On the interpretation of Raman spectra of 1-aminooxy-spermine/DNA complexes

Nucleic Acids Research

Volumn 32, Issue 2, 2004, Pages 579-589

  Ruiz Chica, A J ^a   Medina, M A ^a   Sanchez Jimenez F ^a   Ramirez F J ^a  

^a UNIVERSITY OF MÁLAGA   (Spain)

Author keywords

[No Author keywords available]

Indexed keywords

1 AMINOOXYSPERMINE; ADENINE; CYTOSINE; DNA; DNA MARKER; GENOMIC DNA; GUANINE; NUCLEIC ACID BASE; OLIGODEOXYRIBONUCLEOTIDE; OLIGONUCLEOTIDE; POLYAMINE; SPERMINE; SPERMINE DERIVATIVE; THYMINE; UNCLASSIFIED DRUG;

ANIMAL CELL; BASE PAIRING; BINDING SITE; CALCULATION; CATTLE; CELL PROLIFERATION; COMPLEX FORMATION; CONTROLLED STUDY; DNA STRUCTURE; FOURIER TRANSFORMATION; MACROMOLECULE; MOLECULAR INTERACTION; MOLECULAR MODEL; MOLECULAR STABILITY; NONHUMAN; NUCLEOTIDE SEQUENCE; PRECIPITATION; PRIORITY JOURNAL; RAMAN SPECTROMETRY; RECORDING; REVIEW; SEQUENCE ANALYSIS; SUBSTITUTION REACTION; THEORETICAL STUDY; THYMUS;

ANIMALS; BASE PAIRING; BINDING SITES; CATTLE; DNA; OLIGODEOXYRIBONUCLEOTIDES; PRECIPITATION; SOLUTIONS; SPECTRUM ANALYSIS, RAMAN; SPERMINE; VIBRATION;

EID: 1342327714     PISSN: 03051048     EISSN: None     Source Type: Journal    
DOI: 10.1093/nar/gkh232     Document Type: Review

References (90)

