Abstract
As molecular biology tasks progress from single gene expression to the implementation of entire metabolic pathways and behavioral genetic circuitry, DNA assembly, the process of cloning/constructing a contiguous piece of DNA from a set of composite parts, poses an increasingly formidable challenge. Standardized DNA assembly methodologies have recently emerged that enable and facilitate part re-use, assembly design automation, and high-throughput physical assembly protocols. This chapter reviews the BioBrick, SLIC, Gibson, CPEC and Golden Gate methods, and compares and contrasts their respective strengths, limitations and extents of standardization.
Access this chapter
Tax calculation will be finalised at checkout
Purchases are for personal use only
References
Anderson JC, Dueber JE, Leguia M, Wu GC, Goler JA, Arkin AP, Keasling JD (2010) Bglbricks: a flexible standard for biological part assembly. J Biol Eng 4(1):1
Bitinaite J, Rubino M, Varma KH, Schildkraut I, Vaisvila R, Vaiskunaite R (2007) User friendly dna engineering and cloning method by uracil excision. Nucleic Acids Res 35(6):1992–2002
Densmore D, Kittleson JT, Bilitchenko L, Liu A, Anderson JC (2010a) Rule based constraints for the construction of genetic devices. Circuits and systems (ISCAS), Proceedings of 2010 IEEE international symposium. Paris, pp 557–560
Densmore D, Hsiau TH-C, Kittleson JT, DeLoache W, Batten C, Anderson JC (2010b) Algorithms for automated dna assembly. Nucleic Acids Res 38(8):2607–2616
Engler C, Gruetzner R, Kandzia R, Marillonnet S (2009) Golden gate shuffling: a one-pot dna shuffling method based on type iis restriction enzymes. PLoS One 4(5):e5553
Engler C, Kandzia R, Marillonnet S (2008) A one pot, one step, precision cloning method with high throughput capability. PLoS One 3(11):e3647
Ferrin LJ, Camerini-Otero RD (1991) Selective cleavage of human dna: reca-assisted restriction endonuclease (rare) cleavage. Science 254(5037):1494–1497
Gibson DG, Young L, Chuang R-Y, Venter JC, Hutchison 3rd CA, Smith HO (2009) Enzymatic assembly of dna molecules up to several hundred kilobases. Nat Methods 6(5):343–345
Ho SN, Hunt HD, Horton RM, Pullen JK, Pease LR (1989) Site-directed mutagenesis by overlap extension using the polymerase chain reaction. Gene 77(1):51–59
Knight TF Jr (2002) Darpa biocomp plasmid distribution 1.00 of standard biobrick components. Technical report, Synthetic Biology Working Group, MIT
Li MZ, Elledge SJ (2007) Harnessing homologous recombination in vitro to generate recombinant dna via slic. Nat Methods 4(3):251–256
Quan J, Tian J (2009) Circular polymerase extension cloning of complex gene libraries and pathways. PLoS One 4(7):e6441
Shetty RP, Endy D, Knight TF Jr (2008) Engineering biobrick vectors from biobrick parts. JÂ Biol Eng 2:5
Sone T, Yahata K, Sasaki Y, Hotta J, Kishine H, Chesnut JD, Imamoto F (2008) Multi-gene gateway clone design for expression of multiple heterologous genes in living cells: modular construction of multiple cdna expression elements using recombinant cloning. J Biotechnol 136(3–4):113–121
Acknowledgements
This work conducted by the Joint BioEnergy Institute was supported by the Office of Science, Office of Biological and Environmental Research, of the U.S. Department of Energy under Contract No. DE-AC02-05CH11231.
Author information
Authors and Affiliations
Corresponding author
Editor information
Editors and Affiliations
Rights and permissions
Copyright information
© 2011 Springer Science+Business Media, LLC
About this chapter
Cite this chapter
Hillson, N.J. (2011). DNA Assembly Method Standardization for Synthetic Biomolecular Circuits and Systems. In: Koeppl, H., Setti, G., di Bernardo, M., Densmore, D. (eds) Design and Analysis of Biomolecular Circuits. Springer, New York, NY. https://doi.org/10.1007/978-1-4419-6766-4_14
Download citation
DOI: https://doi.org/10.1007/978-1-4419-6766-4_14
Published:
Publisher Name: Springer, New York, NY
Print ISBN: 978-1-4419-6765-7
Online ISBN: 978-1-4419-6766-4
eBook Packages: EngineeringEngineering (R0)