Interactions of polynucleotides and their components

Abstract

The pK' values of the current bases, nucleosides, nucleotides, nucleotide derivatives and poly U have been determined over a large range of ionic strength. The pK' shifts of the monomers due to variations in ionic strength can be accounted for qualitatively and quantitatively by means of the relation The collision diameters of uracil, uridine, uridine cyclic -2':3'-phosphate and 3' (2') -uridylic acid were determined. The introduction of phosphate affects the charge, resulting into differences in activity coefficient between nucleotides and their corresponding nucleosides and bases. A substitution of -H by ribose at N(3) of uracil or cytosine or at N(9) of adenine or guanine results into an electron withdrawal from the bases with lowering of the pK' value. 2'-Deoxyribose exhibits a weaker electron attraction. Introducing -CH3 at C(5) of uracil yields electrons to the base and the pK values of various thymine derivatives are about 0.5 pH units higher than those of the corresponding uracil derivatives. A phosphate group on C2 or C3 results in an electrostatic attraction of the dissociable proton, so that the pK' is increased at low ionic strengths; at higher ionic strengths screening off occurs and the pK' values of the nucleotides become almost the same as those of the corresponding nucleosides. The site of substitution on the ribose moiety is important: C2'-O-phosphate seems to exert a stronger electrostatic attraction on - NH3 ⊕ groups than C3'-O-phosphate, whereas C5'-O-phosphate exerts in addition an inductive effect that is dependent on the presence of - OH on C2. The electrostatic influence of the phosphate groups on the uracil moiety in UpU, UpC and CpUpC runs roughly parallel to that found in cyclic-2':3'-nucleotides. The pK' shifts experienced in poly U are related to the polyelectrolyte character of this polymer. A new treatment for the evaluation of the electrostatic potential of polynucleotides (poly U) is proposed that is based on the usual rodlike (polyelectrolyte) model.