CH391L/S13/BioBricksAndRegistry - Revision history

Dwight Tyler Fields: /* BioBrick™ Assembly Standard */

2013-05-03T00:02:44Z

BioBrick™ Assembly Standard

←Older revision		Revision as of 00:02, 3 May 2013
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	A BioBrick is a sequence of DNA with a predefined structure and function. This "payload" is held in a circular plasmid, which is an isolated, circular piece of DNA that can replicate in bacteria.		A BioBrick is a sequence of DNA with a predefined structure and function. This "payload" is held in a circular plasmid, which is an isolated, circular piece of DNA that can replicate in bacteria.

-	BioBricks™ are created with the intention of being easily joined and manipulated. In order for this to be possible, the BioBrick™ assembly standard requires the use of defined prefix and suffix sequences (flanking both sides of the BioBrick) that contain specific restriction endonuclease sites. Restriction endonucleases (or restriction enzymes) are proteins that cut DNA at or near specific sites. These sites are recognized as a specific DNA sequence, and go by names such as EcoRI, XbaI, SpeI, PstI and NotI. Assuming the your gene of interest (YGOI for short) exists in a bacterial plasmid or vector (donor plasmid), the restriction enzymes are used to cut YGOI out of the donor plasmid and then cut the recipient plasmid at a specific location in a specific pattern, so that YGOI can then be "pasted" to that location in the recipient plasmid using a process called ligation. The parts must also be engineered such that these sites are not present in the functional region of the sequence. The end of one BioBrick can then be connected, or ligated, together with the end of another BioBrick, allowing you to effectively string together BioBricks end to end to make devices, and then string devices together to make systems.<cite>Canton2008</cite>.	+	BioBricks™ are created with the intention of being easily joined and manipulated. In order for this to be possible, the BioBrick™ assembly standard requires the use of defined prefix and suffix sequences (flanking both sides of the BioBrick) that contain specific restriction endonuclease sites. Restriction endonucleases (or restriction enzymes) are proteins that cut DNA at or near specific sites. These sites are recognized as a specific DNA sequence, and go by names such as EcoRI, XbaI, SpeI, PstI and NotI.
		+
		+	Assuming the your gene of interest (YGOI for short) exists in a bacterial plasmid or vector (donor plasmid), the restriction enzymes are used to cut YGOI out of the donor plasmid and then cut the recipient plasmid at a specific location in a specific pattern, so that YGOI can then be "pasted" to that location in the recipient plasmid using a process called ligation. The parts must also be engineered such that these sites are not present in the functional region of the sequence. The end of one BioBrick can then be connected, or ligated, together with the end of another BioBrick, allowing you to effectively string together BioBricks end to end to make devices, and then string devices together to make systems.<cite>Canton2008</cite>.

	[[Image:Restriction-Enzyme-based-Subcloning.gif\|thumb\|Restriction enzyme cloning, or "subcloning", is a common way to share BioBrick parts.]]		[[Image:Restriction-Enzyme-based-Subcloning.gif\|thumb\|Restriction enzyme cloning, or "subcloning", is a common way to share BioBrick parts.]]

Dwight Tyler Fields: /* BioBrick™ Assembly Standard */

2013-05-03T00:02:03Z

BioBrick™ Assembly Standard

←Older revision		Revision as of 00:02, 3 May 2013
Line 16:		Line 16:
	A BioBrick is a sequence of DNA with a predefined structure and function. This "payload" is held in a circular plasmid, which is an isolated, circular piece of DNA that can replicate in bacteria.		A BioBrick is a sequence of DNA with a predefined structure and function. This "payload" is held in a circular plasmid, which is an isolated, circular piece of DNA that can replicate in bacteria.

