DNA condensation in two dimensions

Abstract

The existence of distinct states of DNA compaction is vital to the functions of viruses, bacteria, and eukaryotic cells (1). The more compact states lead to the efficient packing of colossal genomic DNA molecules within the small confines of the cell nucleus, the bacterial cytoplasm, and viral capsids. Equally important are the less compact states of DNA required during much of the cell life cycle to allow proteins access to the DNA template for a multitude of biological tasks (e.g., gene regulation, transcription, replication). The biologically relevant DNA-condensing agents in vivo include cationic proteins (e.g., histones) and polyamines such as spermidine and spermine with sufficiently high counterion valence (Z ≥ 3) (1–5). In bacteria, polyamine molecules such as spermine (4^{) and spermidine (3) are known to be critical for DNA compaction (}1). Polyamines also are required in DNA catenation (interlocking) by topoisomerases, presumably for locally condensing neighboring DNA segments (1, 6).

There have been a number of theoretical (7–11) and experimental studies aimed at elucidating the fundamental physical mechanisms responsible for DNA condensation. Experimental studies done in vitro have found that DNA condensation from bulk solution critically depends on the valence of the counterions and that a valence of 3 or larger is required to overcome the inherently large electrostatic repulsive barrier between the like-charged polyelectrolytes (2–5). Furthermore, experiments show that counterions with Z = 2 simply provide screening of the electrostatic repulsions but do not lead to DNA collapse. It has been suggested that interactions between like-charged particles in electrolyte solutions may be affected in confined geometries near macroscopic surfaces. In particular, anionic colloidal spheres were found to attract each other in weak monovalent salt solutions near a surface (12, 13).

In this paper we show that the spatial dimension available to DNA plays a key role in the intermolecular interactions. Specifically, DNA chains adsorbed between cationic membranes within the lamellar (L_α^{) phase of cationic lipid (CL)-DNA complexes (}14–17) are found to undergo a collapse transition in the presence of simple divalent cationic biological salts, namely Ca^{, Mg, and Mn. Co also was used because its absorption peak in the visible at 512 nm allowed a direct measurement of binding to DNA in the collapsed phase. Synchrotron x-ray diffraction (XRD) and absorption measurements show that the collapsed phase consists of DNA chains electrostatically tethered by divalent counterions in two dimensions (2D). The trapped counterions form a novel one-dimensional (1D) liquid between the molecular chains at a density of 0.63 ions/DNA base pair. Thus, these simple divalent ions may play a critical role in controlling the compaction state of genomic nucleic acid, for example, in rod-shaped viruses where the genome is adsorbed onto a curved cationic protein surface. Furthermore, the observed enhanced counterion mediated attractive forces, leading to the DNA condensation for Z = 2 in 2D, may act between any like-charged polyelectrolyte macromolecules, such as cytoskeletal fibers or charged polypeptides adsorbed onto or near surfaces} in vivo.

Acknowledgments

Abbreviations

Footnotes