Talk:CH391L/S13/DnaAssembly - Revision history

Evan J. Weaver at 03:14, 15 February 2013

Evan J. Weaver — Fri, 15 Feb 2013 03:14:33 GMT

←Older revision		Revision as of 03:14, 15 February 2013
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	'''[[User:Kevin Baldridge\|Kevin Baldridge]] 15:22, 11 February 2013 (EST)''':Maybe I missed something in today's talk about yeast recombineering, but how does one get the oligos into the yeast for recombination? On the part where he was talking about assembling 1kb pieces within yeast. I have never worked with yeast, are they able to take up linear DNA by itself?		'''[[User:Kevin Baldridge\|Kevin Baldridge]] 15:22, 11 February 2013 (EST)''':Maybe I missed something in today's talk about yeast recombineering, but how does one get the oligos into the yeast for recombination? On the part where he was talking about assembling 1kb pieces within yeast. I have never worked with yeast, are they able to take up linear DNA by itself?
		+	*'''[[User:Evan J WeaverIEvan Weaver]] 17:52, 14 February 2013 (CST)''': I thought he said that he digested the cell wall (if it has one) with some enzyme (I don't remember what exactly). I'd imagine that he would use something like heat shocking or electroporating the the PM, but I don't remember.

		+
	== Assembling nonstandard bases ==		== Assembling nonstandard bases ==
	*'''[[User:Catherine I. Mortensen\|Catherine I. Mortensen]] 22:07, 6 February 2013 (EST)''': I noticed you mentioned that nontraditional bases could be assembled... I'm taking genetics now so I may learn about this soon but could you give an example when a nontraditional base would be useful? I assume a nontraditional base refers to another purine or pyrimidine?		*'''[[User:Catherine I. Mortensen\|Catherine I. Mortensen]] 22:07, 6 February 2013 (EST)''': I noticed you mentioned that nontraditional bases could be assembled... I'm taking genetics now so I may learn about this soon but could you give an example when a nontraditional base would be useful? I assume a nontraditional base refers to another purine or pyrimidine?

Kevin Baldridge at 20:23, 11 February 2013

Kevin Baldridge — Mon, 11 Feb 2013 20:23:01 GMT

←Older revision		Revision as of 20:23, 11 February 2013
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	**'''[[User:Gabriel Wu\|Gabriel Wu]] 01:05, 9 February 2013 (EST)''': RNA applications are pretty different from the ones discussed here. Also, many people who work with RNA will synthesize the RNA from DNA templates. I'm not familiar with what the aptamer labs do, but that is another topic altogether.		**'''[[User:Gabriel Wu\|Gabriel Wu]] 01:05, 9 February 2013 (EST)''': RNA applications are pretty different from the ones discussed here. Also, many people who work with RNA will synthesize the RNA from DNA templates. I'm not familiar with what the aptamer labs do, but that is another topic altogether.

-	**'''[[User:Kevin Baldridge\|Kevin Baldridge]] 15:22, 11 February 2013 (EST)''':Maybe I missed something in today's talk about yeast recombineering, but how does one get the oligos into the yeast for recombination? On the part where he was talking about assembling 1kb pieces within yeast. I have never worked with yeast, are they able to take up linear DNA by itself?	+
		+	'''[[User:Kevin Baldridge\|Kevin Baldridge]] 15:22, 11 February 2013 (EST)''':Maybe I missed something in today's talk about yeast recombineering, but how does one get the oligos into the yeast for recombination? On the part where he was talking about assembling 1kb pieces within yeast. I have never worked with yeast, are they able to take up linear DNA by itself?
		+
	== Assembling nonstandard bases ==		== Assembling nonstandard bases ==
	*'''[[User:Catherine I. Mortensen\|Catherine I. Mortensen]] 22:07, 6 February 2013 (EST)''': I noticed you mentioned that nontraditional bases could be assembled... I'm taking genetics now so I may learn about this soon but could you give an example when a nontraditional base would be useful? I assume a nontraditional base refers to another purine or pyrimidine?		*'''[[User:Catherine I. Mortensen\|Catherine I. Mortensen]] 22:07, 6 February 2013 (EST)''': I noticed you mentioned that nontraditional bases could be assembled... I'm taking genetics now so I may learn about this soon but could you give an example when a nontraditional base would be useful? I assume a nontraditional base refers to another purine or pyrimidine?

Kevin Baldridge at 20:22, 11 February 2013

Kevin Baldridge — Mon, 11 Feb 2013 20:22:37 GMT

←Older revision		Revision as of 20:22, 11 February 2013
Line 40:		Line 40:
	**'''[[User:Gabriel Wu\|Gabriel Wu]] 01:05, 9 February 2013 (EST)''': RNA applications are pretty different from the ones discussed here. Also, many people who work with RNA will synthesize the RNA from DNA templates. I'm not familiar with what the aptamer labs do, but that is another topic altogether.		**'''[[User:Gabriel Wu\|Gabriel Wu]] 01:05, 9 February 2013 (EST)''': RNA applications are pretty different from the ones discussed here. Also, many people who work with RNA will synthesize the RNA from DNA templates. I'm not familiar with what the aptamer labs do, but that is another topic altogether.

