem. 267:4911-15
58. Wang Y-H, Murphy FL, Cech TR, Griffith JD. 1994. Visualization of a tertiary structural domain of the Tetrahymena group I intron by electron microscopy. J. Mol. Biol. 236:64-71
59. Wimberly B, Varani G, Tinoco I Jr. 1993. The conformation of loop E of eukaryotic 5S ribosomal RNA. Biochemistry 32:1078-87
60. Wyatt JR, Tinoco I Jr. 1993. RNA structural elements and RNA function. In The RNA World, ed. RF Gesteland, JF Atkins, 24:465-96. Plainview, NY: Cold Spring Harbor Lab. 630 pp.
61. Yamakawa H, Fujii M. 1973. Translational friction coefficient of wormlike chains. Macramolecules 6:407-15
62. Zacharias M, Hagerman PJ. 1995. Bulge-induced bends in RNA: quantification by transient electric birefringence. J. Mol. Biol. 247:486-500
63. Zacharias M, Hagerman PJ. 1995. The bend in RNA created by the trans-activation response element bulge of human immunodeficiency virus is straightened by arginine and by Tat-derived peptide. Proc. Natl. Acad. Sci. USA 92:6052-56
64. Zacharias M, Hagerman PJ. 1996. The influence of symmetric internal loops on the flexibility of RNA. J. Mol. Biol. 257:276-89
65. Zimm BH. 1980. Chain molecule hydrodynamics by the Monte-Carlo method and the validity of the Kirkwood-Riseman approximation. Macromolecules 13:592-602