THEORETICAL AND EXPERIMENTAL-STUDY OF DNA HELIX-COIL TRANSITION IN ACIDIC AND ALKALINE-MEDIUM

The theoretical approach to the calculation of the influence of select ive binding of small ligands on DNA helix-coil transition has been des cribed in the previous paper (Lando D.Yu., J. Biomol. Struct. Dyn., (1 994)). In the present paper that method is used for the study of DNA p rotonation and deprotonation in acidic and alkaline medium by theoreti cal analysis of pH effect on DNA heat denaturation. The mechanism of D NA protonation in acidic medium and pk values of nucleotides are well known. It gave us an opportunity to check the theory without any fitti ng of pK values. A good agreement between experimental and calculated functions T-m(pK) and Delta T(pH) (melting temperature and melting ran ge width) obtained for acidic medium proved the validity of the theory . However, for alkaline medium there was not even qualitative agreemen t when the agreed-upon mechanism of deprotonation was considered. Look ing into the cause of the discrepancy, we have studied the DNA melting for different mechanisms of deprotonation by calculation of T-m(pH) a nd Delta T(pH). As a result, it has been established that the discrepa ncy is due to deprotonation of bonded GC base pairs of helical DNA reg ions (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.