Abstract
Densely packed DNA arrays exhibit hexagonal and orthorhombic local packings, as well as a weakly first order transition between them. While we have some understanding of the interactions between DNA molecules in aqueous ionic solutions, the structural details of its ordered phases and the mechanism governing the respective phase transitions between them remains less well understood. Since at high DNA densities, i.e., small interaxial spacings, one can neither neglect the atomic details of the interacting macromolecular surfaces nor the atomic details of the intervening ionic solution, the atomistic resolution is a sine qua non to properly describe and analyze the interactions between DNA molecules. In fact, in order to properly understand the details of the observed osmotic equation of state, one needs to implement multiple levels of organization, spanning the range from the molecular order of DNA itself, the possible ordering of counterions, and then all the way to the induced molecular ordering of the aqueous solvent, all coupled together by electrostatic, steric, thermal and direct hydrogen-bonding interactions. Multiscale simulations therefore appear as singularly suited to connect the microscopic details of this system with its macroscopic thermodynamic behavior. We review the details of the simulation of dense atomistically resolved DNA arrays with different packing symmetries and the ensuing osmotic equation of state obtained by enclosing a DNA array in a monovalent salt and multivalent (spermidine) counterions within a solvent permeable membrane, mimicking the behavior of DNA arrays subjected to external osmotic stress. By varying the DNA density, the local packing symmetry, and the counterion type, we are able to analyze the osmotic equation of state together with the full structural characterization of the DNA subphase, the counterion distribution and the solvent structural order in terms of its different order parameters and consequently identify the most important contribution to the DNA-DNA interactions at high DNA densities.
Highlights
The properties of dilute dsDNA solutions do not really suffice in order to understand their behavior in vivo [1,2]
For multivalent counterions at concentrations above a critical value depending on their identity [20], the equation of state (EoS) exhibits pronounced van der Waals-like density discontinuities that are in general larger in the case of monovalent salt solutions, signalling a buildup of attractive interactions [21,22], whose details can be inferred from complementary experiments [23], that eventually lead to DNA condensation [24]
We presented an overview of computational approaches to simulate densely packed
Summary
The properties of dilute (double-stranded) dsDNA solutions do not really suffice in order to understand their behavior in vivo [1,2]. The EoS exhibits a monotonic behavior as a function of the concentration of DNA, characterized by the hydration and fluctuation enhanced electrostatic regimes [3,7,8] It was only recently, through high resolution control of the osmotic pressure based on its known temperature variation [9,10], that a small discontinuous. For multivalent counterions at concentrations above a critical value depending on their identity [20], the EoS exhibits pronounced van der Waals-like density discontinuities that are in general larger in the case of monovalent salt solutions, signalling a buildup of attractive interactions [21,22], whose details can be inferred from complementary experiments [23], that eventually lead to DNA condensation [24]. Important source of DNA attractions and that the way to understand them is to abolish the implicit dielectric continuum model for the solvent
Sign-in/Register to view highlights & summary Sign-in/Register to access full text options 
Talk to us
Join us for a 30 min session where you can share your feedback and ask us any queries you have
Schedule a callDisclaimer: All third-party content on this website/platform is and will remain the property of their respective owners and is provided on "as is" basis without any warranties, express or implied. Use of third-party content does not indicate any affiliation, sponsorship with or endorsement by them. Any references to third-party content is to identify the corresponding services and shall be considered fair use under The CopyrightLaw.
