DNA origami nanorobots allow for the rational design of nanomachines that respond to environmental stimuli with preprogrammed tasks. To date, this mostly is achieved by constructing two-state switches that, upon activation, change their conformation,...
DNA nanotechnology uses predictable interactions of nucleic acids to precisely engineer complex nanostructures. Characterizing these self-assembled structures at the single-structure level is crucial for validating their design and functionality. Nan...
Over the past 15 years, a variety of next-generation sequencing assays have been developed for measuring the 3D conformation of DNA in the nucleus. Each of these assays gives, for a particular cell or tissue type, a distinct picture of 3D chromatin a...
Journal of chemical theory and computation
Aug 29, 2025
Development of suitable scoring functions is essential for the prediction of RNA-protein complex structures. Conventional statistical potential-based scoring functions suffered from deficiencies in handling conformational flexibility. The recent appl...
Identifying novel and functional RNA structures remains a significant challenge in RNA motif design and is crucial for developing RNA-based therapeutics. Here we introduce a computational topology-based approach with unsupervised machine-learning alg...
Journal of chemical information and modeling
Jul 2, 2025
RNA possesses functional significance that extends beyond the transport of genetic information. The functional roles of noncoding RNA can be mediated through their tertiary and secondary structure, and thus, predicting RNA structure holds great promi...
DNA storage has been widely considered as a promising alternative for exponentially growing data. However, the inherent complex secondary structures severely compromise the processes of synthesis, PCR amplification, and sequencing, interfering with r...
RNA molecules are essential in regulating biological processes such as gene expression, cellular differentiation, and development. Accurately predicting RNA secondary structures and designing sequences that fold into specific configurations remain si...
While RNA has recently been recognized as an interesting small-molecule drug target, many challenges remain to be addressed before we take full advantage of it. This emphasizes the necessity to improve our understanding of its structures and function...
DNA topology is essential for regulating cellular processes and maintaining genome stability, yet it is challenging to quantify due to the size and complexity of topologically constrained DNA molecules. By combining high-resolution Atomic Force Micro...
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