RNA binding small molecules: Studies on t-RNA binding by cytotoxic plant alkaloids berberine, palmatine and the comparison to ethidium

Biophysical Chemistry

Volumn 125, Issue 2-3, 2007, Pages 508-520

  Islam, Md Maidul ^a   Sinha, Rangana ^a   Kumar, Gopinatha Suresh ^a  

^a INDIAN INSTITUTE OF CHEMICAL BIOLOGY   (India)

Author keywords

Alkaloid t RNA interaction; Calorimetry; Protoberberine alkaloids; Spectroscopy; t RNA; Thermodynamics

Indexed keywords

ALKALOID; BERBERINE; CYTOTOXIC AGENT; ETHIDIUM BROMIDE; FUNGAL RNA; PALMATINE; TRANSFER RNA;

ARTICLE; BINDING AFFINITY; CIRCULAR DICHROISM; DRUG MECHANISM; ISOTHERMAL TITRATION CALORIMETRY; MEDICINAL PLANT; MOLECULAR INTERACTION; NONHUMAN; PHYTOCHEMISTRY; PRIORITY JOURNAL; RNA BINDING; SPECTROFLUOROMETRY; THERMODYNAMICS;

ALKALOIDS; BERBERINE; BERBERINE ALKALOIDS; ETHIDIUM; INTERCALATING AGENTS; NUCLEIC ACID CONFORMATION; PLANTS; RNA, TRANSFER; RNA, TRANSFER, PHE; SALTS; SPECTRUM ANALYSIS; THERMODYNAMICS;

EID: 33846450257     PISSN: 03014622     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.bpc.2006.11.001     Document Type: Article

References (79)

