Fig. 4: Trumpet AND and OR gates.
From: Trumpet is an operating system for simple and robust cell-free biocomputing
a The general architecture of an AND gate. The gate begins without a gate template. Instead, the inputs are meant to hybridize directly with each other. A complete 106-base AND gate contains a T7 Max promoter sequence, a 30-base random sequence, and ends with the antisense sequence of an RNA aptamer. When zero or one input is present, the DNA polymerase is unable to extend the input to create a double-stranded gate. The T7 RNA polymerase relies on a double-stranded promoter sequence. This prevents the RNA polymerase from transcribing the aptamer, resulting in a 0 signal. When both inputs are present, DNA polymerase is able to extend each end to create a full double-stranded gate template. T7 RNA polymerase is then able to transcribe the RNA aptamer, and the aptamer fluorescent signal is recorded as a 1. b An AND gate truth table. c Fluorescent results of an AND gate encoding a Broccoli aptamer. d The general architecture of an OR gate. The gate template includes both 75-base sense and antisense strands and encodes just the T7 Max promoter sequence followed by an RNA aptamer sequence. When the sense version of the gate template is present with Input 2, DNA polymerase can extend the template in one cycle to create a double-stranded sequence. Likewise, the antisense version of the gate template can be extended when paired with Input 1. When both versions of the gate template and both inputs are present, extension can occur. In all cases, T7 RNA polymerase can transcribe the aptamer on the extended template leading to a 1 signal. When neither input is present, the RNA polymerase is unable to transcribe. The lack of aptamer signal is recorded as a 0. e An OR gate truth table. f Fluorescent results of an OR gate encoding a Broccoli aptamer. 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.
