Synthetic Biology
Traditional Approach Synthetic Biology
Real systems are complex Biology as engineering – bottom-up
Minimise complexity to make approach
system tractable – top-down Basic molecules of life
approach (carbohydrates, nuclei acids etc.)
Assembling and altering new are redesigned and inserted back
genetic pathways for altering into living systems
phenotypes of living cellular Re-design biological systems
organsims Assembling systems from basic
parts
Synthetic Biology (Schmidt, 2012) involves:
A. the design and construction of new biological parts, devices, and systems, &
B. the re - design of existing, natural biological systems for useful purposes.
Synthetic biologists are currently working to:
specify and populate a set of standard parts that
have well - defined performance characteristics
and can be used (and re - used) to build biological
systems,
develop and incorporate design methods and tools
into an integrated engineering environment
reverse engineer and re - design pre - existing
biological parts and devices in order to expand
the set of functions that we can access and
program
reverse engineer and re - design a “ simple ”
natural bacterium
minimize the genome of natural bacteria and
build so - called protocells in the lab, to define the minimal requirements of
living entities
construct orthogonal biological systems, such as a genetic code with an
enlarged alphabet of base pairs
, Biology as Engineering
Real problems are multifactorial, they are complex
Standardisation reduces cost and complexity
Simpler systems are isolated to ensure modularity
Modular assembly enables complex outputs to be
recapitulated robustly and reproducibly
Building the framework
Organism of interest(= chassis)
- Number of chassis being established including viral (bacteriophage), bacterial,
eukaryotic (yeast and higher eukaryotes), archaeal
- Chassis define the structure of the biological parts
Assembling parts
- Compound parts, devices or circuits
Parts and devices can be extensively characterised to test and validate its
robustness and reproducibility
- – Time dependence
- – Localisation
- – Chassis dependence
Integrating devices to obtain function
- Logic gates
- Counters
- Oscillators
- Memory
Complex circuits become increasingly less robust
Devices can be integrated between cells
Standardised part assembly = Biobricks
Biological part = natural nucleic acid sequence that encodes a definable biological
function
Standard biological part = biological part that has been refined in order to conform
to one or more technical standards (Shetty et al., 2008)
Biobrick (Knight, 2003) – a assembly standard for physical composition of biological
parts
Biobrick parts are DNA sequences which conform to a restriction-enzyme assembly
standard
The Lego-like building blocks used to design and assemble synthetic biological
circuits which would then be incorporated into living cells such as E.coli to construct
new biological systems
DNA encoding each BioBrick standard biological part is stored and propagated in
E.coli plasmid-based vectors (can obtain these from the Registry)
Traditional Approach Synthetic Biology
Real systems are complex Biology as engineering – bottom-up
Minimise complexity to make approach
system tractable – top-down Basic molecules of life
approach (carbohydrates, nuclei acids etc.)
Assembling and altering new are redesigned and inserted back
genetic pathways for altering into living systems
phenotypes of living cellular Re-design biological systems
organsims Assembling systems from basic
parts
Synthetic Biology (Schmidt, 2012) involves:
A. the design and construction of new biological parts, devices, and systems, &
B. the re - design of existing, natural biological systems for useful purposes.
Synthetic biologists are currently working to:
specify and populate a set of standard parts that
have well - defined performance characteristics
and can be used (and re - used) to build biological
systems,
develop and incorporate design methods and tools
into an integrated engineering environment
reverse engineer and re - design pre - existing
biological parts and devices in order to expand
the set of functions that we can access and
program
reverse engineer and re - design a “ simple ”
natural bacterium
minimize the genome of natural bacteria and
build so - called protocells in the lab, to define the minimal requirements of
living entities
construct orthogonal biological systems, such as a genetic code with an
enlarged alphabet of base pairs
, Biology as Engineering
Real problems are multifactorial, they are complex
Standardisation reduces cost and complexity
Simpler systems are isolated to ensure modularity
Modular assembly enables complex outputs to be
recapitulated robustly and reproducibly
Building the framework
Organism of interest(= chassis)
- Number of chassis being established including viral (bacteriophage), bacterial,
eukaryotic (yeast and higher eukaryotes), archaeal
- Chassis define the structure of the biological parts
Assembling parts
- Compound parts, devices or circuits
Parts and devices can be extensively characterised to test and validate its
robustness and reproducibility
- – Time dependence
- – Localisation
- – Chassis dependence
Integrating devices to obtain function
- Logic gates
- Counters
- Oscillators
- Memory
Complex circuits become increasingly less robust
Devices can be integrated between cells
Standardised part assembly = Biobricks
Biological part = natural nucleic acid sequence that encodes a definable biological
function
Standard biological part = biological part that has been refined in order to conform
to one or more technical standards (Shetty et al., 2008)
Biobrick (Knight, 2003) – a assembly standard for physical composition of biological
parts
Biobrick parts are DNA sequences which conform to a restriction-enzyme assembly
standard
The Lego-like building blocks used to design and assemble synthetic biological
circuits which would then be incorporated into living cells such as E.coli to construct
new biological systems
DNA encoding each BioBrick standard biological part is stored and propagated in
E.coli plasmid-based vectors (can obtain these from the Registry)
