Conformational Transition of Giant DNA in a Confined Space Surrounded by a Phospholipid Membrane

Abstract

It has been established that a long DNA molecule exhibits a large discrete conformational change from a coiled state to a highly folded state in aqueous solution, depending on the presence of various condensing agents such as polyamines. In this study, T4 DNA labeled with fluorescent dyes was encapsulated in a cell-sized microdroplet covered with a phospholipid membrane to investigate the conformational behavior of a DNA molecule in such a confined space. Fluorescence microscopy showed that the presence of Mg(2+) induced the adsorption of DNA onto the membrane inner-surface of a droplet composed of phosphatidylethanolamine, while no adsorption was observed onto a phosphatidylcholine membrane. Under the presence of spermine (tetravalent amine), DNA had a folded conformation in the bulk solution. However, when these molecules were encapsulated in the microdroplet, DNA adsorbed onto the membrane surface accompanied by unfolding of its structure into an extended coil conformation under high concentrations of Mg(2+). In addition, DNA molecules trapped in large droplets tended not to be adsorbed on the membrane, i.e., no conformational transition occurred. A thermodynamic analysis suggests that the translational entropy loss of a DNA molecule that is accompanied by adsorption is a key factor in these phenomena under micrometer-scale confinement.

Wrinkling of a spherical lipid interface induced by actomyosin cortex

“…In the present study, we fabricated a spherical (in its initial state) cell-sized deformable interface composed of a lipid monolayer [27,28,30] that encapsulates the actomyosin fraction ( Fig. 1(a)).…”

“…Cell-sized water-in-oil (W/O) droplets with a lipid monolayer were prepared as described previously [27,28].…”

Characteristic Behavior of Crowding Macromolecules Confined in Cell-Sized Droplets

“…On axis 3, where e f /k B T $ 0, the free energy of the F 1 state is equal to that of the F 3 state. Reproduced with permission from Kato et al (2009). PEG, these macromolecules (DNA, actin, and alginate) are negatively charged. The persistence lengths of DNA, alginate, and PEG are about 50, 5, and 0.9 nm, respectively, whereas that of actin is much larger comparable to droplet size (i.e., the micrometer scale).…”

“…The left image shows an equatorial section of a droplet, and the middle and right images are focused on the top. Reproduced with permission fromKato et al (2009).…”

Conformations and orientational ordering of semiflexible polymers in spherical confinement

“…Such simulations of generic model systems in thermal equilibrium can provide crucial insights for understanding complex problems such as the structural transitions of actin filaments in cell-sized water droplets confined inside spherical phospholipid membranes, 34 and solutions of ds DNA molecules 35 or mixtures of ds DNA and actin filaments confined in such microspheres. 36 An interesting application of our work could address fragments of ds DNA with contour lengths L comparable to the persistence length p , which is believed to be about 50 nm.…”