Self assembly of poly(o-methoxy aniline) with RNA and RNA/DNA hybrids: Physical properties and conformational change of poly(o-methoxy aniline)

Biophysical Chemistry

Volumn 143, Issue 3, 2009, Pages 145-153

  Routh, Parimal ^a   Mukherjee, Pratap ^a   Dawn, Arnab ^a   Nandi, Arun K ^a  

^a DEPARTMENT OF MATERIALS SCIENCE   (India)

Author keywords

Conductivity; Conformational change; DNA; Poly(o methoxy aniline); RNA; Self assembly

Indexed keywords

DNA; HYDROGEN; PHOSPHATE; POLY(O METHOXYANILINE); POLYANILINE; RNA; UNCLASSIFIED DRUG;

AQUEOUS SOLUTION; ARTICLE; BIOSENSOR; CHEMICAL COMPOSITION; CHEMICAL STRUCTURE; CIRCULAR DICHROISM; COMPLEX FORMATION; CONDUCTANCE; CONFORMATIONAL TRANSITION; CONTROLLED STUDY; DNA RNA HYBRIDIZATION; ELECTRICITY; HYDROGEN BOND; INFRARED SPECTROSCOPY; MOLECULAR INTERACTION; MOLECULAR WEIGHT; PH MEASUREMENT; PHYSICAL CHEMISTRY; PRIORITY JOURNAL; SUPRAMOLECULAR CHEMISTRY; TEMPERATURE DEPENDENCE; TRANSMISSION ELECTRON MICROSCOPY; ULTRAVIOLET SPECTROSCOPY;

ANILINE COMPOUNDS; CIRCULAR DICHROISM; DNA; HYDROGEN BONDING; HYDROGEN-ION CONCENTRATION; MICROSCOPY, ELECTRON, TRANSMISSION; NUCLEIC ACID CONFORMATION; POLYAMINES; RNA; SPECTROPHOTOMETRY, ULTRAVIOLET; SPECTROSCOPY, FOURIER TRANSFORM INFRARED;

PICHIA JADINII;

EID: 67349258966     PISSN: 03014622     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.bpc.2009.05.004     Document Type: Article

References (51)