1. M. Maiti, G.S. Kumar, Molecular aspects on the interaction of protoberberine, benzophenanthridine and aristolochia group of alkaloids with nucleic acid structures and biological perspectives, Med. Res. Rev. (in press), doi:10.1002/med.20087.
2. Hurley L.H. Secondary DNA structures as molecular targets for cancer therapeutics. Biochem. Soc. Trans. 29 (2001) 692-696
3. Dervan P.B. Molecular recognition of DNA by small molecules. Bioorg. Med. Chem. 9 (2001) 2215-2235
4. Chaires J.B. Drug-DNA interactions. Curr. Opin. Struct. Biol. 8 (1998) 314-320
5. McConnaughie A.W., Spychala J., Zhao M., Boykin D., and Wilson W.D. Design and synthesis of RNA-specific groove-binding cations: implications for antiviral drug design. J. Med. Chem. 37 (1994) 1063-1069
6. Tor Y. RNA and the small molecule world. Angew Chem. Int. Ed. 38 (1999) 1579-1582
7. Hermann T. Strategies for the design of drugs targeting RNA and RNA-protein complexes. Angew Chem. Int. Ed. 39 (2002) 1890-1904
8. Hermann T. Rational ligand design for RNA; the role of static structure and conformational flexibility in target design. Biochimie 84 (2002) 869-875
9. Sinha R., Islam Md.M., Bhadra K., Kumar G.S., Banerjee A., and Maiti M. The binding of DNA intercalating and non-intercalating compounds to A-form and protonated form of poly(rC)·poly(rG): spectroscopic and viscometric study. Bioorg. Med. Chem. 14 (2006) 800-814
10. Higgs P.G. RNA secondary structure: physical and computational aspects. Quat. Rev. Biophys. 33 (2000) 199-253
11. Sosnick T.R., and Pan T. RNA folding: models and perspectives. Curr. Opin. Struct. Biol. 13 (2003) 309-316
12. Hermann T., and Westhof E. RNA as a drug target: chemical, modeling, and evolutionary tools. Curr. Opin. Biotechnol. 9 (1998) 66-73
13. Xavier K., Eder P.S., and Giordano T. RNA as a drug target: methods for biophysical characterization and screening. Trends Biotechnol. 18 (2000) 349-356
14. Gallego J., and Varani G. Targeting RNA with small molecule drugs: therapeutic promise and chemical challenges. Acc. Chem. Res. 34 (2001) 836-843
15. Vicens Q., and Westhof E. Molecular recognition of aminoglycoside antibiotics by ribosomal RNA and resistance enzymes: an analysis of X-ray crystal structures. Biopolymer 70 (2003) 42-57
16. Arya D.P. Aminoglycoside-nucleic acid interactions: the case of neomycin. Top. Curr. Chem. 253 (2005) 149-178
17. Tanious F.A., Veal J.M., Buczak H., Ratmeyer L.S., and Wilson W.D. DAPI (4′,6-diamidino-2-phenylindole) binds differently to DNA and RNA: minor-groove binding at AT sites and intercalation at AU sites. Biochemistry 31 (1992) 3103-3112
18. Zhao M., Janda L., Nguyen J., Strekowski L., and Wilson W.D. The interaction of substituted 2-phenylquinoline intercalates with poly(A).poly(U): classical and threading intercalation modes with RNA. Biopolymers 34 (1994) 61-73
19. Fernandez-Saiz M., Werner F., Davis T.M., Schneider H.-J., and Wilson W.D. Studies on the unique RNA duplex destabilization by an azoniacyclophane- NMR titrations with mono- and oligonucleotides of the RNA and DNA types. Eur. J. Org. Chem. 2002 (2002) 1077-1084
20. Toulme J.-J., and Helene C. Anti messenger oligodeoxyribonucleotides: an alternative to antisense RNA for artificial regulation of gene expression- a review. Gene 72 (1988) 51-58
21. Helene C., and Toulme J.-J. Specific regulation of gene expression by antisense, sense and antigene nucleic acids. Biochim. Biophys. Acta 1049 (1990) 99-125
22. Nandi R., Debnath D., and Maiti M. Interactions of berberine with poly(A) and tRNA. Biochim. Biophys. Acta 1049 (1990) 339-342
23. Yadav R.C., Kumar G.S., Bhadra K., Giri P., Sinha R., Pal S., and Maiti M. Berberine, a strong polyriboadenylic acid binding plant alkaloid: spectroscopic, viscometric, and thermodynamic study. Bioorg. Med. Chem. 13 (2005) 165-174
24. Giri P., Hossain M., and Kumar G.S. RNA specific molecules: cytotoxic plant alkaloid palmatine binds strongly to poly(A). Bioorg. Med. Chem. Lett. 16 (2006) 2364-2368
25. Giri P., Hossain M., and Kumar G.S. Molecular aspects on the specific interaction of cytotoxic plant alkaloid palmatine to poly(A). Int. J. Biol. Macromol. 39 (2006) 210-221
26. Xing F., Song G., Ren J., Chaires J.B., and Qu X. Molecular recognition of nucleic acids: coralyne binds strongly to poly(A). FEBS Lett. 579 (2005) 5035-5039
27. Amin A.H., Subbaiah T.V., and Abbasi K.M. Berberine sulfate: antimicrobial activity, bioassay, and mode of action. Can. J. Microbiol. 15 (1969) 1067-1076
