Local conformational changes induced in B-DNA by ethidium intercalation

Biochemistry

Volumn 44, Issue 8, 2005, Pages 2993-2999

  Benevides, James M ^a   Thomas Jr , George J ^a  

^a UNIVERSITY OF MISSOURI KANSAS CITY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

BIOCHEMISTRY; BIOMARKERS; CONFORMATIONS; ESTERS; LASERS; MOLECULAR VIBRATIONS; NUCLEIC ACIDS; RAMAN SCATTERING; RAMAN SPECTROSCOPY; STOICHIOMETRY; SUGARS;

BASE PAIR (BP) FRAGMENTS; ETHIDIUM BROMIDE (ETBR); NEAR-INFRARED (NIR) LASERS; RAMAN DIFFERENCE SPECTROSCOPY;

DNA;

DNA; ESTER DERIVATIVE; ETHIDIUM BROMIDE; INTERCALATING AGENT; NUCLEOTIDE; PHENANTHRIDINE DERIVATIVE; PURINE DERIVATIVE; PYRIMIDINE DERIVATIVE;

ARTICLE; BASE PAIRING; COMPLEX FORMATION; CONFORMATIONAL TRANSITION; DNA DRUG COMPLEX; DNA STRUCTURE; INFRARED RADIATION; INTERCALATION COMPLEX; LASER; NUCLEOSOME; PRIORITY JOURNAL; RAMAN SPECTROMETRY; STOICHIOMETRY; STRUCTURE ANALYSIS; THYMUS;

ANIMALS; CATTLE; DEUTERIUM OXIDE; DNA; ETHIDIUM; INTERCALATING AGENTS; NUCLEIC ACID CONFORMATION; SPECTRUM ANALYSIS, RAMAN;

EID: 14344263607     PISSN: 00062960     EISSN: None     Source Type: Journal    
DOI: 10.1021/bi048651l     Document Type: Article

References (64)

