User:Etienne Robillard/Notebook/Chemtrails911 notebook/Agent Ecoli:Plasmid cloning vectors for gene therapy with phosphohistidine based oligos - Revision history

Etienne Robillard: /* Orthogonal DNA synthesis with Benzoyl-derived phosphotriester protecting groups (dA) */

Etienne Robillard — Fri, 22 Mar 2013 12:25:28 GMT

Orthogonal DNA synthesis with Benzoyl-derived phosphotriester protecting groups (dA)

←Older revision		Revision as of 12:25, 22 March 2013
Line 36:		Line 36:
	* '''Thus phosphohistidine based phosphoramidates can be classified as purine analogues; the substance (Purines) was formally discovered by Emil Fischer during WW1 as a fundamental group of heterocyclic amino acids.'''		* '''Thus phosphohistidine based phosphoramidates can be classified as purine analogues; the substance (Purines) was formally discovered by Emil Fischer during WW1 as a fundamental group of heterocyclic amino acids.'''
	** see Brink et al - Orthogonal translation/transcription and specialized ribosomes: http://www.ncbi.nlm.nih.gov/pubmed/7758959		** see Brink et al - Orthogonal translation/transcription and specialized ribosomes: http://www.ncbi.nlm.nih.gov/pubmed/7758959
		+	*** GenBank annotations (Accession FW420918) - ''Novel shine-dalgarno sequence and method for producing protein using the same'': http://www.ncbi.nlm.nih.gov/nuccore/FW420918

	== References ==		== References ==

Etienne Robillard: /* References */

Etienne Robillard — Fri, 22 Mar 2013 12:08:55 GMT

References

←Older revision		Revision as of 12:08, 22 March 2013
Line 40:		Line 40:

	* http://openwetware.org/images/1/1c/TheBacterialPromoter.pdf		* http://openwetware.org/images/1/1c/TheBacterialPromoter.pdf
-	* http://en.wikipedia.org/wiki/Protecting_group#Carboxylic_acid_protecting_groups protecting groups
-	* http://en.wikipedia.org/wiki/Oligonucleotide_synthesis#Nucleoside_phosphoramidites
	* http://en.wikibooks.org/wiki/Structural_Biochemistry/Nucleic_Acid/Nitrogenous_Bases/Purines		* http://en.wikibooks.org/wiki/Structural_Biochemistry/Nucleic_Acid/Nitrogenous_Bases/Purines

Etienne Robillard: /* Orthogonal DNA synthesis with Benzoyl-derived phosphotriester protecting groups (dA) */

Etienne Robillard — Fri, 22 Mar 2013 12:05:47 GMT

Orthogonal DNA synthesis with Benzoyl-derived phosphotriester protecting groups (dA)

←Older revision		Revision as of 12:05, 22 March 2013
Line 35:		Line 35:
	*** phospho'''tri'''ester = a '''tri'''cyclic N-derived nitrogenous base bound to a Histidine residue made for '''DNA''' synthesis.		*** phospho'''tri'''ester = a '''tri'''cyclic N-derived nitrogenous base bound to a Histidine residue made for '''DNA''' synthesis.
	* '''Thus phosphohistidine based phosphoramidates can be classified as purine analogues; the substance (Purines) was formally discovered by Emil Fischer during WW1 as a fundamental group of heterocyclic amino acids.'''		* '''Thus phosphohistidine based phosphoramidates can be classified as purine analogues; the substance (Purines) was formally discovered by Emil Fischer during WW1 as a fundamental group of heterocyclic amino acids.'''
-	** see ~~also [~~http://en.~~wikipedia~~.~~org/wiki/Piperidine Piperidine] : "Piperidine is also commonly used in chemical degradation reactions, such as the sequencing of DNA in the cleavage of particular modified nucleotides~~. ~~Piperidine is also commonly used as a base for the deprotection of Fmoc-amino acids used in '''[http://openwetware~~.~~org~~/~~wiki~~/~~Solid_Phase_Peptide_Synthesis solid-phase peptide synthesis].'''"~~	+	** see Brink et al - Orthogonal translation/transcription and specialized ribosomes: http://www.ncbi.nlm.nih.gov/pubmed/7758959

	== References ==		== References ==

Etienne Robillard: /* Orthogonal DNA synthesis with Benzoyl-derived phosphotriester protecting groups (dA) */

Etienne Robillard — Fri, 23 Nov 2012 14:01:15 GMT

Orthogonal DNA synthesis with Benzoyl-derived phosphotriester protecting groups (dA)

