Conformation and ion-binding of oligonucleotides

Abstract

The effective charge and the conformation of oligonucleotides may influence their pharmaceutical properties. Therefore, a method based on the convective diffusion process was used to measure both the diffusion coefficient and the effective charge number of four oligonucleotides with different chain lengths. Determinations were carried out at physiological ionic strength and at two temperatures, 20 and 40 °C. The results indicate that the longer oligonucleotides, i.e. number of nucleotides in the molecule from 15 to 30, are strongly ion-paired (75–80%) and the shorter oligonucleotide (seven nucleotides) is only ca. 50% ion-paired. The extent of ion-binding was not dependent on temperature. The conformation of the oligonucleotides appeared to be fairly compact in 0.15 M NaCl solution. The compact conformation and strong ion-pairing may influence the pharmacokinetics of oligonucleotides, possibly facilitating distribution into tissues.