Repository-based plasmid design


Autoři: Joshua J. Timmons aff001;  Doug Densmore aff001
Působiště autorů: Lattice Automation Inc., Boston, Massachusetts, United States of America aff001;  Department of Electrical and Computer Engineering, Boston University, Boston, Massachusetts, United States of America aff002;  Biological Design Center, Boston University, Boston, Massachusetts, United States of America aff003
Vyšlo v časopise: PLoS ONE 15(1)
Kategorie: Research Article
doi: 10.1371/journal.pone.0223935

Souhrn

There was an explosion in the amount of commercially available DNA in sequence repositories over the last decade. The number of such plasmids increased from 12,000 to over 300,000 among three of the largest repositories: iGEM, Addgene, and DNASU. A challenge in biodesign remains how to use these and other repository-based sequences effectively, correctly, and seamlessly. This work describes an approach to plasmid design where a plasmid is specified as simply a DNA sequence or list of features. The proposed software then finds the most cost-effective combination of synthetic and PCR-prepared repository fragments to build the plasmid via Gibson assembly®. It finds existing DNA sequences in both user-specified and public DNA databases: iGEM, Addgene, and DNASU. Such a software application is introduced and characterized against all post-2005 iGEM composite parts and all Addgene vectors submitted in 2018 and found to reduce costs by 34% versus a purely synthetic plasmid design approach. The described software will improve current plasmid assembly workflows by shortening design times, improving build quality, and reducing costs.

Klíčová slova:

BLAST algorithm – Molecular cloning – Plasmid construction – Polymerase chain reaction – Sequence assembly tools – Sequence databases – Synthetic biology – Synthetic plasmids


Zdroje

1. Chen C, Okayama H. High-efficiency transformation of mammalian cells by plasmid DNA. Mol Cell Biol. 1987;7: 2745–2752. doi: 10.1128/mcb.7.8.2745 3670292

2. Nielsen AAK, Der BS, Shin J, Vaidyanathan P, Paralanov V, Strychalski EA, et al. Genetic circuit design automation. Science. 2016;352: aac7341. doi: 10.1126/science.aac7341 27034378

3. Jinek M, East A, Cheng A, Lin S, Ma E, Doudna J. RNA-programmed genome editing in human cells. eLife. 2013;2: e00471. doi: 10.7554/eLife.00471 23386978

4. Lodish H, Berk A, Zipursky SL, Matsudaira P, Baltimore D, Darnell J. DNA Cloning with Plasmid Vectors. Mol Cell Biol 4th Ed. 2000 [cited 5 May 2019]. Available: https://www.ncbi.nlm.nih.gov/books/NBK21498/

5. Brophy JAN, Voigt CA. Principles of Genetic Circuit Design. Nat Methods. 2014;11: 508–520. doi: 10.1038/nmeth.2926 24781324

6. Densmore D, Hassoun S. Design Automation for Synthetic Biological Systems. IEEE Des Test Comput. 2012;29: 7–20. doi: 10.1109/MDT.2012.2193370

7. Peccoud J, Blauvelt MF, Cai Y, Cooper KL, Crasta O, DeLalla EC, et al. Targeted Development of Registries of Biological Parts. PLOS ONE. 2008;3: e2671. doi: 10.1371/journal.pone.0002671 18628824

8. Kamens J. The Addgene repository: an international nonprofit plasmid and data resource. Nucleic Acids Res. 2015;43: D1152–D1157. doi: 10.1093/nar/gku893 25392412

9. Kamens J. Addgene: Making Materials Sharing “Science As Usual.” PLOS Biol. 2014;12: e1001991. doi: 10.1371/journal.pbio.1001991 25387006

10. Kahl L, Molloy J, Patron N, Matthewman C, Haseloff J, Grewal D, et al. Opening options for material transfer. Nat Biotechnol. 2018;36: 923–927. doi: 10.1038/nbt.4263 30307930

11. Brown J. The iGEM competition: building with biology. IET Synth Biol. 2007;1: 3–6.

12. Smolke CD. Building outside of the box: iGEM and the BioBricks Foundation. Nat Biotechnol. 2009;27: 1099. doi: 10.1038/nbt1209-1099 20010584