-	BioBricks™ are created with the intention of being easily joined and manipulated. In order for this to be possible, the BioBrick™ assembly standard requires the use of defined prefix and suffix sequences (flanking both sides of the BioBrick) that contain specific restriction endonuclease sites. Restriction endonucleases (or restriction enzymes) are proteins that cut DNA at or near specific sites. These sites are recognized as a specific DNA sequence, and go by names such as EcoRI, XbaI, SpeI, PstI and NotI. Assuming the your gene of interest (YGOI for short) exists in a bacterial plasmid or vector (donor plasmid), the restriction enzymes are used to cut YGOI out of the donor plasmid and then cut the recipient plasmid at a specific location in a specific pattern, so that YGOI can then be "pasted" to that location in the recipient plasmid using a process called ligation. ~~Naturally, the~~ parts must also be engineered such that these sites are not present in the functional region of the sequence~~<cite>Canton2008</cite>.~~	+	BioBricks™ are created with the intention of being easily joined and manipulated. In order for this to be possible, the BioBrick™ assembly standard requires the use of defined prefix and suffix sequences (flanking both sides of the BioBrick) that contain specific restriction endonuclease sites. Restriction endonucleases (or restriction enzymes) are proteins that cut DNA at or near specific sites. These sites are recognized as a specific DNA sequence, and go by names such as EcoRI, XbaI, SpeI, PstI and NotI. Assuming the your gene of interest (YGOI for short) exists in a bacterial plasmid or vector (donor plasmid), the restriction enzymes are used to cut YGOI out of the donor plasmid and then cut the recipient plasmid at a specific location in a specific pattern, so that YGOI can then be "pasted" to that location in the recipient plasmid using a process called ligation. The parts must also be engineered such that these sites are not present in the functional region of the sequence. The end of one BioBrick can then be connected, or ligated, together with the end of another BioBrick, allowing you to effectively string together BioBricks end to end to make devices, and then string devices together to make systems.<cite>Canton2008</cite>.
-		+
-	~~Cutting the BioBrick at specific restriction sites (using restriction enzymes) is what gives a BioBrick its interlocking ends~~. The end of one BioBrick can then be connected, or ligated, together with the end of another BioBrick, allowing you to effectively string together BioBricks end to end to make devices, and then string devices together to make systems.	+

	[[Image:Restriction-Enzyme-based-Subcloning.gif\|thumb\|Restriction enzyme cloning, or "subcloning", is a common way to share BioBrick parts.]]		[[Image:Restriction-Enzyme-based-Subcloning.gif\|thumb\|Restriction enzyme cloning, or "subcloning", is a common way to share BioBrick parts.]]

Dwight Tyler Fields: /* BioBrick™ Assembly Standard */

2013-05-02T23:58:42Z

BioBrick™ Assembly Standard

←Older revision		Revision as of 23:58, 2 May 2013
Line 16:		Line 16:
	A BioBrick is a sequence of DNA with a predefined structure and function. This "payload" is held in a circular plasmid, which is an isolated, circular piece of DNA that can replicate in bacteria.		A BioBrick is a sequence of DNA with a predefined structure and function. This "payload" is held in a circular plasmid, which is an isolated, circular piece of DNA that can replicate in bacteria.

-	BioBricks™ are created with the intention of being easily joined and manipulated. In order for this to be possible, the BioBrick™ assembly standard requires the use of defined prefix and suffix sequences (flanking both sides of the BioBrick) that contain specific restriction endonuclease sites. These sites are ~~called EcoRI~~, ~~NotI~~ and XbaI ~~in the upstream~~, ~~and~~ SpeI, NotI, and ~~PstI~~ in the ~~downstream~~. Naturally, the parts must also be engineered such that these sites are not present in the functional region of the sequence<cite>Canton2008</cite>.	+	BioBricks™ are created with the intention of being easily joined and manipulated. In order for this to be possible, the BioBrick™ assembly standard requires the use of defined prefix and suffix sequences (flanking both sides of the BioBrick) that contain specific restriction endonuclease sites. Restriction endonucleases (or restriction enzymes) are proteins that cut DNA at or near specific sites. These sites are recognized as a specific DNA sequence, and go by names such as EcoRI, XbaI, SpeI, PstI and NotI. Assuming the your gene of interest (YGOI for short) exists in a bacterial plasmid or vector (donor plasmid), the restriction enzymes are used to cut YGOI out of the donor plasmid and then cut the recipient plasmid at a specific location in a specific pattern, so that YGOI can then be "pasted" to that location in the recipient plasmid using a process called ligation. Naturally, the parts must also be engineered such that these sites are not present in the functional region of the sequence<cite>Canton2008</cite>.