1. Khomutov,A.R. and Khomutov,R.M. (1989) Synthesis of putrescine and spermidine aminooxy analogues. Bioorgan. Khim., 15, 698-703.
2. Khomutov,A.R, Vepsäläinen,J.J., Shevetsov,A.S., Hyvönen,T., Keinänen,T.A., Pustobaev,V.N., Eloranta,T.O. and Khomutov,R.M. (1996) Synthesis of hydroxylamine analogues of polyamines. Tetrahedron, 52, 13751-13766.
3. Hamana,K., Hamana,H., Niitsu,M., Samejima,K. and Itoh,T. (1996) Distribution of long linear and branched polyamines in thermophilic eubacteria and hyper thermophilic archaebacteria. Microbios, 85, 19-33.
4. Tabor,C.W. and Tabor,H. (1984) Polyamines. Annu. Rev. Biochem., 53, 749-790.
5. Pegg,A.E. (1988) Polyamine metabolism and its importance in neoplastic growth and a target for chemotherapy. Cancer Res., 48, 759-774.
6. Heby,O. and Persson,L. (1990) Molecular genetics of polyamine synthesis in eukaryotic cells. Trends Biochem. Sci., 15, 153-158.
7. McMurry,L.M. and Algranati,I.D. (1986) Effect of polyamines on translation fidelity in vivo. Eur. J. Biochem., 155, 383-390.
8. Janne,J., Alhonen,L. and Leinonen,P. (1991) Polyamines: from molecular biology to clinical applications. Ann. Med., 23, 241-259.
9. Ha,H.C., Woster,P.M., Yager,J.D. and Casero,R.A.,Jr (1997) The role of polyamine catabolism in polyamine analogue-induced programmed cell death. Proc. Natl Acad. Sci. USA, 94, 11557-11562.
10. Ha,H.C., Yager,J.D., Woster,P.A. and Casero,R.A.,Jr (1998) Structural specificity of polyamines and polyamine analogues in the protection of DNA from strand breaks induced by reactive oxygen species. Biochem. Biophys. Res. Commun., 244, 298-303.
11. Sy,D., Hugot,S., Savoye,C., Ruiz,S., Charlier,M. and Spotheim-Maurizot,M. (1999) Radioprotection of DNA by spermine: a molecular modelling approach. Int. J. Radiat Biol., 75, 953-961.
12. Braunlin,W.N., Strick,T.J. and Record,M.T.,Jr (1982) Equilibrium dialysis studies of polyamine binding to DNA. Biopolymers, 21, 1301-1314.
13. Raspaud,E., Chaperon,I., Leforestier,A. and Livolant,F. (1999) Spermine-induced aggregation of DNA, nucleosome, and chromatin. Biophys. J., 77, 1547-1555.
14. Thomas,T.J. and Bloomfield,V.A. (1984) Ionic and structural effects on the thermal helix-coil transition of DNA complexed with natural and synthetic polyamines. Biopolymers, 23, 1295-1306.
15. Feurestein,B.G., Wiliiams,L.D., Basu,H.S. and Marton,L.J. (1991) Implications and concepts of polyamine-nucleic acid interactions. J. Cell. Biochem, 46, 37-47.
16. Deng,H., Bloomfield,V.A., Benevides J.M. and Thomas,G.J.,Jr (2000) 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, 3379-3385.
17. Ruiz-Chica,J., Medina,M.A., Sánchez-Jiménez,F. and Ramírez,F.J. (2001) Fourier transform raman study of the structural specificities on the interaction between DNA and biogenic polyamines. Biophys. J., 80, 443-454.
18. Khomutov,R.M., Denisova,G.F., Khomutov,A.R., Belostotskaya,K.M., Shlosman,R.B. and Artamonova,E.Y. (1985) Aminooxypropylamine-effective inhibitor of ornithine decarboxylase in vitro and in vivo. Bioorgan. Khim., 11, 1574-1576.
19. Eloranta,T.O., Khomutov,A.R., Khomutov,R.M. and Hyvönen,T. (1990) Aminooxy anologues of spermidine as inhibitors of spermine synthase and substrates of hepatic polyamine acetylating activity. J. Biochem., 108, 593-598.
