(163h) Protein-to-DNA Converter with High Signal Gain

DNA isothermal amplification techniques have been applied extensively for evaluating nucleic acids inputs but cannot be implemented directly on other types of biomolecules. In this work, we designed a proximity activation mechanism that converts protein inputs into DNA barcodes for the DNA exponential amplification reaction, which we termed PEAR. Several design parameters were identified and experimentally verified, which included the choice of enzymes, sequences of proximity probes and template strand via NUPACK design tool, and the implementation of hairpin lock on the proximity probe structure. Our PEAR system was surprisingly more robust against non-specific DNA amplification, which is a major challenge faced in existing formats of the DNA-based exponential amplification reaction. The as-designed PEAR exhibited good target responsiveness for three protein models with a dynamic range of 4 – 5 orders of magnitude down to femtomolar input concentration. Overall, our proposed protein-to-DNA converter module led to the development of a stable and robust configuration of DNA exponential amplification reaction to achieve high signal gain. We foresee this to enable the use of protein inputs for more complex molecular evaluation as well as ultrasensitive protein detection.