Flexibility of single-stranded DNA: Use of gapped duplex helices to determine the persistence lengths of Poly(dT) and Poly(dA)

Journal of Molecular Biology

Volumn 285, Issue 1, 1999, Pages 245-257

  Mills, Janine B ^a   Vacano, Elsi ^a   Hagerman, Paul J ^a  

^a UNIVERSITY OF COLORADO   (United States)

Author keywords

Birefringence; Hydrodynamics; Nucleic acid structure; Polyelectrolyte; RNA structure

Indexed keywords

MAGNESIUM ION; POLYADENYLIC ACID; POLYELECTROLYTE; POLYTHYMIDYLIC ACID; SINGLE STRANDED DNA;

ARTICLE; NUCLEIC ACID STRUCTURE; PRIORITY JOURNAL; TEMPERATURE;

EID: 0033534516     PISSN: 00222836     EISSN: None     Source Type: Journal    
DOI: 10.1006/jmbi.1998.2287     Document Type: Article

References (62)

1. Achter E. K., Felsenfeld G. The conformation of single-strand polynucleotides in solution: sedimentation studies of apurinic acid. Biopolymers. 10:1971;1625-1634.
2. Anderson C. F., Record M. T. Jr. Polyelectrolyte theories and their applications to DNA. Ann. Rev. Phys. Chem. 33:1982;191-222.
3. Bond J. P., Anderson C. F., Record M. T. Jr. Conformational transitions of duplex and triplex nucleic acid helices: thermodynamic analysis of effects of salt concentration on stability using preferential interaction coefficients. Biophys. J. 67:1994;825-836.
4. Bradley D. F., Stellwagen N. C., O'Konski C. T., Paulson C. M. Electric birefringence and dichroism of acridine orange and methylene blue complexes with polynucleotides. Biopolymers. 11:1972;645-652.
5. Brahms J., Michelson A. M., van Holde K. E. Adenylate oligomers in single- and double-stranded conformation. J. Mol. Biol. 15:1966;467-488.
6. 7. Biophys. Chem. 7:1977;205-209.
7. Camerman N., Fawcett J. K., Camerman A. Molecular structure of a deoxyribose-dinucleotide, sodium thymidylyl-(5′-3′)-thymidylate-(5′) hydrate (pTpT), and a possible structural model for polythymidylate. J. Mol. Biol. 107:1976;601-621.
8. Chan S. I., Schweizer M. P., Ts'o P. O. P. Interaction and association of bases and nucleosides in aqueous solutions. III. A nuclear magnetic resonance study of the self-association of purine and 6-methylpurine. J. Am. Chem. Soc. 86:1964;4182-4188.
9. Charney E., Milstein J. B. Electric dichroism of poly (riboadenylic acid). Biopolymers. 17:1978;1629-1655.
10. Dove W. F., Davidson N. Cation effects on the denaturation of DNA. J. Mol. Biol. 5:1962;467-478.
11. Eisenberg H., Felsenfeld G. Studies of temperature-dependent conformation and phase separation of polyriboadenylic acid solutions at neutral pH. J. Mol. Biol. 30:1967;17-37.
12. n. J. Mol. Biol. 122:1978;465-470.
13. Flory P. J. Statistical Mechanics of Chain Molecules. 1969;Interscience New York. p. 36-43.
14. Fresco J. R., Doty P. Polynucleotides. I. Molecular properties and configurations of polyriboadenylic acid in solution. J. Am. Chem. Soc. 79:1957;3928-3929.
15. Friederich M. W., Gast F.-U., Vacano E., Hagerman P. J. Determination of the angle between the anticodon and aminoacyl acceptor stems of yeast phenylalanyl tRNA in solution. Proc. Natl Acad. Sci. USA. 92:1995;4803-4807.
16. Pheas a model system. Proc. Natl Acad. Sci. USA. 95:1998;3572-3577.
17. Hagerman K. R., Hagerman P. J. Helix rigidity of DNA: the meroduplex as an experimental paradigm. J. Mol. Biol. 260:1996;207-223.
18. Hagerman P. J. Investigation of the flexibility of DNA using transient electric birefringence. Biopolymers. 20:1981;1503-1535.
19. Hagerman P. J. Sometimes a Great Motion: the application of transient electric birefringence to the study of macromolecular structure. Curr. Opin. Struct. Biol. 6:1996;643-649.