20. Hyvönen,T., Alakuijala,L., Andersson,L., Khomutov,A.R., Khomutov,R.M. and Eloranta,T.O. (1988) 1-Amino-oxy-3-aminopropane reversibly prevents the proliferation of cultured baby hamster kidney cells by interfering with polyamine synthesis. J. Biol. Chem., 263, 11138-11144.
21. Hyvönen,T., Keinänen,T.A., Khomutov,A.R., Khomutov,R.M. and Eloranta,T.O. (1995) Aminooxy analogues of spermidine evidence the divergent roles of the charged amino nitrogens in the cellular physiology of spermidine. Life Sci., 56, 349-360.
22. Khomutov,A.R., Shvetsov,A.S., Vepsäläinen,J., Hyvönen,T., Keinanen,T.A., Eloranta,T.O., Krainer,D.L., Porter,C.W. and Khomutov,R.M. (1996) Novel aminooxy analogues of biogenic polyamines. Bioorgan. Khim., 22, 557-559.
23. Turchanowa,L., Shvetsov,A.S., Demin,A.V., Khomutov,A.R., Wallace,H.M., Stein,J. and Milovic,V. (2002) Insufficiently charged isosteric analogue of spermine: interaction with polyamine uptake, and effect of Caco-2 cell growth. Biochem. Pharmacol., 64, 649-655.
24. Ramírez,F.J., Thomas,T.J., Antony,T., Ruiz Chica,J. and Thomas,T. (2002) Effects of aminooxy analogues of biogenic polyamines on the aggregation and stability of calf-thymus DNA. Biopolymers (Biospectroscopy), 65, 148-157.
25. Remy,J.S., Kichler,A., Mordvinov,V., Schuber,F. and Behr,J.P. (1995) Targeted gene transfer into heptaoma cells with lipopolyamine-condensed DNA particles presenting galactose ligands: a stage toward artificial viruses. Proc. Natl Acad. Sci. USA, 92, 1744-1748.
26. Gibson,W., van Breemen,R., Fields,A., LaFemina,R. and Irmiere,A. (1984) D,L-α-difluoromethylornithine inhibits human cytomegalovirus replication. J. Virol., 50, 145-154.
27. Liu,G., Molas,M., Grossmann,G.A., Pasumarthy,M., Perales,J.C., Cooper,M.J. and Hanson,R.W. (2001) Biological properties of poly-L-lysine-DNA complexes generated by cooperative binding of the polycation. J. Biol. Chem., 276, 34379-34387.
28. Thomas,T. and Thomas,T.J. (2001) Polyamines in cell growth and cell death: molecular mechanisms and therapeutic applications. Cell. Mol. Life Sci., 58, 244-258.
29. Ruiz-Chica,J., Medina,M.A., Sánchez-Jiménez,F. and Ramírez,F.J. (2001) Raman Study of the Interaction between Polyamines and a GC Oligonucleotide. Biochem. Biophys. Res. Commun., 285, 437-446.
30. Ruiz-Chica,A.J., Medina,M.A., Sánchez-Jiménez,F. and Ramírez,F.J. (2003) Raman spectroscopy study of the interaction between the ornithine-derived polyamines and an alternating A-T oligodeoxyribonucleotide. Biochim. Biophys Acta, 1628, 11-21.
31. Ulyanov,N.B., Bauer,W.R. and James,T.L. (2002) High-resolution NMR structure of an AT-rich DNA sequence. J. Biomol. NMR, 22, 265-280.
32. Husmann,M., Dragneva,Y., Romahn,E. and Jehnichen,P. (2000) Nuclear receptors modulate the interaction of Sp1 and GC-rich DNA via ternary complex formation. Biochem. J., 352, 763-772.
33. Sarhan,S. and Seiler,N. (1989) On the subcellular localization of the polyamines. Biol. Chem. Hoppe Seyler, 370, 1279-1284.
34. Frisch,M.J., Trucks,G.W., Schlegel,H.B., Gill,P.M.W., Johnson.B.G., Robb,M.A., Cheeseman,J.R., Keith,T., Petersson,G.A., Montgomery,J.A. et al. (1995) Gaussian 94, revision D.3. Gaussian, Inc., Pittsburgh, PA.
35. Clark,T., Chandrasekhar,J., Spitznagel,G.W. and Schleyer,P. (1983) Efficient diffuse function-augmented basis sets for anion calculations III. The 3-21+G basis set for the elements Li-F. J. Comput. Chem., 4, 294-301.
