Fig. 3: Trumpet NOT and NOR gates.
From: Trumpet is an operating system for simple and robust cell-free biocomputing
a The general architecture of a NOT gate. The NOT gate only requires one input, a 26-base single-stranded DNA that is complementary to the region with the restriction enzyme cut site on the gate template. When the input is present (left), it hybridizes with the gate template. The restriction enzyme recognizes the cut site and cleaves the gate template, separating the promoter from the aptamer. The T7 RNA polymerase cannot transcribe the aptamer, and the lack of fluorescence is recorded as a 0 signal. When the input is not present (right), the restriction enzyme cannot cut the single-stranded template. The T7 can transcribe the RNA aptamer from the intact gate template, which results in a fluorescence signal recorded as a 1. b A NOT gate truth table. c Fluorescent results of a NOT gate encoding a Broccoli aptamer. d The general architecture of a NOR gate. A 127-base gate template contains a promoter, first 26-base digest region (10-base random sequence, a restriction enzyme cut site, another 10-base random sequence), a second 26-base digest region (another two random sequences and the same cut site), and ends with the antisense sequence of an RNA aptamer. In this gate, one input consists of one 26-base digest region. When either or both inputs are present with the gate template, hybridization occurs and the restriction enzyme can digest the gate template in one or both locations, separating the promoter from the aptamer sequence. This template cannot be transcribed, and the lack of fluorescence is recorded as a 0 signal. It is only when neither input is present that the gate template remains intact, and transcription of the RNA aptamer occurs. The fluorescence of the transcribed aptamer is recorded as a 1 signal. e A NOR gate truth table. f Fluorescent results of a NOR gate. On all panels, the value of each replicate within a sample set is represented by a gray marker. The green bars are the averages of each sample set (n = 3). All experiments were repeated three times independently. Source data are provided as a Source Data file.
