Polyethyleneimine Derivative for Nucleic Acid Model

  • Lee, Chan-Woo (Department of Innovative Industrial Technology, Hoseo University) ;
  • Chae, Hee-Jeong (Department of Innovative Industrial Technology, Hoseo University, Department of Food and Biotechnology, Hoseo University) ;
  • Kwon, Young-Jin (Department of Disaster prevention and Technology)
  • Published : 2005.06.01

Abstract

Water-soluble polyethyleneimine (PE) derivatives containing nucleic acid bases and hydrophilic amino acids such as homoserine (Hse) and serine were prepared by the activated ester method as nucleic acid models. From spectroscopic measurements, the polymers were found to interact with DNA accompanied by an induction of conformational change. Hypochromicity in UV spectra indicated that a stable polymer complex was formed between poly (A) with PEI­Hse-Ura by complementary hydrogen bonding with equimolar nucleic base units (adenine:uracil=1:1). The induced conformation of DNA by the interaction with the polymer containing uracil and homoserine (PEI-Hse-Ura) was concluded to be a super triple helical structure. The formation of the polymer complex, DNA: PEI-Hse-Ura, was found to be affected by the presence of metal ions such as $Ca^{2+}\;and\;Cu^{2+}$.

Keywords

References

  1. Altmann, K.-H., D. Husken, B. Cuenoud, and C. Garcia- Echeverria (2000) Synthesis and hybridization properties of polyamide based nucleic acid analogues incorporating pyrrolidine-derived nucleoamino acids. Bioorg. Med. Chem. Lett. 10: 929-933 https://doi.org/10.1016/S0960-894X(00)00121-9
  2. Inaki, Y., S.-I. Sugita, T. Takahara, and K. Takemoto (1986) Functional monomers and polymers. CXXXI. Synthesis and interaction studies on polyacrylamide and polymethacrylamide derivatives containing nucleic acid bases. J. Polym. Sci. Part A: Polym. Chem. 24: 3201-3217 https://doi.org/10.1002/pola.1986.080241205
  3. Inaki, Y., K. Ebisutani, and K. Takemoto (1986) Functional monomers and polymers. CXXXII. Template polymerization of methacrylamide derivatives containing nucleic acid bases. J. Polym. Sci. Part A: Polym. Chem. 24: 3249-3262 https://doi.org/10.1002/pola.1986.080241209
  4. Altmann, K.-H., C. S. Chiesi, and C. Garcia-Echeverria (1997) Polyamide based nucleic acid analogs synthesis of amino acids with nucleic acid bases bearing side chains. Bioorg. Med. Chem. Lett. 7: 1119-1122 https://doi.org/10.1016/S0960-894X(97)00172-8
  5. Garcia-Echeverria, C., D. Husken, C. S. Chiesi, and K.-H. Altmann (1997) Novel polyamide based nucleic acid analogs- synthesis of oligomers and RNA-binding properties. Bioorg. Med. Chem. Lett. 7: 1123-1126 https://doi.org/10.1016/S0960-894X(97)00173-X
  6. Inaki, Y. (1992) Synthetic nucleic acid analogs. Prog. Polymer Sci. 17: 515-570 https://doi.org/10.1016/0079-6700(92)90001-F
  7. Overberger, C. G., Y. Inaki, and Y. Nambu (1979) Graft copolymers containing nucleic acid bases and L-amino acids. J. Polymer Sci. Polymer Chem. Ed. 17: 1739-1758 https://doi.org/10.1002/pol.1979.170170616
  8. Overberger, C. G., Y. Inaki, and Y. Nambu (1979) Graft copolymers of nucleic acid bases on polyethyleneimine: Interaction of the polymers. J. Polymer Sci. Polymer Chem. Ed. 17: 1759-1769 https://doi.org/10.1002/pol.1979.170170617
