Relaxation dynamics and structural changes in DNA soft gels

Particle topology-regulated relaxation dynamics in cluster-ordering

The granular materials of soft particles (SPs) demonstrate unique viscoelasticity distinct from general colloidal and polymer systems. Exploiting dynamic light scattering measurements, together with molecular dynamics simulations, we study the diffusive dynamics of soft particle clusters (SPCs) with spherical and cylindrical brush topologies, respectively, in the melts of SPs. A topologically constrained relaxation theory is proposed by quantitatively correlating the relaxation time to the topologies of the SPCs, through the mean free space (Va) of tethered SPs in the cluster. The tethered SPs in SPCs are crowded by SPs of the melts to form the cage zones, and the cooperative diffusion of the tether SPs in the zones is required for the diffusive motion of SPCs. The cage zone serves as an entropic barrier for the diffusion of SP clusters, while its strength is determined by Va. Three characteristic modes can be confirmed: localized non-diffusive mode around critical Va, diffusive mode with Va deviating far from the critical value, and a sub-diffusive mode as an interlude between two limits. Our studies raise attention to the emergent physical properties of materials based on SPs via a topological design while opening new avenues for the design of soft structural materials.

Viscoelastic and Thermoreversible Networks Crosslinked by Non-covalent Interactions Between "Clickable" Nucleic Acids Oligomers and DNA

An approach to efficient and scalable production of oligonucleotide-based gel networks is presented. Specifically, a new class of xenonucleic acid (XNA) synthesized through a scalable and efficient thiol-ene polymerization mechanism, "Clickable" Nucleic Acids (CNAs), were conjugated to a multifunctional poly(ethylene glycol), PEG. In the presence of complementary single stranded DNA (ssDNA), the macromolecular conjugate assembled into a crosslinked 3D gel capable of achieving storage moduli on the order of 1 kPa. Binding studies between the PEG-CNA macromolecule and complementary ssDNA indicate that crosslinking is due to the CNA/DNA interaction. Gel formation was specific to the base sequence and length of the ssDNA crosslinker. The gels were fully thermoreversible, completely melting at temperatures above 60°C and re-forming upon cooling over multiple cycles and with no apparent hysteresis. Shear stress relaxation experiments revealed that relaxation dynamics are dependent on crosslinker length, which is hypothesized to be an effect of the polydisperse CNA chains. Arrhenius analysis of characteristic relaxation times was only possible for shorter crosslinker lengths, and the activation energy for these gels was determined to be 110 ± 20 kJ/mol. Overall, the present work demonstrates that CNA is capable of participating in stimuli-responsive interactions that would be expected from XNAs, and that these interactions support 3D gels that have potential uses in biological and materials science applications.

Multifunctional, fluorescent DNA-derived carbon dots for biomedical applications: bioimaging, luminescent DNA hydrogels, and dopamine detection

Here, we describe the synthesis of 2-3 nm, hydrophilic, blue fluorescence-emitting carbon dots (C-Dots, made using a DNA precursor) by the hydrothermal route from the gelling concentration of 2% (w/v) DNA. These dots exhibited highly efficient internalization in pathogenic fungal cells, negligible cytotoxicity, good PL stability, and high biocompatibility, thus demonstrating their potential as nanotrackers in microbial studies. Bioimaging was performed using Candida albicans as the representative for microbial pathogens. The novelty of these dots is that they formed fluorescent nanocomposite hydrogels with the same DNA much below the gelation concentration (1% w/v) and the tunable gels possessed strength between 20 and 80 Pa with the corresponding gelation temperature T_gel between 40 to 50 °C. The network density and gelation free energy data supported the superior crosslinking ability of these dots. The as-prepared hydrogels can replace the existing toxic quantum dot-based hydrogels for drug delivery. We also demonstrated the use of a DNA hydrogel-fabricated working electrode (DNA-C-Dot/ITO electrode) for the biosensing of dopamine. Our electrochemical biosensor had a detection limit of 5 × 10^-3 mM for dopamine. These multifunctional, fluorescent C-Dots and hydrogel after suitable conjugation or loading with molecules and drugs hold promising potential for further exploitation in bioimaging, targeted drug delivery, wound healing, and biosensing applications.

Small-angle neutron scattering and molecular dynamics structural study of gelling DNA nanostars

DNA oligomers with properly designed sequences self-assemble into well defined constructs. Here, we exploit this methodology to produce bulk quantities of tetravalent DNA nanostars (each one composed of 196 nucleotides) and to explore the structural signatures of their aggregation process. We report small-angle neutron scattering experiments focused on the evaluation of both the form factor and the temperature evolution of the scattered intensity at a nanostar concentration where the system forms a tetravalent equilibrium gel. We also perform molecular dynamics simulations of one isolated tetramer to evaluate the form factor numerically, without resorting to any approximate shape. The numerical form factor is found to be in very good agreement with the experimental one. Simulations predict an essentially temperature-independent form factor, offering the possibility to extract the effective structure factor and its evolution during the equilibrium gelation.