Photophysical and calorimetric studies on the binding of 9-O-substituted analogs of the plant alkaloid berberine to double stranded poly(A)

Journal of Photochemistry and Photobiology B: Biology

Volumn 125, Issue , 2013, Pages 105-114

  Basu, Anirban ^a   Jaisankar, Parasuraman ^a   Kumar, Gopinatha Suresh ^a  

^a INDIAN INSTITUTE OF CHEMICAL BIOLOGY   (India)

Author keywords

9 O berberine analogs; Cooperativity; Double stranded poly(A) binding; Thermodynamic parameters

Indexed keywords

ADENINE; ALKYL ETHER; BERBERINE; CARBONYL DERIVATIVE; FERROCYANIDE; METHYL GROUP; POLYADENYLIC ACID;

ARTICLE; BINDING AFFINITY; CHEMICAL STRUCTURE; CIRCULAR DICHROISM; CONFORMATIONAL TRANSITION; ENERGY TRANSFER; ENTHALPY; ENTROPY; HYDRODYNAMICS; ISOTHERMAL TITRATION CALORIMETRY; PRIORITY JOURNAL; QUANTUM CHEMISTRY; SPECTROFLUOROMETRY; STOICHIOMETRY; TEMPERATURE DEPENDENCE; THERMODYNAMICS; VISCOSITY;

EID: 84879215519     PISSN: 10111344     EISSN: 18732682     Source Type: Journal    
DOI: 10.1016/j.jphotobiol.2013.05.009     Document Type: Article

References (54)