	Cutting the BioBrick at specific restriction sites (using restriction enzymes) is what gives a BioBrick its interlocking ends. The end of one BioBrick can then be connected, or ligated, together with the end of another BioBrick, allowing you to effectively string together BioBricks end to end to make devices, and then string devices together to make systems.		Cutting the BioBrick at specific restriction sites (using restriction enzymes) is what gives a BioBrick its interlocking ends. The end of one BioBrick can then be connected, or ligated, together with the end of another BioBrick, allowing you to effectively string together BioBricks end to end to make devices, and then string devices together to make systems.

-	For example, to join together two BioBricks, you would first cut both plasmids with restriction enzymes, turning one into an "insert" by getting rid of the rest of the plasmid, and turning the other into a "vector" by opening a space in the plasmid in front of the BioBrick. Because A's always pair with T's and G's always pair with C's, the overhanging edges of single-stranded DNA that your restriction enzymes left behind will match up to make double stranded DNA. You then mix together the insert and vector with a special enzyme called a "ligase" that can join together two broken pieces of DNA. The result is a composite plasmid that contains two BioBricks, now side by side<cite>agapakis</cite>.	+	[[Image:Restriction-Enzyme-based-Subcloning.gif\|thumb\|Restriction enzyme cloning, or "subcloning", is a common way to share BioBrick parts.]]
		+	For example, to join together two BioBricks, you would first cut both plasmids with restriction enzymes, turning one into an "insert" by getting rid of the rest of the plasmid, and turning the other into a "vector" by opening a space in the plasmid in front of the BioBrick. Because A's always pair with T's and G's always pair with C's, the overhanging edges of single-stranded DNA that your restriction enzymes left behind will match up to make double stranded DNA. You then mix together the insert and vector with a special enzyme called a "ligase" that can join together two broken pieces of DNA. The result is a composite plasmid that contains two BioBricks, now side by side<cite>agapakis</cite><cite>CloningColdSpringHarbor</cite> <cite>CloningNikosPinotsis</cite>.

	It is important to note that this new larger composite part has the same restriction sites as the smaller parts it was originally made from. This is what is meant by preserving "key structural elements" that allow one component of any size to be easily connected to any other component<cite>Knight2003</cite>. Also note that the "scar" (point of ligation between BioBricks) doesn't match the restriction sites anymore, so the bond between BioBricks will hold through though subsequent rounds of splicing.		It is important to note that this new larger composite part has the same restriction sites as the smaller parts it was originally made from. This is what is meant by preserving "key structural elements" that allow one component of any size to be easily connected to any other component<cite>Knight2003</cite>. Also note that the "scar" (point of ligation between BioBricks) doesn't match the restriction sites anymore, so the bond between BioBricks will hold through though subsequent rounds of splicing.
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	A tutorial on BioBrick™ assembly is available on the [[BioBricks construction tutorial]] page.		A tutorial on BioBrick™ assembly is available on the [[BioBricks construction tutorial]] page.
	Specific assembly standards for different types of BioBricks can be found at the [http://partsregistry.org/Help:BioBrick_Assembly ''Help:BioBrick Assembly] page.		Specific assembly standards for different types of BioBricks can be found at the [http://partsregistry.org/Help:BioBrick_Assembly ''Help:BioBrick Assembly] page.
-
-

	==History==		==History==

Dwight Tyler Fields: /* Sharing BioBricks */

2013-05-02T23:53:42Z

Sharing BioBricks

←Older revision		Revision as of 23:53, 2 May 2013
Line 29:		Line 29:
	Specific assembly standards for different types of BioBricks can be found at the [http://partsregistry.org/Help:BioBrick_Assembly ''Help:BioBrick Assembly] page.		Specific assembly standards for different types of BioBricks can be found at the [http://partsregistry.org/Help:BioBrick_Assembly ''Help:BioBrick Assembly] page.