		+	**'''[[User:Kevin Baldridge\|Kevin Baldridge]] 15:22, 11 February 2013 (EST)''':Maybe I missed something in today's talk about yeast recombineering, but how does one get the oligos into the yeast for recombination? On the part where he was talking about assembling 1kb pieces within yeast. I have never worked with yeast, are they able to take up linear DNA by itself?
	== Assembling nonstandard bases ==		== Assembling nonstandard bases ==
	*'''[[User:Catherine I. Mortensen\|Catherine I. Mortensen]] 22:07, 6 February 2013 (EST)''': I noticed you mentioned that nontraditional bases could be assembled... I'm taking genetics now so I may learn about this soon but could you give an example when a nontraditional base would be useful? I assume a nontraditional base refers to another purine or pyrimidine?		*'''[[User:Catherine I. Mortensen\|Catherine I. Mortensen]] 22:07, 6 February 2013 (EST)''': I noticed you mentioned that nontraditional bases could be assembled... I'm taking genetics now so I may learn about this soon but could you give an example when a nontraditional base would be useful? I assume a nontraditional base refers to another purine or pyrimidine?

Gabriel Wu at 06:21, 11 February 2013

Gabriel Wu — Mon, 11 Feb 2013 06:21:28 GMT

←Older revision		Revision as of 06:21, 11 February 2013
Line 54:		Line 54:
	**'''[[User:Max E. Rubinson\|Max E. Rubinson]] 22:43, 7 February 2013 (EST)''':I don't know if CPEC was started as an iGEM project, but [http://2009.igem.org/Team:Duke this group] at Duke (where the method was developed) used CPEC to assemble a metabolic pathway for the production of plastic polymers in ''E. coli''.		**'''[[User:Max E. Rubinson\|Max E. Rubinson]] 22:43, 7 February 2013 (EST)''':I don't know if CPEC was started as an iGEM project, but [http://2009.igem.org/Team:Duke this group] at Duke (where the method was developed) used CPEC to assemble a metabolic pathway for the production of plastic polymers in ''E. coli''.
	**'''[[User:Thomas Wall\|Thomas Wall]] 20:33, 7 February 2013 (EST)''': http://2009.igem.org/Team:Duke		**'''[[User:Thomas Wall\|Thomas Wall]] 20:33, 7 February 2013 (EST)''': http://2009.igem.org/Team:Duke
-	**'''[[User:Gabriel Wu\|Gabriel Wu]] 01:17, 11 February 2013 (EST)''':The paper on CPEC was published in July 2009. The only authors on the paper are the graduate student and PI involved in the iGEM team. [http://www.ncbi.nlm.nih.gov/pubmed/19649325] Considering the typical iGEM timeline and the publication date, it's unclear if CPEC "started" as an iGEM project, but the students may have played some role in preparing it for publication.	+	**'''[[User:Gabriel Wu\|Gabriel Wu]] 01:17, 11 February 2013 (EST)''':The paper on CPEC was published in July 2009. The only authors on the paper are the graduate student and PI involved in the iGEM team. [http://www.ncbi.nlm.nih.gov/pubmed/19649325] Considering the typical iGEM timeline and the publication date, as well as the lack of authorship for any of the undergraduate students, it's unclear if CPEC "started" as an iGEM project, but the students may have played some role in preparing it for publication.

Gabriel Wu: /* iGEM connection */

Gabriel Wu — Mon, 11 Feb 2013 06:17:50 GMT

iGEM connection

←Older revision		Revision as of 06:17, 11 February 2013
Line 53:		Line 53:
	*'''[[User:Jeffrey E. Barrick\|Jeffrey E. Barrick]] 00:35, 7 February 2013 (EST)''':Someone mentioned that CPEC was started as an iGEM project. Can you link to the relevant team website as part of the topic so that we can take a look at it?		*'''[[User:Jeffrey E. Barrick\|Jeffrey E. Barrick]] 00:35, 7 February 2013 (EST)''':Someone mentioned that CPEC was started as an iGEM project. Can you link to the relevant team website as part of the topic so that we can take a look at it?
	**'''[[User:Max E. Rubinson\|Max E. Rubinson]] 22:43, 7 February 2013 (EST)''':I don't know if CPEC was started as an iGEM project, but [http://2009.igem.org/Team:Duke this group] at Duke (where the method was developed) used CPEC to assemble a metabolic pathway for the production of plastic polymers in ''E. coli''.		**'''[[User:Max E. Rubinson\|Max E. Rubinson]] 22:43, 7 February 2013 (EST)''':I don't know if CPEC was started as an iGEM project, but [http://2009.igem.org/Team:Duke this group] at Duke (where the method was developed) used CPEC to assemble a metabolic pathway for the production of plastic polymers in ''E. coli''.
-	*'''[[User:Thomas Wall\|Thomas Wall]] 20:33, 7 February 2013 (EST)''': http://2009.igem.org/Team:Duke	+	**'''[[User:Thomas Wall\|Thomas Wall]] 20:33, 7 February 2013 (EST)''': http://2009.igem.org/Team:Duke
	**'''[[User:Gabriel Wu\|Gabriel Wu]] 01:17, 11 February 2013 (EST)''':The paper on CPEC was published in July 2009. The only authors on the paper are the graduate student and PI involved in the iGEM team. [http://www.ncbi.nlm.nih.gov/pubmed/19649325] Considering the typical iGEM timeline and the publication date, it's unclear if CPEC "started" as an iGEM project, but the students may have played some role in preparing it for publication.		**'''[[User:Gabriel Wu\|Gabriel Wu]] 01:17, 11 February 2013 (EST)''':The paper on CPEC was published in July 2009. The only authors on the paper are the graduate student and PI involved in the iGEM team. [http://www.ncbi.nlm.nih.gov/pubmed/19649325] Considering the typical iGEM timeline and the publication date, it's unclear if CPEC "started" as an iGEM project, but the students may have played some role in preparing it for publication.

