Ability of spermine to differentiate between DNA sequences-Preferential stabilization of A-tracts

Biophysical Chemistry

Volumn 122, Issue 1, 2006, Pages 5-15

  Patel, Mayank M ^a   Anchordoquy, Thomas J ^a  

^a UNIVERSITY OF COLORADO   (United States)

Author keywords

A tracts; G tracts; Isothermal Titration Calorimetry (ITC); Sequence specific spermine DNA binding; Thermodynamics of spermine DNA binding

Indexed keywords

DNA; PROTEIN; SPERMINE;

ARTICLE; CHROMATIN STRUCTURE; CIRCULAR DICHROISM; DNA DETERMINATION; DNA PACKAGING; DNA SEQUENCE; DNA STRUCTURE; ISOTHERMAL TITRATION CALORIMETRY; OLIGOMERIZATION; PRIORITY JOURNAL; PROTEIN DNA BINDING; PROTEIN SECONDARY STRUCTURE; PROTEIN STABILITY; PROTEIN TERTIARY STRUCTURE; SEQUENCE ANALYSIS;

BASE SEQUENCE; BINDING SITES; CALORIMETRY; CIRCULAR DICHROISM; DNA; ENTROPY; HYDROGEN BONDING; MOLECULAR STRUCTURE; NUCLEIC ACID CONFORMATION; POLYDEOXYRIBONUCLEOTIDES; SENSITIVITY AND SPECIFICITY; SPERMINE; TITRIMETRY;

EID: 33746861517     PISSN: 03014622     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.bpc.2006.02.001     Document Type: Article

References (85)

