Electrophoretic study of conformational transitions in poly(G) as a function of monovalent cations
DOI:
https://doi.org/10.7124/bc.00075EKeywords:
poly(G), conformational transitions of homopolyribonucleotides, electrophoresis, toluidine blue, electronic absorption spectrumsAbstract
Conformational transitions in poly(G) as a function of salt concentration has been studied first by the method of electrophoresis. It was shown that only one band of polymer is observed at concentration of monovalent cations > 10 mM. This band corresponds to the four-stranded form of poly(G). At lower salt concentration two overlapping bands are observed. The band with lower electrophoretic mobility corresponds to four-stranded form of polymer and the band with higher mobility corresponds to single-stranded form. Electronic absorption spectrums of several homopolyribonucleotides after their staining with toluidine blue in agarose gels have been presented. It was discovered that the shape of spectrum depends both on polymer and its form. The Δλmax of absorption spectrums of four-stranded and single-stranded forms of poly(G) is about 20 nM.References
Zarudna MI, Hovorun DM. Self-associated homopolymer tracts of cellular RNAs: physical mechanisms of formation and function. Physics of the Alive. 1999; 7(2): 38-52.
Saenger W. Principles of nucleic acid structure. New York: Springer, 1984; 556 p.
Zarudnaya MI, Potyahaylo AL, Kolomiets IM, Hovorun DM. Auxiliary elements of mammalian pre-mRNAs polyadenylation signals. Biopolym Cell. 2002; 18(6):500-17.
Matunis MJ, Xing J, Dreyfuss G. The hnRNP F protein: unique primary structure, nucleic acid-binding properties, and subcellular localization. Nucleic Acids Res. 1994;22(6):1059-67.
Gwack Y, Kim DW, Han JH, Choe J. Characterization of RNA binding activity and RNA helicase activity of the hepatitis C virus NS3 protein. Biochem Biophys Res Commun. 1996;225(2):654-9.
Achsel T, Stark H, Lührmann R. The Sm domain is an ancient RNA-binding motif with oligo(U) specificity. Proc Natl Acad Sci U S A. 2001;98(7):3685-9.
Zarudnaya MI, Zheltovsky NV. Determination of association constants for the interaction between homopolyribonucleotides and lysine derivative by agarose gel electrophoresis. Mol Biol (Mosk). 1989; 23(1):215–224.
Zarudnaya MI, Zheltovsky NV. Affinity electrophoresis study on the interaction between homopolyribonucleotides and divalent lysine complex. Mol Biol (Mosk). 1992; 26(1):110-7.
Zarudnaia MI, ZHeltovskiĭ NV. [Electrophoretic study of conformational transitions in poly(A) at acid pHs]. Mol Biol (Mosk). 1995;29(5):1040-7.
Zarudnaia MI. [Study of conformational transitions in poly(A) using the buffer capacity method]. Mol Biol (Mosk). 1998;32(3):508-14.
Zarudnaya MI, Potyahaylo AL, Hovorun DM. Conformational transitions of poly(C) and poly(dC): study by the proton buffer capacity method. Biopolym Cell. 2000; 16(6):495-504.
Zarudnaya MI, Samijlenko SP, Potyahaylo AL, Hovorun DM. Structural transitions in polycytidylic acid: proton buffer capacity data. Nucleosides Nucleotides Nucleic Acids. 2002;21(2):125-37.
Fresco JR, Massoulie J. Polynucleotides. V. Helix-coil transition of polyriboguanylic acid. J Am Chem Soc. 1963;85(9):1352–3.
Pochon F, Michelson AM. Polynucleotides. VI. Interaction between polyguanylic acid and polycytidylic acid. Proc Natl Acad Sci U S A. 1965;53(6):1425-30.
Lesnik EA, Kochkina IM, Tikhonenko AS, Varshavskiĭ IaM. [Structure of polyriboguanylic acid in solution]. Mol Biol (Mosk). 1980;14(4):820-9.
Lesnik EA, Maslova RN, Varshavskiĭ IaM. [Influence of ionic strength and temperature on the structure of poly(G) in solution 1H replaced by 3H exchange method]. Mol Biol (Mosk). 1981;15(1):161-6.
Souleil C, Panijel J. Immunochemistry of polyribonucleotides. Study of polyriboinosinic and polyriboguanylic acids. Biochemistry. 1968;7(1):7-13.
Rice J, Lafleur L, Medeiros GC, Thomas GJ. Raman studies of nucleic acids. IX: A salt-induced structural transition in poly(rG). J Raman Spectrosc. 1973;1(2):207–15.
Mergny JL, De Cian A, Ghelab A, Saccà B, Lacroix L. Kinetics of tetramolecular quadruplexes. Nucleic Acids Res. 2005;33(1):81-94.
Zarudnaya MI, Stepanyugin AV, Potyahaylo AL, Hovorun DM. Conformational transitions in homopolyribonucleotides under electrophoresis. IV Congress of Ukrainian Biophysical Society: Abstracts book. Donets'k, 2006:295-6.
Antony T, Atreyi M, Rao MV. Spectroscopic studies on the binding of methylene blue to poly(riboadenylic acid). J Biomol Struct Dyn. 1993;11(1):67-81.
Imae T, Hayashi S, Ikeda S, Sakaki T. Interaction between acridine orange and polyriboadenylic acid. Int J Biol Macromol. 1981;3(4):259–66.
Imae T, Hayashi S, Ikeda S. Calculation of induced circular dichroism of acridine orange-poly(riboadenylic acid) complexes and confirmation of their structure. Macromolecules. 1987;20(3):589–97.