An elastic rod model to evaluate effects of ionic concentration on equilibrium configuration of DNA in salt solution

Modulation of DNA conformation in electrolytic nanodroplets

The behavior of deoxyribonucleic acid (DNA) molecules in confinement is of profound importance in various bioengineering and medical applications. In the present study, all-atom molecular dynamics simulation is utilized to investigate the transition of the double-strand DNA (dsDNA) conformation in the electrolytic nanodroplet. Three typical conformations, i.e., C-shaped, folded S-shaped, and double C-shaped, are observed for different droplet sizes and ionic concentrations. To reveal the physics underlying this phenomenon, the characteristics of the dsDNA molecules, such as the overcharging intensity, the end-to-end distance, the radius of gyration, etc. are analyzed in detail based on the numerical results. It is found that the transition can be ascribed to the buckling of the polymer molecules under the compression due to the confinement of the nanodroplet, and it can be modulated by the ionic concentration in the electrolyte. Generally, nanoscale confinement dominates dsDNA behavior over the electrostatic effects in smaller nanodroplets, while the latter becomes more important for larger nanodroplets. This competition results in the persistence length increasing with the nanodroplet radii. Based on these discussions, a non-dimensional elasto-capillary number μ is proposed to classify the dsDNA conformations into three regions.

3D Deformation Patterns of S Shaped Elastic Rods as a Pathogenesis Model for Spinal Deformity in Adolescent Idiopathic Scoliosis

Adolescent idiopathic scoliosis (AIS) is a three-dimensional (3D) deformity of the spinal column in pediatric population. The primary cause of scoliosis remains unknown. The lack of such understanding has hampered development of effective preventive methods for management of this disease. A long-held assumption in pathogenesis of AIS is that the upright spine in human plays an important role in induction of scoliosis. Here, the variations in the sagittal curve of the scoliotic and non-scoliotic pediatric spines were used to study whether specific sagittal curves, under physiological loadings, are prone to 3D deformation leading to scoliosis. To this end, finite element models of the S shaped elastic rods, which their curves were derived from the radiographs of 129 sagittal spinal curves of adolescents with and without scoliosis, were generated. Using the mechanics of deformation in elastic rods, this study showed that the 3D deformation patterns of the two-dimensional S shaped slender elastic rods mimics the 3D patterns of the spinal deformity in AIS patients with the same S shaped sagittal spinal curve. On the other hand, the rods representing the non-scoliotic sagittal spinal curves, under the same mechanical loading, did not twist thus did not lead to a 3D deformation. This study provided strong evidence that the shape of the sagittal profile in individuals can be a leading cause of the 3D spinal deformity as is observed in the AIS population.

Ionic effects on the temperature-force phase diagram of DNA

Double-stranded DNA (dsDNA) undergoes a structural transition to single-stranded DNA (ssDNA) in many biologically important processes such as replication and transcription. This strand separation arises in response either to thermal fluctuations or to external forces. The roles of ions are twofold, shortening the range of the interstrand potential and renormalizing the DNA elastic modulus. The dsDNA-to-ssDNA transition is studied on the basis that dsDNA is regarded as a bound state while ssDNA is regarded as an unbound state. The ground state energy of DNA is obtained by mapping the statistical mechanics problem to the imaginary time quantum mechanics problem. In the temperature-force phase diagram the critical force F _c (T) increases logarithmically with the Na⁺ concentration in the range from 32 to 110 mM. Discussing this logarithmic dependence of F _c (T) within the framework of polyelectrolyte theory, it inevitably suggests a constraint on the difference between the interstrand separation and the length per unit charge during the dsDNA-to-ssDNA transition.