DNA Condensation Process Research Articles

Nucleic acids packaging processes: effects of adenine tracts and sequence-dependent curvature.

The effects of short runs of adenines (A-tracts) upon nucleic acids packaging processes and the properties of the resulting condensates were investigated by using random DNA sequences isolated from natural sources, as well as synthetic segments obtained by an extensive ligation of specific oligomers. Reiteration of short A-tracts (A(N) where N less than 3) within the DNA molecules is found to be compatible with a long-range chiral organization of the strands in the nucleic acid condensed phases. This chiral order, whose occurrence necessitates a high degree of flexibility, is shown, however, to differ from that exhibited by packed species originating from random AT-rich fragments; the altered patterns are interpreted in terms of a reduced overall flexibility of the DNA strands. Repetition of longer A-tracts (where N greater than 3), in which the distinct structural features that characterize this motif are fully expressed, results in a complete suppression of any chiral order in the packed particles, assigned to a significantly enhanced rigidity. DNA fragments where A-tracts are reiterated in phase, leading to a stable macroscopic curvature, are found to undergo condensation through altered pathways and to form toroidal shapes of unusually small dimensions. The results point towards the intriguing possibility that A-tracts and, in particular, the global, intrinsic curvature associated with such motifs, might be involved in the determination of nucleic acids packaging pathways, and underline the usefulness of defined sequences in the study of DNA condensation processes.

Thermodynamics of Cation-Induced DNA Condensation

An estimation of the various free energy contributions to DNA collapse into toroidal particles is made, considering DNA bending and segment mobility, electrostatic repulsions between DNA chains, and attractive forces resulting from correlated counterion fluctuations. It is shown that the process of DNA condensation becomes spontaneous in the presence of divalent cations in methanol, and in the presence of tri- or tetravalent cations in water media. This is a consequence of the large decrease in the electrostatic repulsion between charged DNA segments, allowing the attractive force resulting from correlated fluctuations of bound counterions to become dominant. Our calculations indicate that short DNA fragments would condense into multimolecular particles in order to maximize the attractive force due to counterion fluctuations.