J5 DNA assembly design automation

Methods in Molecular Biology

Volumn 1116, Issue , 2014, Pages 245-269

  Hillson, Nathan J ^a  

^a NONE

Author keywords

BioCAD; Combinatorial library; Design automation; DNA assembly; Synthetic biology

Indexed keywords

DNA; ENDONUCLEASE;

ARTICLE; BIOTECHNOLOGICAL PROCEDURES; COMPUTER INTERFACE; COMPUTER PROGRAM; COST BENEFIT ANALYSIS; DNA FLANKING REGION; DNA SEQUENCE; DNA SYNTHESIS; GENETIC ENGINEERING; INTERNET; LABORATORY AUTOMATION; LIQUID; MEDICAL TECHNOLOGY; PRIORITY JOURNAL; PROCESS OPTIMIZATION; ROBOTICS; SEQUENCE HOMOLOGY;

AUTOMATION; DNA; GENETIC TECHNIQUES; INTERNET; MOLECULAR SEQUENCE ANNOTATION; SOFTWARE; TEMPERATURE; USER-COMPUTER INTERFACE;

EID: 84903366037     PISSN: 10643745     EISSN: None     Source Type: Book Series    
DOI: 10.1007/978-1-62703-764-8_17     Document Type: Article

References (64)

1. Ellis T, Adie T, Baldwin GS (2011) DNA assembly for synthetic biology: from parts to pathways and beyond. Integr Biol (Camb) 3:109-118. doi: 10.1039/c0ib00070a
2. Hillson NJ (2011) DNA assembly method standardization for synthetic biomolecular circuits and systems. In: Koeppl H, Densmore D, di Bernardo M, Setti G (eds) Design and analysis of bio-molecular circuits, 1st edn. Springer, New York, pp 295-314
3. Densmore D, Hsiau TH, Kittleson JT et al (2010) Algorithms for automated DNA assembly. Nucleic Acids Res 38:2607-2616. doi: 10.1093/nar/gkq165
4. Shetty RP, Endy D, Knight TF Jr (2008) Engineering BioBrick vectors from BioBrick parts. J Biol Eng 2:5. doi: 10.1186/1754-1611-2-5 (Pubitemid 351827652)
5. Anderson JC, Dueber JE, Leguia M et al (2010) BglBricks: a flexible standard for biological part assembly. J Biol Eng 4:1. doi: 10.1186/1754-1611-4- 1
6. Leguia M, Brophy J, Densmore D et al (2011) Automated assembly of standard biological parts. Methods Enzymol 498:363-397. doi: 10.1016/B978-0-12-385120-8.00016-4
7. Beal J, Weiss R, Densmore D et al (2012) An end-to-end workflow for engineering of biological networks from high-level specifications. ACS Synth Biol 1:317. doi: 10.1021/sb300030d
8. Weber E, Engler C, Gruetzner R et al (2011) A modular cloning system for standardized assembly of multigene constructs. PLoS One 6:e16765. doi: 10.1371/journal.pone.0016765
9. Sarrion-Perdigones A, Falconi EE, Zandalinas SI et al (2011) GoldenBraid: an iterative cloning system for standardized assembly of reusable genetic modules. PLoS One 6:e21622. doi: 10.1371/journal.pone.0021622
10. Quan J, Tian J (2009) Circular polymerase extension cloning of complex gene libraries and pathways. PLoS One 4:e6441. doi: 10.1371/journal.pone.0006441
11. Shao Z, Luo Y, Zhao H (2011) Rapid characterization and engineering of natural product biosynthetic pathways via DNA assembler. Mol Biosyst 7:1056-1059. doi: 10.1039/c0mb00338g
12. Carothers JM, Goler JA, Juminaga D et al (2011) Model-driven engineering of RNA devices to quantitatively program gene expression. Science 334:1716-1719. doi: 10.1126/science.1212209
13. Salis HM, Mirsky EA, Voigt CA (2009) Automated design of synthetic ribosome binding sites to control protein expression. Nat Biotechnol 27:946-950. doi: 10.1038/nbt.1568
14. Egbert RG, Klavins E (2012) Fine-tuning gene networks using simple sequence repeats. Proc Natl Acad Sci U S A 109:16817-16822. doi: 10.1073/pnas.1205693109
