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 OJPC  Vol.5 No.3 , August 2015
Structural Study of Methylated and Non-Methylated Duplexes by IR Fourier Spectroscopy
V. G. Kunitsyn, P. A. Kuznetsov, E. N. Demchenko, O. I. Gimautdinova
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Abstract: Structure of the duplex consisting of 23 pairs of bases was studied before and after the methylation of two cytosine molecules from different chains of the duplex. The study was performed in a buffer solution using an IR Fourier spectrometer. The absorption bands corresponding to the duplex backbone were found to change their characteristics after the methylation. Firstly, the integrated intensity ratio of the absorption bands, S1044/S1085, decreased by a factor of 1.5. The absorption band at 1044 cm-1 corresponds to the COC bond of deoxyribose, and the band at 1085 cm-1 to the PO2symm.vibr bond. Secondly, a substantial shift of the absorption band 1085→1112 cm-1 (Δν = 27 cm-1) was observed. In addition, pronounced changes in the absorption region of CH stretching vibrations took place. In particular, shifting of some absorption bands assigned to the stretching vibrations of CH bonds; the 2979→2945.7 shift was equal to 33.3 cm-1. In addition to the indicated changes, some bands corresponding to the Z structure appeared in the methylated duplex. Thus, methylation of two cytosine molecules in the duplex leads to the order→order structural transition, most likely to the B→Z transition.
Keywords: Duplex, Duplm, Structural Study, FTIR Spectroscopy
Cite this paper: Kunitsyn, V. , Kuznetsov, P. , Demchenko, E. and Gimautdinova, O. (2015) Structural Study of Methylated and Non-Methylated Duplexes by IR Fourier Spectroscopy. Open Journal of Physical Chemistry, 5, 87-92. doi: 10.4236/ojpc.2015.53009.
References

[1]   Dyachenko, O.V., Shevchyk, T.V. and Buryanov, Y.I. (2010) Structural and Functional Features of the 5-Methylcytosine Distribution in the Eukaryotic Genome. Molecular Biology, 44, 171-185.
http://dx.doi.org/10.1134/S0026893310020019

[2]   Klenov, M.S. and Gvozdev, V.A. (2005) Heterochromatin Formation: Role of Short RNAs and DNA Methylation. Biochemistry (Moscow), 70, 1187-1198.
http://dx.doi.org/10.1007/s10541-005-0247-4

[3]   Vanyushin, B.F. (2007) A View of an Elemental Naturalist at the DNA World (Base Composition, Sequences, Methylation). Biochemistry (Moscow), 72, 1289-1298.
http://dx.doi.org/10.1134/S0006297907120036

[4]   Banyay, M. and Graslund, A. (2002) Structural Effects of Cytosine Methylation on DNA Sugar Pucker Studied by FTIR. Journal of Molecular Biology, 324, 667-676.
http://dx.doi.org/10.1016/S0022-2836(02)01104-X

[5]   Temiz, N.A., Donohue, D.E., Bacolla, A., Luke, B.T. and Collins, J.R. (2012) Role of Methylation in the Intrinsic Dynamics of B and Z-DNA. PLoS One, 7, e35558.
http://dx.doi.org/10.1371/journal.pone.0035558

[6]   Rauch, C., Pichler, A., Trieb, M., Wellensohn, B., Liedt, K.R. and Mayer, E. (2005) Z-DNA’s Conformer Substrates Revealed by FT-IR Difference Spectroscopy of Nonoriented Left-Handed Double Helical Poly (dG-dC). Journal of Biomolecular Structure and Dynamics, 22, 595-614.
http://dx.doi.org/10.1080/07391102.2005.10507029

[7]   Panin, L.E., Kunitsyn, V.G. and Tusikov, F.V. (2005) Effect of Glucocorticoids and Their Complexes with Apolipoprotein A-I on the Secondary Structure of Eukaryotic DNA. International Journal of Quantum Chemistry, 101, 450- 467.
http://dx.doi.org/10.1002/qua.20200

[8]   Panin, L.E., Kunitsyn, V.G. and Tuzikov, F.V. (2006) Changes in the Secondary Structure of Highly Polymeric DNA and CC(GCC)n-Type Oligonucleotides under the Action of Steroid Hormones and Their Complexes with Apolipoprotein A-I. Journal of Physical Chemistry B, 110, 13560-13571.
http://dx.doi.org/10.1021/jp068011n

[9]   Panin, L.E. and Kunitsyn, V.G. (2009) The Initiation Mechanism of Gene Expression in Ascitic Hepatoma Cells under the Action of Dehydroepiandrosterone in a Complex with Apolipoprotein A-I. Current Chemical Biology, 3, 306-314.

[10]   Chmuzh, E.V., Kashirina, Yu.G., Tomilova, Yu.E., Chernukhin, V.A., Okhapkina, S.S., Gonchar, D.A., Dedkov, V.S., Abdurashitov, M.A. and Degtyarev, S.H. (2007) Gene Cloning, Comparative Analysis of the Protein Structures from Fsp4HI Restriction-Modification System and Biochemical Characterization of the Recombinant DNA Methyltransferase М. Fsp4HI. Molecular Biology, 41, 43-50.
http://dx.doi.org/10.1134/S0026893307010062

[11]   Ingold, K. (1973) Theoretical Bases of Organic Chemistry. Nauka, Moscow.

[12]   Smith, A. (1980) Applied Spectroscopy. Mir, Moscow.

[13]   Ovchinnikov, Yu.A. (1987) Bioorganic Chemistry. Nauka, Moscow.

[14]   Rubin, B.A. (1990) Biophysics. Vyschaya Shkola.

 
 
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