13. Zuo D, Mohr SE, Hu Y, Taycher E, Rolfs A, Kramer J, et al. PlasmID: a centralized repository for plasmid clone information and distribution. Nucleic Acids Res. 2007;35: D680–D684. doi: 10.1093/nar/gkl898 17132831

14. The Fungal Genetics Stock Center: a repository for 50 years of fungal genetics research | SpringerLink. [cited 11 May 2019]. Available: https://link.springer.com/article/10.1007/s12038-010-0014-6

15. Iverson SV, Haddock TL, Beal J, Densmore DM. CIDAR MoClo: Improved MoClo Assembly Standard and New E. coli Part Library Enable Rapid Combinatorial Design for Synthetic and Traditional Biology. ACS Synth Biol. 2016;5: 99–103. doi: 10.1021/acssynbio.5b00124 26479688

16. Engler C, Youles M, Gruetzner R, Ehnert T-M, Werner S, Jones JDG, et al. A Golden Gate Modular Cloning Toolbox for Plants. ACS Synth Biol. 2014;3: 839–843. doi: 10.1021/sb4001504 24933124

17. Sarrion-Perdigones A, Falconi EE, Zandalinas SI, Juárez P, Fernández-del-Carmen A, Granell A, et al. GoldenBraid: An Iterative Cloning System for Standardized Assembly of Reusable Genetic Modules. PLOS ONE. 2011;6: e21622. doi: 10.1371/journal.pone.0021622 21750718

18. Oberortner E, Cheng J-F, Hillson NJ, Deutsch S. Streamlining the Design-to-Build Transition with Build-Optimization Software Tools. ACS Synth Biol. 2017;6: 485–496. doi: 10.1021/acssynbio.6b00200 28004921

19. Gibson DG. Enzymatic assembly of overlapping DNA fragments. Methods in enzymology. Elsevier; 2011. pp. 349–361. doi: 10.1016/B978-0-12-385120-8.00015-2 21601685

20. Gibson DG, Young L, Chuang R-Y, Venter JC, Hutchison III CA, Smith HO. Enzymatic assembly of DNA molecules up to several hundred kilobases. Nat Methods. 2009;6: 343. doi: 10.1038/nmeth.1318 19363495

21. Casini A, Storch M, Baldwin GS, Ellis T. Bricks and blueprints: methods and standards for DNA assembly. Nat Rev Mol Cell Biol. 2015;16: 568–576. doi: 10.1038/nrm4014 26081612

22. Timmons J. REPP. 2019. Available: https://github.com/Lattice-Automation/repp

23. Repp—Manage Files at SourceForge.net. [cited 26 Jun 2019]. Available: https://sourceforge.net/projects/repplasmid/files/

24. Herscovitch M, Perkins E, Baltus A, Fan M. Addgene provides an open forum for plasmid sharing. Nat Biotechnol. 2012;30: 316–317. doi: 10.1038/nbt.2177 22491276

25. Seiler CY, Park JG, Sharma A, Hunter P, Surapaneni P, Sedillo C, et al. DNASU plasmid and PSI: Biology-Materials repositories: resources to accelerate biological research. Nucleic Acids Res. 2013;42: D1253–D1260. doi: 10.1093/nar/gkt1060 24225319

26. Registry API—parts.igem.org. [cited 23 Apr 2019]. Available: http://parts.igem.org/Registry_API

27. Information NC for B, Pike USNL of M 8600 R, MD B, Usa 20894. Building a BLAST database with local sequences. National Center for Biotechnology Information (US); 2008. Available: https://www.ncbi.nlm.nih.gov/books/NBK279688/

28. SnapGene | Software for everyday molecular biology. In: SnapGene [Internet]. [cited 30 Apr 2019]. Available: https://www.snapgene.com/

29. Adames NR, Wilson ML, Fang G, Lux MW, Glick BS, Peccoud J. GenoLIB: a database of biological parts derived from a library of common plasmid features. Nucleic Acids Res. 2015;43: 4823–4832. doi: 10.1093/nar/gkv272 25925571

