Enzyme-Powered Self-Propelled DNA Nanoparticles for Disruption and Antibiotic Delivery in Topical Biofilms - PROJECT SUMMARY/ABSTRACT Bacterial biofilms are responsible for most human infections, causing tens of thousands of deaths and billions in medical costs per year. Topical biofilms alone cause significant harm to patients by growing on open wounds, skin lesions, burn injuries, or diabetic ulcers, and elsewhere. Biofilms are notoriously difficult to eradicate, in large part because of the extracellular polymeric substance (EPS), a self-produced extracellular matrix in which biofilm bacteria reside. The EPS benefits bacteria in many ways, including mediating quorum sensing, providing nutrients, and blocking transport of antibiotics and host immune response. The ability to actively penetrate the EPS and deliver anti-bacterial cargo where it is most needed would bypass many of these protections and could thus have a transformative impact on the remediation of biofilms. First introduced in 2004, artificial self-propelled particles (SPPs) can propel themselves through complex biological media and deliver cargo to specific locations. Thus, SPPs hold significant potential for biomedical applications such as biofilm remediation. However, SPPs must overcome significant challenges in the form of biocompatibility, tracking, and control to be viable for clinical use. Here, we propose to leverage the burgeoning field of DNA nanotechnology to develop urease-powered DNA-origami-based self-propelled particles (DNA-SPPs) for biofilm remediation. As a model organism, we focus on the well-studied pathogen Pseudomonas aeruginosa. Aim 1 of this study will quantify the dependence of DNA-SPPs’ locomotion on local urea concentration and pH and elucidate the extent to which they perform chemotaxis in urea gradients. Aim 2 will test the hypothesis that if DNA-SPPs are decorated with glycosyl hydrolase enzymes (which are widely used to disrupt the biofilm matrix, specifically in the case of P. aeruginosa), they will degrade the biofilm matrix as they move through it, weakening the protection the EPS normally provides to bacteria. The success of Aim 2 will be marked by greater efficacy of a model antibiotic (ceftazidime, which has demonstrated efficacy at treating P. aeruginosa biofilms) administered topically. In Aim 3, we will load ceftazidime directly onto DNA-SPPs using a pH-sensitive motif (e.g., I-motif) that undergoes structural changes in response to pH decrease, thus releasing cargo only in acidic regions. By correlating the delivered payload to the pH distribution, we will confirm the ability of DNA-SPPs to deliver cargo preferentially in acidic regions, where hard- to-reach bacteria tend to cluster. Finally, we will assess the combinatorial benefits of the approaches in Aims 2 and 3 by using DNA-SPPs to both increase the biofilm’s permeability and to deliver antibiotics deep inside the biofilm. The major output of this study will be design criteria for DNA-based enzyme-powered SPPs to disrupt and deliver cargo in extracellular matrix (ECM) environments, which could have a major impact on the treatment of biofilms, and will lay the foundation for a customizable platform technology applicable to a wide range of ECM- mediated diseases.
