title: Fluorescence dynamics of DNA condensed by the molecular crowding agent poly(ethylene glycol).
abstract: Condensation of extended DNA into compact structures is encountered in a variety of situations, both natural and artificial. While condensation of DNA has been routinely carried out by the use of multivalent cations, cationic lipids, detergents, and polyvalent cationic polymers, the use of molecular crowding agents in condensing DNA is rather striking. In this work, we have studied the dynamics of plasmid DNA condensed in the presence of a molecular crowding agent, polyethylene glycol (PEG). Steady-state and time-resolved fluorescence of the recently established condensation-indicating DNA binder, YOYO-1 [G. Krishnamoorthy, G. Duportail, and Y. Mely (2002), Biochemistry 41, 15277-15287] was used in inferring the dynamic aspects of DNA condensates. It is shown that DNA condensed by PEG is more flexible and less compact when compared to DNA condensed by binding agents such as polyethyleneimine. The relevance of such differences in dynamics toward functional aspects of condensed DNA is discussed.
authors.affiliation: Department of Chemical Sciences, Tata Institute of Fundamental Research, Mumbai, India.
authors.forename: Mamata H
authors.initials: MH
authors.lastname: Kombrabail
authors.forename: G
authors.initials: G
authors.lastname: Krishnamoorthy
mesh_terms: D001583:Benzoxazoles / Q000737:chemistry; D004278:DNA, Superhelical / Q000737:chemistry* / Q000187:drug effects*; D005456:Fluorescent Dyes / Q000737:chemistry; D007700:Kinetics; D009690:Nucleic Acid Conformation; D010957:Plasmids / Q000737:chemistry / Q000187:drug effects; D011092:Polyethylene Glycols / Q000494:pharmacology*; D011806:Quinolinium Compounds / Q000737:chemistry; D013050:Spectrometry, Fluorescence
chemical_list: D001583:Benzoxazoles; D004278:DNA, Superhelical; D005456:Fluorescent Dyes; D011806:Quinolinium Compounds; C075296:1,1'-((4,4,7,7-tetramethyl)-4,7-diazaundecamethylene)bis-4-(3-methyl-2,3-dihydro(benzo-1,3-oxazole)-2-methylidene)quinolinium; D011092:Polyethylene Glycols