BioBricks

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BioBricks
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Part Types

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

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Chassis

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

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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?

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Parts

• Protein Coding
• Ribosome Binding Sites
• Conjugation

• Regulatory
• Terminators
• RNA
• DNA

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Regulatory
www.ntu.edu.sg/home5/pg04325488/dfl.htm
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Terminators
http//www.sparknotes.com/biology/molecular/dnatra
nscription/section2.rhtml
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RNA
Nature Biotechnology 22, 841 - 847 (2004)
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DNA

• Spacers
• Add Biobricks site
• Insertion
• Transpososome

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Protein coding

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

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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

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Conjugation

• Genes and plasmids for the transfer of genetic
  material via conjugation.

kentsimmons.uwinnipeg.ca/16cm05/1116/16monera.htm
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Devices

• Protein Generator
• Composite Devices
• Measurement

• Reporters
• Inverters
• Signalling

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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

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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

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Signalling

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

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Protein Generation

• RBS-gene-terminator
• promoter-RBS-gene-terminator
• operator-promoter-RBS-gene-terminator

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Composite devices

• Catch all device category

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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

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Other

• PCR primers
• Tags degradation, binding and restriction sites

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General info

• Biobricks http//parts.mit.edu/registry/index.php
  /Main_Page
• Search biobricks http//parts.mit.edu/r/parts/par
  tsdb/search.cgi