Synthetic in Vitro Circuits

Overview

Journal Curr Opin Chem Biol

Publisher Elsevier

Specialty Biochemistry

Date 2012 Jun 9

PMID 22676890

Citations 19

Authors

Adam J Hockenberry

Michael C Jewett

Affiliations

Soon will be listed here.

Abstract

Inspired by advances in the ability to construct programmable circuits in living organisms, in vitro circuits are emerging as a viable platform for designing, understanding, and exploiting dynamic biochemical circuitry. In vitro systems allow researchers to directly access and manipulate biomolecular parts without the unwieldy complexity and intertwined dependencies that often exist in vivo. Experimental and computational foundations in DNA, DNA/RNA, and DNA/RNA/protein based circuitry have given rise to systems with more than 100 programmed molecular constituents. Functionally, they have diverse capabilities including: complex mathematical calculations, associative memory tasks, and sensing of small molecules. Progress in this field is showing that cell-free synthetic biology is a versatile testing ground for understanding native biological circuits and engineering novel functionality.

Citing Articles

Lipid vesicle-based molecular robots.

Peng Z, Iwabuchi S, Izumi K, Takiguchi S, Yamaji M, Fujita S Lab Chip. 2024; 24(5):996-1029.

PMID: 38239102 PMC: 10898420. DOI: 10.1039/d3lc00860f.

Programmable Biomolecule-Mediated Processors.

Shu J, Tan Z, Wang Q, Yong K J Am Chem Soc. 2023; 145(46):25033-25042.

PMID: 37864571 PMC: 10682996. DOI: 10.1021/jacs.3c04142.

Evolution and synthetic biology.

Ornelas M, Cournoyer J, Bram S, Mehta A Curr Opin Microbiol. 2023; 76:102394.

PMID: 37801925 PMC: 10842511. DOI: 10.1016/j.mib.2023.102394.

Cell-free TXTL synthesis of infectious bacteriophage T4 in a single test tube reaction.

Rustad M, Eastlund A, Jardine P, Noireaux V Synth Biol (Oxf). 2020; 3(1):ysy002.

PMID: 32995511 PMC: 7445788. DOI: 10.1093/synbio/ysy002.

Cell-Free Protein Synthesis: Chassis toward the Minimal Cell.

Yue K, Zhu Y, Kai L Cells. 2019; 8(4).

PMID: 30959805 PMC: 6523147. DOI: 10.3390/cells8040315.

References

Phillips A, Cardelli L . A programming language for composable DNA circuits. J R Soc Interface. 2009; 6 Suppl 4:S419-36. PMC: 2843959. DOI: 10.1098/rsif.2009.0072.focus. View

Genot A, Bath J, Turberfield A . Reversible logic circuits made of DNA. J Am Chem Soc. 2011; 133(50):20080-3. DOI: 10.1021/ja208497p. View

Franco E, Friedrichs E, Kim J, Jungmann R, Murray R, Winfree E . Timing molecular motion and production with a synthetic transcriptional clock. Proc Natl Acad Sci U S A. 2011; 108(40):E784-93. PMC: 3189071. DOI: 10.1073/pnas.1100060108. View

Ahn J, Kang T, Kim D . Tuning the expression level of recombinant proteins by modulating mRNA stability in a cell-free protein synthesis system. Biotechnol Bioeng. 2008; 101(2):422-7. DOI: 10.1002/bit.21884. View

Qian L, Winfree E . Scaling up digital circuit computation with DNA strand displacement cascades. Science. 2011; 332(6034):1196-201. DOI: 10.1126/science.1200520. View

Ahn J, Keum J, Kim D . High-throughput, combinatorial engineering of initial codons for tunable expression of recombinant proteins. J Proteome Res. 2008; 7(5):2107-13. DOI: 10.1021/pr700856s. View

Benenson Y, Paz-Elizur T, Adar R, Keinan E, Livneh Z, Shapiro E . Programmable and autonomous computing machine made of biomolecules. Nature. 2001; 414(6862):430-4. DOI: 10.1038/35106533. View

Jungmann R, Steinhauer C, Scheible M, Kuzyk A, Tinnefeld P, Simmel F . Single-molecule kinetics and super-resolution microscopy by fluorescence imaging of transient binding on DNA origami. Nano Lett. 2010; 10(11):4756-61. DOI: 10.1021/nl103427w. View

Simpson Z, Tsai T, Nguyen N, Chen X, Ellington A . Modelling amorphous computations with transcription networks. J R Soc Interface. 2009; 6 Suppl 4:S523-33. PMC: 2843957. DOI: 10.1098/rsif.2009.0014.focus. View

10.

Purnick P, Weiss R . The second wave of synthetic biology: from modules to systems. Nat Rev Mol Cell Biol. 2009; 10(6):410-22. DOI: 10.1038/nrm2698. View

11.

Jewett M, Forster A . Update on designing and building minimal cells. Curr Opin Biotechnol. 2010; 21(5):697-703. PMC: 2952674. DOI: 10.1016/j.copbio.2010.06.008. View

12.

Kim J, Winfree E . Synthetic in vitro transcriptional oscillators. Mol Syst Biol. 2011; 7:465. PMC: 3063688. DOI: 10.1038/msb.2010.119. View

13.

Xie Z, Liu S, Bleris L, Benenson Y . Logic integration of mRNA signals by an RNAi-based molecular computer. Nucleic Acids Res. 2010; 38(8):2692-701. PMC: 2860122. DOI: 10.1093/nar/gkq117. View

14.

Prokup A, Hemphill J, Deiters A . DNA computation: a photochemically controlled AND gate. J Am Chem Soc. 2012; 134(8):3810-5. DOI: 10.1021/ja210050s. View

15.

Zadeh J, Steenberg C, Bois J, Wolfe B, Pierce M, Khan A . NUPACK: Analysis and design of nucleic acid systems. J Comput Chem. 2010; 32(1):170-3. DOI: 10.1002/jcc.21596. View

16.

Venkataraman S, Dirks R, Ueda C, Pierce N . Selective cell death mediated by small conditional RNAs. Proc Natl Acad Sci U S A. 2010; 107(39):16777-82. PMC: 2947873. DOI: 10.1073/pnas.1006377107. View

17.

Harris D, Jewett M . Cell-free biology: exploiting the interface between synthetic biology and synthetic chemistry. Curr Opin Biotechnol. 2012; 23(5):672-8. PMC: 4038125. DOI: 10.1016/j.copbio.2012.02.002. View

18.

Qian L, Winfree E, Bruck J . Neural network computation with DNA strand displacement cascades. Nature. 2011; 475(7356):368-72. DOI: 10.1038/nature10262. View

19.

Shin J, Noireaux V . Efficient cell-free expression with the endogenous E. Coli RNA polymerase and sigma factor 70. J Biol Eng. 2010; 4:8. PMC: 3161345. DOI: 10.1186/1754-1611-4-8. View

20.

Hodgman C, Jewett M . Cell-free synthetic biology: thinking outside the cell. Metab Eng. 2011; 14(3):261-9. PMC: 3322310. DOI: 10.1016/j.ymben.2011.09.002. View