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

Biochemistry. 1993 Jan 26;32(3):961-7. doi: 10.1021/bi00054a029.

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.

Publication types

  • Research Support, Non-U.S. Gov't
  • Research Support, U.S. Gov't, P.H.S.

MeSH terms

  • Animals
  • Cattle
  • DNA / chemistry
  • DNA / metabolism*
  • Diffusion
  • Magnetic Resonance Spectroscopy
  • Models, Chemical
  • Nucleic Acid Conformation
  • Spermidine / analogs & derivatives*
  • Spermidine / chemistry
  • Spermidine / metabolism
  • Thymus Gland / chemistry

Substances

  • N-octamethylspermidine
  • DNA
  • Spermidine