-	~~===Sharing BioBricks===~~
-	~~[[Image:Restriction-Enzyme-based-Subcloning.gif\|thumb\|Restriction enzyme cloning, or "subcloning", is a common way to share BioBrick parts.]]~~
-	~~Molecular parts are shared using one of several cloning techniques. One of these techniques is called restriction enzyme cloning, or "subcloning".~~

-	Restriction enzymes (or restriction endonucleases) are proteins that cut DNA at or near specific sites. These sites are recognized as a specific DNA sequence, and go by names such as EcoRI, XbaI, SpeI, PstI and NotI. Assuming the your gene of interest (YGOI for short) exists in a bacterial plasmid or vector (donor plasmid), the restriction enzymes are used to cut YGOI out of the donor plasmid and then cut the recipient plasmid at a specific location in a specific pattern, so that YGOI can then be "pasted" to that location in the recipient plasmid using a process called ligation<cite>CloningColdSpringHarbor</cite> <cite>CloningNikosPinotsis</cite>.

	==History==		==History==

Dwight Tyler Fields: /* History */

2013-05-02T23:49:30Z

History

←Older revision		Revision as of 23:49, 2 May 2013
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	==History==		==History==
-	~~The registry is an effort that was~~ founded by Tom Knight of the Artificial Intelligence Lab at MIT in 2003. He coined the term "BioBrick" in his paper, "Idempotent Vector Design for Standard Assembly of Biobricks". Idempotent, a term borrowed from mathematics and computer science, in this context means that, during the assembly of complex biological components, the chemical reactions should not alter the key structural elements of the components<cite>Knight2003</cite>.	+	Both the Registry and the assembly standard were founded by Tom Knight of the Artificial Intelligence Lab at MIT in 2003. He coined the term "BioBrick" in his paper, "Idempotent Vector Design for Standard Assembly of Biobricks". Idempotent, a term borrowed from mathematics and computer science, in this context means that, during the assembly of complex biological components, the chemical reactions should not alter the key structural elements of the components<cite>Knight2003</cite>. The latest draft of the assembly standard, from 2008, is called BB2: [http://hdl.handle.net/1721.1/45139 Draft Standard for Biobrick BB-2 Biological Parts]. The standard is still required to be used in all iGEM competitions (as of 2013).

	In the summer of 2004, the registry contained about 100 basic parts; today, this has expanded to over 700 available and 2000 defined parts<cite>iGEMRegistry</cite>.		In the summer of 2004, the registry contained about 100 basic parts; today, this has expanded to over 700 available and 2000 defined parts<cite>iGEMRegistry</cite>.

Dwight Tyler Fields: /* BioBrick™ Assembly Standard */

2013-05-02T23:47:54Z

BioBrick™ Assembly Standard

←Older revision		Revision as of 23:47, 2 May 2013
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	A tutorial on BioBrick™ assembly is available on the [[BioBricks construction tutorial]] page.		A tutorial on BioBrick™ assembly is available on the [[BioBricks construction tutorial]] page.
	Specific assembly standards for different types of BioBricks can be found at the [http://partsregistry.org/Help:BioBrick_Assembly ''Help:BioBrick Assembly] page.		Specific assembly standards for different types of BioBricks can be found at the [http://partsregistry.org/Help:BioBrick_Assembly ''Help:BioBrick Assembly] page.
-
-	The BioBrick assembly standard was first introduced by Tom Knight in 2003, and he has updated it several times since. The latest draft, from 2008, is called BB2: [http://hdl.handle.net/1721.1/45139 Draft Standard for Biobrick BB-2 Biological Parts]. The standard is still required to be used in all iGEM competitions (as of 2013).