Gabriel Wu: /* iGEM connection */

Gabriel Wu — Mon, 11 Feb 2013 06:17:33 GMT

iGEM connection

←Older revision		Revision as of 06:17, 11 February 2013
Line 51:		Line 51:

	== iGEM connection ==		== iGEM connection ==
-	*'''[[User:Jeffrey E. Barrick\|Jeffrey E. Barrick]] 00:35, 7 February 2013 (EST)''':Someone mentioned that CPEC was started as an iGEM project. Can you ~~like~~ to the relevant team website as part of the topic so that we can take a look at it?	+	*'''[[User:Jeffrey E. Barrick\|Jeffrey E. Barrick]] 00:35, 7 February 2013 (EST)''':Someone mentioned that CPEC was started as an iGEM project. Can you link to the relevant team website as part of the topic so that we can take a look at it?
	**'''[[User:Max E. Rubinson\|Max E. Rubinson]] 22:43, 7 February 2013 (EST)''':I don't know if CPEC was started as an iGEM project, but [http://2009.igem.org/Team:Duke this group] at Duke (where the method was developed) used CPEC to assemble a metabolic pathway for the production of plastic polymers in ''E. coli''.		**'''[[User:Max E. Rubinson\|Max E. Rubinson]] 22:43, 7 February 2013 (EST)''':I don't know if CPEC was started as an iGEM project, but [http://2009.igem.org/Team:Duke this group] at Duke (where the method was developed) used CPEC to assemble a metabolic pathway for the production of plastic polymers in ''E. coli''.
	*'''[[User:Thomas Wall\|Thomas Wall]] 20:33, 7 February 2013 (EST)''': http://2009.igem.org/Team:Duke		*'''[[User:Thomas Wall\|Thomas Wall]] 20:33, 7 February 2013 (EST)''': http://2009.igem.org/Team:Duke
		+	**'''[[User:Gabriel Wu\|Gabriel Wu]] 01:17, 11 February 2013 (EST)''':The paper on CPEC was published in July 2009. The only authors on the paper are the graduate student and PI involved in the iGEM team. [http://www.ncbi.nlm.nih.gov/pubmed/19649325] Considering the typical iGEM timeline and the publication date, it's unclear if CPEC "started" as an iGEM project, but the students may have played some role in preparing it for publication.

Gabriel Wu: /* Assembling nonstandard bases */

Gabriel Wu — Mon, 11 Feb 2013 06:10:49 GMT

Assembling nonstandard bases

←Older revision		Revision as of 06:10, 11 February 2013
Line 44:		Line 44:
	**'''[[User:Yunle Huang\|Yunle Huang]] 10:02, 7 February 2013 (EST)''': One example I found was 2-Aminopurine. 2-Aminopurine is a fluorescent nucleic acid analogues can be used in nucleic acid research. Since it pairs with both thymine and cytosine, it can also be used for mutagenesis. http://www.pnas.org/content/83/15/5434		**'''[[User:Yunle Huang\|Yunle Huang]] 10:02, 7 February 2013 (EST)''': One example I found was 2-Aminopurine. 2-Aminopurine is a fluorescent nucleic acid analogues can be used in nucleic acid research. Since it pairs with both thymine and cytosine, it can also be used for mutagenesis. http://www.pnas.org/content/83/15/5434
	**'''[[User:Benjamin Gilman\|Benjamin Gilman]] 16:02, 7 February 2013 (EST)''': Unnatural bases are often used in synthetic DNA oligos to broaden the range of binding interactions or chemistry available (like what [http://www.somalogic.com Somalogic] has done with DNA aptamers). Are there any applications where genes with synthetic, unnatural bases were used ''in vivo''?		**'''[[User:Benjamin Gilman\|Benjamin Gilman]] 16:02, 7 February 2013 (EST)''': Unnatural bases are often used in synthetic DNA oligos to broaden the range of binding interactions or chemistry available (like what [http://www.somalogic.com Somalogic] has done with DNA aptamers). Are there any applications where genes with synthetic, unnatural bases were used ''in vivo''?
-	***''''[[User:Gabriel Wu\|Gabriel Wu]] 01:10, 11 February 2013 (EST)'''': I don't know of any "in vivo" applications for unnatural bases.	+	***'''[[User:Gabriel Wu\|Gabriel Wu]] 01:10, 11 February 2013 (EST)''': I don't know of any "in vivo" applications for unnatural bases.
	***'''[[User:Aurko Dasgupta\|Aurko Dasgupta]] 20:34, 7 February 2013 (EST)''':So I'm guessing they handle stuff like promoter/transcription factor binding affinity? Unless you use some kind of unnatural tRNA as well, I doubt you'd be able get that stuff translated.		***'''[[User:Aurko Dasgupta\|Aurko Dasgupta]] 20:34, 7 February 2013 (EST)''':So I'm guessing they handle stuff like promoter/transcription factor binding affinity? Unless you use some kind of unnatural tRNA as well, I doubt you'd be able get that stuff translated.
	****'''[[User:Gabriel Wu\|Gabriel Wu]] 00:27, 11 February 2013 (EST)''': In the article, the mention of non-traditional bases is simply an extension of the chemistry of DNA synthesis. Nucleotides all share a common deoxyribose phosphate backbone. The base that defines the nucleotide is not involved in the extension of the DNA molecule; therefore, any base can be incorporated into a growing chain (so long as it maintains the deoxyribose backbone).		****'''[[User:Gabriel Wu\|Gabriel Wu]] 00:27, 11 February 2013 (EST)''': In the article, the mention of non-traditional bases is simply an extension of the chemistry of DNA synthesis. Nucleotides all share a common deoxyribose phosphate backbone. The base that defines the nucleotide is not involved in the extension of the DNA molecule; therefore, any base can be incorporated into a growing chain (so long as it maintains the deoxyribose backbone).
	****'''[[User:Gabriel Wu\|Gabriel Wu]] 00:27, 11 February 2013 (EST)''': However, I think it's interesting to note that researchers have studied how to synthesize XNA, or "xeno-nucleic acid," in order to understand the fundamental dynamics of the basic chemical nature of life and its ability to store information. They've actually made XNA polymerases that replicate XNA templates. While they haven't shown transcription of XNA into some RNA-equivalent molecule, the ability to have an XNA polymerase suggests that it is possible to create such a protein. [http://www.ncbi.nlm.nih.gov/pubmed/22517858]		****'''[[User:Gabriel Wu\|Gabriel Wu]] 00:27, 11 February 2013 (EST)''': However, I think it's interesting to note that researchers have studied how to synthesize XNA, or "xeno-nucleic acid," in order to understand the fundamental dynamics of the basic chemical nature of life and its ability to store information. They've actually made XNA polymerases that replicate XNA templates. While they haven't shown transcription of XNA into some RNA-equivalent molecule, the ability to have an XNA polymerase suggests that it is possible to create such a protein. [http://www.ncbi.nlm.nih.gov/pubmed/22517858]
-	****''''[[User:Gabriel Wu\|Gabriel Wu]] 01:09, 11 February 2013 (EST)'''': Finally, there has been a significant amount of work on unnatural amino acid incorporation. In this case, they modify a tRNA to incorporate an amino acid that is not its natural partner. This unnatural amino acid is then incorporated into the growing peptide chain. [http://www.ncbi.nlm.nih.gov/pubmed/2649980] While this modification is done to existing tRNAs that recognize natural codons (typically a stop codon), it is possible to imagine a scenario where a tRNA could be modified to recognize a transcribed XNA codon and used to incorporate an unnatural amino acid from XNA.	+	****'''[[User:Gabriel Wu\|Gabriel Wu]] 01:09, 11 February 2013 (EST)''': Finally, there has been a significant amount of work on unnatural amino acid incorporation. In this case, they modify a tRNA to incorporate an amino acid that is not its natural partner. This unnatural amino acid is then incorporated into the growing peptide chain. [http://www.ncbi.nlm.nih.gov/pubmed/2649980] While this modification is done to existing tRNAs that recognize natural codons (typically a stop codon), it is possible to imagine a scenario where a tRNA could be modified to recognize a transcribed XNA codon and used to incorporate an unnatural amino acid from XNA.

