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 Conjugation, bacteriophage, signalling etc.

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?

Parts Protein Coding Regulatory Ribosome Binding Sites Terminators RNA Conjugation Regulatory Terminators RNA DNA

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

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

RNA Nature Biotechnology 22, 841 - 847 (2004)

DNA Spacers Add Biobricks site Insertion Transpososome

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

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

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

Devices Protein Generator Reporters Composite Devices Inverters Signalling Protein Generator Composite Devices Measurement

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

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

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

Protein Generation RBS-gene-terminator promoter-RBS-gene-terminator operator-promoter-RBS-gene-terminator

Composite devices Catch all device category

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

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

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