Difference between revisions of "CH391L/S14/BioBricks"
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== What are BioBricks, and what is their purpose? == | == What are BioBricks, and what is their purpose? == | ||
| − | A BioBrick is a sequence of DNA with a | + | A BioBrick is a sequence of DNA with a predefined structure and function. The information is held in a plasmid, or a circular piece of DNA that can be inserted, and replicated into bacteria. |
Before BioBricks, there was little standardization in assembly techniques for DNA sequences. It was necessary to create a standardized system of biological building blocks to enable scientists to go beyond the experiment of DNA assembly and allow them to focus on more complicated research. BioBricks were created as a set of standard and interchangeable “parts” that could be assembled into sub-components. According to the Registry of Standard Biological Parts, which contains DNA for thousands of previously created parts submitted by iGEM members, a standard biological part is “a functional unit of DNA that encodes for a specific biological function. Parts have been standardized so they can be used to efficiently develop biological systems in living cells." The advantage of BioBricks is that the assembly of these parts could be outsourced to others and new experimentation could rely heavily on previously manufactured components. The BioBricks foundation was co-founded in 2005 by Drew Endy. Tom Knight and Drew Endy also helped co-found the Registry of Standard Biological Parts.[http://parts.igem.org/Main_Page] | Before BioBricks, there was little standardization in assembly techniques for DNA sequences. It was necessary to create a standardized system of biological building blocks to enable scientists to go beyond the experiment of DNA assembly and allow them to focus on more complicated research. BioBricks were created as a set of standard and interchangeable “parts” that could be assembled into sub-components. According to the Registry of Standard Biological Parts, which contains DNA for thousands of previously created parts submitted by iGEM members, a standard biological part is “a functional unit of DNA that encodes for a specific biological function. Parts have been standardized so they can be used to efficiently develop biological systems in living cells." The advantage of BioBricks is that the assembly of these parts could be outsourced to others and new experimentation could rely heavily on previously manufactured components. The BioBricks foundation was co-founded in 2005 by Drew Endy. Tom Knight and Drew Endy also helped co-found the Registry of Standard Biological Parts.[http://parts.igem.org/Main_Page] | ||
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The original BioBrick assembly standard created by Tom Knight: | The original BioBrick assembly standard created by Tom Knight: | ||
| − | In order to easily joint and manipulate segments of DNA, BioBrick assembly standards requires the use of defined prefix and suffix sequences that flank both sides of the BioBrick. These prefix and suffix regions (such as EcoRI, NotI, XbaI, SpeI, and PtsI) can be cut by specific restriction endonucleases. Restriction endonucleases are a key element in the cutting and conjoining of segments of DNA, and will be elaborated in further detail in a later section. | + | In order to easily joint and manipulate segments of DNA, BioBrick assembly standards requires the use of defined prefix and suffix sequences that flank both sides of the BioBrick. These prefix and suffix regions (such as EcoRI, NotI, XbaI, SpeI, and PtsI) can be cut by specific restriction endonucleases. Restriction endonucleases are a key element in the cutting and conjoining of segments of DNA, and will be elaborated in further detail in a later section. (insert hyperlink here.. ask dennis how to do that) |
The upstream end (Prefix) contains vector insert restriction sites with the following sequence: | The upstream end (Prefix) contains vector insert restriction sites with the following sequence: | ||
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3' --cgt CTTAAG CGCCGGCG A ACATCT -------- A TGATCA T CGCCGGC GACGTC gca-- | 3' --cgt CTTAAG CGCCGGCG A ACATCT -------- A TGATCA T CGCCGGC GACGTC gca-- | ||
EcoRI NotI XbaI SpeI NotI PstI | EcoRI NotI XbaI SpeI NotI PstI | ||
| − | The component vector cannot contain any of the restriction sites to avoid any unwanted cutting by restriction enzymes, and any such sites are removed by point mutations. | + | The component vector (the insert) cannot contain any of the restriction sites to avoid any unwanted cutting by restriction enzymes, and any such sites are removed by point mutations. |
== BioBrick Composition Techniques == | == BioBrick Composition Techniques == | ||
Revision as of 19:28, 18 January 2014
What are BioBricks, and what is their purpose?
A BioBrick is a sequence of DNA with a predefined structure and function. The information is held in a plasmid, or a circular piece of DNA that can be inserted, and replicated into bacteria.
Before BioBricks, there was little standardization in assembly techniques for DNA sequences. It was necessary to create a standardized system of biological building blocks to enable scientists to go beyond the experiment of DNA assembly and allow them to focus on more complicated research. BioBricks were created as a set of standard and interchangeable “parts” that could be assembled into sub-components. According to the Registry of Standard Biological Parts, which contains DNA for thousands of previously created parts submitted by iGEM members, a standard biological part is “a functional unit of DNA that encodes for a specific biological function. Parts have been standardized so they can be used to efficiently develop biological systems in living cells." The advantage of BioBricks is that the assembly of these parts could be outsourced to others and new experimentation could rely heavily on previously manufactured components. The BioBricks foundation was co-founded in 2005 by Drew Endy. Tom Knight and Drew Endy also helped co-found the Registry of Standard Biological Parts.[1]
The creation of a standard sequence interface for all BioBricks:
The original BioBrick assembly standard created by Tom Knight:
In order to easily joint and manipulate segments of DNA, BioBrick assembly standards requires the use of defined prefix and suffix sequences that flank both sides of the BioBrick. These prefix and suffix regions (such as EcoRI, NotI, XbaI, SpeI, and PtsI) can be cut by specific restriction endonucleases. Restriction endonucleases are a key element in the cutting and conjoining of segments of DNA, and will be elaborated in further detail in a later section. (insert hyperlink here.. ask dennis how to do that)
The upstream end (Prefix) contains vector insert restriction sites with the following sequence:
5' --gca GAATTC GCGGCCGC T TCTAGA G --- 3'
3' --cgt CTTAAG CGCCGGCG A ACATCT C --- 5'
EcoRI NotI XbaI
The downstream end (Suffix) contains vector insert restriction sites with the following sequence:
5' --- T ACTAGT A GCGGCCG CTGCAG gct--- 3'
3' --- A TGATCA T CGCCGGC GACGTC cga--- 5'
SpeI NotI PstI
When combined, the entire component vector looks like this:
5’ --gca GAATTC GCGGCCGC T TCTAGA --insert--T ACTAGT A GCGGCCG CTGCAG gct--
3' --cgt CTTAAG CGCCGGCG A ACATCT -------- A TGATCA T CGCCGGC GACGTC gca--
EcoRI NotI XbaI SpeI NotI PstI
The component vector (the insert) cannot contain any of the restriction sites to avoid any unwanted cutting by restriction enzymes, and any such sites are removed by point mutations.
