Biological analog-to-digital and digital-to-analog converters

Patent metadata

Field	Value
Publication number	US-10614353-B2
Application number	US-201715499202-A
Country	US
Kind code	B2
Filing date	Apr 27, 2017
Priority date	Nov 30, 2009
Publication date	Apr 7, 2020
Grant date	Apr 7, 2020

Abstract

Described herein are novel biological converter switches that utilize modular components, such as genetic toggle switches and single invertase memory modules (SIMMs), for converting analog inputs to digital outputs, and digital inputs to analog outputs, in cells and cellular systems. Flexibility in these biological converter switches is provided by combining individual modular components, i.e., SIMMs and genetic toggle switches, together. These biological converter switches can be combined in a variety of network topologies to create circuits that act, for example, as switchboards, and regulate the production of an output product(s) based on the combination and nature of input signals received.

First claim

We claim:

1. A digital-to-analog biological converter switch, the digital-to-analog biological converter switch comprising at least two single invertase memory modules (SIMM), wherein each SIMM is an engineered nucleic acid construct comprising nucleic acid sequences in following order; an inducible promoter sequence (iP), a forward recombinase recognition site sequence (RRS for ), an inverted promoter sequence (P inv ), a recombinase gene sequence (RC), a reverse recombinase recognition site sequence (RRS rev ), an inverted second inducible promoter sequence (iP inv, 2 ), and an output product sequence (OP), (iP-RRS for -P inv -RC-RRS rev -iP inv, 2 -OP) n ;
wherein the recombinase gene sequence of each SIMM encodes a recombinase that recognizes the RRS for and RRS rev of that SIMM; and wherein n≥2.

2. The digital-to-analog biological converter switch of claim 1 , wherein the inverted promoter sequence (P inv ) of each SIMM has a different promoter strength.

3. The digital-to-analog biological converter switch of claim 1 , wherein the recombinases encoded by each SIMM is different.

4. The digital-to-analog biological converter switch of claim 1 , wherein the inverted second inducible promoter sequence of each SIMM is induced by the same inducing agent.

5. The digital-to-analog biological converter switch of claim 1 , wherein the output product is a reporter protein, a transcriptional repressor, a transcriptional activator, a selection marker, an enzyme, a receptor protein, a ligand protein, an RNA, an iRNA molecule, a riboswitch, or a short-hairpin RNA.

6. The digital-to-analog biological converter switch of claim 1 , wherein the output product sequence of each SIMM encodes for the same output product.

7. The digital-to-analog biological converter switch of claim 1 , wherein the output product sequence of each SIMM encodes for a different output product.

8. The digital-to-analog biological converter switch of claim 1 , wherein the output product sequence of each SIMM encodes for the same reporter protein.

9. The digital-to-analog biological converter switch of claim 8 , wherein the reporter protein is a fluorescent reporter.

10. The digital-to-analog biological converter switch of claim 1 , wherein the number of SIMMs in the switch is an integer value between and including 2 and 100.

11. The digital-to-analog biological converter switch of claim 1 , further comprising at least one ribosome binding sequence.

12. The digital-to-analog biological converter switch of claim 1 , further comprising at least one terminator sequence.

13. The digital-to-analog biological converter switch of claim 1 , further comprising at least one degradation tag sequence.

14. The digital-to-analog biological converter switch of claim 1 , further comprising at least one sequence encoding an iRNA molecule specific for at least one protein encoded by the digital-to-analog biological converter switch.

15. The digital-to-analog biological converter switch of claim 14 , wherein the iRNA molecule specific for at least one protein is specific for the recombinase encoded by the SIMM.

16. The digital-to-analog biological converter switch of claim 1 , where the promoter sequence of the inducible promoters comprises a sequence selected from any of the promoter sequences of SEQ ID NOs: 1-7, SEQ ID NOs: 167-843, and SEQ ID NOs: 1009-1010.

17. The digital-to-analog biological converter switch of claim 1 , where the promoter sequence of the inverted promoter (P inv ) comprises a sequence selected from any of the promoter sequences of SEQ ID NOs: 41-198, SEQ ID NOs: 205-319, and SEQ ID NOs: 1005-1008.

Assignees

• Univ Boston
• Massachusetts Inst Technology

Inventors

• Collins James J
• Lu Timothy Kuan-Ta

Classifications

• H03M1/74

  Simultaneous conversion · CPC title

• G06N3/002 Primary

  Biomolecular computers, i.e. using biomolecules, proteins, cells (using DNA G06N3/123; using neurons G06N3/061) · CPC title

• H03M1/361 Primary

  having a separate comparator and reference value for each quantisation level, i.e. full flash converter type · CPC title