36. Hariharan,P.C. and Pople,J.A. (1973) The influence of polarization functions on molecular orbital hydrogenation energies. Theoret. Chim. Acta, 28, 213-222.
37. Becke,A.D. (1988) Density-functional exchange-energy approximation with correct asymptotic behaviour. Phys. Rev. A, 38, 3098-3100.
38. Perdew,J.P. and Wang,Y. (1992) Accurate and simple analytic representation of the electron-gas correlation energy. Phys. Rev. B, 45, 13244-13249.
39. Tortonda,F.R., Pascual-Ahuir,J.L., Silla,E., Tuñon,I. and Ramírez,F.J. (1998) Aminoacid Zwitterions in solution: geometric, energetic, and vibrational analysis using density functional theory-contimuum model calculations. J. Chem. Phys., 109, 592-602.
40. Collado,J.A., Tuñon,I., Silla,E. and Ramírez,F.J. (2000) Vibrational dynamics of histamine monocation in solution: an experimental (FT-IR, FT-Raman) and theoretical (SCRF-DFF) study. J. Phys. Chem. A, 104, 2120-2131.
41. Ramírez,F.J., Tuñón,I., Collado,J.A. and Silla,E. (2003) Structural and vibrational study of the tautomerism of histamine free-base in solution. J. Am. Chem. Soc., 125, 2328-2340.
42. Wong,M.W., Frisch,M.J. and Wiberg,K.B. (1991) Solvent effects. 1. Mediation of electrostatic effects by solvent. J. Am. Chem. Soc., 113, 4776-4782.
43. Wong,M.W., Frisch,M.J. and Wiberg, K.B. (1992) Solvent effects. 2. Medium effect on the structure, energy, charge density and vibrational frequencies of sulfamic acid. J. Am. Chem. Soc., 114, 523-529.
44. Wong,M.W., Frisch,M.J. and Wiberg,K.B. (1992) Solvent effects. 3. Tautomeric equilibria of formamide and 2-pyridone in the gas phase and solution: an ab initio SCRF study. J. Am. Chem. Soc., 114, 1645-4652.
45. Pulay,P., Fogarasi,G., Pang,P. and Boggs,J.E. (1979) Systematic ab initio gradient calculation of molecular geometries, force constants and dipole moment derivatives. J. Am. Chem. Soc., 101, 2550-2560.
46. Wilson,E.B., Decius,J.C. and Cross,P.C. (1955) Molecular Vibrations. Dover, New York, NY, pp. 208-239.
47. Gosule,L.C. and Schellman,J.A. (1976) Compact form of DNA induced by spermidine. Nature, 259, 333-335.
48. Peticolas,W.L., Kubasek,W.L., Thomas,G.A. and Tsuboi,M. (1987) Nucleic Acids. In Spiro,T. (ed.), Biological Applications of Raman Spectroscopy. John Wiley & Sons, New York, NY, Vol 1, pp. 81-131.
49. Thomas,G.J.,Jr. and Tsuboi,M. (1993) Raman spectroscopy of nucleic acids and their complexes. Adv. Biophys. Chem., 3, 1-70.
50. Ghomi,M., Letellier,R., Liquier,J. and Taillandier,E. (1990) Interpretation of DNA vibrational spectra by normal coordinate analysis. Int. J. Biochem., 22, 691-699.
51. Krafft,C., Hinrichs,W., Orth,P., Saenger,W. and Welfle,H. (1998) Raman spectroscopic analysis of Tet repressor-operator DNA interaction in deuterium oxide. Cell Mol. Biol., 44, 239-250.
52. Wen,Z.Q., Overman,S.A. and Thomas,G.J.,Jr (1997) Structure and interactions of the single-stranded DNA genome of filamentous virus fd: investigation by ultraviolet resonance Raman spectroscopy. Biochemistry, 36, 7810-7820.
53. Overman,S.A., Aubrey,K.L., Reilly,K.E., Osman,O., Hayes,S.J., Serwer,P. and Thomas,G.J.,Jr (1998) Conformation and interactions of the packaged double-stranded DNA genome of bacteriophage T7. Biospectroscopy, 4, S47-56.