1. Haq, I., and Ladbury, J. (2000) Drug-DNA recognition: energetics and implications for design, J. Mol. Recognit. 13, 188-197.
2. Han, X., and Gao, X. (2001) Sequence specific recognition of ligand-DNA complexes studied by NMR, Curr. Med. Chem. 8, 551-581.
3. Haq, I. (2002) Thermodynamics of drug-DNA interactions, Arch. Biochem. Biophys. 403, 1-15.
4. Jain, S. C., and Sobell, H. M. (1984) Visualization of drug-nucleic acid interactions at atomic resolution. VIII. Structures of two ethidium/dinucleoside monophosphate crystalline complexes containing ethidium:cytidylyl(3′- 5′) guanosine, J. Biomol. Struct. Dyn. 1, 1179-1194.
5. Jain, S. C., and Sobell, H. M. (1984) Visualization of drug-nucleic acid interactions at atomic resolution. VII. Structure of an ethidium/dinucleoside monophosphate crystalline complex, ethidium: uridylyl(3′-5′) adenosine, J. Biomol. Struct. Dyn. 1, 1161-1177.
6. Sakore, T. D., Bhandary, K. K., and Sobell, H. M. (1984) Visualization of drug-nucleic acid interactions at atomic resolution. X. Structure of a N,N-dimethylproflavine:deoxycytidylyl-(3′-5′)deoxyguanosine crystalline complex, J. Biomol. Struct. Dyn. 1, 1219-1227.
7. Bhandary, K. K., Sakore, T. D., Sobell, H. M., King, D., and Gabbay, E. J. (1984) Visualization of drug-nucleic acid interactions at atomic resolution. IX. Structures of two N,N-dimethylproflavine:5-iodocytidylyl (3′-5′) guanosine crystalline complexes, J. Biomol. Struct. Dyn. 1, 1195-1217.
8. Lybrand, T., and Kollman, P. (1985) Molecular mechanical calculations on the interaction of ethidium cation with double-helical DNA, Biopolymers 24, 1863-1879.
9. Moravek, Z., Neidle, S., and Schneider, B. (2002) Protein and drug interactions in the minor groove of DNA, Nucleic Acids Res. 30, 1182-1191.
10. Patel, D. J. (1997) Structural analysis of nucleic acid aptamers, Curr. Opin. Chem. Biol. 1, 32-46.
11. 1H NMR study, Nucleic Acids Res. 10, 749-762.
12. 1H NMR structural analysis of ethidium bromide complexation with self-complementary deoxytetranucleotides 5′-d(ApCpGpT), 5′-d(ApGpCpT), and 5′-d(TpGpCpA) in aqueous solution, Biopolymers 38, 745-757.
13. 1H NMR determination of the thermodynamics of drug complexation with single-stranded and double-stranded oligonucleotides in solution: ethidium bromide complexation with the deoxytetranucleotides 5′-d(ApCpGpT), 5′-d(ApGpCpT), and 5′-d(TpGpCpA), Biopolymers 42, 285-295.
14. Davies, D. B., Pahomov, V. I., and Veselkov, A. N. (1997) NMR determination of the conformational and drug binding properties of the DNA heptamer d(GpCpGpApApGpC) in aqueous solution, Nucleic Acids Res. 25, 4523-4531.
15. Ren, J., and Chaires, J. B. (1999) Sequence and structural selectivity of nucleic acid binding ligands, Biochemistry 38, 16067-16075.
16. Ren, J., Jenkins, T. C., and Chaires, J. B. (2000) Energetics of DNA intercalation reactions, Biochemistry 39, 8439-8447.
17. Chaires, J. B. (2001) Analysis and interpretation of ligand-DNA binding isotherms, Methods Enzymol. 340, 3-22.
18. Lu, D. S., Nonaka, Y., Tsuboi, M., and Nakamoto, K. (1990) Molecular distortion of distamycin on binding to DNA as revealed by Raman spectroscopy, J. Raman Spectrosc. 21, 321-326.
19. Thomas, G. J., Jr., and Tsuboi, M. (1993) Raman spectroscopy of nucleic acids and their complexes, in Advances in Biophysical Chemistry (Bush, C. A., Ed.) Vol. 3, pp 1-70, JAI Press Inc., Greenwich, CT.
20. Benevides, J. M., Chan, G., Lu, X. J., Olson, W. K., Weiss, M. A., and Thomas, G. J., Jr. (2000) Protein-directed DNA structure. I. Raman spectroscopy of a high-mobility-group box with application to human sex reversal, Biochemistry 39, 537-547.
21. Benevides, J. M., Li, T., Lu, X. J., Srinivasan, A. R., Olson, W. K., Weiss, M. A., and Thomas, G. J., Jr. (2000) Protein-directed DNA structure II. Raman spectroscopy of a leucine zipper bZIP complex, Biochemistry 39, 548-556.
