Polyammonium cation diffusion in aqueous solutions of DNA as studied by pulsed field gradient NMR

An NMR self-diffusion study of the interactions between spermidine and oligonucleotides

Self-diffusion coefficients have been determined by pulsed field gradient nmr methods for spermidine in solutions of the oligonucleotides d(GC)4 and d(GGAATTCC). The self-diffusion behavior of spermidine in solution of d(GC)4 is very similar to that observed previously for methylspermidine (completely N-methylated spermidine). Moreover, the self-diffusion behaviors of spermidine in solutions of d(GC)4 and d(GGAATTCC) are also quite similar, indicating that there is no significant influenceon on self-diffusion of oligonucleotide base composition. Furthermore, self-diffusion coefficients of the oligonucleotide d(GC)8 show only a small dependence on oligonucleotide concentration, and no measurable dependence on sodium ion or magnesium ion concentration.

Localized interaction of the polyamine methylspermidine with double-helical DNA as monitored by 1H NMR self-diffusion measurements

The 1H NMR pulsed field gradient self-diffusion method has been used to measure the diffusion coefficient of the polyamine analogue methylspermidine (completely N-methylated spermidine) in DNA solution, as a function of the concentration ratio of methylspermidine to DNA phosphate. Three different DNA's have been investigated: d(GC)4 (8 base pairs), core length calf thymus DNA (approximately 120 base pairs), and sonicated high molecular weight calf thymus DNA (average 7500 base pairs). For a constant ratio of methylspermidine to DNA phosphate, the diffusion coefficient decreases with increasing DNA length. Moreover, at low concentration ratios the diffusion coefficient of methylspermidine approaches a limiting value that is close to that of the DNA molecule. The experimental data are well reproduced by a two-state diffusion model. In this model the diffusion coefficient of the polyamine is a population-weighted average of polyamine associated with DNA (with a diffusion coefficient given by that of the DNA molecule) and polyamine free in solution.