15. Mutalik VK, Guimaraes JC, Cambray G et al (2013) Quantitative estimation of activity and quality for collections of functional genetic elements. Nat Methods 10(4):347-353. doi: -10.1038/nmeth.2403
16. Mutalik VK, Guimaraes JC, Cambray G et al (2013) Precise and reliable gene expression via standard transcription and translation initiation elements. Nat Methods 10(4):354-360
17. Hillson NJ, Rosengarten RD, Keasling JD (2012) j5 DNA assembly design automation software. ACS Synth Biol 1:14-21. doi: 10.1021/Sb2000116
18. Chen J, Densmore D, Ham TS et al (2012) DeviceEditor visual biological CAD canvas. J Biol Eng 6:1. doi: 10.1186/1754-1611-6-1
19. Ham TS, Dmytriv Z, Plahar H et al (2012) Design, implementation and practice of JBEIICE: an open source biological part registry platform and tools. Nucleic Acids Res 40:e141. doi: 10.1093/nar/gks531
20. Linshiz G, Stawski N, Poust S et al (2012) PaR-PaR laboratory automation platform. ACS Synth Biol 2:216-222. doi: 10.1021/sb300075t
21. Thieme F, Engler C, Kandzia R et al (2011) Quick and clean cloning: a ligation- independent cloning strategy for selective cloning of specific PCR products from non-specific mixes. PLoS One 6:e20556. doi: 10.1371/journal.pone. 0020556
22. Li MZ, Elledge SJ (2007) Harnessing homologous recombination in vitro to generate recombinant DNA via SLIC. Nat Methods 4:251-256. doi: 10.1038/nmeth1010 (Pubitemid 46358876)
23. You C, Zhang XZ, Zhang YH (2012) Simple cloning via direct transformation of PCR product (DNA Multimer) to Escherichia coli and Bacillus subtilis . Appl Environ Microbiol 78:1593-1595. doi: 10.1128/AEM.07105-11
24. Quan J, Tian J (2011) Circular polymerase extension cloning for high-throughput cloning of complex and combinatorial DNA libraries. Nat Protoc 6:242-251. doi: 10.1038/nprot.2010.181
25. Erijman A, Dantes A, Bernheim R et al (2011) Transfer-PCR (TPCR): a highway for DNA cloning and protein engineering. J Struct Biol 175:171-177. doi: 10.1016/j.jsb.2011.04.005
26. Zhang Y, Werling U, Edelmann W (2012) SLiCE: a novel bacterial cell extract-based DNA cloning method. Nucleic Acids Res 40:e55. doi: 10.1093/nar/gkr1288
27. Gibson DG, Young L, Chuang RY et al (2009) Enzymatic assembly of DNA molecules up to several hundred kilobases. Nat Methods 6:343-345. doi: 10.1038/nmeth.1318
28. Ramon A, Smith HO (2011) Single-step linker-based combinatorial assembly of promoter and gene cassettes for pathway engineering. Biotechnol Lett 33:549-555. doi: 10.1007/s10529-010-0455-x
29. Shao Z, Zhao H, Zhao H (2009) DNA assembler, an in vivo genetic method for rapid construction of biochemical pathways. Nucleic Acids Res 37:e16. doi: 10.1093/nar/gkn991
30. Wingler LM, Cornish VW (2011) Reiterative recombination for the in vivo assembly of libraries of multigene pathways. Proc Natl Acad Sci U S A 108:15135-15140. doi: 10.1073/pnas.1100507108
31. j5 website. http://j5.jbei.org
32. Gibthon website. http://gibthon.org
33. Richardson SM, Liu S, Boeke JD et al (2012) Design-A-Gene with GeneDesign. Methods Mol Biol 852:235-247. doi: 10.1007/978-1-61779-564-0-18
34. Richardson SM, Nunley PW, Yarrington RM et al (2010) GeneDesign 3.0 is an updated synthetic biology toolkit. Nucleic Acids Res 38:2603-2606. doi: 10.1093/nar/gkq143
35. GeneDesign website. http://54.235.254.95/gd/