  9. Inaki, Y., T. Ishikawa, and K. Takemoto (1980) Synthesis and interactions of poly-L-lysines containing nucleic acid bases. Nucleic Acids Symp. Ser. 8: 137-140
  10. Sakuma, Y., Y. Inaki, and K. Takemoto (1982) Functional monomers and polymers. CII. Synthesis and properties of oligomer models of polyethyleneimine derivatives containing pendant adenine bases. J. Polymer Sci. Polymer Chem. Ed. 20: 3431-3446 https://doi.org/10.1002/pol.1982.170201215
  11. Sakuma, Y., Y. Inaki, and K. Takemoto (1982) Intramolecular interaction of thymine and adenine bases in synthetic oligo- and polynucleotide models. Nucleic Acids Symp. Ser. 11: 269-272
  12. Shimazaki, Y., M. Mitsuishi, S. Ito, M. Yamamoto, and Y. Inaki (1998) Preparation of the nucleoside-containing nanolayered film by the layer-by-layer deposition technique. Thin Solid Films 333: 5-8 https://doi.org/10.1016/S0040-6090(98)00966-3
  13. Nakauchi, G., Y. Inaki, S. Kitaoka, C. Yokoyama, and T. Tanabe (2002) Application of L-cystein derivative to DNA microarray. Nucleic Acids Res. Suppl. 2: 257-258 https://doi.org/10.1093/nar/2.2.257
  14. Yoo, S. M., K. C. Keum, S. Y. Yoo, J. Y. Choi, K. H. Chang, N. C. Yoo, W. M. Yoo, J. M. Kim, D. Lee, and S. Y. Lee (2004) Development of DNA microarray for pathogen detection. Biotechnol. Bioprocess Eng. 9: 93-99 https://doi.org/10.1007/BF02932990
  15. You, K. M., S. H. Lee, A. Im, and S. B. Lee (2004) Aptamers as functional nucleic acids: In vitro selection and biotechnological applications. Biotechnol. Bioprocess Eng. 8: 64-75 https://doi.org/10.1007/BF02940259
  16. Inaki, Y., K. Matsukawa, H. Kawano, W. Hong, T. Wada, E. Mochizuki, and K. Takemoto (1992) Immobilization of nucleoside on silica gel and specific separation of oligonucleotides. Nucleic Acids Symp. Ser. 27: 29-30
  17. Inaki, Y. and K. Takemoto (1988) Nucleic acid analogs for high performance liquid chromatography. Nucleic Acids Symp. Ser. 19: 45-48
  18. Inaki, Y., K. Matsukawa, H. Kawano, W. Hong, T. Wada, E. Mochizuki, and K. Takemoto (1992) Immobilization of nucleoside on silica gel and specific separation of oligonucleotides. Nucleic Acids Symp. Ser. 27: 29-30
  19. Wada, T., Y. Inaki, and K. Takemoto (1988) Functional monomers and olymers. CLXXII. Synthesis and interaction studies on water-soluble nucleic acid analogs: Poly (ethylenimine) derivatives containing thymine and adenine. Polymer J. 20: 1059-1068 https://doi.org/10.1295/polymj.20.1059
  20. Wada, T., Y. Inaki, and K. Takemoto (1989) Functional monomers and polymers. CLXXI. Synthesis and interaction studies on water soluble nucleic acid analogs: Polyethylenimine derivatives containing cytosine and hypoxanthine. Polymer J. 21: 11-18 https://doi.org/10.1295/polymj.21.11
  21. Wada T., N. Masumi, E. Mochizuki, Y. Inaki, and K. Takemoto (1992) Synthesis and interaction studies of watersoluble nucleic acid analogs containing serine as a spacer. Nucleic Acids Symp. Ser. 27: 115-116
  22. Wada, T., E. Mochizuki, Y. Inaki, and K. Takemoto (1990) Water soluble synthetic nucleic acid analogs-polyethyleneimine derivatives containing nucleic acid bases-conformation and interaction with nucleic acids. Nucleic Acids Symp. Ser. 22: 113-114