	== iGEM connection ==		== iGEM connection ==

Gabriel Wu: /* Assembling nonstandard bases */

Gabriel Wu — Mon, 11 Feb 2013 06:10:18 GMT

Assembling nonstandard bases

←Older revision		Revision as of 06:10, 11 February 2013
Line 44:		Line 44:
	**'''[[User:Yunle Huang\|Yunle Huang]] 10:02, 7 February 2013 (EST)''': One example I found was 2-Aminopurine. 2-Aminopurine is a fluorescent nucleic acid analogues can be used in nucleic acid research. Since it pairs with both thymine and cytosine, it can also be used for mutagenesis. http://www.pnas.org/content/83/15/5434		**'''[[User:Yunle Huang\|Yunle Huang]] 10:02, 7 February 2013 (EST)''': One example I found was 2-Aminopurine. 2-Aminopurine is a fluorescent nucleic acid analogues can be used in nucleic acid research. Since it pairs with both thymine and cytosine, it can also be used for mutagenesis. http://www.pnas.org/content/83/15/5434
	**'''[[User:Benjamin Gilman\|Benjamin Gilman]] 16:02, 7 February 2013 (EST)''': Unnatural bases are often used in synthetic DNA oligos to broaden the range of binding interactions or chemistry available (like what [http://www.somalogic.com Somalogic] has done with DNA aptamers). Are there any applications where genes with synthetic, unnatural bases were used ''in vivo''?		**'''[[User:Benjamin Gilman\|Benjamin Gilman]] 16:02, 7 February 2013 (EST)''': Unnatural bases are often used in synthetic DNA oligos to broaden the range of binding interactions or chemistry available (like what [http://www.somalogic.com Somalogic] has done with DNA aptamers). Are there any applications where genes with synthetic, unnatural bases were used ''in vivo''?
		+	***''''[[User:Gabriel Wu\|Gabriel Wu]] 01:10, 11 February 2013 (EST)'''': I don't know of any "in vivo" applications for unnatural bases.
	***'''[[User:Aurko Dasgupta\|Aurko Dasgupta]] 20:34, 7 February 2013 (EST)''':So I'm guessing they handle stuff like promoter/transcription factor binding affinity? Unless you use some kind of unnatural tRNA as well, I doubt you'd be able get that stuff translated.		***'''[[User:Aurko Dasgupta\|Aurko Dasgupta]] 20:34, 7 February 2013 (EST)''':So I'm guessing they handle stuff like promoter/transcription factor binding affinity? Unless you use some kind of unnatural tRNA as well, I doubt you'd be able get that stuff translated.
	****'''[[User:Gabriel Wu\|Gabriel Wu]] 00:27, 11 February 2013 (EST)''': In the article, the mention of non-traditional bases is simply an extension of the chemistry of DNA synthesis. Nucleotides all share a common deoxyribose phosphate backbone. The base that defines the nucleotide is not involved in the extension of the DNA molecule; therefore, any base can be incorporated into a growing chain (so long as it maintains the deoxyribose backbone).		****'''[[User:Gabriel Wu\|Gabriel Wu]] 00:27, 11 February 2013 (EST)''': In the article, the mention of non-traditional bases is simply an extension of the chemistry of DNA synthesis. Nucleotides all share a common deoxyribose phosphate backbone. The base that defines the nucleotide is not involved in the extension of the DNA molecule; therefore, any base can be incorporated into a growing chain (so long as it maintains the deoxyribose backbone).

