Equilibrium phase diagram and thermal responses of charged DNA-virus rod-suspensions at low ionic strengths

Abstract

The collective behavior of DNA is important for exploring new types of bacteria in the means of detection, which is greatly interested in the understanding of interactions between DNAs in living systems. How they self-organize themselves is a physical common phenomenon for broad ranges of thermodynamic systems. In this work, the equilibrium phase diagrams of charged chiral rods (fd viruses) at low ionic strengths (below a few mM) are provided to demonstrate both replicas of (or self-organized) twist orders and replica symmetry breaking near high concentration glass-states. By varying the ionic strengths, it appears that a critical ionic strength is obtained below 1–2 mM salt, where the twist and freezing of nematic domains diverge. Also, the microscopic relaxation is revealed by the ionic strength-dependent effective Debye screening length. At a fixed low ionic strength, the local orientations of twist are shown by two different length scales of optical pitch, in the chiral-nematic N* phase and the helical domains $$H_{D}$$ H D , for low and high concentration, respectively. RSB occurs in several cases of crossing phase boundary lines in the equilibrium phase diagram of DNA-rod concentration and ionic strength, including long-time kinetic arrests in the presence of twist orders. The different pathways of PATH I, II and III are due to many-body effects of randomized orientations for charged fd rods undergoing long-range electrostatic interactions in bulk elastic medium. In addition, the thermal stability are shown for chiral pitches of the N* phase and the abnormal cooling process of a specific heat in a structural glass. Here, the concentration-driven twist-effects of charged DNA rods are explored using various experimental methods involving image-time correlation, microscopic dynamics in small angle dynamic light scattering, optical activity in second harmonic generation, and differential scanning calorimetry for the glass state.

Orientation Kinetics of Chiral-Nematic N* Domains in Suspensions of Charged DNA Rods

“…More direct evidence of physical observations for the replica symmetry breaking (RSB) appears in the middle concentrations (of the X-pattern), occasionally in the fast time scale with mechanical kinks [14]. Without any loss of information, maintaining reliable continu- relation functions are also shown in Fig.…”

“…In particular, there is a divergence of length scales in the component of q D ⊥ and the relevant chiral pitch q P in the X-pattern, where the effective decoupling of q D ⊥ and q D then leads to RSB. The further realization of RSB is accurately observed in the ITCs of FTs at a concentration of DNA rods of 5.4 mg/ml, which is the concentration where the mechanical kink randomly appears in the real space in a short period of time before reaching an equilibrium [14,19,27]. This can be understood as the density of the system being compensated by the orientation orders of chiral nematic N* domains at the N*-X transition line, with the FIG.…”

“…The trend is also seen in the lower binodal, relating to the intrinsic microscopic relaxations of charged DNA rods where the effective diffusion of the given concentration (or the crowding) is considered compared to the orientations. The reorientation of the aligned planar nematic phase at higher ionic strengths is shown to be much faster than the perpendicular diffusion [14,19]. (iii) The increase of the FT spectral spacing corresponds to a decrease of the N* domain size as the replica of half-sized twisted helical domains at higher concentrations (at the HD phase) near the X-pattern above the N* phase in the equilibrium diagram in Fig.…”

“…Further details on the equilibrium phase diagram of charged DNA rods at low ionic strengths can be found in Ref. [14,19].…”

“…Here, the suspensions of charged DNA rods in equilibrium phase behaviors at low ionic strengths are introduced as a good lyotropic system, where the orientation kinetics are analyzed and characterized by means of an advanced method of image-time correlations (ITCs) in the Fourier transforms (FTs). The equilibrium phase behaviors are explored systematically by varying the concentration of DNA rods at a given low ionic strength: the chiral-nematic N* phase and the hierarchical chiral mesophases, Xpattern and helical domain (HD) phase are observed above the isotropic-nematic coexistence concentrations [14]. In particular, the intermediate concentration of DNA rods, the Xpattern is formed as a new type of glass (forming the cavity loops, a chiral glass) where replica symmetry breaking (RSB) occurs, in contrast to the structural glass [19].…”