S. V. Kornilova

Study of Ca2+, Mn2+ and Cu2+ binding to DNA in solution by means of IR spectroscopy

The interaction of Cu2+, Mn2+ and Ca2+ ions with the DNA macromolecule was studied in aqueous solutions at different metal ion concentrations. All these ions interact with both the bases and the phosphate groups of DNA. Cu2+ ions alter the DNA B-conformation at [Cu2+] > 2 × 10−2M. Metal ions binding to DNA induce DNA compactisation. The highly positive cooperativity of this process was shown. The binding constants and parameters of cooperativity of the metal ions binding to DNA were estimated.

IR-SPECTROSCOPIC STUDIES OF DIVALENT METAL ION EFFECTS ON DNA HYDRATION

Abstract The metal (Mn 2+ , Ca 2+ , Cu 2+ ) ion effect on the DNA structure in films is studied at different relative humidities (5–98%) by IR-spectroscopy. The results obtained suggest the interaction of the ions both with the DNA phosphate groups and with the nucleic bases. The formation of the secondary structure of DNA complexed with metal ions is shown to take place at a greater number of water molecules bound to the polymer than it is the case of DNA without ions. The interaction of DNA with metal ions inhibits its transition into the A form and induces essential changes in the hydration energy.

Complexes of (dG-dC)20 with Mn2+ ions: a study by vibrational circular dichroism and infrared absorption spectroscopy.

The B-Z transition of the synthetic oligonucleotide, (dG-dC)20, induced by Mn2+ ions at room temperature, was investigated by absorption and Vibrational Circular Dichroism (VCD) spectroscopy in the range of 1800-800 cm(-1). Metal ion concentration was varied from 0 to 0.73 M Mn2+ (0 to 8.5 moles of Mn2+ per mole of oligonucleotide phosphate, [Mn]/[P]). While both types of spectra showed considerable changes as the Mn2+ concentrations were raised, differences between the two were often complementary in their expression and extent, those displayed by VCD being more clearly evident due to the inversion of the opposite helical sense from the right-handed to the left-handed conformation. The main phase of the transition occurred in the metal ion concentration between 0.8-1.1 [Mn]/[P]. Gradual changes that took place in the spectra were interpreted in terms of simultaneous processes that depended on metal ion concentration, namely B-Z transformation, binding of Mn2+ to phosphates and to nitrogen bases, and partial denaturation. Below approximately 0.6 [Mn]/[P], only a small portion of the oligonucleotide adopted the Z conformation within a 3 hour period, whereas conversion was completed in the same time interval for concentrations between 0.9-1.2 [Mn]/[P]. At [Mn]/[P] >1.7, complete transition to the Z-form took place immediately on adding Mn2+. Applying VCD spectroscopy in combination with conventional infrared absorption proved most useful for corroborating changes in the absorption spectra, and for detecting in an unique manner, not attainable by absorption methods, conformational changes that lead to the inversion of the helical sense of the oligonucleotide.

DNA interaction with biologically active metal ions. Cooperativity of metal ion binding at compacting of DNA

In this review we summarize stress factors that affect the lactic acid bacteria (LAB) and cause different molecular stress responses. LAB belong to a group of bacteria that is very widespread in food and beverages. They are present, and desired, in fermented products like yogurts, cheese, vegetables, meat or wine. In most of them, LAB are providing positive sensory and nutritive features. However, as harmless and desired microbes in one product, LAB can cause spoilage and a bad taste of others, especially in juices and beverages. LAB are resistant to many stress factors which allows them to survive in harsh environments. The most common stress factors they have to deal with are: heat, cold, acidity, NaCl and high hydrostatic pressure (HHP). Their ability to survive depends on their skills to cope with stress factors. Under stress conditions, LAB activate mechanisms that allow them to adjust to the new conditions, which can influence their viability and technological properties. This ability to adapt to different stress conditions may come from the cross-protection systems they have, as resistance to one factor may help them to deal with the other stress effectors. LAB are highly valuable for the food industry and that is why it is important to understand their stress response mechanisms.

Vibrational spectroscopic studies of the divalent metal ion effect on DNA structural transitions

Raman spectroscopy is used to study DNA complexes with Cu2+, Mn2+ and Ca2+ ions in 0.001 M NaCl, pH 7.0. The changes observed in the spectra permit us to conclude that all the ions interact both with the DNA phosphate groups and with the nucleic bases, changing the DNA structure. Ca2+ and Mn2+ ions bind to N7 of guanine and adenine only, but Cu2+ ions can probably bind to N7, O6 of guanine and N3 of cytosine as well. The latter type of binding occurs as the base is turning around the glycoside bonds and a G-C pair transition from anti to syn conformation takes place. Besides, at high concentrations of Ca2+ ions a partial B-A transition takes place in DNA.

Studies of formation of bivalent copper complexes with native and denatured DNA

The formation of Cu2+ complexes with native and denatured DNA is studied by the methods of differential UV spectroscopy, CD spectroscopy, and viscometry. On ion binding to the bases of native DNA the latter transforms into a new conformation. This transition is accompanied with a sharp increase in UV absorption and a decrease in the intrinsic viscosity though the high degree of helicity persists. Possible sites of Cu2+ ion binding on DNA of various conformations are found along with corresponding constants of complex formation.

Spectroscopic studies of divalent metal ions effect on DNA and polynucleotides structural transitions

The active biological role of divalent metal in the function of the genetic apparatus in cancerogenesis and mutagenesis has been attracting permanent interest in the interaction of these ions with nucleic acids. The present work studies using the IR-, Raman spectroscopy, CD and differential UV-spectroscopy methods Mn2+, Ca2+, Mg2+ and Cu 2+ ion interactions with DNA in solutions and films at various relative humidities. The method used gives information on metal ion binding sites, the metal ion effects on the macromolecule transition into the double helical conformation and on properties of the hydrate water of the complex.

Urea effect on DNA structural transitions under Cu2+ ions action in solution

Recently we have shown that DNA transition into compact state under Cu2+ ions in mixed solution containing alcohols, depends not only on the solution dielectric permeability but on the solution structure [1]. Alcohols studied (ethanol, 1, 2-PD) at their small volume concentrations in solution stabilize the water structure therefore it seems interesting to study DNA structural transitions due to the Cu2+ ion action in aqueous solution of urea destructing the water structure [2].

Spectroscopic studies of ionising radiation and metal ion effects on DNA structure and dynamics

After the accident at Chernobyl APS it is actual to study changes in DNA of animals exposed to prolonged radiation in this zone. Using IR-, UV-spectroscopic, viscometry, thermal denaturation and nucleic-physics methods, we investigated properties of DNA extracted from liver and spleen of such animals — rats of the fourth-seventh generations and different age groups.

IR-Spectroscopic and Theoretical Studies of the Divalent Metal Ion Binding To DNA

Metal ion binding to DNA plays the essential role in the appearance of disturbances of genetic apparatus functioning such as carcinogenesis, mutagenesis. The IR spectroscopy method gives information on metal ion binding sites, the metal ion effects on the macromolecule transition into the double helical conformation and on properties of hydrate water of the complex and can be used to solve the above problems. IR spectra of DNA complexes with divalent metal ions (Mn2+, Cu2+, Ca2+) at different relative humidities (5–98%) were recorded with an IR-spectrophotometer UR-20. The methods of the DNA films preparation and IR spectra recording as well as DNA samples characteristics were described in detail in [ 1 ].