Volume 9, Number 2, p.p. 77–82
Consequences of an acidic environment for the structural and functional characteristics of DNA
T. Mdzinarashvili,1, 2 T. Partskhaladze, 1M. Khvedelidze 1, 2 and T. Lomidze1
1
Department of Physics, Faculty of Exact and Natural Sciences, Ivane Javakhishvili Tbilisi State University, 3 Chavchavadze Ave, 0128 Tbilisi, Georgia
2
Institute of Molecular Biology and Biophysics, 12 Gotua St, 0160 Tbilisi, Georgia
Experiments to identify protein interaction and the mechanism of protein recognition of several DNA fragments have been conducted. Calorimetry has revealed that DNA structural lability strongly depends on solvent pH; the enthalpy of DNA denaturation decreases when the solvent becomes more acidic and increases with little change in denaturation temperature under alkaline conditions. As the solvent becomes more alkaline, these negligible changes of denaturation temperature are marked by a narrowing of the heat absorption peak width, signifying increasing phase transition coöperativity; the thermostability of the AT and GC pairs becomes less distinguishable as new bonds to the AT pair are formed. Under acidic conditions (pH 2.8–7.0), the structure of ds-DNA undergoes considerable destabilization; protonation of DNA leads to a significant reduction in melting enthalpy and the transition temperature, inferred to be caused by the decreasing number of hydrogen bonds between the base pairs (despite the destabilizing influence of the acidic environment on the DNA structure, after returning to physiological conditions the DNA accurately returns to its native double helix structure without any defects). From the experimental results a model of protein–DNA specific site recognition can be inferred, which includes first ds-DNA strand separation of specific (AT-rich) regions by the protein and then interaction of the protein with the opened DNA sites.
Keywords:
DNA-protein interaction, DSC, pH influence on DNA