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BioBricks

BioBricks. Part Types. Chassis – organism (E. coli, yeast, mammalian) Vectors – plasmids, strains Parts - Proteins, RBS Devices – Inverters, reporters. Chassis. Constructing systems in bacteria (E. coli) This chassis can interact with most other organisms

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BioBricks

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  1. BioBricks

  2. Part Types • Chassis – organism (E. coli, yeast, mammalian) • Vectors – plasmids, strains • Parts - Proteins, RBS • Devices – Inverters, reporters

  3. Chassis • Constructing systems in bacteria (E. coli) • This chassis can interact with most other organisms • Conjugation, bacteriophage, signalling etc.

  4. Vectors • Plasmid – circle of extra chromosomal DNA that can be inserted into cells • These can contain biobrick pieces or be a “backbone” into which one can place biobrick pieces • Strains?

  5. Parts • Regulatory • Terminators • RNA • DNA • Protein Coding • Ribosome Binding Sites • Conjugation

  6. Regulatory www.ntu.edu.sg/home5/pg04325488/dfl.htm

  7. Terminators http://www.sparknotes.com/biology/molecular/dnatranscription/section2.rhtml

  8. RNA Nature Biotechnology 22, 841 - 847 (2004)

  9. DNA • Spacers • Add Biobricks site • Insertion • Transpososome

  10. Protein coding • Genes that code for useful proteins • Repressors, activators • Integrases, Excisionases • Enzymes • Reporters

  11. Ribosome binding sites • Site where the ribosome binds (obviously) • Different sequences lead to change in translation • These sites can be used for riboregulators or other regulation

  12. Conjugation • Genes and plasmids for the transfer of genetic material via conjugation. kentsimmons.uwinnipeg.ca/16cm05/1116/16monera.htm

  13. Protein Generator Composite Devices Measurement Devices • Reporters • Inverters • Signalling

  14. Reporters • Semi-rudundant to DNA as there are genes of reporters in this category • Also reporters expressed by constitutive and regulated promoters • Some more complex systems using reporters

  15. Inverters, Logic devices • PoPs -Polymerase Per Second (or PoPS) is defined as the number of times that an RNA polymerase molecule passes a specific point on DNA per unit time

  16. Signalling • Communication between an individual cell and its neighbors • Signal Senders • Signal Receivers • devices using signalling

  17. Protein Generation • RBS-gene-terminator • promoter-RBS-gene-terminator • operator-promoter-RBS-gene-terminator

  18. Composite devices • Catch all device category

  19. Measurement • Promoter output measurements • RBS characterization • QPI refers to a Quad-Part Inverter: an RBS, repressor protein, terminator and promoter • Screening plasmids: promoter, reporter, cloning site, reporter

  20. “Other” • PCR primers • Tags – degradation, binding and restriction sites

  21. General info • Biobricks: http://parts.mit.edu/registry/index.php/Main_Page • Search biobricks: http://parts.mit.edu/r/parts/partsdb/search.cgi

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