The importance of pK in an analysis of the interaction of compounds with DNA.

pK of a compound is crucial for determining the contributions of different forms of it towards overall binding with DNA. Hence it is important to use correct pK values in DNA interaction studies. This study takes a look at the importance of pK values to realize binding of compounds with DNA. Since pK of a compound determined in the presence of DNA is quite different from that determined in its absence hence, presence of different forms of a compound during interaction with DNA is different from that realized if the determination of pK is done in normal aqueous solution in absence of DNA. Hence, calculations determining contributions of different forms of a compound interacting with DNA are affected accordingly. Two simple analogues of anthracyclines, alizarin and purpurin, were used to investigate the influence DNA has on pK values. Indeed, they were different in presence of DNA than when determined in normal aqueous solution. pK for alizarin and purpurin determined in the absence and presence of calf thymus DNA were used in equations that determine contributions of two forms (neutral and anionic) towards overall binding with DNA. The study concludes that correct pK values, determined correctly i.e. under appropriate conditions, must be used for DNA binding experiments to evaluate contributions of individual forms.