Department of Molecular and Quantum Biophysics

The fundamental research program is focused on:

search for universal physical and chemical foundations of the specificity of interaction between components of nucleoproteid complexes and the determination of the role, that prototropic tautomerism of nuclear acids and proton transmission play in elementary processes of protein - nucleic and nucleic-nucleic recognition.

Our current research and recent achievements:

• Using the methods of molecular spectroscopy (IR, UV, Raman Spectroscopy, NMR) and quantum-chemical calculations of different range of accuracy, the changes in the tautomeric state of nucleotide bases under the effect of oxygenic bonding or interaction with ligands of peptide nature and cations of alkali metals are being investigated. Similar changes in the tautomeric state of nucleotide bases, expected under the influence of heterogeneous environment in cells are postulated/stated to be a mechanism responsible for structural-dynamic transformations in protein-nucleic complexes.
• Theoretical and experimental investigations of the tautomeric state of nucleotide bases in model complexes of protein-nucleic recognition provide grounds to prove/support the concept that high-energy tautomers play a significant role in biochemical processes
• The properties/regularities of spatial organisation such as secondary and tertiary structures of cellular and viral RNA and their signal sequences are being studied using modern methods of electrophoresis, protonic buffer capacity, molecular modelling and bioinformatics.
• Applied branch of research is related to experimental and theoretical studies on structural-dynamic and physical-chemical properties of some pharmaceutically important compounds.
• Recently, a novel original technique, covered by the patent of Ukraine, has been elaborated in the Department and offered for experimental use. According to this technique, a multi-induced full reflection of light can be used to obtain a high-quality IR spectrum of fine films of nucleic acids and nucleoproteid complexes.

Selected publications:

1. S.A.Trygubenko, T.V.Bogdan, S.P.Samijlenko, D.M.Hovorun, M.Kabelac, P.Hobza Acetic acis anion preferentially binds to he higher-energy adenine prototropic tautomer over the canonical one: a molecular dynamics and ab initio quantum chemical studies // Physics of the Alive. – 2002. – V. 10, № 2. – P.39-46
2. M.I.Zarudnaya, I.M.Kolomiets, A.L.Potyahaylo, D.M.Hovorun Downstream elements of mammalian pre-mRNA polyadenylation signals: primary, secondary and higher-order structures // Nucleic Acids Research. – 2003. – V.31, N 5. – P.1375-86.
3. A.V.Stepanyugin, S.P.Samijlenko, O.I.Martynenko, D.M.Hovorun. ATR-IR Spectroscopy as applied to nucleic acid films // Spectrochimica Acta Part A: Molecular and Biomolecular Spectroscopy. - 2004. - V.00, N. 00. - P.00-00.