Book of Abstracts: Albany 2011

category image Albany 2011
Conversation 17
June 14-18 2011
©Adenine Press (2010)

The Influence of Aliphatic Alcohols on Oligonucleotide Hybridization

The biological activity of nucleic acids is correlates strongly with their physico-chemical properties, in particular their thermodynamic properties. The thermal stability of nucleic acids depends strongly on the properties of intracellular environment such as ionic strength, polarity of the medium and presence of various osmolites, compartmentalization and etc (1-3). The influence of monovalent (Na+ and K+) and divalent (Mg2+) cations has been widely studied (4, 5). By contrast the thermodynamics properties of nucleic acids in the presence of various co-solvents have not been studied in details previously, excepting the molecular crowding effect (5). Here we begin the systematic study of the thermodynamics of DNA duplex formation in the presence of a large variety of co-solvents. In this work the efficiency of oligodeoxyribolnucleotides hybridization and DNA duplex secondary structure in the presence of various aliphatic alcohols (ethanol, ethylene glycol, diethylene glycol, 2,2,2-trifluoroethanol, 2-cyanoethanol) in water solution (10 mM sodium cacodylate, pH 7.2) has been characterized. It has been shown that the increase of concentration of aliphatic alcohol in solution from 0 to 50 % (v/v) does not change the conformation of DNA helix. We have demonstrated that for most alcohols (ethanol, cyanoethanol, ethylene glycol and diethylene glycol) rising of their concentration up to 50 % in a aqueous solution lead to monotonous decrease in melting temperature for DNA duplexes of various length (12, 15 or 20 b.p.) and GC-content (27 – 60 %). In the case of trifluoroethanol the stability of double stranded DNA decreases with the increase of the alcohol concentration up to 20 %. The higher concentrations of trifluoroethanol (up to 75 %) resulted in slight stabilization of DNA duplexes. The analysis of the data obtained has shown the possibility of using a simple model for the description of thermal stability of duplexes in mixed water/alcohol solutions except 2,2,2-trifluoroethanol. The model assume that the number of solvents molecules (water and со-solvent) which are bound to DNA changes at helix-to-coil transition. The proposed model describes the dependence of melting temperatures of oligonucleotide complexes on concentration of ethanol, cyanoethanol, ethylene glycol and diethylene glycol with accuracy 1.1, 1.7, 1.0, 2.2 °С, respectively.

The results obtained can be applied in hybridization analysis in various buffer conditions, for example, with the use of exciplexes (7); in studying nucleic acid – protein interactions and in the development of molecular-imprinted polymers (8).

This research has been supported by Russian Government (P1073), SB RAS, RFBR and by MCB and FBNN programs of RAS.


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  2. I. A. Il’icheva, P. K. Vlasov, N. G. Esipova, V. G. Tumanyan, J Biomol Struct Dyn 27,677-693 (2010).
  3. T. C. Mou, M. C. Shen, T.C. Terwilliger, D.M. Gray, Biopolymers 70, 637-648 (2003).
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  5. R. Owczarzy, B. G.Moreira, Y. You, M. A. Behlke, J. A. Walder, Biochemistry 47, 5336-5353 (2008).
  6. D. Miyoshi, N. Sugimoto, Biochimie 90, 1040-1051 (2008).
  7. E. V. Bichenkova, A. Gbaj, L. Walsh, H. E. Savage, C. Rogert, A. R. Sardarian, L. L. Etchells, K. T. Douglas, Org. Biomol. Chem. 5, 1039-1051 (2007).
  8. E. V. Dmitrienko, I. A. Pyshnaya, A. V. Rogoza, D. V. Pyshnyi, Patent of Russian Federation # 2385889, (2010).

Alexander A. Lomzov1,2*
Irina V. Khalo1,2
Dmitrii V. Pyshnyi1

1Institute of Chemical Biology and Fundamental Medicine SB RAS
Lavrent'v ave., 8, 630090,
Novosibirsk, Russia
2Novosibirsk State University
Pirogova st., 2, 630090
Novosibirsk, Russia

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