22. Benevides, J. M., and Thomas, G. J., Jr. (2002) DNA unwinding: analysis by near-infrared Raman spectroscopy of ethidium-DNA complexes. Biophys. J. 82, 125d.
23. Serban, D., Benevides, J. M., and Thomas, G. J., Jr. (2003) HU protein employs similar mechanisms of minor-groove recognition in binding to different B-DNA sites: demonstration by Raman spectroscopy, Biochemistry 42, 7390-7399.
24. Wang, J. C. (1974) The degree of unwinding of the DNA helix by ethidium. I. Titration of twisted PM2 DNA molecules in alkaline cesium chloride density gradients, J. Mol. Biol. 89, 783-801.
25. Liu, L. F., and Wang, J. C. (1975) On the degree of unwinding of the DNA helix by ethidium. II. Studies by electron microscopy, Biochim. Biophys. Acta 395, 401-412.
26. Wang, J. C., Barkley, M. D., and Bourgeois, S. (1974) Measurements of unwinding of lac operator by repressor, Nature 251, 247-249.
27. Werner, M. H., Huth, J. R., Gronenborn, A. M., and Clore, G. M. (1995) Molecular basis of human 46X,Y sex reversal revealed from the three-dimensional solution structure of the human SRY-DNA complex, Cell 81, 705-714.
28. Giese, K., Pagel, J., and Grosschedl, R. (1997) Functional analysis of DNA bending and unwinding by the high mobility group domain of LEF-1, Proc. Natl. Acad. Sci. U.S.A. 94, 12845-12850.
29. Dhavan, G. M., Crothers, D. M., Chance, M. R., and Brenowitz, M. (2002) Concerted binding and bending of DNA by Escherichia coli integration host factor, J. Mol. Biol. 315, 1027-1037.
30. Rice, P. A., Yang, S., Mizuuchi, K., and Nash, H. A. (1996) Crystal structure of an IHF-DNA complex: a protein-induced DNA U-turn, Cell 87, 1295-1306.
31. Prescott, B., Steinmetz, W., and Thomas, G. J., Jr. (1984) Characterization of DNA structures by laser Raman spectroscopy, Biopolymers 23, 235-256.
32. Thomas, G. J., Jr., and Benevides, J. M. (1985) An A-helix structure for poly(dA-dT)·poly(dA-dT), Biopolymers 24, 1101-1105.
33. Tung, C. S., and Harvey, S. C. (1986) Base sequence, local helix structure, and macroscopic curvature of A-DNA and B-DNA, J. Biol. Chem. 261, 3700-3709.
34. Wang, L., Ferrari, M., and Bloomfield, V. A. (1990) Large-scale preparation of mononucleosomal DNA from calf thymus for biophysical studies, Biotechniques 9, 24, 26-24, 27.
35. Duguid, J., Bloomfield, V. A., Benevides, J., and Thomas, G. J., Jr. (1993) Raman spectroscopy of DNA-metal complexes. I. Interactions and conformational effects of the divalent cations: Mg, Ca, Sr, Ba, Mn, Co, Ni, Cu, Pd, and Cd, Biophys. J. 65, 1916-1928.
36. Overman, S. A., and Thomas, G. J., Jr. (1995) Raman spectroscopy of the filamentous virus Ff (fd, fl, M13): structural interpretation for coat protein aromatics, Biochemistry 34, 5440-5451.
37. Tsuboi, M., Benevides, J. M., and Thomas, G. J., Jr. (2004) Structural analysis of drug intercalation: polarized Raman microspectroscopy of the complex between ethidium and genomic DNA, Biophys. J. 86, 138a.
38. Thomas, G. J., Jr., Prescott, B., and Olins, D. E. (1977) Secondary structure of histones and DNA in chromatin, Science 197, 385-388.
39. Erfurth, S. C., Bond, P. J., and Peticolas, W. L. (1975) Characterization of the A D B transition of DNA in fibers and gels by laser Raman spectroscopy, Biopolymers 14, 1245-1257.
40. Duguid, J. G., Bloomfield, V. A., Benevides, J. M., and Thomas, G. J., Jr. (1996) DNA melting investigated by differential scanning calorimetry and Raman spectroscopy, Biophys. J. 71, 3350-3360.
41. Serban, D., Benevides, J. M., and Thomas, G. J., Jr. (2002) DNA secondary structure and Raman markers of supercoiling in Escherichia coli plasmid pUC19, Biochemistry 41, 847-853.
42. Winkle, S. A., Rosenberg, L. S., and Krugh, T. R. (1982) On the cooperative and noncooperative binding of ethidium to DNA, Nucleic Acids Res. 10, 8211-8223.
43. Movileanu, L., Benevides, J. M., and Thomas, G. J., Jr. (2002) Determination of base and backbone contributions to the thermodynamics of premelting and melting transitions in B DNA, Nucleic Acids Res. 30, 3767-3777.