1. T. Hermann, D.J. Patel, Adaptive recognition by nucleic acid aptamers, Science 287 (2000) 820-825. (Pubitemid 30084318)
2. D.E. Graves, L.M. Velea, Intercalative binding of small molecules to nucleic acids, Curr. Org. Chem. 4 (2000) 915-929.
3. A. Paul, S. Bhattacharya, Chemistry and biology of DNA-binding small molecules, Curr. Sci. 102 (2012) 212-231.
4. M. Wickens, P. Anderson, R.J. Jackson, Life and death in the cytoplasm: messages from the 3′ end, Curr. Opin. Genet. Dev. 7 (1997) 220-232. (Pubitemid 27206761)
5. K. Dower, N. Kuperwasser, H. Merrikh, M. Rosbash, A synthetic A tail rescues yeast nuclear accumulation of a ribozyme-terminated transcript, RNA 10 (2004) 1888-1899. (Pubitemid 39557826)
6. S.L. Topalian, S. Kaneko, M.I. Gonzales, G.L. Bond, Y. Ward, J.L. Manley, Identification and functional characterization of neo-poly(A) polymerase, an RNA processing enzyme overexpressed in human tumors, Mol. Cell. Biol. 21 (2001) 5614-5623. (Pubitemid 32702464)
7. S.L. Topalian, M.I. Gonzales, Y. Ward, X. Wang, R.F. Wang, Revelation of a cryptic major histocompatibility complex class II-restricted tumor epitope in a novel RNA-processing enzyme, Cancer Res. 62 (2002) 5505-5509.
8. S.B. Zimmerman, D.R. Davies, M.A. Navia, An ordered single-stranded structure for polyadenylic acid in denaturing solvents. An X-ray fibre diffraction and model building study, J. Mol. Biol. 116 (1977) 317-330. (Pubitemid 8215110)
9. W. Saenger, J. Riecke, D. Suck, A structural model for the polyadenylic acid single helix, J. Mol. Biol. 93 (1975) 529-534.
10. S. Chakraborty, S. Sharma, P.K. Maiti, Y. Krishnan, The poly dA helix: a new structural motif for high performance DNA-based molecular switches, Nucl. Acids Res. 37 (2009) 2810-2817.
11. A. Sachs, E. Wahle, Poly(A) tail metabolism and function in eucaryotes, J. Biol. Chem. 268 (1993) 22955-22958. (Pubitemid 23327995)
12. H. Le, K.S. Browning, D.R. Gallie, The phosphorylation state of poly(A)-binding protein specifies its binding to poly(A) RNA and its interaction with eukaryotic initiation factor (eIF) 4F, eIFiso4F, and eIF4B, J. Biol. Chem. 275 (2000) 17452-17462. (Pubitemid 30430784)
13. A. Rich, D.R. Davies, F.H.C. Crick, J.D. Watson, The molecular structure of polyadenylic acid, J. Mol. Biol. 3 (1961) 71-86.
14. J.R. Fresco, Polynucleotides II: the X-Ray diffraction patterns of solutions of the randomly coiled and helical forms of polyriboadenylic acid, J. Mol. Biol. 1 (1959) 106-110.
15. P.O.P. Ts'o, G.K. Helmkamp, C. Sander, Interaction of nucleosides and related compounds with nucleic acids as indicated by the change of helixcoil transition temperature, Proc. Natl. Acad. Sci. USA 48 (1962) 686-697.
16. M.I. Zarudnaya, D.M. Hovorun, Structural transitions in polyadenylic acid and hypothesis on biological role of its double-stranded forms, Ukr. Biokhim. Zh. 71 (1999) 15-20.
17. M.I. Zarudnaia, A.V. Stepaniugin, A.L. Potiagaǐlo, D.N. Govorun, Intramolecular double-stranded helices of polyadenylic acid and their possible biological significance, Ukr. Biokhim. Zh. 80 (2008) 74-81.
18. M.I. Zarudnaya, D.M. Hovorun, Hypothetical double-helical poly(A) formation in a cell and its possible biological significance, IUBMB Life 48 (1999) 581-584. (Pubitemid 30043802)
19. S. Ravindranathan, S.E. Butche, J. Feigon, Adenine protonation in domain B of the hairpin ribozyme, Biochemistry 39 (2000) 16026-16032. (Pubitemid 32038265)
20. E. Bernstein, A.A. Caudy, S.M. Hammond, G.J. Hannon, Role for a bidentate ribonuclease in the initiation step of RNA interference, Nature 409 (2001) 363-366. (Pubitemid 32151243)
21. B.R. Williams, PKR; a sentinel kinase for cellular stress, Oncogene 18 (1999) 6112-6120.
22. T. Melcher, S. Maas, A. Herb, R. Sprengel, P.H. Seeburg, M. Higuchi, A mammalian RNA editing enzyme, Nature 379 (1996) 460-464. (Pubitemid 26039528)
23. M.A. O'Connell, A. Gerber, W. Keller, Purification of human double-stranded RNA-specific editase 1 (hRED1) involved in editing of brain glutamate receptor B pre-mRNA, J. Biol. Chem. 272 (1997) 473-478. (Pubitemid 27021182)
24. C.B. Carlson, O.M. Stephens, P.A. Beal, Recognition of double-stranded RNA by proteins and small molecules, Biopolymers 70 (2003) 86-102. (Pubitemid 37092909)
25. T. Imae, S. Hayashi, S. Ikeda, T. Sakaki, Interaction between acridine orange and polyriboadenylic acid, Int. J. Biol. Macromol. 3 (1981) 259-266.
26. C. Ciatto, M.L. D'Amico, G. Natile, F. Secco, M. Venturini, Intercalation of proflavine and a platinum derivative of proflavine into double-helical poly(A), Biophys. J. 77 (1999) 2717-2724. (Pubitemid 29519516)
27. L.M. Tumir, I. Piantanida, I.J. Cindric, T. Hrenar, Z. Meic, M. Zinic, New permanently charged phenanthridinium-nucleobase conjugates. Interactions with nucleotides and polynucleotides and recognition of ds-polyAH+, J. Phys. Org. Chem. 16 (2003) 891-899.
28. P. Giri, G. Suresh Kumar, Spectroscopic and calorimetric studies on the binding of the phototoxic and cytotoxic plant alkaloid sanguinarine with double helical poly(A), J. Photochem. Photobiol. A: Chem. 194 (2008) 111-121.
