Quantification of the effect of excluded volume on double-stranded DNA

Donna Louie, Philip Serwer

Research output: Contribution to journalArticlepeer-review

31 Scopus citations

Abstract

By steric exclusion of volume, neutral polymers both condense and increase the effective concentration of DEJA random coils. Neutral polymers also stimulate the in vitro packaging of DNA in the capsids of some double-stranded DNA bacteriophages. In the present study, the physical effects of neutral polymers on DNA random coils have been quantified by assaying the DNA products at equilibrium of the following two reactions of the 12 nucleotide single-stranded complementary (cohesive) ends of mature bacteriophage R DNA: bimolecular joining of half-molecules of mature λ DNA, and cyclization of intact a DNA; cyclization is used as a probe for unimolecular DNA condensation. The smaller neutral molecules, including polyethylene glycol of molecular mass 200 Da (PEG200), shift both reactions towards dissociation; this shift is partially correlated with reduced water activity. The larger PEGs (molecular mass of 1540 or more) shift both reactions towards association. Water activity-corrected equilibrium constants for the larger PEGs are found to increase as a function of PEG concentration. Below 2% to 3% (w/v) PEG, these equilibrium constants are independent of PEG; molecular mass; at higher PEG concentrations, these equilibrium constants increase as the molecular mass of the PEG increases. The following conclusions are drawn. (1) Volume exclusion among PEG molecules is the primary cause of the PEG molecular mass-dependence of excluded volume. (2) At the lower PEG concentrations, the PEG radius obtained by quantification of excluded volume is usually equal to the hydrodynamic PEG radius. (3) At any given PEG concentration, the PEG-DNA excluded volume is approximately the same for bimolecular DNA joining as it is for unimolecular DNA cyclization. (4) Polymer-induced stimulation of in vitro bacteriophage DNA packaging is derived primarily from alteration of water activity, not alteration of excluded volume.

Original languageEnglish (US)
Pages (from-to)547-558
Number of pages12
JournalJournal of Molecular Biology
Volume242
Issue number4
DOIs
StatePublished - Sep 29 1994

Keywords

  • Agarose gel
  • Cohesive-ended joining of
  • DNA
  • DNA
  • Electrophoresis
  • Excluded volume
  • Packaging of
  • Polyethylene glycol

ASJC Scopus subject areas

  • Structural Biology
  • Molecular Biology

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