Cancer remains the deadliest disease for mankind, and hence, the need for effective, reliable, and functioning cancer treatment is crucial. A promising minimally invasive oncological treatment called photodynamic therapy (PDT) involves irradiation of a photosensitizing drug injected into the vasculature which in turn transfers energy to the surrounding oxygen, generating heavily cytotoxic reactive oxygen species (ROS), either directly or indirectly killing the cell. Although simple in theory, many problems need to be addressed like oxygen waste and hence resupply, light source delivery to the photosensitizer (PS), or the cancer cell targeting with the PS. Promising new agents to tackle multiple issues in PDT are metal nanoclusters (NCs), especially with gold as the core. They turn out to accumulate well in cancer cells, be very biocompatible, and even function as PS themselves. A less common way to surpass the light source delivery problem is to use X-rays due to low in vivo scattering and absorption cross section, giving rise to what we will call X-ray photodynamic therapy (X-PDT). It shows great potential for demolishing cancer cells, prompted by their high energy. The energy transfer in both cases, PDT and X-PDT, from PS or NC to oxygen is poorly understood and the subject of current research. This Tutorial gives an easy to understand introduction to PDT and X-PDT and their different agents, explains the use of metal NCs in both heavily related treatment methods, gives an overview of the known elementary transfer mechanisms between the typical contributors to PDT and X-PDT, and briefly sketches realized and possible simulation strategies. It aims to give an understanding of where current research is lacking and thus what new experiments, theories, and simulations should be targeted as well as an outlook for possible further theoretical and computational X-PDT research.

RNA aptamers play essential roles in gene regulation, sensing, and therapeutics, relying on ligand-induced kinetic changes for function. The theophylline aptamer has been engineered to regulate synthetic gene networks in response to the presence of the theophylline small molecule ligand, but the thermodynamic and kinetic parameters behind theophylline's unique function are not known. Here, we use optical tweezers single-molecule force spectroscopy to measure the folding dynamics of the theophylline aptamer in the presence and absence of ligand. We find that theophylline binding does not affect folding rates but significantly slows unfolding by stabilizing the aptamer by ∼3.6 k B T, or ∼2.1 kcal/mol. These results support a conformational selection model of ligand binding and reveal no evidence of large structural rearrangement upon ligand association. Our findings suggest that theophylline-induced stabilization, rather than structural remodeling, drives aptamer function in synthetic biology applications to regulate gene expression. This kinetic stabilization supports prior work proposing a kinetic trap mechanism, in which the long-lived, folded ligand-bound state delays ribosome binding and translation. These insights emphasize the kinetic basis of RNA-mediated regulation and inform the future design of ptamer-based tools in synthetic biology and therapeutics.