54. Puppels,G.J., Otto,C., Greve,J., Robert-Nicoud,M., Arndt-Jovin,D.J. and Jovin,T.M. (1994) Raman microspectroscopic study of low-pH-induced changes in DNA structure of polytene chromosomes. Biochemistry, 33, 3386-3395.
55. Lord,R.C. and Thomas,G.J.,Jr (1967) Raman studies of nucleic acids. II. Aqueous purine and pyrimidine mixtures. Biochim. Biophys. Acta, 142, 1-11.
56. Thomas,G.J. and Wang,A.H. (1988) Laser Raman spectroscopy of nucleic acids. In Eckstein,F. and Lilley,D.M.J. (eds), Nucleic Acids and Molecular Biology. Springer-Verlag, Berlin, Germany, pp. 1-30.
57. Benevides,J.M., Wang,A.H., van der Marel,G.A., van Boom,J.H. and Thomas,G.J.,Jr (1988) Crystal and solution structures of the B-DNA dodecamer d(CGCAAATTTGCG) probed by Raman spectroscopy: heterogeneity in the crystal structure does not persist in the solution structure. Biochemistry, 27, 931-938.
58. Duguid,J.G., Bloomfield,V.A., Benevides,J.M. and Thomas,G.J.,Jr (1996) DNA melting investigated by differential scanning caforimetry and Raman spectroscopy. Biophys. J., 71, 3350-3360.
59. 2O solutions and application to B, Z and A-DNA. Nucleic Acids Res., 11, 5747-5761.
60. Tinoco,I., Bustamante,C. and Maestre,M.F. (1990) The optical activity of nucleic acids and their aggregates. Annu. Rev. Biophys. Bioeng., 9, 107-141.
61. Raspaud,E., Olvera de la Cruz,M., Sikorav,J.L. and Livolant,F. (1998) Precipitation of DNA by polyamines: a polyelectrolyte behavior. Biophys. J., 74, 381-393.
62. Olvera de la Cruz,M., Belloni,L., Delsanti,M., Dalbiez,J. P., Spalla,O. and Drifford,M. (1995) Precipitation of highly charged polyelectrolyte solutions in the presence of multivalent salts. J. Chem. Phys., 103, 5781-5791.
63. Benevides,J.M., Wang,A.H., van der Marel,G.A., van Boom,J.H. and Thomas,G.J.,Jr (1989) Effect of the G.T mismatch on backbone and sugar conformations of Z-DNA and B-DNA: analysis by Raman spectroscopy of crystal and solution structures of d(CGCGTG) and d(CGCGCG). Biochemistry, 28, 304-310.
64. Cao,A., Liquier,J. and Taillandier,E. (1995) Infrared and Raman spectroscopy of Biomolecules. In Spiro,T.G. (ed.), Infrared and Raman Spectroscopy: Methods and Applications. VCH, Weinheim, Germany, pp. 344-372.
65. Zacharias,W., Martin,J.C. and Wells,R.D. (1983) Condensed form of (dG-dC)n′(dG-dC), as an intermediate between the B- and Z-type conformations induced by sodium acetate. Biochemistry, 22, 2398-2405.
66. Jovin,T.M., Mcintosh,L.P. and Soumpasis,D.M. (1987) The transition between B-DNA and Z-DNA. Annu. Rev. Phys. Chem., 38, 521-560.
67. Van Holde,K.E., Johnson,W.C. and Ho,P.S. (1998) Principles of Physical Biochemistry. Prentice-Hall, New Jersey, pp. 166-178.
68. O'Connor,T., Kilpatrick,M.W., Klysik,J., Larson,J.E., Martin,J.C., Singleton,C.K., Stirdivant,S.M., Zacharias,W. and Wells,R.D. (1983) Left-handed Z-DNA helices in polymers, restriction fragments, and recombinant plasmids. J. Biomol. Struct. Dyn., 1, 999-1009.
69. Thomas,G.J.,Jr and Benevides,J.M. (1985) An A-helix structure for poly(dA-dT) × poly(dA-dT). Biopolymers, 24, 1101-1105.
70. Katahira,M., Nishimura,Y., Tsuboi,M., Sato,T., Mitsui,Y. and Iitaka,Y. (1986) Local and overall conformations of DNA double helices with the A-T base pairs. Biochim. Biophys. Acta, 867, 256-267.
71. Loprete,D.M. and Hartman,K.A (1990) Conditions for the stability ofthe alternative structures of duplex poly/dA-dT. Biopolymers, 30, 753-761.