28. Creasey W.A. Biochemical effects of berberine. Biochem. Pharmacol. 28 (1979) 1081-1084
29. Schmeller T., Latz-Bruning B., and Wink M. Biochemical activities of berberine, palmatine and sanguinarine mediating chemical defence against microorganisms and herbivores. Phytochemistry 44 (1997) 257-266
30. Kuo C.L., Chi C.W., and Liu T.Y. Modulation of apoptosis by berberine through inhibition of cyclooxygenase-2 and Mc1-1 expression in oral cancer cells. In Vivo 1 (2005) 247-252
31. Nishida S., Kikuichi S., Yoshioka S., Tsubaki M., Fujii Y., Matsuda H., Kubo M., and Irimajiri K. Induction of apoptosis in HL-60 cells treated with medicinal herbs. Am. J. Chin. Med. 4 (2003) 551-562
32. Letašiová S., Jantová S., Čipák L., and Múčková M. Berberine-antiproliferative activity in vitro and induction of apoptosis/necrosis of the U937 and B16 cells. Cancer Lett. 239 (2006) 254-262
33. Letašiová S., Jantová S., Miko M., Ovadekova R., and Horvathova M. Effect of berberine on proliferation, biosynthesis of macromolecules, cell cycle and induction of intercalation with DNA, ds DNA damage and apoptosis in Ehrlich ascites carcinoma cells. J. Pharm. Pharmacol. 58 (2006) 263-270
34. Hwang J.-M., Kuo H.-C., Tseng T.-H., Liu J.-Y., and Chu C.-Y. Berberine induces apoptosis through a mitochondria/caspases pathway in human hepatoma cells. Arch. Toxicol. 80 (2006) 62-73
35. Debnath D., Kumar G.S., Nandi R., and Maiti M. Interaction of berberine chloride with deoxyribonucleic acids: evidence for base and sequence specificity. Indian J. Biochem. Biophys. 26 (1989) 201-208
36. Kumar G.S., Debnath D., Sen A., and Maiti M. Thermodynamics of the interaction of berberine with DNA. Biochem. Pharmacol. 46 (1993) 1665-1667
37. 1H NMR investigation of the interaction of berberine and sanguinarine with DNA. Indian J. Biochem. Biophys. 32 (1995) 74-77
38. Pilch D.S., Yu C., Makhey D., LaVoie E.J., Srinivasan A.R., Olson W.K., Sauers R.R., Breslauer K.J., Geacintov N.E., and Liu L.F. Minor groove-directed and intercalative ligand-DNA interactions in the poisoning of human DNA topoisomerase I by protoberberine analogs. Biochemistry 36 (1997) 12542-12553
39. Bhadra K., Kumar G.S., Das S., Islam Md.M., and Maiti M. Protonated structures of naturally occurring deoxyribonucleic acids and their interaction with berberine. Biorg. Med. Chem. 13 (2005) 4851-4863
40. K. Bhadra, M. Maiti, G.S. Kumar, Molecular recognition of nucleic acids by small molecules: AT base pair specific intercalative binding of cytotoxic alkaloid palmatine (Communicated).
41. Antony T., Atreyi M., and Rao M.V.R. Interaction of methylene blue with transfer RNA- a spectroscopic study. Chem. Biol. Inter. 97 (1995) 199-214
42. Gomori G. In: Colowick S.P., and Kaplan N.O. (Eds). Preparation of Buffers for Use in Enzyme Studies, in Methods Enzymol vol. 1 (1955), Academic Press 138-146
43. Kumar G.S., and Maiti M. DNA polymorphism under the influence of low pH and low temperature. J. Biomol. Struct. Dyn. 12 (1994) 183-201
44. Das S., Kumar G.S., and Maiti M. Conversions of the left-handed form and the protonated form of DNA back to the bound right-handed form by sanguinarine and ethidium: a comparative study. Biophys. Chem. 76 (1999) 199-218
45. Nandi R., Chakraborty S., and Maiti M. Base- and sequence-dependent binding of aristololactam β-d-glucoside to deoxyribonucleic acid. Biochemistry 30 (1991) 3715-3720
46. C.R. Cantor, P.R. Schimmel, Biophysical Chemistry Part III, pp. 1135-1139, W.H. Freeman, New York.
47. Huang C.Y. In: Colowick S.P., and Kaplan N.O. (Eds). Determination of binding stoichiometry by the continuous variation method: the job plot, in Methods Enzymol vol. 87 (1982), Academic Press 509-525
48. McGhee J.D., and von Hippel P.H. Theoretical aspects of DNA-protein interactions: co-operative and non-co-operative binding of large ligands to a one-dimensional homogeneous lattice. J. Mol. Biol. 86 (1974) 469-489
49. Ray A., Maiti M., and Nandy A. Scatplot: a computer program for determination of binding parameters of non-linear non-cooperative ligand-substrate interactions. Comput. Biol. Med. 26 (1996) 497-503
50. L-form deoxyribonucleic acid structures. J. Biomol. Struct. Dyn. 21 (2003) 141-151
51. Marky L.A., and Breslauer K.J. Calculating thermodynamic data for transitions of any molecularity from equilibrium melting curves. Biopolymers 26 (1987) 1601-1620