20. Hagerman P. J., Zimm B. H. Monte Carlo approach to the analysis of the rotational diffusion of wormlike chains. Biopolymers. 20:1981;1481-1502.
21. Helmkamp G. K., Kondo N. S. Preferred orientations in purine stacking. Biochim. Biophys. Acta. 145:1967;27-30.
22. Hingerty B. E., Broyde S. B., Olson W. K. The poly(rU) coil: a minimum-energy model that matches experimental observations. Biopolymers. 21:1982;1167-1188.
23. Hoffmann G. W., Pörschke D. Cooperative nonenzymatic base recognition. Thermodynamics of the helix-coil transition of a monomer-polymer double helix. Biopolymers. 12:1973;1611-1623.
24. Holcomb D. N., Tinoco I. Jr. Conformation of polyriboadenylic acid: pH and temperature dependence. Biopolymers. 3:1965;121-133.
25. Howard F. B., Singer M. F. Helix formation between nucleosides and polyribonucleotides: helices as substrates for polynucleoside phosphorylase. Fed. Proc. Fed. Am. Soc. Exp. Biol. 24:1965;483.
26. Howard F. B., Frazier J., Lipsett M. N. Infrared demonstration of two- and three-strand helix formation between poly C and guanosine mononucleotides and oligonucleotides. Biochem. Biophys. Res. Commun. 17:1964;93-102.
27. Howard F. B., Frazier J., Singer M. F., Miles H. T. Helix formation between polyribonucleotides and purines, purine nucleosides and nucleotides. II. J. Mol. Biol. 16:1966;415-439.
28. Huang W. M., Ts'o P. O. P. Physicochemical basis of the recognition process in nucleic acid interactions I. Interactions of polyuridylic acid and nucleosides. J. Mol. Biol. 16:1966;523-543.
29. Inners L. D., Felsenfeld G. Conformation of polyribouridylic acid in solution. J. Mol. Biol. 50:1970;373-389.
30. 2+ions to polyadenylate, polyuridylate, and their complexes. Biopolymers. 10:1971;2459-2490.
31. Krakauer H., Sturtevant J. M. Heats of the helix-coil transitions of the poly A- poly U complexes. Biopolymers. 6:1968;491-512.
32. Leng M., Felsenfeld G. A study of polyadenylic acid at neutral pH. J. Mol. Biol. 15:1966;455-466.
33. Luzzati V., Mathis A., Mason F., Witz J. Structure transitions observed in DNA and poly A in solution as a function of temperature and pH. J. Mol. Biol. 10:1964;28-41.
34. Manning G. S. The application of polyelectrolyte limiting laws to the helix-coil transition of DNA. VI. The numerical value of the axial phosphate spacing for the coil form. Biopolymers. 15:1976;2385-2390.
35. Martel P. Base crystallization and base stacking in water. Eur. J. Biochem. 96:1979;213-219.
36. Maxwell E. S., Barnett L. M. Helix formation between purine nucleosides and polyribonucleotides: Behavior of the ordered structure in polynucleotide-directed amino acid incorporating systems. Fed. Proc. Fed. Am. Soc. Exp. Biol. Proc. 24:1965;483.
37. Miles H. T., Frazier J. Helix formation between nucleosides and polyribonucleotides. Fed. Proc. Fed. Am. Soc. Exp. Biol. 24:1965;483.
38. Mills J. B., Cooper J. P., Hagerman P. J. Electrophoretic evidence that single-stranded regions of one or more nucleotides dramatically increase the flexibility of DNA. Biochemistry. 33:1994;1797-1803.
39. Mitchell P. R., Sigel H. A proton nuclear-magnetic-resonance study of self-stacking in purine and pyrimidine nucleosides and nucleotides. Eur. J. Biochem. 88:1978;149-154.
40. Olsthoorn C. S. M., Bostelaar L. J., van Boom J. H., Altona C. Conformational characteristics of the trinucleotide diphosphate dApdApdA and its constituents from nuclear magnetic resonance and circular dichroism studies. Extrapolation to the stacked conformers. Eur. J. Biochem. 112:1980;95-110.