1. Childs A.C., Mehta D.J., and Gerner E.W. Polyamine-dependent gene expression. Cell. Mol. Life Sci. 60 (2003) 1394-1406
2. Cohen S.S. Introduction of the Polyamines (1971), Prentice-Hall, Englewood Cliffs, NJ
3. Cohen S.S. A Guide to Polyamines (1998), Oxford University Press, New York, NY
4. Tabor C.W., and Tabor H. Polyamines. Ann. Rev. Biochem. 53 (1984) 749-790
5. Watanabe S., Kusama-Eguchi K., Kobayashi H., and Igarashi K. Estimation of polyamine binding to macromolecules and ATP in bovine lymphocytes and rat liver. J. Biol. Chem. 266 (1991) 20803-20809
6. Igarashi K., and Kashiwagi K. Polyamines: mysterious modulators of cellular functions. Biochem. Biophys. Res. Commun. 271 (2000) 559-564
7. Chen H.H., Behe M.J., and Rau D.C. Critical amount of oligovalent ion binding required for the B-Z transition of poly (dG-m5dC). Nucleic Acids Res. 12 (1984) 2381-2389
8. Thomas T.J., and Messner R.P. A left-handed (Z) conformation of poly(dA-C).poly(dG-dT) induced by polyamines. Nucleic Acids Res. 14 (1986) 6721-6733
9. Egli M., Williams L.D., Gao Q., and Rich A. Structure of the pure-spermine form of Z-DNA (magnesium free) at 1-A resolution. Biochemistry 30 (1991) 11388-11402
10. Thomas T.J., and Bloomfield V.A. Ionic and structural effects on the thermal helix-coil transition of DNA complexed with natural and synthetic polyamines. Biopolymers 23 (1984) 1295-1306
11. Hougaard D.M., Bolund L., Fujiwara K., and Larsson L.-J. Endogenous polyamines are intimately associated with highly condensed chromatin in vivo. A fluorescence cytochemical and immunocytochemical study of spermine and spermidine during the cell cycle and in reactivated nuclei. Eur. J. Cell Biol. 44 (1987) 151-155
12. Smirnov I.V., Dimitrov S.I., and Makarov V.L. Polyamine-DNA interactions. Condensation of chromatin and naked DNA. J. Biomol. Struct. Dyn. 5 (1988) 1149-1161
13. Kolata G. New clues to gene regulation. Science 224 (1984) 588-589
14. Behe M. The DNA sequence of the human β-globin region is strongly biased in favor of long strings of contiguous purine or pyrimidine residues. Biochemistry 26 (1987) 7870-7875
15. Karlin S., Blaisdell B.E., Sapolsky R.J., Cardon L., and Burge C. Assessments of DNA inhomogeneities in yeast chromosome III. Nucleic Acids Res. 21 (1993) 703-711
16. Alleman R.K., M., and Egli. DNA recognition and bending. Chem. Biol. 4 (1997) 643-650
17. Lew J.M., Fei Y.L., Aleck K., Blencowe B.J., Weksberg R., and Sadowski P.D. CDKN1C mutation in Wiedemann-Beckwith syndrome patients reduces RNA splicing efficiency and identifies a splicing enhancer. Am. J. Med. Genet. A 127 (2004) 268-276
18. Hardin C.C., Henderson E., Watson T., and Prosser J.K. Monovalent cation-induced structural transitions in telomeric DNAs: G-DNA folding intermediates. Biochemistry 30 (1991) 4460-4472
19. Ahmed S., and Henderson E. Formation of novel hairpin structures by telomeric C-strand oligonucleotides. Nucleic Acids Res. 20 (1992) 507-511
20. Jain S., Zon G., and Sundaralingam M. Base only binding of spermine in the deep groove of the A-DNA octamer d(GTGTACAC). Biochemistry 28 (1989) 2360-2364
21. Xu Q., Shoemaker R.K., and Braunlin W.H. Induction of B-A transitions of deoxyoligonucleotides by multivalent cations in dilute aqueous solution. Biophys. J. 65 (1993) 1039-1049
22. Lindqvist M., and Gräslund A. An FTIR and CD study of the structural effects of G-tract length and sequence context on DNA conformation in solution. J. Mol. Biol. 314 (2001) 423-432
23. Vargason J.M., Henderson K., and Ho P.S. A crystallographic map of the transition from B-DNA to A-DNA. Proc. Natl. Acad. Sci. U. S. A. 98 (2001) 7265-7270
24. Dickerson R.E., and Ng H.L. DNA structure from A to B. Proc. Natl. Acad. Sci. U. S. A. 98 (2001) 6986-6988
25. Braun C.S., Jas G.S., Choosakoonkriang S., Koe G.S., Smith J.G., and Middaugh C.R. The structure of DNA within cationic lipid/DNA complexes. Biophys. J. 84 (2003) 1114-1123
26. Hirschman S., Leng M., and Felsenfield G. Interaction of spermine and DNA. Biopolymers 5 (1967) 227-233
27. Morgan J.E., Blankenship J.W., and Matthews H.R. Association constants for the interaction of double-stranded and single-stranded DNA with spermine, spermidine, putrescine, diaminopropane, N1- and N8-acetylspermidine, and magnesium: determination from analysis of the broadening of thermal denaturation curves. Arch. Biochem. Biophys. 246 (1986) 225-232
28. Igarashi K., Sakamoto I., Goto N., Kashiwagi K., Honma R., and Hirose S. Interaction between polyamines and nucleic acids or phospholipids. Arch. Biochem. Biophys. 219 (1982) 438-443
29. Stewart K.D. The effect of structural changes in a polyamine backbone on its DNA-binding properties. Biochem. Biophys. Res. Commun. 152 (1988) 1441-1446
