Validation of a fully integrated platform and disposable microfluidic chips enabling parallel purification of genome segments for assembly

Biotechnology and Bioengineering

Volumn 111, Issue 8, 2014, Pages 1627-1637

  Kersaudy Kerhoas, M ^a   Amalou, F ^a   Che, A ^b   Kelly, J ^b   Liu, Y ^a   Desmulliez, M P Y ^a   Shu, W ^a  

^a HERIOT WATT UNIVERSITY   (United Kingdom)

^b Ginkgo Bioworks   (United States)

Author keywords

Lab on a chip; Microfluidics; Purification; Synthetic biology

Indexed keywords

BIOLOGY; FLUIDIC DEVICES; GENES; GENETIC ENGINEERING; LAB-ON-A-CHIP; PURIFICATION;

DECOUPLING CONTROL STRATEGY; FULLY INTEGRATED; KEY TECHNOLOGIES; MICRO-FLUIDIC DEVICES; MICROFLUIDIC CHIP; MICROFLUIDIC TECHNOLOGIES; RECENT PROGRESS; SYNTHETIC BIOLOGY;

MICROFLUIDICS;

ARTICLE; CONTAMINATION; CONTROL STRATEGY; COST; DISPOSABLE EQUIPMENT; DNA PURIFICATION; EQUIPMENT DESIGN; FLOW RATE; FLUID FLOW; GENOME ANALYSIS; LAB ON A CHIP; MAGNET; MICROFLUIDICS; PHENOTYPE; PNEUMATIC TOOL; RECYCLING; SYNTHETIC BIOLOGY; TEMPERATURE; VALIDATION STUDY; VISCOSITY; COMBINATORIAL CHEMISTRY; DEVICES; GENOME; ISOLATION AND PURIFICATION; MICROFLUIDIC ANALYSIS; REPRODUCIBILITY; SYNTHESIS;

DNA;

COMBINATORIAL CHEMISTRY TECHNIQUES; DNA; EQUIPMENT DESIGN; GENOME; MICROFLUIDIC ANALYTICAL TECHNIQUES; REPRODUCIBILITY OF RESULTS;

EID: 84903306895     PISSN: 00063592     EISSN: 10970290     Source Type: Journal    
DOI: 10.1002/bit.25225     Document Type: Article

References (35)