Gabriel Wu: /* Assembling nonstandard bases */

Gabriel Wu — Mon, 11 Feb 2013 06:09:00 GMT

Assembling nonstandard bases

←Older revision		Revision as of 06:09, 11 February 2013
Line 45:		Line 45:
	**'''[[User:Benjamin Gilman\|Benjamin Gilman]] 16:02, 7 February 2013 (EST)''': Unnatural bases are often used in synthetic DNA oligos to broaden the range of binding interactions or chemistry available (like what [http://www.somalogic.com Somalogic] has done with DNA aptamers). Are there any applications where genes with synthetic, unnatural bases were used ''in vivo''?		**'''[[User:Benjamin Gilman\|Benjamin Gilman]] 16:02, 7 February 2013 (EST)''': Unnatural bases are often used in synthetic DNA oligos to broaden the range of binding interactions or chemistry available (like what [http://www.somalogic.com Somalogic] has done with DNA aptamers). Are there any applications where genes with synthetic, unnatural bases were used ''in vivo''?
	***'''[[User:Aurko Dasgupta\|Aurko Dasgupta]] 20:34, 7 February 2013 (EST)''':So I'm guessing they handle stuff like promoter/transcription factor binding affinity? Unless you use some kind of unnatural tRNA as well, I doubt you'd be able get that stuff translated.		***'''[[User:Aurko Dasgupta\|Aurko Dasgupta]] 20:34, 7 February 2013 (EST)''':So I'm guessing they handle stuff like promoter/transcription factor binding affinity? Unless you use some kind of unnatural tRNA as well, I doubt you'd be able get that stuff translated.
-	**'''[[User:Gabriel Wu\|Gabriel Wu]] 00:27, 11 February 2013 (EST)''': In the article, the mention of non-traditional bases is simply an extension of the chemistry of DNA synthesis. Nucleotides all share a common deoxyribose phosphate backbone. The base that defines the nucleotide is not involved in the extension of the DNA molecule; therefore, any base can be incorporated into a growing chain (so long as it maintains the deoxyribose backbone).	+	****'''[[User:Gabriel Wu\|Gabriel Wu]] 00:27, 11 February 2013 (EST)''': In the article, the mention of non-traditional bases is simply an extension of the chemistry of DNA synthesis. Nucleotides all share a common deoxyribose phosphate backbone. The base that defines the nucleotide is not involved in the extension of the DNA molecule; therefore, any base can be incorporated into a growing chain (so long as it maintains the deoxyribose backbone).
-	**'''[[User:Gabriel Wu\|Gabriel Wu]] 00:27, 11 February 2013 (EST)''': However, I think it's interesting to note that researchers have studied how to synthesize XNA, or "xeno-nucleic acid," in order to understand the fundamental dynamics of the basic chemical nature of life and its ability to store information. [http://www.ncbi.nlm.nih.gov/pubmed/22517858]	+	****'''[[User:Gabriel Wu\|Gabriel Wu]] 00:27, 11 February 2013 (EST)''': However, I think it's interesting to note that researchers have studied how to synthesize XNA, or "xeno-nucleic acid," in order to understand the fundamental dynamics of the basic chemical nature of life and its ability to store information. They've actually made XNA polymerases that replicate XNA templates. While they haven't shown transcription of XNA into some RNA-equivalent molecule, the ability to have an XNA polymerase suggests that it is possible to create such a protein. [http://www.ncbi.nlm.nih.gov/pubmed/22517858]
		+	****''''[[User:Gabriel Wu\|Gabriel Wu]] 01:09, 11 February 2013 (EST)'''': Finally, there has been a significant amount of work on unnatural amino acid incorporation. In this case, they modify a tRNA to incorporate an amino acid that is not its natural partner. This unnatural amino acid is then incorporated into the growing peptide chain. [http://www.ncbi.nlm.nih.gov/pubmed/2649980] While this modification is done to existing tRNAs that recognize natural codons (typically a stop codon), it is possible to imagine a scenario where a tRNA could be modified to recognize a transcribed XNA codon and used to incorporate an unnatural amino acid from XNA.

