Time Study of DNA Condensate Morphology:  Implications Regarding the Nucleation, Growth, and Equilibrium Populations of Toroids and Rods

Abstract

It is well known that multivalent cations cause free DNA in solution to condense into nanometer-scale particles with toroidal and rod-like morphologies. However, it has not been shown to what degree kinetic factors (e.g., condensate nucleation) versus thermodynamic factors (e.g., DNA bending energy) determine experimentally observed relative populations of toroids and rods. It is also not clear how multimolecular DNA toroids and rods interconvert in solution. We have conducted a series of condensation studies in which DNA condensate morphology statistics were measured as a function of time and DNA structure. Here, we show that in a typical in vitro DNA condensation reaction, the relative rod population 2 min after the initiation of condensation is substantially greater than that measured after morphological equilibrium is reached (ca. 20 min). This higher population of rods at earlier time points is consistent with theoretical studies that have suggested a favorable kinetic pathway for rod nucleation. By using static DNA loops to alter the kinetics and thermodynamics of condensation, we further demonstrate that reported increases in rod populations associated with decreasing DNA length are primarily due to a change in the thermodynamics of DNA condensation, rather than a change in the kinetics of condensate nucleation or growth. The results presented also reveal that the redistribution of DNA from rods to toroids is mediated through the exchange of DNA strands with solution.

Compaction of bacterial genomic DNA: clarifying the concepts

“…In line with this remark, it was shown about 40 years ago that it is possible to condense DNA into very compact structures by adding polyamines with three or four positive charges to very dilute solutions of DNA [55,56,57]. Since that time, this phenomenon has been investigated by many polymer physicists (as a model for the behavior of polyelectrolytes in the presence of multivalent counterions) and biophysicists (as a model for DNA packaging into viruses) and it is now well established that the size and morphology (toroids, rods, or spheres) of condensed DNA depends crucially on the ionic strength and solvent polarity of the solution, as well as the charge and density of the condensing agent (see for example [58,59,60] This expression leads to estimates of the fluctuation correlation energy of the order of -0.3 T k B per base pair at the condensation threshold, a value which is indeed sufficient to It may be worth emphasizing that complex coacervation (discussed in the previous subsection) and condensation by small cations are rather different mechanisms, although the polycations that trigger them may differ only in their respective number of monomers. The coacervation mechanism is indeed much more efficient than forces arising from fluctuation (2)), are shown for each interaction potential, and the value of the radius of gyration of the compacted DNA is indicated close to the corresponding vignette.…”

“…In line with this remark, it was shown about 40 years ago that it is possible to condense DNA into very compact structures by adding polyamines with three or four positive charges to very dilute solutions of DNA [55,56,57]. Since that time, this phenomenon has been investigated by many polymer physicists (as a model for the behavior of polyelectrolytes in the presence of multivalent counterions) and biophysicists (as a model for DNA packaging into viruses) and it is now well established that the size and morphology (toroids, rods, or spheres) of condensed DNA depends crucially on the ionic strength and solvent polarity of the solution, as well as the charge and density of the condensing agent (see for example [58,59,60] and references therein). A remarkable result has been obtained by Wilson and Bloomfield, who studied the compaction of T7 bacteriophage DNA by trivalent spermidine, tetravalent spermine and other multivalent cations, at varying monovalent salt concentrations [54].…”

DNA Hydrogel Fiber with Self‐Entanglement Prepared by Using an Ionic Liquid

“…[15] When DNA strands are condensed by binding to cations, the amplitudes of positive CD bands are decreased and the amplitudes of negative CD bands are increased. [16,17] Upon addition of the RTIL, the DNA strand in the spinning solution was condensed efficiently because the amplitude of the positive CD band decreased proportionately to the amount of RTIL added. When salt is removed from DNA, there is normally a shift of the wavelength crossover from 255 to 261 nm and an increase in the amplitude of negative CD bands.…”

Single-molecule stretching studies of RNA chaperones

“…22 Therefore some mechanisms to lower these energetic barriers, decrease persistence length and facilitate aggregation must be relevant in vivo. Indeed, it is known 23 that physiologically relevant small multivalent cations with a net charge of +3 or higher, such as Spermidine 3+ or Spermine 4+ , [22][23][24][25][26][27][28][29][30][31][32] induce aggregation (or condensation) of dsDNA and RNA. 33,34 In addition, protamines, 35 synthetic multivalent cations (such as CoHex 3+ ), and many unstructured cationic peptides or proteins with high positive charge density also condense DNA and RNA.…”