1. Balagadde FK, You LC, Hansen CL, Arnold FH, Quake SR. 2005. Long-term monitoring of bacteria undergoing programmed population control in a microchemostat. Science 309(5731):137-140.
2. Becker H. 2010. Mind the gap! Lab Chip 10(3):271-273.
3. Boehm CR, Freemont PS, Ces O. 2013. Design of a prototype flow microreactor for synthetic biology in vitro. Lab Chip 13(17):3426-3432.
4. Carr PA, Church GM. 2009. Genome engineering. Nat Biotechnol 27(12):1151-1162.
5. Che A. 2008. Registry of Standard Parts: http://parts.igem.org/Part:pSB1C3.
6. Che A, Knight T, Canton B, Kelly J, Shetty R; Iti Scotland Limited, assignee. 2012. Method For Assembly Of Polynucleic Acid Sequences. US.
7. Colin VL, Rodriguez A, Cristobal HA. 2011. The role of synthetic biology in the design of microbial cell factories for biofuel production. J Biomed Biotechnol 2011:601834.
8. Fu AF, Chou H, Spence C, Arnold FH, Quake SR. 2002. An integrated microfabricated cell sorter. Anal Chem 74:2451-2457.
9. Gomez-Sjoeberg R, Leyrat AA, Pirone DM, Chen CS, Quake SR. 2007. Versatile, fully automated, microfluidic cell culture system. Anal Chem 79(22):8557-8563.
10. Grover WH, von Muhlen MG, Manalis SR. 2008. Teflon films for chemically-inert microfluidic valves and pumps. Lab Chip 8(6):913-918.
11. Gu W, Zhu XY, Futai N, Cho BS, Takayama S. 2004. Computerized microfluidic cell culture using elastomeric channels and Braille displays. PNAS 101(45):15861-15866.
12. Gulati S, Rouilly V, Niu X, Chappell J, Kitney RI, Edel JB, Freemont PS, deMello AJ. 2009. Opportunities for microfluidic technologies in synthetic biology. J R Soc Interface 6(Suppl 4):S493-S506.
13. Hong JW, Quake SR. 2003. Integrated nanoliter systems. Nat Biotechnol 21(10):1179-1183.
14. Karle M, Miwa J, Roth G, Zengerle R, Von Stetten F. 2009. A novel microfluidic platform for continuous DNA extraction and purification using laminar flow magnetophoresis. In: IEEE, IEEE 22nd International Conference on Micro Electro Mechanical Systems, 2009. IEEE. p. 276-279.
15. Ko Y-J, Maeng J-H, Ahn Y, Hwang SY. 2011. DNA ligation using a disposable microfluidic device combined with a micromixer and microchannel reactor. Sens Actuat B Chem 157(2):735-741.
16. Kong DS, Carr PA, Chen L, Zhang S, Jacobson JM. 2007. Parallel gene synthesis in a microfluidic device. Nucleic Acids Res 35(8):e61.
17. Lee C-C, Snyder TM, Quake SR. 2010. A microfluidic oligonucleotide synthesizer. Nucleic Acids Res 38(8):2514-2521.
18. Leslie DC, Easley CJ, Seker E, Karlinsey JM, Utz M, Begley MR, Landers JP. 2009. Frequency-specific flow control in microfluidic circuits with passive elastomeric features. Nat Phys 5(3):231-235.
19. Lin H-C, Liu Y-J, Yao D-J. 2010. Core-shell droplets for parallel DNA ligation of an ultra-micro volume using an EWOD microfluidic system. JALA 15(3):210-215.
20. Oblath EA, Henley WH, Alarie JP, Ramsey JM. 2013. A microfluidic chip integrating DNA extraction and real-time PCR for the detection of bacteria in saliva. Lab Chip 13(7):1325-1332.
21. Richmond KE, Li MH, Rodesch MJ, Patel M, Lowe AM, Kim C, Chu LL, Venkataramaian N, Flickinger SF, Kaysen J, Belshaw PJ, Sussman MR, Cerrina F. 2004. Amplification and assembly of chip-eluted DNA (AACED): A method for high-throughput gene synthesis. Nucleic Acids Res 32(17):5011-5018.
22. Shaikh KA, Ryu KS, Goluch ED, Nam J-M, Liu J, Thaxton CS, Chiesl TN, Barron AE, Lu Y, Mirkin CA, Liu C. 2005. A modular microfluidic architecture for integrated biochemical analysis. PNAS 102(28):9745-9750.
23. Skafte-Pedersen P, Sip CG, Folch A, Dufva M. 2013. Modular microfluidic systems using reversibly attached PDMS fluid control modules. J Micromech Microeng 23(5):055011.
24. Smolke CD, Silver PA. 2011. Informing biological design by integration of systems and synthetic biology. Cell 144(6):855-859.
25. Sollier E, Murray C, Maoddi P, Di Carlo D. 2011. Rapid prototyping polymers for microfluidic devices and high pressure injections. Lab Chip 11(22):3752-3765.
26. Squires TM, Quake SR. 2005. Microfluidics: Fluid physics at the nanoliter scale. Rev Mod Phys 77(3):977-1026.
27. Szita N, Polizzi K, Jaccard N, Baganz F. 2010. Microfluidic approaches for systems and synthetic biology. Curr Opin Biotechnol 21(4):517-523.
28. Tian JD, Gong H, Sheng NJ, Zhou XC, Gulari E, Gao XL, Church G. 2004. Accurate multiplex gene synthesis from programmable DNA microchips. Nature 432(7020):1050-1054.
29. Vinuselvi P, Park S, Kim M, Park JM, Kim T, Lee SK. 2011. Microfluidic technologies for synthetic biology. Int J Mol Sci 12(6):3576-3593.
30. Webb DP, Knauf B, Liu C, Hutt D, Conway P. 2009. Productionisation issues for commercialisation of microfluidic based devices. Sens Rev 29(4):349-354.
31. Wu AR, Hiatt JB, Lu R, Attema JL, Lobo NA, Weissman IL, Clarke MF, Quake SR. 2009a. Automated microfluidic chromatin immunoprecipitation from 2, 000 cells. Lab Chip 9(10):1365-1370.
32. Wu AR, Hiatt JB, Lu R, Attema JL, Lobo NA, Weissman IL, Clarke MF, Quake SR. 2009b. Automated microfluidic chromatin immunoprecipitation from 2000 cells. Lab Chip 9:1365-1370.
33. Xia YN, Whitesides GM. 1998. Soft lithography. Angew Chem Int Ed 37(5):551-575.
34. Zhang W, Lin S, Wang C, Hu J, Li C, Zhuang Z, Zhou Y, Mathies RA, Yang CJ. 2009. PMMA/PDMS valves and pumps for disposable microfluidics. Lab Chip 9(21):3088-3094.
35. Zhou XC, Cai SY, Hong AL, You QM, Yu PL, Sheng NJ, Srivannavit O, Muranjan S, Rouillard JM, Xia YM, Zhang XL, Xiang Q, Ganesh R, Zhu Q, Matejko A, Gulari E, Gao XL. 2004. Microfluidic PicoArray synthesis of oligodeoxynucleotides and simultaneous assembling of multiple DNA sequences. Nucleic Acids Res 32(18):5409-5417.