	== iGEM connection ==		== iGEM connection ==

Gabriel Wu at 05:31, 11 February 2013

Gabriel Wu — Mon, 11 Feb 2013 05:31:53 GMT

←Older revision		Revision as of 05:31, 11 February 2013
Line 46:		Line 46:
	***'''[[User:Aurko Dasgupta\|Aurko Dasgupta]] 20:34, 7 February 2013 (EST)''':So I'm guessing they handle stuff like promoter/transcription factor binding affinity? Unless you use some kind of unnatural tRNA as well, I doubt you'd be able get that stuff translated.		***'''[[User:Aurko Dasgupta\|Aurko Dasgupta]] 20:34, 7 February 2013 (EST)''':So I'm guessing they handle stuff like promoter/transcription factor binding affinity? Unless you use some kind of unnatural tRNA as well, I doubt you'd be able get that stuff translated.
	**'''[[User:Gabriel Wu\|Gabriel Wu]] 00:27, 11 February 2013 (EST)''': In the article, the mention of non-traditional bases is simply an extension of the chemistry of DNA synthesis. Nucleotides all share a common deoxyribose phosphate backbone. The base that defines the nucleotide is not involved in the extension of the DNA molecule; therefore, any base can be incorporated into a growing chain (so long as it maintains the deoxyribose backbone).		**'''[[User:Gabriel Wu\|Gabriel Wu]] 00:27, 11 February 2013 (EST)''': In the article, the mention of non-traditional bases is simply an extension of the chemistry of DNA synthesis. Nucleotides all share a common deoxyribose phosphate backbone. The base that defines the nucleotide is not involved in the extension of the DNA molecule; therefore, any base can be incorporated into a growing chain (so long as it maintains the deoxyribose backbone).
-	**'''[[User:Gabriel Wu\|Gabriel Wu]] 00:27, 11 February 2013 (EST)''': However, I think it's interesting to note that researchers have studied how to synthesize XNA, or "xeno-nucleic acid," in order to understand the fundamental dynamics of the basic chemical nature of life and its ability to store information. [~~DOI 10.1126~~/~~science~~.~~1217622~~]	+	**'''[[User:Gabriel Wu\|Gabriel Wu]] 00:27, 11 February 2013 (EST)''': However, I think it's interesting to note that researchers have studied how to synthesize XNA, or "xeno-nucleic acid," in order to understand the fundamental dynamics of the basic chemical nature of life and its ability to store information. [http://www.ncbi.nlm.nih.gov/pubmed/22517858]

	== iGEM connection ==		== iGEM connection ==

←Older revision		Revision as of 06:21, 11 February 2013
Line 54:		Line 54:
	**'''[[User:Max E. Rubinson\|Max E. Rubinson]] 22:43, 7 February 2013 (EST)''':I don't know if CPEC was started as an iGEM project, but [http://2009.igem.org/Team:Duke this group] at Duke (where the method was developed) used CPEC to assemble a metabolic pathway for the production of plastic polymers in ''E. coli''.		**'''[[User:Max E. Rubinson\|Max E. Rubinson]] 22:43, 7 February 2013 (EST)''':I don't know if CPEC was started as an iGEM project, but [http://2009.igem.org/Team:Duke this group] at Duke (where the method was developed) used CPEC to assemble a metabolic pathway for the production of plastic polymers in ''E. coli''.
	**'''[[User:Thomas Wall\|Thomas Wall]] 20:33, 7 February 2013 (EST)''': http://2009.igem.org/Team:Duke		**'''[[User:Thomas Wall\|Thomas Wall]] 20:33, 7 February 2013 (EST)''': http://2009.igem.org/Team:Duke
-	**'''[[User:Gabriel Wu\|Gabriel Wu]] 01:17, 11 February 2013 (EST)''':The paper on CPEC was published in July 2009. The only authors on the paper are the graduate student and PI involved in the iGEM team. [http://www.ncbi.nlm.nih.gov/pubmed/19649325] Considering the typical iGEM timeline and the publication date, it's unclear if CPEC "started" as an iGEM project, but the students may have played some role in preparing it for publication.	+	**'''[[User:Gabriel Wu\|Gabriel Wu]] 01:17, 11 February 2013 (EST)''':The paper on CPEC was published in July 2009. The only authors on the paper are the graduate student and PI involved in the iGEM team. [http://www.ncbi.nlm.nih.gov/pubmed/19649325] Considering the typical iGEM timeline and the publication date, as well as the lack of authorship for any of the undergraduate students, it's unclear if CPEC "started" as an iGEM project, but the students may have played some role in preparing it for publication.

←Older revision		Revision as of 06:17, 11 February 2013
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	*'''[[User:Jeffrey E. Barrick\|Jeffrey E. Barrick]] 00:35, 7 February 2013 (EST)''':Someone mentioned that CPEC was started as an iGEM project. Can you link to the relevant team website as part of the topic so that we can take a look at it?		*'''[[User:Jeffrey E. Barrick\|Jeffrey E. Barrick]] 00:35, 7 February 2013 (EST)''':Someone mentioned that CPEC was started as an iGEM project. Can you link to the relevant team website as part of the topic so that we can take a look at it?
	**'''[[User:Max E. Rubinson\|Max E. Rubinson]] 22:43, 7 February 2013 (EST)''':I don't know if CPEC was started as an iGEM project, but [http://2009.igem.org/Team:Duke this group] at Duke (where the method was developed) used CPEC to assemble a metabolic pathway for the production of plastic polymers in ''E. coli''.		**'''[[User:Max E. Rubinson\|Max E. Rubinson]] 22:43, 7 February 2013 (EST)''':I don't know if CPEC was started as an iGEM project, but [http://2009.igem.org/Team:Duke this group] at Duke (where the method was developed) used CPEC to assemble a metabolic pathway for the production of plastic polymers in ''E. coli''.
-	*'''[[User:Thomas Wall\|Thomas Wall]] 20:33, 7 February 2013 (EST)''': http://2009.igem.org/Team:Duke	+	**'''[[User:Thomas Wall\|Thomas Wall]] 20:33, 7 February 2013 (EST)''': http://2009.igem.org/Team:Duke
	**'''[[User:Gabriel Wu\|Gabriel Wu]] 01:17, 11 February 2013 (EST)''':The paper on CPEC was published in July 2009. The only authors on the paper are the graduate student and PI involved in the iGEM team. [http://www.ncbi.nlm.nih.gov/pubmed/19649325] Considering the typical iGEM timeline and the publication date, it's unclear if CPEC "started" as an iGEM project, but the students may have played some role in preparing it for publication.		**'''[[User:Gabriel Wu\|Gabriel Wu]] 01:17, 11 February 2013 (EST)''':The paper on CPEC was published in July 2009. The only authors on the paper are the graduate student and PI involved in the iGEM team. [http://www.ncbi.nlm.nih.gov/pubmed/19649325] Considering the typical iGEM timeline and the publication date, it's unclear if CPEC "started" as an iGEM project, but the students may have played some role in preparing it for publication.

