Publications

Nucleic acid hybridization in bimolecular and folding reactions is a fundamental kinetic process susceptible to water solvation, counterions, and chemical modifications with intricate enthalpy-entropy compensation effects. Such effects hinder the typically weak temperature dependencies of enthalpies and entropies quantified by the heat capacity change upon duplex formation. Using a temperature-jump optical trap, we investigate the folding thermodynamics and kinetics of DNA hairpins of varying stem sequences and loop sizes in the temperature range of 5-40 circle C. From a kinetic analysis and using a Clausius-Clapeyron equation in force, we derive the hybridization heat capacity changes Delta Cp per GC and AT bp, finding 36 +/- 3 and 29 +/- 3 cal/(mol K), respectively. The almost equal values imply similar degrees of freedom arrest upon GC and AT bp formation during duplex formation. Folding kinetics on DNA hairpins of varying loop sizes show that the transition states (TS) in duplex formation have high free energies but low Delta Cp values relative to the native state. Consequently, TS have low configurational entropy in agreement with the funnel-like energy landscape hypotheses. Our study underlines the validity of general principles in the hybridization and folding of nucleic acids determined by the TS's Delta Cp values.

JTD Keywords: Binding, Duplex, Force, Free-energy-landscape, Heat-capacity changes, Kinetics, Protein, Stability, Thermodynamic, Transition-state

When exposed to the oral environment, dental implants, like natural surfaces, become substrates for microbial adhesion and accumulation, often leading to implant-related infections-one of the main causes of implant failure. These failures impose significant costs on patients, clinicians, and healthcare systems. Despite extensive research, there is no consensus on the most effective protocol for managing peri-implantitis. Biomedical engineering has aimed to address this challenge by developing biocompatible implants with surface properties designed to enhance biological responses and reduce polymicrobial accumulation. Due to the complexity of interactions between implants and biological systems, no single material property can drive these processes. Instead, a combination of physical, chemical, and mechanical properties is required to ensure a safe and effective response. Antimicrobial coatings are developed either by incorporating antimicrobial agents onto surfaces or modifying the material's physicochemical properties. These coatings utilize a range of compounds for contact-killing or as drug-delivery systems. While biomaterials science has advanced rapidly in enhancing implant surfaces, these bioengineering techniques have progressed more rapidly than our understanding of the pathogenesis of implant infections. To bridge this gap, biomedical engineering must address emerging knowledge about implant infections, focusing on controlling microbial accumulation while simultaneously managing inflammatory responses to support tissue healing. This review critically evaluates current evidence on implant infection pathogenesis, antimicrobial coating technologies, and systematically assesses their in vivo (animal and human evidence) efficacy to guide future advancements in implant infection mitigation.

JTD Keywords: Antimicrobial, Bacterial adhesion, Biofilm formation, Biomaterials, Coating, Dental implant, Drug-deliver, Free-energy, In-vivo antibacterial, Infectio, Infection, Peri-implantitis, Pure titanium, Quality-of-life, Resistant staphylococcus-aureus, Titanium implant