  23. Fang, S. B., Y. Inaki, and K. Takemoto (1984) Functional monomers and polymers. CX. Methylation and interaction studies on uracil-containing polymethacrylate derivatives. J. Polymer Sci. Polymer Chem. Ed. 22: 2455-2467 https://doi.org/10.1002/pol.1984.170221014
  24. Brahms, J., A. M. Michelson, and K. E. van Holde (1966) Adenylate oligomers in single- and double-strand conformation. J. Mol. Biol. 15: 467-488 https://doi.org/10.1016/S0022-2836(66)80122-5
  25. Arnott, S. and D. W. Hukins (1973) Refinement of the structure of B-DNA and implications for the analysis of xray diffraction data from fibers of biopolymers. J. Mol. Biol. 81: 93-105 https://doi.org/10.1016/0022-2836(73)90182-4
  26. Neault, J. F., M. Naoui, and H. A. Tajmir-Riahi (1995) DNA-drug interaction. The effects of vitamin C on the solution structure of calf-thymus DNA studied by FTIR and laser Raman difference spectroscopy. J. Biomol. Struct. Dynamics 13: 387-397 https://doi.org/10.1080/07391102.1995.10508847
  27. Ivanov, V. I., L. E. Minchenkova, A. K. Shchelkina, and A. I. Poletaev (1973) Different conformations of doublestranded nucleic acid in solution as revealed by circular dichroism. Biopolymers 12: 89-110 https://doi.org/10.1002/bip.1973.360120109
  28. Maniatis, T., J. H. Jr Venable, and L. S. Lerman (1974) The structure of psi DNA. J. Mol. Biol. 84: 37-64 https://doi.org/10.1016/0022-2836(74)90211-3
  29. Huey, R. and S. C. Mohr (1981) Condensed states of nucleic acids. III. psi(+) and psi(-) conformational transitions of DNA induced by ethanol and salt. Biopolymers 20: 2533-2552 https://doi.org/10.1002/bip.1981.360201205
  30. Shin, Y. A. and G. L. Eichhorn (1984) Formation of y(+) and y(-) DNA. Biopolymers 23: 325-335 https://doi.org/10.1002/bip.360230211
  31. Pohl, F. M. and T. M. Jovin (1972) Salt-induced cooperative conformational change of a synthetic DNA: Equilibrium and kinetic studies with poly (dG-dC). J. Mol. Biol. 67: 375-396 https://doi.org/10.1016/0022-2836(72)90457-3
  32. Marmur, J. and P. Doty (1962) Determination of the base composition of deoxyribonucleic acid from its thermal denaturation temperature. J. Mol. Biol. 5: 109-118 https://doi.org/10.1016/S0022-2836(62)80066-7
  33. Eichhorn, G. L. and Y. A. Shin (1968) Interaction of metal ions with polynucleotides and related compounds. XII. The relative effect of various metal ions on DNA helicity. J. Am. Chem. Soc. 90: 7323-7328 https://doi.org/10.1021/ja01028a024
  34. Khutsishvili, I. G., D. G. Chkhaberidze, E. Z. Mchedlishvili, K. G. Sologashvili, and V. G. Bregadze (2003) Spectrophotometric study of the reaction of cadmium ions with DNA. Sakartvelos Mecnierebata Akademiis Macne Kimiis Seria 29: 293-301
  35. Shin, Y. A., J. J. Butzow, L. D. Sinsel, P. Clark, R. P. Pillai, W. C. Johnson, and G. L. Eichhorn (1988) Metal-induced sequential transitions among DNA conformations. Biopolymers 27: 1415-1432 https://doi.org/10.1002/bip.360270908
  36. Arnott, S., D. W. Hukins, S. D. Dover, W. Fuller, and A. R. Hodgson (1973) Structures of synthetic polynucleotides in the A-RNA and A'-RNA conformations: X-ray diffraction analyses of the molecular conformations of polyadenylic acid-polyuridylic acid and polyinosinic acid-polycytidylic acid. J. Mol. Biol. 81: 107-122 https://doi.org/10.1016/0022-2836(73)90183-6