	===Sharing BioBricks===		===Sharing BioBricks===

Dwight Tyler Fields: /* References */

2013-05-02T23:43:30Z

References

←Older revision		Revision as of 23:43, 2 May 2013
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	#Knight2003 Knight, Tom. Idempotent vector design for standard assembly of biobricks. MASSACHUSETTS INST OF TECH CAMBRIDGE ARTIFICIAL INTELLIGENCE LAB, 2003.		#Knight2003 Knight, Tom. Idempotent vector design for standard assembly of biobricks. MASSACHUSETTS INST OF TECH CAMBRIDGE ARTIFICIAL INTELLIGENCE LAB, 2003.
	#agapakis http://agapakis.com/hssp/biobricks.html		#agapakis http://agapakis.com/hssp/biobricks.html
		+	#Bonnet [http://www.sciencemag.org/content/early/2013/03/27/science.1232758 Bonnet et. al., "Amplifying Genetic Logic Gates", Published Online March 28 2013, Science DOI: 10.1126/science.1232758]
	</biblio>		</biblio>

Dwight Tyler Fields: /* PoPS (Polymerase per Second) */

2013-05-02T23:43:06Z

PoPS (Polymerase per Second)

←Older revision		Revision as of 23:43, 2 May 2013
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	PoPS is a useful abstraction that we can use to think about transcription-based logic devices and characterize BioBrick™ parts. MIT initially used a unit of measurement called TIPS (Transcription Initiations per Second) for measure rates of transcription at the ends of its parts; however, this was insufficient because there are places on the DNA (e.g. terminators) where transcription initiations are not taking place. [[PoPS]] is a relatively new unit developed during construction of standardized "ends" of DNA pieces that measures the inputs and outputs of BioBrick™ parts. PoPS measure the rate at which RNA polymerase moves past a point in the DNA, similar to measuring the current flow across a specific point in a wire. Devices that have an input and output in PoPS are composable - that is, they can be arbitrarily joined together to create complex devices and systems. Creation of devices allows us to characterize devices and eventually more complex systems, thus PoPS is important as a common signal carrier. PoPS differs from transcription rate in that it can also be measured at terminator sites; upstream, they are theoretically equivalent.		PoPS is a useful abstraction that we can use to think about transcription-based logic devices and characterize BioBrick™ parts. MIT initially used a unit of measurement called TIPS (Transcription Initiations per Second) for measure rates of transcription at the ends of its parts; however, this was insufficient because there are places on the DNA (e.g. terminators) where transcription initiations are not taking place. [[PoPS]] is a relatively new unit developed during construction of standardized "ends" of DNA pieces that measures the inputs and outputs of BioBrick™ parts. PoPS measure the rate at which RNA polymerase moves past a point in the DNA, similar to measuring the current flow across a specific point in a wire. Devices that have an input and output in PoPS are composable - that is, they can be arbitrarily joined together to create complex devices and systems. Creation of devices allows us to characterize devices and eventually more complex systems, thus PoPS is important as a common signal carrier. PoPS differs from transcription rate in that it can also be measured at terminator sites; upstream, they are theoretically equivalent.

-	An example of a system from which PoPS is understandable is a PoPS based inverter, which takes in a PoPS signal and inverts it. A PoPS based inverter consists of a ribosome-binding site, repressor coding region, terminator and cognate promoter. A high PoPS input cause expression of the repressor, which then binds to the promoter and produces a low output signal. A low PoPS input means very little repressor expression, so the promoter is free to generate PoPS.<cite>PoPS</cite>.	+	An example of a system from which PoPS is understandable is a PoPS based inverter, which takes in a PoPS signal and inverts it. A PoPS based inverter consists of a ribosome-binding site, repressor coding region, terminator and cognate promoter. A high PoPS input cause expression of the repressor, which then binds to the promoter and produces a low output signal. A low PoPS input means very little repressor expression, so the promoter is free to generate PoPS.<cite>PoPS</cite><cite>#Bonnet</cite>.

