Modular nucleic acid-based circuits for counters, binary operations, memory, and logic

An inducer engineered genetic counter nucleic acid molecule comprising a nucleic acid sequence comprising an inducible promoter sequence (iPA), at least one single invertase memory module (SIMM), and an output nucleic acid sequence encoding an output product (OP), where the SIMM comprises a forward recombinase recognition sequence (RRSfor), an inverted inducible promoter sequence (iP1,inv), a ribosome binding site (RBS), a recombinase gene sequence (RC), a degradation tag sequence (D), a transcriptional terminator sequence (T), and a reverse recombinase recognition sequence (RRSrev), such that the inducer engineered genetic counter nucleic acid molecule comprises a nucleic acid molecule encoding the following components:

• iPA-[RRS1,for-iP1,inv-RBS-RC1-D-T-RRS1,rev]n-OP,
• wherein iPA and the iP1 of each SIMM are responsive to the same inducer, wherein the recombinase encoded by each at least one SIMM is specific for the forward and reverse recombinase recognition site of that SIMM, and wherein n is an integer value≧1.

A single-inducer engineered genetic counter nucleic acid molecule comprising a nucleic acid sequence encoding:

• an inducible promoter sequence (iPA), one single invertase memory module (SIMM), and an output nucleic acid sequence encoding an output product (OP), where the SIMM comprises a forward recombinase recognition sequence (RRSfor), an inverted inducible promoter sequence (iP1,inv), a ribosome binding site (RBS), a recombinase gene sequence (RC), a degradation tag sequence (D), a transcriptional terminator sequence (T), and a reverse recombinase recognition sequence (RRSrev), such that the single-inducer engineered genetic counter nucleic acid molecule comprises a nucleic acid sequence encoding the following components:
• iPA-[RRS1,for-RBS-RC1-D-T-RRS1,rev]-OP,
• wherein iPA and iP1 are responsive to the same inducer, and wherein the recombinase encoded by the SIMM is specific for the forward and reverse recombinase recognition site of the SIMM.

A single-inducer engineered genetic counter nucleic acid molecule comprising a nucleic acid sequence encoding:

• an inducible promoter sequence (iPA), two single invertase memory modules (SIMMs), and an output nucleic acid sequence encoding an output product (OP), where each SIMM comprises a forward recombinase recognition sequence (RRSfor), an inverted inducible promoter sequence (iPinv), a ribosome binding site (RBS), a recombinase gene sequence (RC), a degradation tag sequence (D), a transcriptional terminator sequence (T), and a reverse recombinase recognition sequence (RRSrev), such that the single-inducer engineered genetic counter nucleic acid molecule comprising a nucleic acid sequence encoding the following components:
• iPA-[RRS1,for-iP1,inv-RBS-RC1-D-T-RRS1,rev]-[RRS2,for-iP1,inv-RBS-RC2-D-T-RRS2,rev]-OP,
• wherein iPA and iP1 are responsive to the same inducer, and wherein the recombinase encoded by each SIMM is specific for the forward and reverse recombinase recognition site of that SIMM.

A multiple-inducer engineered genetic counter nucleic acid molecule comprising a nucleic acid sequence encoding:

• an inducible promoter sequence (iPA), two single invertase memory modules (SIMM), and an output nucleic sequence encoding an output product (OP), where each SIMM comprises a forward recombinase recognition sequence (RRSfor), an inverted inducible promoter sequence (iPinv), a ribosome binding site (RBS), a recombinase gene sequence (RC), a degradation tag sequence (D), a transcriptional terminator sequence (T), and a reverse recombinase recognition sequence (RRSrev), such that the multiple-inducer engineered genetic counter nucleic acid molecule comprising a nucleic acid sequence encoding the following components:
• iPA-[RRS1,for-iP1,inv-RBS-RC1-D-T-RRS1,rev]-[RRS2,for-iP2,inv-RBS-RC2-D-T-RRS2,rev]OP,
• wherein iPA and the iP of at least one SIMM are responsive to different inducers from each other, and wherein the recombinase encoded by each SIMM is specific for the forward and reverse recombinase recognition site of that SIMM.