1. Wallace G.G., and Kane-Maguire L.A.P. Manipulating and monitoring biomolecular interactions with conducting electroactive polymers. Adv. Mater. 14 (2002) 953-960
2. Nilsson K.P.R., Herland A., Hammarstrom P., and Inganas O. Conjugated polyelectrolytes: conformation-sensitive optical probes for detection of amyloid fibril formation. Biochemistry 44 (2005) 3718-3724
3. Nilsson K.P.R., and Inganas O. Chip and solution detection of DNA hybridization using a luminescent zwitterionic polythiophene derivative. Nature Materials 2 (2003) 419-424
4. Gaylord B.S., Heeger A.J., and Bazan G.C. DNA hybridization detection with water-soluble conjugated polymers and chromophore-labeled single-stranded DNA. J. Am. Chem. Soc. 125 (2003) 896-900
5. Thompson L.A., Kowalik J., Josowicz M., and Janata J. Label-free DNA hybridization probe based on a conducting polymer. J. Am. Chem. Soc. 125 (2003) 324-325
6. Wang J., and Jiang M. Toward genolelectronics: nucleic acid doped conducting polymers. Langmuir 16 (2000) 2269-2274
7. Ho H.-A., Najari A., and Leclerc M. Optical detection of DNA and proteins with cationic polythiophenes. Acc. Chem. Res. 41 (2008) 168-178
8. Gibbs J.M., Park S.-J., Anderson D.R., Watson K.J., Mirkin C.A., and Nguyen S.T. Polymer-DNA hybrids as electrochemical probes for the detection of DNA. J. Am. Chem. Soc. 127 (2005) 1170-1178
9. Lassalle N., Mailley P., Vieil E., Livache T., Roget A., Correia J.P., and Abrantes L.M. Electronically conductive polymer grafted with oligonucleotides as electrosensors of DNA: preliminary study of real time monitoring by in situ techniques. J. Electroanal. Chem. 509 (2001) 48-57
10. Liu B., and Bazan G.C. Interpolyelectrolyte complexes of conjugated copolymers and DNA: platforms for multicolor biosensors. J. Am. Chem. Soc. 126 (2004) 1942-1943
11. Finnegan E.J., and Matzke M.A. The small RNA world. J. Cell Sci. 116 (2003) 4689-4693
12. Hentze M.W., Izaurralde E., and Séraphin B. A new era for the RNA world conference: RNA 2000. EMBO reports 5 (2000) 394-398
13. Recksiedler C.L., Deore B.A., and Freund M.S.A. Novel layer-by-layer approach for the fabrication of conducting polymer/RNA multilayer films for controlled release. Langmuir 22 (2006) 2811-2815
14. Fan Y., Chen X., Trigg A.D., Tung C.-h., Kong J., and Gao Z. Detection of microRNAs using target-guided formation of conducting polymer nanowires in nanogaps. J. Am. Chem. Soc. 129 (2007) 5437-5443
15. Medalia O., Heim M., Guckenberger R., Sperling R., and Sperling J. Gold-tagged RNA - a probe for macromolecular assemblies. J. Struct. Biol. 127 (1999) 113-119
16. Liu D., Gugliotti L.A., Wu T., Dolska M., Tkachenko A.G., Shipton M.K., Eaton B.E., and Feldheim D.L. RNA-mediated synthesis of palladium nanoparticles on Au surfaces. Langmuir 22 (2006) 5862-5866
17. Dawn A., and Nandi A.K. Biomolecular hybrid of a conducting polymer with DNA: morphology, structure, and doping behavior. Macromol. Biosci. 5 (2005) 441-450
18. Dawn A., and Nandi A.K. Slow doping rate in DNA-poly(o-methoxyaniline) hybrid: uncoiling of poly(o-methoxyaniline) chain on DNA template. Macromolecules 38 (2005) 10067-10073
19. Dawn A., and Nandi A.K. Simple method for the preparation of DNA-poly(o-methoxyaniline) hybrid: structure, morphology, and uncoiling of poly(o-methoxyaniline) on the DNA surface. Langmuir 22 (2006) 3273-3279
20. Dawn A., and Nandi A.K. Nanostructured self-assembly of double-stranded DNA/poly(o-methoxyaniline) hybrid. J. Phys. Chem. C 111 (2007) 6268-6274
21. Erie D.A. The many conformational states of RNA polymerase elongation complexes and their roles in the regulation of transcription. Biochim. Biophys. Acta 1577 (2002) 224-239
22. Shilatifard A., Conaway R.C., and Conaway J.W. The RNA polymerase II elongation complex. Ann. Rev. Biochem. 72 (2003) 693-715
23. Mattoso L.H.C., Faria R.M., Bulhões L.O.S., and MacDiarmid A.G. Synthesis, doping, and processing of high molecular weight poly(o-methoxyaniline). J. Polym. Sci.: Part A: Polym. Chem. 32 (1994) 2147-2153
24. Andreatta A., Cao Y., Chiang J.C., Heeger A.J., and Smith P. Electrically-conductive fibers of polyaniline spun from solutions in concentrated sulfuric acid. Synthetic Metals 26 (1988) 383-389
25. Baird D.G., and Smith J.K. Dilute solution properties of poly(1,4-phenylene terephthalamide) in sulfuric acid. J. Polym. Sci. Polym. Chem. 16 (1978) 61-70
26. Dawn A., and Nandi A.K. Formation of silver nanoparticles in deoxyribonucleic acid-poly(o-methoxyaniline) hybrid: a novel nano-biocomposite. J. Phys. Chem. B 110 (2006) 18291-18298