72. Movileanu,L., Benevides,J.M. and Thomas,G.J.,Jr (1999) Temperature dependence of the Raman spectrum of DNA. Part I-Raman signatures of premelting and melting transitions of poly(dA-dT)-poly(dA-dT). J. Raman Spectroscopy, 30, 637-649.
73. Movileanu,L., Benevides,J.M. and Thomas,G.J.,Jr (2002) 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(dA-dT)·poly(dA-dT). Biopolymers, 63, 181-194.
74. 13C substitution products. Spectrochim. Acta, 41A, 209-216.
75. Dhaouadi,Z., Ghomi,M., Austi,J.C., Girling,R.B., Hester,E., Mojzes,P., Chinsky,L., Turpin,P.Y., Coulombeau,C., Jobic,H. and Tomkinson,J. (1993) Vibrational motions of bases of nucleic acids as revealed by neutron inelastic scattering and resonance Raman Spectroscopy. I. Adenine and its deuterated species. J. Phys. Chem., 97, 1074-1084.
76. Zhang,S.L., Michaelian,K.H. and Loppnow,G.R. (1998) Vibrational spectra and experimental assigments of thymine and nine of its isotopomers. J. Phys. Chem. A, 102, 461-470.
77. Livolant,F. and Leforestier,A. (1996) Condensed phases of DNA: structures and phase transitions. Prog. Polym. Sci., 21, 1115-1164.
78. Yevdokimov,Y.M., Salyanov,V.I., Buligin,L.V., Dembo,A.T., Gedig,E., Spener,F. and Palumbo,M. (1997) Liquid-crystalline structure of nucleic acids: effect of antracycline drugs and copper ions. J. Biomol. Struct. Dyn., 15, 97-105.
79. Saminathan,M., Thomas,T., Shirahata,A., Pillai,C.K. and Thomas,T.J. (2002) Polyamine structural effects on the induction and stabilization of liquid crystalline DNA: potential applications to DNA packaging, gene therapy and polyamine therapeutics. Nucleic Acids Res., 30, 3722-3731.
80. HyperChem. Release 5.0 (1996) Hypercube, Inc., Ontario, Canada.
81. Marques,M.P.M. and Batista de Carvalho,L.A.E. (2000) Theoretical approach to the conformational preferences of putrescine. In Morgan,D.M.L., White,A., Sánchez-Jiménez,F. and Bardócz,S. (eds), Biologically Active Amines in Food. Office for Official Publications of the European Communities, Luxembourg, Vol. IV, pp. 122-129.
82. Howell,M.L., Schroth,G.P. and Ho,P.S. (1996) Sequence-dependent effects of spermine on the thermodynamics of the B-DNA to Z-DNA transition. Biochemistry, 35, 15373-15382.
83. Cohen,S.S. (1998) A Guide to the Polyamines. Oxford University Press, New York, NY.
84. Torbet,J. and DiCapua,E. (1989) Supercoiled DNA is interwound in liquid crystalline solutions. EMBO J., 8, 4351-4356.
85. Igarashi,K. and Kashiwagi,K. (2000) Polyamines: mysterious modulators of cellular functions. Biochem. Biophys. Res. Commun., 271, 559-564.
86. Tabor,H. (1962) The protective effect of spermidine and other polyamines against heat denaturation of deoxyribonucleic acid. Biochemistry, 1, 496-501.
87. Thomas,T.J. and Messner,R.P. (1988) Structural specificity of polyamines in left handed Z-DNA formation. Immunological and spectroscopic studies. J. Mol. Biol., 201, 463-467.
88. Rich,A., Nordheim,A. and Wang,A.H. (1984) The chemistry and biology of left-handed Z-DNA. Annu. Rev. Biochem., 53, 791-846.
89. Feuerstein,B.G., Pattabiraman,N. and Marton,L.J. (1986) Spermine-DNA interactions: a theoretical study. Proc. Natl Acad. Sci. USA, 83, 5948-5952.
90. Feuerstein,B.G., Pattabiraman,N. and Marton,L.J. (1989) Molecular dynamics of spermine-DNA interactions: sequence specificity and DNA bending for a simple ligand. Nucleic Acids Res., 17, 6883-6892.