30. Yuki M., Grukhin V., Lee C.-S., and Haworth I.S. Spermine binding to GC-rich DNA: experimental and theoretical studies. Arch. Biochem. Biophys. 325 (1996) 39-46
31. Deng H., Bloomfield V.A., Benevides J.M., and Thomas Jr. G.J. Structural basis of polyamine-DNA recognition: spermidine and spermine interactions with genomic B-DNAs of different GC content probed by Raman spectroscopy. Nucleic Acids Res. 28 (2000) 3379-3385
32. Schmid N., and Behr J.P. Location of spermine and other polyamines on DNA as revealed by photoaffinity cleavage with polyaminobenzenediazonium salts. Biochemistry 30 (1991) 4357-4361
33. Lindemose S., Nielsen P.E., and Møllegaard N.E. Polyamines preferentially interact with bent adenine tracts in double-stranded DNA. Nucleic Acids Res. 33 (2005) 1709-1803
34. Feuerstein B.G., Pattabiraman N., and Marton L.J. Molecular mechanics of the interactions of spermine with DNA: DNA bending as a result of ligand binding. Nucleic Acids Res. 18 (1990) 1271-1282
35. Feuerstein B.G., Pattabiraman N., and Marton L.J. Spermine-DNA interactions: a theoretical study. Proc. Natl. Acad. Sci. U. S. A. 83 (1986) 5948-5952
36. Zakrzewska K., and Pullman B. Spermine-nucleic acid interactions: a theoretical study. Biopolymers 25 (1986) 375-392
37. Dickerson R.E., Kopka M.L., and Pjura P.E. NATO ASI Ser., A 137 (1987) 45-62
38. Chan S.S., Breslauer K.J., Hogan M.E., Kessler D.J., Austin R.H., Ojemann J., Passner J.M., and Wiles N.C. Physical studies of DNA premelting equilibria in duplexes with and without homo dA.dT tracts: correlations with DNA bending. Biochemistry 29 (1990) 6161-6171
39. Cantor C.R., and Schimmel P.R. Biophysical Chemistry Part II (1980), Freeman, CA 384
40. Wiseman T., Williston S., Brands J.F., and Lin L.-N. Rapid measurement of binding constants and heats of binding using a new titration calorimeter. Anal. Biochem. 179 (1989) 131-137
41. Indyk L., and Fisher H.F. Theoretical aspects of isothermal titration calorimetry. Methods Enzymol. 295 (1998) 350-364
42. Brahms J., and Mommerts W.F.H.M. A study of conformation of nucleic acids in solution by means of circular dichroism. J. Mol. Biol. 10 (1964) 73-88
43. Wells R.D., Larson J.E., Grant R.C., Shortle B.E., and Cantor C.R. Physicochemical studies on polydeoxyribonucleotides containing defined repeating nucleotide sequences. J. Mol. Biol. 54 (1970) 465-497
44. Gennis R.B., and Cantor C.R. Optical studies of a conformational change in DNA before melting. J. Mol. Biol. 65 (1972) 381-399
45. Greve J., Maestre M.F., and Leving A. Circular dichroism of adenine and thymine containing synthetic polynucleotides. Biopolymers 16 (1977) 1489-1504
46. Fasman G.D. Circular Dichroism and the Conformational Analysis of Biomolecules (1996), Plenum Press, New York
47. Alexeev D.G., Lipanov A.A., and Skuratovskii I.Ya. Poly(dA).poly(dT) is a B-type double helix with a distinctively narrow minor groove. Nature 325 (1987) 821-823
48. Nelson H.C.M., Finch J.T., Luisi B.F., and Klug A. The structure of an oligo(dA).oligo(dT) tract and its biological implications. Nature 330 (1987) 221-226
49. Chandrasekaran R., and Radha A. Structure of poly d(A).poly d(T). J. Biomol. Struct. Dyn. 10 (1992) 153-168
50. Wang A.H., Fujii S., van Boom J.H., and Rich A. Molecular structure of the octamer d(G-G-C-C-GG- C-C): modified A-DNA. Proc. Natl. Acad. Sci. U. S. A. 79 (1982) 3968-3972
51. Mooers B.H., Schroth G.P., Baxter W.W., and Ho P.S. Alternating and non-alternating dG-dC hexanucleotides crystallize as canonical A-DNA. J. Mol. Biol. 249 (1995) 772-784
52. Ivanov V.I., Minchenkova L.E., Minyat E.E., Frank-Kamenetskii M.D., and Schyolkina A.K. The B to A transition of DNA in solution. J. Mol. Biol. 87 (1974) 817-833
53. Cheatham III T.E., Srinivasan J., Case D.A., and Kollman P.A. Molecular dynamics and continuum solvent studies of the stability of polyG-polyC and polyA-polyT DNA duplexes in solution. J. Biomol. Struct. Dyn. 16 (1998) 265-280
54. Gao Y.-G., Robinson H., and Wang A.H.-J. High-resolution A-DNA crystal structures of d(AGGGGCCCCT)-an A-DNA model of poly(dG)·poly(dC). Eur. J. Biochem. 261 (1999) 413-420
55. Girod J.C., Johnson Jr. W.C., Huntington S.K., and Maestre M.F. Conformation of deoxyribonucleic acid in alcohol solutions. Biochemistry 12 (1973) 5092-5096
56. Riazance J.H., Baase W.A., Johnson Jr. W.C., Hall K., Cruz P., and Tinoco Jr. I. Evidence for Z-form RNA by vacuum UV circular dichroism. Nucleic Acids Res. 13 (1985) 4983-4989
57. Ng H.-L., Kopka M.L., and Dickerson R.E. The structure of a stable intermediate in the A ↔ B DNA helix transition. Proc. Natl. Acad. Sci. U. S. A. 97 (2000) 2035-2039
