BioBrick
Encyclopedia
BioBrick standard biological parts are DNA
sequences of defined structure and function; they share a common interface and are designed to be composed and incorporated into living cells such as E. coli to construct new biological systems. BioBrick parts represent an effort to introduce the engineering principles of abstraction and standardization into synthetic biology
. The trademarked words BioBrick and BioBricks are correctly used as adjectives (not nouns) and refer to a specific "brand" of open source genetic parts as defined via an open technical standards setting process that is led by the BioBricks Foundation.
BioBrick parts were introduced by Tom Knight at MIT in 2003. Drew Endy
, now at Stanford, and Christopher Voigt
, at UCSF, are also heavily involved in the project. A registry of several thousand public domain BioBrick parts is maintained by Randy Rettberg team at http://partsregistry.org. The annual iGEM
competition promotes the BioBrick parts concept by involving undergraduate and graduate students in the design of biological systems.
One of the goals of the BioBricks project is to provide a workable approach to nanotechnology
employing biological organisms. Another, more long-term goal is to produce a synthetic living organism from standard parts that are completely understood.
Each BioBrick part is a DNA sequence held in a circular plasmid
; the "payload" of the BioBrick part is flanked by universal and precisely defined upstream and downstream sequences which are technically not considered part of the BioBrick part. These sequences contain six restriction sites for specific restriction enzyme
s (at least two of which are isocaudomer
s), which allows for the simple creation of larger BioBrick parts by chaining together smaller ones in any desired order. In the process of chaining parts together, the restriction sites between the two parts are removed, allowing the use of those restriction enzymes without breaking the new, larger BioBrick apart. To facilitate this assembly process, the BioBrick part itself may not contain any of these restriction sites.
There are three levels of BioBrick parts: "parts", "devices" and "systems". "Parts" are the building blocks and encode basic biological functions (such as encoding a certain protein
, or providing a promoter to let RNA polymerase
bind and initiate transcription of downstream sequences); "devices" are collections of parts that implement some human-defined function (such as a riboregulator
producing a fluorescent
protein whenever the environment contains a certain chemical); "systems" perform high-level tasks (such as oscillating between two colors at a predefined frequency).
Example BioBrick systems honored at previous iGEM competitions include:
Two measures for the performance of biological parts have been defined by Drew Endy's team: PoPS or Polymerase per second, the number of times a RNA polymerase
passes by a certain DNA point per second; and RiPS or Ribosomal initiations per second, the number of times a ribosome
passes a certain point on mRNA each second.
DNA
Deoxyribonucleic acid is a nucleic acid that contains the genetic instructions used in the development and functioning of all known living organisms . The DNA segments that carry this genetic information are called genes, but other DNA sequences have structural purposes, or are involved in...
sequences of defined structure and function; they share a common interface and are designed to be composed and incorporated into living cells such as E. coli to construct new biological systems. BioBrick parts represent an effort to introduce the engineering principles of abstraction and standardization into synthetic biology
Synthetic biology
Synthetic biology is a new area of biological research that combines science and engineering. It encompasses a variety of different approaches, methodologies, and disciplines with a variety of definitions...
. The trademarked words BioBrick and BioBricks are correctly used as adjectives (not nouns) and refer to a specific "brand" of open source genetic parts as defined via an open technical standards setting process that is led by the BioBricks Foundation.
BioBrick parts were introduced by Tom Knight at MIT in 2003. Drew Endy
Drew Endy
Drew Endy is a synthetic biologist.He was a junior fellow for 3 years and later an assistant professor in the Department of Biological Engineering at MIT. In September 2008, he moved to Palo Alto to become an assistant professor in the Department of Bioengineering at Stanford University...
, now at Stanford, and Christopher Voigt
Christopher Voigt
Christopher Voigt is an American synthetic biologist, molecular biophysicist, and engineer. He is currently an Associate Professor in the of the with appointments in the and the graduate student programs. His research interests focus on the reprogramming of bacterial organisms to perform...
, at UCSF, are also heavily involved in the project. A registry of several thousand public domain BioBrick parts is maintained by Randy Rettberg team at http://partsregistry.org. The annual iGEM
IGEM
The International Genetically Engineered Machine competition is a worldwide Synthetic Biology competition aimed at undergraduate university students.- Competition details :...
competition promotes the BioBrick parts concept by involving undergraduate and graduate students in the design of biological systems.
One of the goals of the BioBricks project is to provide a workable approach to nanotechnology
Nanotechnology
Nanotechnology is the study of manipulating matter on an atomic and molecular scale. Generally, nanotechnology deals with developing materials, devices, or other structures possessing at least one dimension sized from 1 to 100 nanometres...
employing biological organisms. Another, more long-term goal is to produce a synthetic living organism from standard parts that are completely understood.
