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BioBricks

Learn about the different types of biobricks used in synthetic biology, including chassis organisms, vectors, parts, and devices. Discover their function and how they can be used to construct genetic systems in bacteria. Find resources and information on terminators, protein coding genes, ribosome binding sites, conjugation, reporters, and more.

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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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