Fig. 5: A layered OR gate built from NAND gates.
From: Trumpet is an operating system for simple and robust cell-free biocomputing
a A schematic showing a full circuit of three NAND gates performing an OR gate operation. Within the processor, two unique NAND gates produce single-stranded DNA outputs, which become inputs for a third unique NAND gate. The final output of the third NAND gate is RNA aptamer fluorescence. b The general architecture of the first two NAND gates (NAND 1 or NAND 2) in the circuit. c When both pairs of inputs are present with NAND 1 or NAND 2, a restriction enzyme cleaves the gate templates, leaving the promoter-annealed portion of the templates attached to the magnetic bead. The cut portions of the templates can be removed by discarding the supernatant. When the release oligo is added to the digested versions of the gates, there is no complementary site for the release oligo to hybridize to. d When zero inputs are present with NAND 1 or NAND 2, the restriction enzyme does not cleave the gate template. The entire 106-base template remains attached to the beads, and remains bound to the magnetic beads. When the release oligo is added, it hybridizes with its complementary region on the gate template. When each output from NAND 1 and NAND 2 are added to NAND 3, they act as the single-stranded inputs and can hybridize with the NAND 3 gate template. The restriction enzyme can digest the template, which prevents the transcription of the downstream RNA aptamer. The lack of transcribed fluorescent signal is recorded as a 0. e NAND 1 truth table. (f)Fluorescence results of NAND 3 in all input conditions of NAND 1. (g)NAND 2 truth table. h Fluorescence results of NAND 3 in all input conditions of NAND 2. i Depiction of input conditions of NAND 1 and 2 where the outputs become the inputs for NAND 3. j Fluorescence results of the OR gate processor with all three NAND gates. 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.