Each BioBrick part is a DNA sequence held in a circular plasmid
Plasmid
In microbiology and genetics, a plasmid is a DNA molecule that is separate from, and can replicate independently of, the chromosomal DNA. They are double-stranded and, in many cases, circular...
; the "payload" of the BioBrick part is flanked by universal and precisely defined upstream and downstream sequences which are technically not considered part of the BioBrick part. These sequences contain six restriction sites for specific restriction enzyme
Restriction enzyme
A Restriction Enzyme is an enzyme that cuts double-stranded DNA at specific recognition nucleotide sequences known as restriction sites. Such enzymes, found in bacteria and archaea, are thought to have evolved to provide a defense mechanism against invading viruses...
s (at least two of which are isocaudomer
Isocaudomer
Isocaudomers are pairs of restriction enzymes that have slightly different recognition sequences but upon cleavage generate identical termini. For example the enzymes Mbo I and BamH I are isocaudomers: Mbo I N*GATC N N CTAG*N BamH I G*GATC C...
s), which allows for the simple creation of larger BioBrick parts by chaining together smaller ones in any desired order. In the process of chaining parts together, the restriction sites between the two parts are removed, allowing the use of those restriction enzymes without breaking the new, larger BioBrick apart. To facilitate this assembly process, the BioBrick part itself may not contain any of these restriction sites.
There are three levels of BioBrick parts: "parts", "devices" and "systems". "Parts" are the building blocks and encode basic biological functions (such as encoding a certain protein
Protein
Proteins are biochemical compounds consisting of one or more polypeptides typically folded into a globular or fibrous form, facilitating a biological function. A polypeptide is a single linear polymer chain of amino acids bonded together by peptide bonds between the carboxyl and amino groups of...
, or providing a promoter to let RNA polymerase
RNA polymerase
RNA polymerase is an enzyme that produces RNA. In cells, RNAP is needed for constructing RNA chains from DNA genes as templates, a process called transcription. RNA polymerase enzymes are essential to life and are found in all organisms and many viruses...
bind and initiate transcription of downstream sequences); "devices" are collections of parts that implement some human-defined function (such as a riboregulator
Riboregulator
In molecular biology, a riboregulator is a ribonucleic acid that responds to a signal nucleic acid molecule by Watson-Crick base pairing. A riboregulator may respond to a signal molecule in any number of manners including, translation of the RNA into a protein, activation of a ribozyme, release...
producing a fluorescent
Fluorescence
Fluorescence is the emission of light by a substance that has absorbed light or other electromagnetic radiation of a different wavelength. It is a form of luminescence. In most cases, emitted light has a longer wavelength, and therefore lower energy, than the absorbed radiation...
protein whenever the environment contains a certain chemical); "systems" perform high-level tasks (such as oscillating between two colors at a predefined frequency).
Example BioBrick systems honored at previous iGEM competitions include:
- E. coli detector for arsenicArsenicArsenic is a chemical element with the symbol As, atomic number 33 and relative atomic mass 74.92. Arsenic occurs in many minerals, usually in conjunction with sulfur and metals, and also as a pure elemental crystal. It was first documented by Albertus Magnus in 1250.Arsenic is a metalloid...
that responds with pHPHIn chemistry, pH is a measure of the acidity or basicity of an aqueous solution. Pure water is said to be neutral, with a pH close to 7.0 at . Solutions with a pH less than 7 are said to be acidic and solutions with a pH greater than 7 are basic or alkaline...
change; - E. coli producer of various scents such as banana or mint;
- human cell line engineered to inhibit excessive response to Toll-like receptorToll-like receptorToll-like receptors are a class of proteins that play a key role in the innate immune system. They are single, membrane-spanning, non-catalytic receptors that recognize structurally conserved molecules derived from microbes...
activation, so as to avoid sepsisSepsisSepsis is a potentially deadly medical condition that is characterized by a whole-body inflammatory state and the presence of a known or suspected infection. The body may develop this inflammatory response by the immune system to microbes in the blood, urine, lungs, skin, or other tissues...
.
Two measures for the performance of biological parts have been defined by Drew Endy's team: PoPS or Polymerase per second, the number of times a RNA polymerase
RNA polymerase
RNA polymerase is an enzyme that produces RNA. In cells, RNAP is needed for constructing RNA chains from DNA genes as templates, a process called transcription. RNA polymerase enzymes are essential to life and are found in all organisms and many viruses...
passes by a certain DNA point per second; and RiPS or Ribosomal initiations per second, the number of times a ribosome
Ribosome
A ribosome is a component of cells that assembles the twenty specific amino acid molecules to form the particular protein molecule determined by the nucleotide sequence of an RNA molecule....
passes a certain point on mRNA each second.