30. Labs Program—igem.org. [cited 4 May 2019]. Available: https://igem.org/Labs_Program

31. Information NC for B, Pike USNL of M 8600 R, MD B, Usa 20894. Appendices. National Center for Biotechnology Information (US); 2018. Available: https://www.ncbi.nlm.nih.gov/books/NBK279684/

32. Untergasser A, Cutcutache I, Koressaar T, Ye J, Faircloth BC, Remm M, et al. Primer3—new capabilities and interfaces. Nucleic Acids Res. 2012;40: e115. doi: 10.1093/nar/gks596 22730293

33. Koressaar T, Remm M. Enhancements and modifications of primer design program Primer3. Bioinformatics. 2007;23: 1289–1291. doi: 10.1093/bioinformatics/btm091 17379693

34. Ye J, Coulouris G, Zaretskaya I, Cutcutache I, Rozen S, Madden TL. Primer-BLAST: a tool to design target-specific primers for polymerase chain reaction. BMC Bioinformatics. 2012;13: 134. doi: 10.1186/1471-2105-13-134 22708584

35. parts.igem.org. [cited 20 Apr 2019]. Available: http://parts.igem.org/Main_Page

36. Addgene: Homepage. [cited 23 Apr 2019]. Available: https://www.addgene.org/

37. Shetty RP, Endy D, Knight TF. Engineering BioBrick vectors from BioBrick parts. J Biol Eng. 2008;2: 5. doi: 10.1186/1754-1611-2-5 18410688

38. Wan X, Volpetti F, Petrova E, French C, Maerkl SJ, Wang B. Cascaded amplifying circuits enable ultrasensitive cellular sensors for toxic metals. Nat Chem Biol. 2019;15: 540–548. doi: 10.1038/s41589-019-0244-3 30911179

39. Christen M, Deutsch S, Christen B. Genome Calligrapher: A Web Tool for Refactoring Bacterial Genome Sequences for de Novo DNA Synthesis. ACS Synth Biol. 2015;4: 927–934. doi: 10.1021/acssynbio.5b00087 26107775

40. Hillson NJ, Rosengarten RD, Keasling JD. j5 DNA Assembly Design Automation Software. ACS Synth Biol. 2012;1: 14–21. doi: 10.1021/sb2000116 23651006

41. Benchling | The Life Sciences R&D Cloud. In: Benchling [Internet]. [cited 5 May 2019]. Available: https://www.benchling.com/

42. Geneious | Bioinformatics Software for Sequence Data Analysis. In: Geneious [Internet]. [cited 5 May 2019]. Available: https://www.geneious.com/

43. Apt KR. Logic Programming. Handb Theor Comput Sci Vol B Form Models Semat B. 1990;1990: 493–574.

44. dnaweaver-webapp. [cited 17 Jun 2019]. Available: https://dnaweaver.genomefoundry.org/#/

45. Engler C, Marillonnet S. Golden Gate Cloning. In: Valla S, Lale R, editors. DNA Cloning and Assembly Methods. Totowa, NJ: Humana Press; 2014. pp. 119–131. doi: 10.1007/978-1-62703-764-8_9

46. McLaughlin JA, Myers CJ, Zundel Z, Mısırlı G, Zhang M, Ofiteru ID, et al. SynBioHub: A Standards-Enabled Design Repository for Synthetic Biology. ACS Synth Biol. 2018;7: 682–688. doi: 10.1021/acssynbio.7b00403 29316788

47. Eugene–A Domain Specific Language for Specifying and Constraining Synthetic Biological Parts, Devices, and Systems. [cited 16 Jun 2019]. Available: https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0018882

48. Double Dutch: A Tool for Designing Combinatorial Libraries of Biological Systems | ACS Synthetic Biology. [cited 16 Jun 2019]. Available: https://pubs.acs.org/doi/abs/10.1021/acssynbio.5b00232


Článek vyšel v časopise

PLOS One


2020 Číslo 1