29. P. Giri, G. Suresh Kumar, Binding of protoberberine alkaloid coralyne with double stranded poly(A): a biophysical study, Mol. BioSyst. 4 (2008) 341-348. (Pubitemid 351422589)
30. A. Das, K. Bhadra, B. Achari, P. Chakraborty, G. Suresh Kumar, Interaction of aristololactam-b-D-glucoside and daunomycin with poly(A): spectroscopic and calorimetric studies, Biophys. Chem. 155 (2011) 10-19.
31. P. Centikol, N.V. Hud, Molecular recognition of poly(A) by small ligands: an alternative method of analysis reveals nanomolar, cooperative and shapeselective binding, Nucl. Acids Res. 37 (2009) 611-621.
32. M.M. Islam, A. Basu, G. Suresh Kumar, Binding of 9-O-(x-amino) alkyl ether analogs of the plant alkaloid berberine to poly(A): insights into self-structure induction, Med. Chem. Commun. 2 (2011) 631-637.
33. A. Basu, P. Jaisankar, G. Suresh Kumar, 9-O-N-aryl/arylalkyl amino carbonyl methyl substituted berberine analogs induce self-structure in polyadenylic acid, RSC Adv. 2 (2012) 7714-7723.
34. R.C. Yadav, G. Suresh Kumar, K. Bhadra, P. Giri, R. Sinha, S. Pal, M. Maiti, Berberine, a strong polyriboadenylic acid binding plant alkaloid: spectroscopic, viscometric and thermodynamic study, Bioorg. Med. Chem. 13 (2005) 165-174. (Pubitemid 39575701)
35. A. Basu, P. Jaisankar, G. Suresh Kumar, Synthesis of novel 9-O-N-aryl/aryl-alkyl amino carbonyl methyl substituted berberine analogs and evaluation of DNA binding aspects, Bioorg. Med. Chem. 20 (2012) 2498-2505.
36. J.Y. Pang, Y. Qin, W.H. Chen, G.A. Luo, Z.H. Jiang, Synthesis and DNA-binding affinities of monomodified berberines, Bioorg. Med. Chem. 13 (2005) 5835-5840. (Pubitemid 41247768)
37. M. Halimani, S.P. Chandran, S. Kashyap, V.M. Jadhav, B.L.V. Prasad, S. Hotha, S. Maiti, Dendritic effect of ligand-coated nanoparticles: enhanced apoptotic activity of silica-berberine nanoconjugates, Langmuir 25 (2009) 2339-2347.
38. M.M. Islam, S. Roy Chowdhury, G. Suresh Kumar, Spectroscopic and calorimetric studies on the binding of alkaloids berberine, palmatine and coralyne to double stranded RNA polynucleotides, J. Phys. Chem. B 113 (2009) 1210-1224.
39. K. Bhadra, M. Maiti, G. Suresh Kumar, Molecular recognition of nucleic acids by small molecules: mode and base specificity of DNA binding of cytotoxic alkaloid palmatine, Biochim. Biophys. Acta 1770 (2007) 1071-1080. (Pubitemid 46678609)
40. K. Bhadra, M. Maiti, G. Suresh Kumar, Interaction of isoquinoline alkaloids with polymorphic DNA structures, Chem. Biodivers. 6 (2009) 1323-1342.
41. J.D. McGhee, P.H. von Hippel, Theoretical aspects of DNA-protein interactions: cooperative and noncooperative binding of large ligands to a one dimensional homogeneous lattice, J. Mol. Biol. 86 (1974) 469-489.
42. H. Benesi, J. Hildebrand, A spectrophotometric investigation of the interaction of iodine with aromatic hydrocarbons, J. Am. Chem. Soc. 71 (1949) 2703-2707.
43. N.C. Garbett, N.B. Hammond, D.E. Graves, Influence of the amino substituents in the interaction of ethidium bromide with DNA, Biophys. J. 87 (2004) 3974-3981. (Pubitemid 39602902)
44. P. Job, Formation and stability of inorganic complexes in solution, Ann. Chim. 9 (1928) 113-203.
45. M.M. Islam, R. Sinha, G. Suresh Kumar, RNA binding small molecules: studies on t-RNA binding by cytotoxic plant alkaloids berberine, palmatine and the comparison to ethidium, Biophys. Chem. 125 (2007) 508-520. (Pubitemid 46138021)
46. J.R. Lakowicz, Principles of Fluorescence Spectroscopy, Plenum Press, New York, 1983. pp 257-295.
47. L.S. Lerman, Structural considerations in the interaction of DNA and acridines, J. Mol. Biol. 3 (1961) 18-30.
48. K.M. Guthrie, A.D. Parenty, L.V. Smith, L. Cronin, A. Cooper, Microcalorimetry of interaction of dihydro-imidazo-phenanthridinium (DIP)-based compounds with duplex DNA, Biophys. Chem. 126 (2007) 117-123. (Pubitemid 46186632)
49. J. Ren, T.C. Jenkins, J.B. Chaires, Energetics of DNA intercalation reactions, Biochemistry 39 (2000) 8439-8447. (Pubitemid 30489940)
50. K.L. Buchmueller, S.L. Bailey, D.A. Matthews, Z.T. Taherbhai, J.K. Register, Z.S. Davis, C.D. Bruce, C. O'Hare, J.A. Hartley, M. Lee, Physical and structural basis for the strong interactions of the -ImPy-central pairing motif in the polyamide f-ImPyIm, Biochemistry 45 (2006) 13551-13565. (Pubitemid 44748501)
51. B. Nguyen, J. Stanek, W.D. Wilson, Binding-linked protonation of a DNA minorgroove agent, Biophys. J. 90 (2006) 1319-1328.
52. F.V. Murphy, M.E. Churchill, Nonsequence-specific DNA recognition: a structural perspective, Structure 8 (2000) R83-R89. (Pubitemid 30202894)
53. M.T. Record Jr., C.F. Anderson, T.M. Lohman, Thermodynamic analysis of ion effects on the binding and conformational equilibria of proteins and nucleic acids: the role of ion association or release, screening, and ion effects on water activity, Q. Rev. Biophys. 11 (1978) 103-178. (Pubitemid 8373664)
54. E.B. Starikov, B. Norden, Enthalpy-entropy compensation: a phantom or something useful, J. Phys. Chem. B 111 (2007) 14431-14435.