←Older revision		Revision as of 06:17, 11 February 2013
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	== iGEM connection ==		== iGEM connection ==
-	*'''[[User:Jeffrey E. Barrick\|Jeffrey E. Barrick]] 00:35, 7 February 2013 (EST)''':Someone mentioned that CPEC was started as an iGEM project. Can you ~~like~~ to the relevant team website as part of the topic so that we can take a look at it?	+	*'''[[User:Jeffrey E. Barrick\|Jeffrey E. Barrick]] 00:35, 7 February 2013 (EST)''':Someone mentioned that CPEC was started as an iGEM project. Can you link to the relevant team website as part of the topic so that we can take a look at it?
	**'''[[User:Max E. Rubinson\|Max E. Rubinson]] 22:43, 7 February 2013 (EST)''':I don't know if CPEC was started as an iGEM project, but [http://2009.igem.org/Team:Duke this group] at Duke (where the method was developed) used CPEC to assemble a metabolic pathway for the production of plastic polymers in ''E. coli''.		**'''[[User:Max E. Rubinson\|Max E. Rubinson]] 22:43, 7 February 2013 (EST)''':I don't know if CPEC was started as an iGEM project, but [http://2009.igem.org/Team:Duke this group] at Duke (where the method was developed) used CPEC to assemble a metabolic pathway for the production of plastic polymers in ''E. coli''.
	*'''[[User:Thomas Wall\|Thomas Wall]] 20:33, 7 February 2013 (EST)''': http://2009.igem.org/Team:Duke		*'''[[User:Thomas Wall\|Thomas Wall]] 20:33, 7 February 2013 (EST)''': http://2009.igem.org/Team:Duke
		+	**'''[[User:Gabriel Wu\|Gabriel Wu]] 01:17, 11 February 2013 (EST)''':The paper on CPEC was published in July 2009. The only authors on the paper are the graduate student and PI involved in the iGEM team. [http://www.ncbi.nlm.nih.gov/pubmed/19649325] Considering the typical iGEM timeline and the publication date, it's unclear if CPEC "started" as an iGEM project, but the students may have played some role in preparing it for publication.

←Older revision		Revision as of 06:10, 11 February 2013
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	**'''[[User:Yunle Huang\|Yunle Huang]] 10:02, 7 February 2013 (EST)''': One example I found was 2-Aminopurine. 2-Aminopurine is a fluorescent nucleic acid analogues can be used in nucleic acid research. Since it pairs with both thymine and cytosine, it can also be used for mutagenesis. http://www.pnas.org/content/83/15/5434		**'''[[User:Yunle Huang\|Yunle Huang]] 10:02, 7 February 2013 (EST)''': One example I found was 2-Aminopurine. 2-Aminopurine is a fluorescent nucleic acid analogues can be used in nucleic acid research. Since it pairs with both thymine and cytosine, it can also be used for mutagenesis. http://www.pnas.org/content/83/15/5434
	**'''[[User:Benjamin Gilman\|Benjamin Gilman]] 16:02, 7 February 2013 (EST)''': Unnatural bases are often used in synthetic DNA oligos to broaden the range of binding interactions or chemistry available (like what [http://www.somalogic.com Somalogic] has done with DNA aptamers). Are there any applications where genes with synthetic, unnatural bases were used ''in vivo''?		**'''[[User:Benjamin Gilman\|Benjamin Gilman]] 16:02, 7 February 2013 (EST)''': Unnatural bases are often used in synthetic DNA oligos to broaden the range of binding interactions or chemistry available (like what [http://www.somalogic.com Somalogic] has done with DNA aptamers). Are there any applications where genes with synthetic, unnatural bases were used ''in vivo''?
-	***''''[[User:Gabriel Wu\|Gabriel Wu]] 01:10, 11 February 2013 (EST)'''': I don't know of any "in vivo" applications for unnatural bases.	+	***'''[[User:Gabriel Wu\|Gabriel Wu]] 01:10, 11 February 2013 (EST)''': I don't know of any "in vivo" applications for unnatural bases.
	***'''[[User:Aurko Dasgupta\|Aurko Dasgupta]] 20:34, 7 February 2013 (EST)''':So I'm guessing they handle stuff like promoter/transcription factor binding affinity? Unless you use some kind of unnatural tRNA as well, I doubt you'd be able get that stuff translated.		***'''[[User:Aurko Dasgupta\|Aurko Dasgupta]] 20:34, 7 February 2013 (EST)''':So I'm guessing they handle stuff like promoter/transcription factor binding affinity? Unless you use some kind of unnatural tRNA as well, I doubt you'd be able get that stuff translated.
	****'''[[User:Gabriel Wu\|Gabriel Wu]] 00:27, 11 February 2013 (EST)''': In the article, the mention of non-traditional bases is simply an extension of the chemistry of DNA synthesis. Nucleotides all share a common deoxyribose phosphate backbone. The base that defines the nucleotide is not involved in the extension of the DNA molecule; therefore, any base can be incorporated into a growing chain (so long as it maintains the deoxyribose backbone).		****'''[[User:Gabriel Wu\|Gabriel Wu]] 00:27, 11 February 2013 (EST)''': In the article, the mention of non-traditional bases is simply an extension of the chemistry of DNA synthesis. Nucleotides all share a common deoxyribose phosphate backbone. The base that defines the nucleotide is not involved in the extension of the DNA molecule; therefore, any base can be incorporated into a growing chain (so long as it maintains the deoxyribose backbone).
	****'''[[User:Gabriel Wu\|Gabriel Wu]] 00:27, 11 February 2013 (EST)''': However, I think it's interesting to note that researchers have studied how to synthesize XNA, or "xeno-nucleic acid," in order to understand the fundamental dynamics of the basic chemical nature of life and its ability to store information. They've actually made XNA polymerases that replicate XNA templates. While they haven't shown transcription of XNA into some RNA-equivalent molecule, the ability to have an XNA polymerase suggests that it is possible to create such a protein. [http://www.ncbi.nlm.nih.gov/pubmed/22517858]		****'''[[User:Gabriel Wu\|Gabriel Wu]] 00:27, 11 February 2013 (EST)''': However, I think it's interesting to note that researchers have studied how to synthesize XNA, or "xeno-nucleic acid," in order to understand the fundamental dynamics of the basic chemical nature of life and its ability to store information. They've actually made XNA polymerases that replicate XNA templates. While they haven't shown transcription of XNA into some RNA-equivalent molecule, the ability to have an XNA polymerase suggests that it is possible to create such a protein. [http://www.ncbi.nlm.nih.gov/pubmed/22517858]
-	****''''[[User:Gabriel Wu\|Gabriel Wu]] 01:09, 11 February 2013 (EST)'''': Finally, there has been a significant amount of work on unnatural amino acid incorporation. In this case, they modify a tRNA to incorporate an amino acid that is not its natural partner. This unnatural amino acid is then incorporated into the growing peptide chain. [http://www.ncbi.nlm.nih.gov/pubmed/2649980] While this modification is done to existing tRNAs that recognize natural codons (typically a stop codon), it is possible to imagine a scenario where a tRNA could be modified to recognize a transcribed XNA codon and used to incorporate an unnatural amino acid from XNA.	+	****'''[[User:Gabriel Wu\|Gabriel Wu]] 01:09, 11 February 2013 (EST)''': Finally, there has been a significant amount of work on unnatural amino acid incorporation. In this case, they modify a tRNA to incorporate an amino acid that is not its natural partner. This unnatural amino acid is then incorporated into the growing peptide chain. [http://www.ncbi.nlm.nih.gov/pubmed/2649980] While this modification is done to existing tRNAs that recognize natural codons (typically a stop codon), it is possible to imagine a scenario where a tRNA could be modified to recognize a transcribed XNA codon and used to incorporate an unnatural amino acid from XNA.

