New biocomputing method uses enzymes as catalysts for DNA-based molecular computing UMNews NatureComms
A typical NOT gate reaction consists of 1 μL of a restriction enzyme, 3 μL of 5X aHOT 7.9 buffer, 1 μL of 25 μM gate template, 1 μL of 25 μM T7 Max promoter sense complement, 3 μL of 25 μM input when applicable, and ddHO to bring the volume up to 15 μl. Reaction A was subjected to the same annealing and digest incubation protocols mentioned above.
The AND gate Reaction A utilizes New England Biolabs OneTaq Polymerase PCR recommendations. However, instead of running the reaction for 30 cycles, the AND gate only requires one cycle. Each AND gate reaction has a final volume of 25μL and includes 5μL of OneTaq 5X Standard Reaction Buffer , 1 μL of 100 μM Input 1, 1 μL of 100 μM Input 2, 0.
All gate Reaction As were used as the template for a cell-free transcription reaction that produces a fluorescent RNA aptamer. This transcription reaction will be referred to as Reaction B in this Methods. Typical cell-free transcription reactions are quite compact in volume , but because Reaction A volumes were a minimum of 7 μL and often contained highly concentrated gate templates, the concentration of reagents were increased to compensate.
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