Theoretical and Experimental Study of DNA Helix-Coil Transition in Acidic and Alkaline Medium

Abstract

The theoretical approach to the calculation of the influence of selective binding of small ligands on DNA helix-coil transition has been described in the previous paper (Lando D. Yu., J. Biomol. Struct. Dyn., (1994)). In the present paper that method is used for the study of DNA protonation and deprotonation in acidic and alkaline medium by theoretical analysis of pH effect on DNA heat denaturation. The mechanism of DNA protonation in acidic medium and pK values of nucleotides are well known. It gave us an opportunity to check the theory without any fitting of pK values. A good agreement between experimental and calculated functions Tm(pH) and delta T(pH) (melting temperature and melting range width) obtained for acidic medium proved the validity of the theory. However, for alkaline medium there was not even qualitative agreement when the agreed-upon mechanism of deprotonation was considered. Looking into the cause of the discrepancy, we have studied the DNA melting for different mechanisms of deprotonation by calculation of Tm(pH) and delta T(pH). As a result, it has been established that the discrepancy is due to deprotonation of bonded GC base pairs of helical DNA regions (pK = 11). It was shown that the early known protonation and newly found deprotonation of helical DNA essentially stabilised double helix in alkaline and acidic medium.

Force-dependent melting of supercoiled DNA at thermophilic temperatures

“…F char at low temperatures) is known to change as a function of salt concentration and pH [8]. Furthermore, we predict that the midpoint temperature will be lower under conditions favoring unwinding, such as low salt concentration or ATrich sequence, consistent with a reduction in melting temperature under these conditions [5,6].…”

“…This balance is dependent on environmental variables such as salt concentration, pH, torque, force, superhelical density (σ = ΔLk/Lk 0 ; i.e. the percent of extra or missing turns compared to B-form DNA), and temperature [5][6][7][8]. Interestingly, there are differences in superhelical density that correlate with differences in environmental temperature between Mesophiles (20°C b T b 45°C; σ b 0), Thermophiles (45°C b T b 80°C; σ ≈ 0), and Hyperthermophiles (80°C b T b 122°C; σ N 0) [9][10][11].…”

Temporal behavior of DNA thermal stability in the presence of platinum compounds. Role of monofunctional and bifunctional adducts

“…DNA deprotonation causes a destabilizing effect at pH >10, i.e., when pH is higher than pK's of nitrogen bases (see [53,72] for detail). In alkaline medium, thermal destabilization takes place for both unmodified and platinated DNA because the majority protons able to dissociate from DNA in alkaline medium are included in the formation hydrogen bonds that generate the double helix [53,72]. Binding of platinum compounds decreases DNA charge density in helical regions adjacent to destroyed sites of platination.…”

DNA conformational equilibrium in the presence of Zn2+ ions in neutral and alkaline solutions

“…For example, deprotonation and subsequent change in structure occurs in alkaline medium at temperatures above 40 • C (pH 10.2, temperature of deprotonation T dep = 45 • C, T m = 65 • C) [22]. …”