	== iGEM connection ==		== iGEM connection ==

←Older revision		Revision as of 06:10, 11 February 2013
Line 44:		Line 44:
	**'''[[User:Yunle Huang\|Yunle Huang]] 10:02, 7 February 2013 (EST)''': One example I found was 2-Aminopurine. 2-Aminopurine is a fluorescent nucleic acid analogues can be used in nucleic acid research. Since it pairs with both thymine and cytosine, it can also be used for mutagenesis. http://www.pnas.org/content/83/15/5434		**'''[[User:Yunle Huang\|Yunle Huang]] 10:02, 7 February 2013 (EST)''': One example I found was 2-Aminopurine. 2-Aminopurine is a fluorescent nucleic acid analogues can be used in nucleic acid research. Since it pairs with both thymine and cytosine, it can also be used for mutagenesis. http://www.pnas.org/content/83/15/5434
	**'''[[User:Benjamin Gilman\|Benjamin Gilman]] 16:02, 7 February 2013 (EST)''': Unnatural bases are often used in synthetic DNA oligos to broaden the range of binding interactions or chemistry available (like what [http://www.somalogic.com Somalogic] has done with DNA aptamers). Are there any applications where genes with synthetic, unnatural bases were used ''in vivo''?		**'''[[User:Benjamin Gilman\|Benjamin Gilman]] 16:02, 7 February 2013 (EST)''': Unnatural bases are often used in synthetic DNA oligos to broaden the range of binding interactions or chemistry available (like what [http://www.somalogic.com Somalogic] has done with DNA aptamers). Are there any applications where genes with synthetic, unnatural bases were used ''in vivo''?
		+	***''''[[User:Gabriel Wu\|Gabriel Wu]] 01:10, 11 February 2013 (EST)'''': I don't know of any "in vivo" applications for unnatural bases.
	***'''[[User:Aurko Dasgupta\|Aurko Dasgupta]] 20:34, 7 February 2013 (EST)''':So I'm guessing they handle stuff like promoter/transcription factor binding affinity? Unless you use some kind of unnatural tRNA as well, I doubt you'd be able get that stuff translated.		***'''[[User:Aurko Dasgupta\|Aurko Dasgupta]] 20:34, 7 February 2013 (EST)''':So I'm guessing they handle stuff like promoter/transcription factor binding affinity? Unless you use some kind of unnatural tRNA as well, I doubt you'd be able get that stuff translated.
	****'''[[User:Gabriel Wu\|Gabriel Wu]] 00:27, 11 February 2013 (EST)''': In the article, the mention of non-traditional bases is simply an extension of the chemistry of DNA synthesis. Nucleotides all share a common deoxyribose phosphate backbone. The base that defines the nucleotide is not involved in the extension of the DNA molecule; therefore, any base can be incorporated into a growing chain (so long as it maintains the deoxyribose backbone).		****'''[[User:Gabriel Wu\|Gabriel Wu]] 00:27, 11 February 2013 (EST)''': In the article, the mention of non-traditional bases is simply an extension of the chemistry of DNA synthesis. Nucleotides all share a common deoxyribose phosphate backbone. The base that defines the nucleotide is not involved in the extension of the DNA molecule; therefore, any base can be incorporated into a growing chain (so long as it maintains the deoxyribose backbone).