36. Convert PCR Primers Into In-Fusion ® Primers website. http://www.clontech.com/US/Products/Cloning-and-Competent-Cells/Cloning-Kits/ xxclt-onlineToolsLoad.jsp?citemId=http://bioinfo.clontech.com/infusion/ convertPcrPrimersInit.do&xxheight=750
37. GeneArt ® Primer and Construct Design Tool website. http://bioinfo.invitrogen.com/oligoDesigner
38. Engler C, Gruetzner R, Kandzia R et al (2009) Golden gate shuffling: a one-pot DNA shuffling method based on type IIS restriction enzymes. PLoS One 4:e5553. doi: 10.1371/journal.pone.0005553
39. Engler C, Kandzia R, Marillonnet S (2008) A one pot, one step, precision cloning method with high throughput capability. PLoS One 3:e3647. doi: 10.1371/journal.pone.0003647
40. Engler C, Marillonnet S (2011) Generation of families of construct variants using golden gate shuffling. Methods Mol Biol 729:167-181. doi: 10.1007/978-1-61779-065-2-11
41. Geertsma ER, Dutzler R (2011) A versatile and effi cient high-throughput cloning tool for structural biology. Biochemistry 50:3272-3278. doi: 10.1021/bi200178z
42. Bitinaite J, Rubino M, Varma KH et al (2007) USER™ friendly DNA engineering and cloning method by uracil excision. Nucleic Acids Res 35:1992. doi: 10.1093/nar/gkm041 (Pubitemid 47061665)
43. Annaluru N, Muller H, Ramalingam S (2012) Assembling DNA fragments by USER fusion. Methods Mol Biol 852:77-95. doi: 10.1007/978-1-61779-564-0-7
44. Olsen LR, Hansen NB, Bonde MT et al (2011) PHUSER (Primer Help for USER): a novel tool for USER fusion primer design. Nucleic Acids Res 39:W61-W67. doi: 10.1093/nar/gkr394
45. PHUSER website. http://www.cbs.dtu.dk/services/phuser/
46. TeselaGen website. http://teselagen.com
47. VectorEditor stand-alone software. https://public-registr y.jbei.org/static/vesa/VectorEditor.html
48. Public instance of the JBEI Parts Registry. http://public-registry.jbei. org
49. VectorEditor Project. http://code.google.com/p/vectoreditor/
50. PaR-PaR website. http://prpr.jbei.org
51. PaR-PaR source code github repository. https://github.com/jbei/prpr
52. Synthetic Biology Open Language visual standard. http://www.sbolstandard. org/visual
53. j5 user's manual. http://j5.jbei.org/j5manual/index.html
54. Eugene website. http://eugenecad.org/
55. Bilitchenko L, Liu A, Cheung S et al (2011) Eugene-a domain specific language for specifying and constraining synthetic biological parts, devices, and systems. PLoS One 6:e18882. doi: 10.1371/journal.pone.0018882
56. Rozen S, Skaletsky H (2000) Primer3 on the WWW for general users and for biologist programmers. Methods Mol Biol 132:365-386
57. DINAMelt web server. http://mfold.rna.albany.edu/?q=DINAMelt/Quickfold
58. j5, DeviceEditor, and VectorEditor demonstration video. http://j5.jbei.org/j5-and-DeviceEditor-Demo-Movie.mov
59. DeviceEditor user's manual. http://j5.jbei.org/DeviceEditor-manual/index. html
60. A plasmid Editor (ApE) software. http://biologylabs.utah.edu/jorgensen/ wayned/ape/
61. j5 web-form interface. http://j5.jbei.org/bin/j5-entry-form.pl
62. Clotho website. http://clothocad.org
63. Xia B, Bhatia S, Bubenheim B (2011) Developer's and user's guide to Clotho v2.0 A software platform for the creation of synthetic biological systems. Methods Enzymol 498:97-135. doi: 10.1016/B978-0-12-385120-8.00005-X
64. DeviceEditor software. http://j5.jbei.org/bin/deviceeditor.pl