The importance of pKa in an analysis of the interaction of compounds with DNA

Anthracycline analogues alizarin and purpurin were used to find how DNA influences determination of pKa. pKa1 and pKa2 were different when evaluated in presence of DNA. pKa1 determined in presence of DNA was used to evaluate contributions of two forms of the molecules towards overall binding with calf thymus DNA. Revised calculations show contribution of the neutral form was different while that of the anionic form was same.