58. Nickol J., Behe M., and Felsenfeld G. Effect of the B-Z transition in poly(dG-m5dC). poly(dGm5dC) on nucleosome formation. Proc. Natl. Acad. Sci. U. S. A. 79 (1982) 1771-1774
59. Marquet R., and Houssier C. Different binding modes of spermine to A-T and G-C base pairs modulate the bending and stiffening of the DNA double helix. J. Biomol. Struct. Dyn. 6 (1988) 235-246
60. Hall K.B., and Maestre M.F. Temperature-dependent reversible transition of poly(dCdG):poly(dCdG) in ethanolic and methanolic solutions. Biopolymers 23 (1984) 2127-2139
61. II form in crystals. Nucleic Acids Res. 18 (1990) 2141-2148
62. Herrera J.E., and Chaires J.B. A premelting conformational transition in poly(dA):poly(dT) coupled to daunomycin binding. Biochemistry 28 (1989) 1993-2000
63. Chan S.S., Austin R.H., Mukerji I., and Spiro T.G. Temperature-dependent ultraviolet resonance Raman spectroscopy of the premelting state of dA·dT DNA. Biophys. J. 72 (1997) 1512-1520
64. Movileanu L., Benevides J.M., and Thomas Jr. G.J. Temperature dependence of the Raman spectrum of DNA: II. Raman signatures of premelting and melting transitions of poly(dA):poly(dT) and comparison with poly(dA5dT):poly(dA-dT). Biopolymers 63 (2002) 181-194
65. Movileanu L., Benevides J.M., and Thomas Jr. G.J. Determination of base and backbone contributions to the thermodynamics of premelting and melting transitions in B DNA. Nucleic Acids Res. 30 (2002) 3767-3777
66. Bloomfield V.A., Crothers D.M., and Tinoco Jr. I. Nucleic Acids-Structures, Properties, and Functions (2000), University Science Books, Sausalito, CA 29
67. Matulis D., Rouzina I., and Bloomfield V.A. Thermodynamics of DNA binding and condensation: isothermal calorimetry and electrostatic mechanism. J. Mol. Biol. 296 (2000) 1053-1063
68. Patel M.M., and Anchordoquy T.J. Contribution of hydrophobicity to thermodynamics of ligand-DNA binding and DNA collapse. Biophys. J. 88 (2005) 2089-2103
69. 6. J. Mol. Biol. 144 (1980) 431-453
70. Marquet R., Wyart A., and Houssier C. Influence of DNA length on spermine-induced condensation. Importance of the bending and stiffening of DNA. Biochim. Biophys. Acta 909 (1987) 165-172
71. Wu H.M., and Crothers D.M. The locus of sequence-directed and protein-induced DNA bending. Nature 308 (1984) 509-513
72. In: Olson W.K., Sarma M.H., Sarma R.H., and Sundaralingam M. (Eds). Structure and Expression Volume 3: DNA Bending and Curvature (1988), Adenine Press, Schenectady, NY
73. Yoon C., Prive G.G., Goodsell D.S., and Dickerson R.E. Structure of an alternating B-DNA helix and its relationship to A-tract DNA. Proc. Natl. Acad. Sci. U. S. A. 85 (1988) 6332-6336
74. Aymami J., Coll M., Frederick C.A., Wang A.H.-J., and Rich A. The propeller DNA conformation of poly(dA) · poly(dT). Nucleic Acids Res. 17 (1989) 3229-3245
75. n double helices in dilute solution. Nature 340 (1989) 321-322
76. Shui X., McFail-Isom L., Hu G.G., and Williams L.D. The B-DNA dodecamer at high resolution reveals a spine of water on sodium. Biochemistry 37 (1998) 8341-8355
77. Liepinsh E., Otting G., and Wuthrich K. NMR observation of individual molecules of hydration water bound to DNA duplexes: direct evidence for a spine of hydration water present in aqueous solution. Nucleic Acids Res. 20 (1992) 6549-6553
78. Halle B., and Denisov V.P. Water and monovalent ions in the minor groove of B-DNA oligonucleotides as seen by NMR. Biopolymers 48 (1998) 210-233
79. McGhee J.D., and Felsenfeld G. Nucleosome structure. Ann. Rev. Biochem. 49 (1980) 1115-11156
80. Shatzky-Schwartz M., Hiller Y., Reich Z., Ghirlando R., Weinberger S., and Minsky A. Attenuation of DNA-protein interactions associated with intrinsic, sequence-dependent DNA curvature. Biochemistry 31 (1992) 2339-2346
81. Puhl H.L., and Behe M.J. Poly(dA)·poly(dT) forms very stable nucleosomes at higher temperatures. J. Mol. Biol. 245 (1995) 559-567
82. Prunell A. Nucleosome reconstitution on plasmid-inserted poly(dA).poly(dT). EMBO J. 1 (1982) 173-179
83. Peng H.F., and Jackson V. In vitro studies on the maintenance of transcription-induced stress by histones and polyamines. J. Biol. Chem. 275 (2000) 657-668
84. Chalikian T.V., Sarvazyan A.P., Plum G.E., and Breslauer K.J. Influence of base composition, base sequence, and duplex structure on DNA hydration: apparent molar volumes and apparent molar adiabatic compressibilities of synthetic and natural DNA duplexes at 25 degrees C (1994). Biochemistry 33 (1994) 2394-2401
85. Chalikian T.V., Völker J., Srinivasan A.R., Olson W.K., and Breslauer K.J. The hydration of nucleic acid duplexes as assessed by a combination of volumetric and structural techniques. Biopolymers 50 (1999) 459-471