Allosteric DNAzyme-based encoder for molecular information transfer

Abstract

Dynamic DNA nanotechnology plays a significant role in nanomedicine and information science due to its high programmability based on Watson-Crick base pairing and nanoscale dimensions. Intelligent DNA machines and networks have been widely used in various fields, including molecular imaging, biosensors, drug delivery, information processing, and logic operations. Encoders serve as crucial components for information compilation and transfer, allowing the conversion of information from diverse application scenarios into a format recognized and applied by DNA circuits. However, there are only a few encoder designs with DNA outputs. Moreover, the molecular priority encoder is hardly designed. In this study, we introduce allosteric DNAzyme-based encoders for information transfer. The design of the allosteric domain and the recognition arm allows the input and output to be independent of each other and freely programmable. The pre-packaged mode design achieves uniformity of baseline dynamics and dynamics controllability. We also integrated non-nucleic acid molecules into the encoder through the aptamer design of the allosteric domain. Furthermore, we developed the 2n-n encoder and the Endo IV-assisted priority encoder inspired by immunoglobulin's molecular structure and effector patterns. To our knowledge, the proposed encoder is the first enzyme-free DNA encoder with DNA output, and the priority encoder is the first molecular priority encoder in the DNA reaction network. Our encoders avoid complex operations on a single molecule, and their simple structure facilitates their application in complex DNA circuits and biological scenarios.