41. Pörschke D., Eggers F. Thermodynamics and kinetics of base-stacking interactions. Eur. J. Biochem. 26:1972;490-498.
42. Press W. H., Vetterling W. T., Teukolsky S. A. Numerical Recipes in Fortran: The Art of Scientific Computing. 1992;Cambridge University Press, Cambridge. p. 678-683.
43. +effects on transition of DNA and polynucleotides of variable linear charge density. Biopolymers. 15:1976;893-915.
44. Rich A., Davies D. R., Crick F. H. C., Watson J. D. The molecular structure of polyadenylic acid. J. Mol. Biol. 3:1961;71-86.
45. Riley M., Maling B. Physical and chemical characterization of two- and three-stranded adenine-thymine and adenine-uracil homopolymer complexes. J. Mol. Biol. 20:1966;359-389.
46. Rivetti C., Walker C., Bustamante C. Overstretching B-DNA: the elastic response of individual double-stranded and single-stranded DNA molecules. J. Mol. Biol. 280:1998;41-59.
47. Roitman D. B., Zimm B. An elastic hinge model for dynamics of stiff chains. I. Viscoelastic properties. J. Chem. Phys. 81:1984a;6340-6347.
48. Roitman D. B., Zimm B. An elastic hinge model for dynamics of stiff chains. II. Transient electro-optical properties. J. Chem. Phys. 81:1984b;6348-6354.
49. Saenger W. Principles of Nucleic Acid Structure. 1984;Springer-Verlag, New York. p. 298-320.
50. Smith S. B., Cui Y., Bustamante C. Overstretching B-DNA: the elastic response of individual double-stranded and single-stranded DNA molecules. Science. 271:1996;795-799.
51. Stannard B. S., Felsenfeld G. The conformation of polyriboadenylic acid at low temperature and neutral pH. A single-stranded rodlike structure. Biopolymers. 14:1975;299-307.
52. Strauss U. P., Ander P. Molecular dimensions and interactions of lithium polyphosphate in aqueous lithium bromide solutions. J. Phys. Chem. 66:1962;2235-2239.
53. Strauss U. P., Wineman P. L. Molecular dimensions and interactions of long-chain polyphosphates in sodium bromide solutions. J. Am. Chem. Soc. 80:1958;2366-2371.
54. Sundaralingam M. Stereochemistry of nucleic acids and their constituents. IV. Allowed and preferred conformations of nucleosides, nucleoside mono-, di-, tri-, tetraphosphates, nucleic acids and polynucleotides. Biopolymers. 7:1969;821-860.
55. Thomas R. Recherches sur la dénaturation des acides desoxyribonucléiques. Biochim. Biophys. Acta. 14:1954;231-240.
56. Ts'o P. O. P., Melvin I. S., Olsen A. C. Interaction and association of bases and nucleosides in aqueous solutions. J. Am. Chem. Soc. 85:1963;1289-1296.
57. Vacano E., Hagerman P. J. Analysis of birefringence decay profiles for nucleic acid helices possessing bends: The τ-ratio approach. Biophys. J. 73:1997;306-317.
58. van Holde K. E., Brahms J., Michelson A. M. Base interactions of nucleotide polymers in aqueous solution. J. Mol. Biol. 12:1965;726-739.
59. Witz J., Luzzati V. La structure des acides polyadenylique et polyuridilique en solution: etude par diffusion centrale des rayons X. J. Mol. Biol. 11:1965;620-630.
60. Zacharias M., Hagerman P. J. Bulge-induced bends in RNA: Quantification by transient electric birefringence. J. Mol. Biol. 247:1995;486-500.
61. Zacharias M., Hagerman P. J. The influence of symmetric internal loops on the flexibility of RNA. J. Mol. Biol. 257:1996;276-289.
62. Zacharias M., Hagerman P. J. Influence of static and dynamic bends on the birefringence decay profile of RNA helices: Brownian dynamics simulations. Biophys. J. 73:1997;318-332.