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

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Abstract
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.