27. Metzger A.U., Schindler T., Willbold D., Kraft M., Steegborn C., Volkmann A., Frank R.W., and Rosch P. Structural rearrangements on HIV-1 Tat (32-72) TAR complex formation. FEBS Lett. 384 (1996) 255-259
28. Arakawa H., Neault J.F., and Tajmir-Riahi H.A. Silver(I) complexes with DNA and RNA studied by Fourier transform infrared spectroscopy and capillary electrophoresis. Biophys. J. 81 (2001) 1580-1587
29. Ruoying T., and Alan F.D. Circular dichroism studies suggest that TAR RNA changes conformation upon specific binding of arginine or guanidine. Biochemistry 31 (1992) 10288-10294
30. Spiro T.G. Biological Application of Raman Spectroscopy (1987), John Wiley and Sons
31. Loprete D.M., and Hartman K.A. Conditions for the stability of the B, C, and Z structural forms of poly(dG-dC) in the presence of lithium, potassium, magnesium, calcium, and zinc cations. Biochemistry 32 (1993) 4077-4082
32. Starikov E.B., Semenov M.A., Maleev V.Ya., and Gasan A.I. Evidential study of correlated events in biochemistry: physicochemical mechanisms of nucleic acid hydration as revealed by factor analysis. Biopolymers 31 (1991) 255-273
33. Prevette L.E., Kodger T.E., Reineke T.M., and Lynch M.L. Deciphering the role of hydrogen bonding in enhancing pDNA-polycation interactions. Langmuir 23 (2007) 9773-9784
34. Arakawa H., Ahmad R., Naoui M., and Tajmir-Riahi H.-A. A comparative study of calf thymus DNA binding to Cr(III) and Cr(VI) ions. Evidence for the guanine N-7-chromium-phosphate chelate formation. J. Biol. Chem. 275 (2000) 10150-10153
35. Taillandier E., Liquier J., and Taboury J.A. Advances in Infrared and Raman Spectroscopy (1985)
36. Brahms S., Brahms J., and Pilet J. Infrared studies on the backbone conformation of nucleic acids. Isr. J. Chem. 12 (1974) 153-163
37. Tajmir-Riahi H.A., Neault J.F., and Naoui M. Does DNA acid fixation produce left-handed Z structure?. FEBS Lett. 370 (1995) 105-108
38. Tajmir-Riahi H.A., Langlais M., and Savoir R. A laser Raman spectroscopic study of the interaction of calf-thymus DNA with Cu(II) and Pb(II) ions: metal ion binding and DNA conformational changes. Nucleic Acids Res. 16 (1988) 751-762
39. Huang W.S., and MacDiarmid A.G. Optical properties of polyaniline. Polymer 34 (1993) 1833-1845
40. Xia Y., Wiesinger J.M., MacDiarmid A.G., and Epstein A.J. Camphorsulfonic acid fully doped polyaniline emeraldine salt: conformations in different solvents studied by an ultraviolet/visible/near-infrared spectroscopic method. Chem. Mater. 7 (1995) 443-445
41. Stejskal J., Kratochvíl P., and Radhakrishnan N. Polyaniline dispersions 2. UV-Vis absorption spectra. Synthetic Metals 61 (1993) 225-231
42. Ruokolainen J., Eerikainen H., Torkkeli M., Serimaa R., Jussila M., and Ikkala O. Comb-shaped supramolecules of emeraldine base form of polyaniline due to coordination with zinc dodecyl benzenesulfonate and their plasticized self-organized structures. Macromolecules 33 (2000) 9272-9276
43. Garai A., Kuila B.K., and Nandi A.K. Montmorillonite clay nanocomposites of sulfonic acid doped thermoreversible polyaniline gel: physical and mechanical properties. Macromolecules 39 (2006) 5410-5418
44. Shibaev P.V., Schaumburg K., Bjornholm T., and Norgaard K. Conformation of polythiophene derivatives in solution. Synthetic Metals 97 (1998) 97-104
45. Malik S., Jana T., and Nandi A.K. Thermoreversible gelation of regioregular poly(3-hexylthiophene) in xylene. Macromolecules 34 (2001) 275-282
46. Farmer B.L., Hopfinger A.J., and Lando J.B. Polymorphism of poly(vinylidene fluoride): potential energy calculations of the effects of head-to-head units on the chain conformation and packing of poly(vinylidene fluoride). J. Appl. Phys. 43 (1972) 4293-4303
47. Mal S., and Nandi A.K. Gelation mechanism of thermoreversible poly(vinylidene fluoride) gels in glyceryl tributyrate. Polymer 39 (1998) 6301-6307
48. Dikshit A.K., and Nandi A.K. Thermoreversible gelation of poly(vinylidene flouride) in diethyl adipate: a concerted mechanism. Macromolecules 31 (1998) 8886-8892
49. Eley D.D., and Spivey D.I. Semiconductivity of organic substances, part 9 - nucleic acid in the dry state. Trans. Faraday Soc. 58 (1962) 411-415
50. Porath D., Bezryadin A., Vries S.D., and Dekker C. Direct measurement of electrical transport through DNA molecules. Nature 403 (2000) 635-638
51. Berlin Y.A., Burin A.L., and Ratner M.A. Charge hopping in DNA. J. Am. Chem. Soc. 123 (2001) 260-268