52. Chaires J.B., Satyanarayana S., Suh D., Fokt I., Przewloka T., and Priebe W. Parsing the free energy of anthracycline antibiotic binding to DNA. Biochemistry 35 (1996) 2047-2053
53. Chaires J.B. Dissecting the free energy of drug binding to DNA. Anti-Cancer Drug Des. 11 (1996) 569-580
54. 6 cationic peptide with short nucleic acid oligomers: demonstration of large Columbic end effects on binding at 0.1-0.2 M salt. Nucleic Acids Res. 32 (2004) 3271-3281
55. Suh D., and Chaires J.B. Criteria for the mode of binding of DNA binding agents. Bioorg. Med. Chem. 3 (1995) 723-728
56. O'Brien R., and Haq I. Applications of biocalorimetry: binding, stability and enzyme kinetics. In: Ladbury J.E., and Doyle M. (Eds). Biocalorimetry (2004), John Wiley and Sons Ltd.
57. Rich A., and RajBhandary U.L. Transfer RNA: molecular structure, sequence and properties. Ann. Rev. Biochem. 45 (1976) 805-860
58. Stein A., and Crothers D.M. Conformational changes of transfer RNA, The role of magnesium (II). Biochemistry 15 (1976) 160-168
59. Friederich M.W., and Hagerman P.J. The angle between the anticodon and aminoacyl acceptor stems of yeast tRNA(Phe) is strongly modulated by magnesium ions. Biochemistry 36 (1977) 6090-6099
60. Phe thermal unfolding equilibria by UV spectroscopy and multivariate curve resolution. J. Inorg. Biochem. 89 (2002) 115-122
61. Maglott E.J., Deo S.S., Przykorska A., and Glick G.D. Conformational transitions of an unmodified tRNA: implications for RNA folding. Biochemistry 37 (1998) 16349-16359
62. 2+-induced tRNA folding. Biochemistry 40 (2001) 6688-6698
63. Bina-Stein M., and Crothers D.M. Conformational changes of transfer ribonucleic acid. The pH phase diagram under acidic conditions. Biochemistry 13 (1974) 2771-2775
64. Steinmetz-Kayne M., Benigno R., and Kallenbach N.R. Proton nuclear magnetic resonance study of the effect of pH on tRNA structure. Biochemistry 16 (1977) 1064-2073
65. Römer R., Riesner D., Maass G., Wintermeyer W., Thiebe R., and Zachau H.G. Cooperative helix-coil transitions in half molecules of phenylalanine specific tRNA from yeast. FEBS Lett. 5 (1969) 15-19
66. Phe fragments. Eur. J. Biochem. 36 (1973) 76-88
67. phe. Biochemistry 16 (1977) 5261-5273
68. Dahl K.S., Pardi A., and Tinoco Jr. I. Structural effects on the circular dichroism of ethidium ion-nucleic acid complexes. Biochemistry 21 (1982) 2730-2737
69. Xu H., Liang Y., Zhang P., Du F., Zhou B.-R., Wu J., Liu J.-H., Liu Z.-G., and Ji L.N. Biophysical studies of a ruthenium (II) polypyridyl complex binding to DNA and RNA prove that nucleic acid structure has significant effect on binding behaviors. J. Biol. Inorg. Chem. 10 (2005) 529-538
70. Kaul M., and Pilch D.S. Thermodynamics of aminoglycoside-rRNA recognition: the binding of neomycin-class aminoglycosides to the A site of 16S rRNA. Biochemistry 41 (2002) 7695-7706
71. Pilch D.S., Kaul M., Barbieri C.M., and Kerrigan J.E. Thermodynamics of aminoglycoside-rRNA recognition. Biopolymers 70 (2003) 58-79
72. Guthrie K.M., Parenty A.D.C., Smith L.V., Cronin L., and Cooper A. Microcalorimetry of interaction of dihydro-imidazo-phenanthridinium (DIP)-based compounds with duplex DNA. Biophys. Chem. (2006) (on line)
73. Bittman R. Studies of the binding of ethidium bromide to transfer ribonucleic acid: absorption, fluorescence, ultracentrifugation and kinetic investigations. J. Mol. Biol. 46 (1969) 251-268
74. Sakai T.T., Torget R., Josephine I., Freda C.E., and Cohen S.S. The binding of polyamines and of ethidium bromide to tRNA. Nucleic Acids Res. 2 (1975) 1005-1022
75. Tao T., Nelson J.H., and Cantor C.R. Conformational studies on transfer ribonucleic acid. Fluorescence lifetime and nanosecond depolarization measurements on bound ethidium bromide. Biochemistry 9 (1970) 3514-3524
76. Phe by high resolution (300 MHz) nuclear magnetic resonance. Biochemistry 14 (1975) 2660-2665
77. Jones C.R., Bolton P.H., and Kearns D.R. Ethidium bromide binding to transfer RNA: transfer RNA as a model system for studying drug-RNA interactions. Biochemistry 17 (1978) 601-607
78. Liebman M., Rubin J., and Sundaralingam M. Nonintercalative binding of ethidium bromide to nucleic acids: crystal structure of an ethidium-tRNA molecular complex. Proc. Natl. Acad. Sci. U. S. A. 74 (1977) 4821-4825
79. Chu W.-C., Liu J.C.-H., and Horowitz J. Localization of the major ethidium bromide binding site on tRNA. Nucleic Acids Res. 25 (1997) 3944-3949