	==Using the Registry==		==Using the Registry==

Dwight Tyler Fields: /* PoPS (Polymerase per Second) */

2013-05-02T23:39:47Z

PoPS (Polymerase per Second)

←Older revision		Revision as of 23:39, 2 May 2013
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	==PoPS (Polymerase per Second)==		==PoPS (Polymerase per Second)==
-	MIT initially used a unit of measurement called TIPS (Transcription Initiations per Second) for measure rates of transcription at the ends of its parts; however, this was insufficient because there are places on the DNA (e.g. terminators) where transcription initiations are not taking place. [[PoPS]] is a relatively new unit developed during construction of standardized "ends" of DNA pieces that measures the inputs and outputs of BioBrick™ parts. PoPS measure the rate at which RNA polymerase moves past a point in the DNA, similar to measuring the current flow across a specific point in a wire. Devices that have an input and output in PoPS are composable - that is, they can be arbitrarily joined together to create complex devices and systems. Creation of devices allows us to characterize devices and eventually more complex systems, thus PoPS is important as a common signal carrier. PoPS differs from transcription rate in that it can also be measured at terminator sites; upstream, they are theoretically equivalent.	+	PoPS is a useful abstraction that we can use to think about transcription-based logic devices and characterize BioBrick™ parts. MIT initially used a unit of measurement called TIPS (Transcription Initiations per Second) for measure rates of transcription at the ends of its parts; however, this was insufficient because there are places on the DNA (e.g. terminators) where transcription initiations are not taking place. [[PoPS]] is a relatively new unit developed during construction of standardized "ends" of DNA pieces that measures the inputs and outputs of BioBrick™ parts. PoPS measure the rate at which RNA polymerase moves past a point in the DNA, similar to measuring the current flow across a specific point in a wire. Devices that have an input and output in PoPS are composable - that is, they can be arbitrarily joined together to create complex devices and systems. Creation of devices allows us to characterize devices and eventually more complex systems, thus PoPS is important as a common signal carrier. PoPS differs from transcription rate in that it can also be measured at terminator sites; upstream, they are theoretically equivalent.

-	An example of a system from which PoPS is understandable is a PoPS based inverter, which takes in a PoPS signal and inverts it. A PoPS based inverter consists of a ribosome-binding site, repressor coding region, terminator and cognate promoter. A high PoPS input cause expression of the repressor, which then binds to the promoter and produces a low output signal. A low PoPS input means very little repressor expression, so the promoter is free to generate PoPS.	+	An example of a system from which PoPS is understandable is a PoPS based inverter, which takes in a PoPS signal and inverts it. A PoPS based inverter consists of a ribosome-binding site, repressor coding region, terminator and cognate promoter. A high PoPS input cause expression of the repressor, which then binds to the promoter and produces a low output signal. A low PoPS input means very little repressor expression, so the promoter is free to generate PoPS.<cite>PoPS</cite>.
-		+
-	At the end of the day PoPS is a useful abstraction that we can use to think about transcription-based logic devices and characterize BioBrick™ parts; up to this point, there has been to way of measuring it ''in vivo''<cite>PoPS</cite>.	+

	==Using the Registry==		==Using the Registry==

Dwight Tyler Fields: /* BioBrick™ Types */

2013-05-02T23:37:50Z

BioBrick™ Types

←Older revision		Revision as of 23:37, 2 May 2013
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	* Ribosomal binding sites are sequences of mRNA that are bound by the ribosome when initiating protein translation.		* Ribosomal binding sites are sequences of mRNA that are bound by the ribosome when initiating protein translation.

-	* A terminator~~, or transcription terminator,~~ is a section of DNA that marks the end of gene or operon on genomic DNA for transcription.	+	* A terminator is a section of DNA that marks the end of gene or operon on genomic DNA for transcription.

	===BioBrick™ Names===		===BioBrick™ Names===