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

Patent metadata

Field	Value
Publication number	US-9697460-B2
Application number	US-201013512449-A
Country	US
Kind code	B2
Filing date	Nov 30, 2010
Priority date	Nov 30, 2009
Publication date	Jul 4, 2017
Grant date	Jul 4, 2017

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. An analog-to-digital biological converter switch, the biological converter switch comprising at least two nucleic acid modules, wherein each of the at least two nucleic acid modules comprise:
an inducible promoter nucleic acid sequence (iP A ) operably linked to a repressor nucleic acid sequence (R A ) encoding a repressor sequence, and
a toggle switch nucleic acid (TS A ), (iP A -R A -TS A ) n ; wherein the toggle switch nucleic acid comprises a first repressible promoter nucleic acid sequence (rP 1 ) operably linked to and capable of driving expression of a second repressor nucleic acid sequence (R 2 ) encoding a second repressor protein, and a second repressible promoter nucleic acid sequence (rP 2 ) operably linked to and capable of driving expression of: (i) a first repressor nucleic acid sequence (R 1 ) encoding a first repressor protein, and (ii) an output nucleic acid sequence encoding an output product (OP) (rP 1 -R 2 and rP 2 -R 1 -OP), wherein the first repressible promoter nucleic acid sequence rP 1 is capable of being inhibited by the first repressor protein and the second repressible promoter nucleic acid sequence rP 2 is capable of being inhibited by the second repressor protein, and
wherein the inducible nucleic acid promoter nucleic acid sequence of each of the at least two nucleic acid modules has a different threshold for induction by a same inducing agent.

2. The analog-to-digital biological converter switch of claim 1 , wherein the repressor protein encoded by the first repressor nucleic acid sequence of the toggle switch (R 1 ) and the repressor protein encoded by the module (R A ) are the same repressor protein.

3. The analog-to-digital biological converter switch of claim 1 , wherein the repressor proteins encoded by the at least two nucleic acid modules are different repressor proteins.

4. The analog-to-digital 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.

5. The analog-to-digital biological converter switch of claim 1 , wherein the output nucleic acid sequence of each toggle switch of each module encodes a same output product.

6. The analog-to-digital biological converter switch of claim 1 , wherein the output nucleic acid sequence of each toggle switch of each module encodes a reporter protein.

7. The analog-to-digital biological converter switch of claim 1 , wherein the output nucleic acid sequence of each toggle switch of each module encodes a different output product.

8. The analog-to-digital biological converter switch of claim 1 , wherein n is an integer value between and including 2 and 100.

9. The analog-to-digital biological converter switch of claim 1 , wherein n is an integer value between and including 2 and 10.

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

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

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

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

14. The analog-to-digital biological converter switch of claim 1 , wherein at least one repressor protein is an engineered zinc-finger protein.

15. The analog-to-digital biological converter switch of claim 1 , where the inducible promoter nucleic acid sequence, the first repressible promoter nucleic acid sequence, and the second repressible promoter nucleic acid sequence of each of the at least two nucleic acid modules comprises a nucleic acid 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.

16. An analog-to-digital biological converter switch comprising the nucleic acid circuit depicted in FIG. 1A , the content of which is herein incorporated by reference in its entirety.

Assignees

• Collins James J
• Lu Timothy Kuan-Ta
• Univ Boston
• Massachusetts Inst Technology

Inventors

• Collins James J
• Lu Timothy Kuan-Ta

Classifications

• H03M1/74

  Simultaneous conversion · CPC title

• H03M1/361 Primary

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

• G06N3/002 Primary

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