44. Reilly, K. E., and Thomas, G. J., Jr. (1994) Hydrogen exchange dynamics of the P22 virion determined by time-resolved Raman spectroscopy: effects of chromosome packaging on the kinetics of nucleotide exchanges, J. Mol. Biol. 241, 68-82.
45. Zama, M., Olins, D. E., Prescott, B., and Thomas, G. J., Jr. (1978) Nucleosome conformation: pH and organic solvent effects, Nucleic Acids Res. 5, 3881-3897.
46. 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-S56.
47. Thomas, G. J., Jr. (1999) Raman spectroscopy of protein and nucleic acid assemblies, Annu. Rev. Biophys. Biomol. Struct. 28, 1-27.
48. 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.
49. Tuma, R., and Thomas, G. J., Jr. (2002) in Handbook of Vibrational Spectroscopy, Volume 5, Applications in Life, Pharmaceutical and Natural Sciences (Chalmers, J. M., and Griffiths, P. R., Eds.) pp 3519-3535, John Wiley & Sons, Chichester, U.K.
50. Peticolas, W. L., and Evertsz, E. (1992) Conformation of DNA in vitro and in vivo from laser Raman scattering, Methods Enzymol. 211, 335-352.
51. Nishimura, Y., Tsuboi, M., Nakano, T., Higuchi, S., Sato, T., Shida, T., Uesugi, S., Ohtsuka, E., and Ikehara, M. (1983) Raman diagnosis of nucleic acid structure: sugar-puckering and glycosidic conformation in the guanosine moiety, Nucleic Acids Res. 11, 1579-1588.
52. 2O solutions and application to B, Z and A-DNA, Nucleic Acids Res. 11, 5747-5761.
53. Nishimura, Y., Tsuboi, M., Sato, T., and Aoki, K. (1986) Conformation-sensitive Raman lines of mononucleotides and their use in a structure analysis of polynucleotides: guanine and cytosine nucleotides, J. Mol. Struct. 146, 123-153.
54. Dijkstra, S., Benevides, J. M., and Thomas, G. J., Jr. (1991) Solution conformations of nucleoside analogues exhibiting antiviral activity against human immunodeficiency virus, J. Mol. Struct. 242, 283-301.
55. Movileanu, L., Benevides, J. M., and Thomas, G. J., Jr. (1999) Temperature dependence of the Raman spectrum of DNA. I. Raman signatures of premelting and melting transitions of poly-(dA-dT)·poly(dA-dT), J. Raman Spectrosc. 30, 637-649.
56. 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.
57. Benevides, J. M., Overman, S. A., and Thomas, G. J., Jr. (2003) in Current Protocols in Protein Science (Coligan, J. E., Dunn, B. M., Ploegh, H. L., Speicher, D. W., and Wingfield, P. T., Eds.) pp 17.8.1-17.8.35, John Wiley and Sons, New York.
58. Erfurth, S. C., Kiser, E. J., and Peticolas, W. L. (1972) Determination of the backbone structure of nucleic acids and nucleic acid oligomers by laser Raman scattering, Proc. Natl. Acad. Sci. U.S.A. 69, 938-941.
59. Thomas, G. J., Jr., and Hartman, K. A. (1973) Raman studies of nucleic acids. VIII. Estimation of RNA secondary structure from Raman scattering by phosphate group vibrations, Biochim. Biophys. Acta 312, 311-322.
60. Small, E. W. and Peticolas, W. L. (1971) Conformational dependence of the Raman scattering intensities from polynucleotides, Biopolymers 10, 69-88.
61. Benevides, J. M., Wang, A. H. J., Rich, A., Kyogoku, Y., van der Marel, G. A., van Boom, J. H., and Thomas, G. J., Jr. (1986) Raman spectra of single crystals of r(GCG)d(CGC) and d(C-CCCGGGG) as models for A DNA, their structure transitions in aqueous solution, and comparison with double-helical poly(dG)·poly(dC), Biochemistry 25, 41-50.
62. 8 determined by NMR and Raman spectroscopy, J. Am. Chem. Soc. 112, 4508-4512.
63. Thomas, G. J., Jr., Prescott, B., Opella, S. J., and Day, L. A. (1988) Sugar pucker and phosphodiester conformations in viral genomes of filamentous bacteriophages: fd, If1, IKe, Pf1, Xf, and Pf3, Biochemistry 27, 4350-4357.
64. Evertsz, E. M., Thomas, G. A., and Peticolas, W. L. (1991) Raman spectroscopic studies of the DNA cro binding site conformation, free and bound to cro protein, Biochemistry 30, 1149-1155.