Condensation of DNA by multivalent cations: Experimental studies of condensation kinetics

• Published in: BIOPOLYM Vol. 53; no. 4; pp. 329 - 341
• Main Authors: He, Siqian, Arscott, Patricia G., Bloomfield, Victor A.
• Format: Journal Article
• Language: English
• Published: New York John Wiley & Sons, Inc 05.04.2000
• Subjects: Cells; Cobalt - metabolism; Cobalt compounds; Condensation; condensation kinetics; DNA - chemistry; DNA - metabolism; DNA condensation; Kinetics; Microscopy, Electron; Molecular dynamics; multivalent cations; Organometallics; Phase equilibria; Plasmids - chemistry; Plasmids - metabolism; Positive ions; Reaction kinetics; Salts; Scattering, Radiation; Ultracentrifugation; Viruses
• ISSN: 0006-3525; 1097-0282
• DOI: 10.1002/(SICI)1097-0282(20000405)53:4<329::AID-BIP5>3.0.CO;2-6

DNA in viruses and cells exists in highly condensed, tightly packaged states. We have undertaken an in vitro study of the kinetics of DNA condensation by the trivalent cation hexaammine cobalt (III) with the aim of formulating a quantitative, mechanistic model of the condensation process. Experimental approaches included total intensity and dynamic light scattering, electron microscopy, and differential sedimentation. We determined the average degree of condensation, the distribution of condensate sizes, and the fraction of uncondensed DNA as a function of reaction time for a range of [DNA] and [Co(NH3) 3+6]. We find the following: (1) DNA condensation occurs only above a critical [Co(NH3) 3+6] for a given DNA and salt concentration. At the onset of condensation, [Co(NH3) 3+6]/[DNA‐phosphate] is close to the average value of 0.54, which reflects the 89–90% charge neutralization criterion for condensation. (2) The equilibrium weight average hydrodynamic radius 〈RH 〉 of the condensates first decreases, then increases with increasing [Co(NH3) 3+6] as they undergo a transition from intramolecular (monomolecular) to intermolecular (multimolecular) condensation. However, 〈RH 〉 is insensitive to [DNA]. (3) The uncondensed DNA fraction decays approximately exponentially with time. The equilibrium uncondensed DNA fraction and relaxation time decrease with increasing [Co(NH3) 3+6] but are insensitive to [DNA]. (4) The condensation rate in its early stages is insensitive to [DNA] but proportional to [Co(NH3) 3+6]xs = [Co(NH3) 3+6] − [Co(NH3) 3+6]crit. (5) Data for low [DNA] and low [Co(NH3) 3+6] at early stages of condensation are most reliable for kinetic modeling since under these conditions there is minimal clumping and network formation among separate condensates. A mechanism with initial monomolecular nucleation and subsequent bimolecular association and unimolecular dissociation steps with rate constants that depend on the number of DNA molecules in the condensate, accounts reasonably well for these observations. © 2000 John Wiley & Sons, Inc. Biopoly 53: 329–341, 2000