←Older revision		Revision as of 14:01, 23 November 2012
Line 35:		Line 35:
	*** phospho'''tri'''ester = a '''tri'''cyclic N-derived nitrogenous base bound to a Histidine residue made for '''DNA''' synthesis.		*** phospho'''tri'''ester = a '''tri'''cyclic N-derived nitrogenous base bound to a Histidine residue made for '''DNA''' synthesis.
	* '''Thus phosphohistidine based phosphoramidates can be classified as purine analogues; the substance (Purines) was formally discovered by Emil Fischer during WW1 as a fundamental group of heterocyclic amino acids.'''		* '''Thus phosphohistidine based phosphoramidates can be classified as purine analogues; the substance (Purines) was formally discovered by Emil Fischer during WW1 as a fundamental group of heterocyclic amino acids.'''
-	** see also [http://en.wikipedia.org/wiki/Piperidine Piperidine] : "Piperidine is also commonly used in chemical degradation reactions, such as the sequencing of DNA in the cleavage of particular modified nucleotides. Piperidine is also commonly used as a base for the deprotection of Fmoc-amino acids used in '''solid-phase peptide synthesis.'''"	+	** see also [http://en.wikipedia.org/wiki/Piperidine Piperidine] : "Piperidine is also commonly used in chemical degradation reactions, such as the sequencing of DNA in the cleavage of particular modified nucleotides. Piperidine is also commonly used as a base for the deprotection of Fmoc-amino acids used in '''[http://openwetware.org/wiki/Solid_Phase_Peptide_Synthesis solid-phase peptide synthesis].'''"

	== References ==		== References ==

Etienne Robillard: /* Orthogonal DNA synthesis with Benzoyl-derived phosphotriester protecting groups (dA) */

Etienne Robillard — Thu, 22 Nov 2012 12:51:38 GMT

Orthogonal DNA synthesis with Benzoyl-derived phosphotriester protecting groups (dA)

←Older revision		Revision as of 12:51, 22 November 2012
Line 35:		Line 35:
	*** phospho'''tri'''ester = a '''tri'''cyclic N-derived nitrogenous base bound to a Histidine residue made for '''DNA''' synthesis.		*** phospho'''tri'''ester = a '''tri'''cyclic N-derived nitrogenous base bound to a Histidine residue made for '''DNA''' synthesis.
	* '''Thus phosphohistidine based phosphoramidates can be classified as purine analogues; the substance (Purines) was formally discovered by Emil Fischer during WW1 as a fundamental group of heterocyclic amino acids.'''		* '''Thus phosphohistidine based phosphoramidates can be classified as purine analogues; the substance (Purines) was formally discovered by Emil Fischer during WW1 as a fundamental group of heterocyclic amino acids.'''
-	** see also [http://en.wikipedia.org/wiki/Piperidine Piperidine]	+	** see also [http://en.wikipedia.org/wiki/Piperidine Piperidine] : "Piperidine is also commonly used in chemical degradation reactions, such as the sequencing of DNA in the cleavage of particular modified nucleotides. Piperidine is also commonly used as a base for the deprotection of Fmoc-amino acids used in '''solid-phase peptide synthesis.'''"

	== References ==		== References ==

Etienne Robillard: /* Orthogonal DNA synthesis with Benzoyl-derived phosphotriester protecting groups (dA) */

Etienne Robillard — Thu, 22 Nov 2012 12:44:45 GMT

Orthogonal DNA synthesis with Benzoyl-derived phosphotriester protecting groups (dA)

←Older revision		Revision as of 12:44, 22 November 2012
Line 35:		Line 35:
	*** phospho'''tri'''ester = a '''tri'''cyclic N-derived nitrogenous base bound to a Histidine residue made for '''DNA''' synthesis.		*** phospho'''tri'''ester = a '''tri'''cyclic N-derived nitrogenous base bound to a Histidine residue made for '''DNA''' synthesis.
	* '''Thus phosphohistidine based phosphoramidates can be classified as purine analogues; the substance (Purines) was formally discovered by Emil Fischer during WW1 as a fundamental group of heterocyclic amino acids.'''		* '''Thus phosphohistidine based phosphoramidates can be classified as purine analogues; the substance (Purines) was formally discovered by Emil Fischer during WW1 as a fundamental group of heterocyclic amino acids.'''
-	** see also [[http://en.wikipedia.org/wiki/Piperidine Piperidine]]	+	** see also [http://en.wikipedia.org/wiki/Piperidine Piperidine]

	== References ==		== References ==

Etienne Robillard: /* Orthogonal DNA synthesis with Benzoyl-derived phosphotriester protecting groups (dA) */

Etienne Robillard — Thu, 22 Nov 2012 12:44:23 GMT

Orthogonal DNA synthesis with Benzoyl-derived phosphotriester protecting groups (dA)

←Older revision		Revision as of 12:44, 22 November 2012
Line 34:		Line 34:
	*** araBAD XXX		*** araBAD XXX
	*** phospho'''tri'''ester = a '''tri'''cyclic N-derived nitrogenous base bound to a Histidine residue made for '''DNA''' synthesis.		*** phospho'''tri'''ester = a '''tri'''cyclic N-derived nitrogenous base bound to a Histidine residue made for '''DNA''' synthesis.
-	~~**~~ Thus phosphohistidine based phosphoramidates can be classified as purine analogues; the substance (Purines) was formally discovered by Emil Fischer during WW1 as a fundamental group of heterocyclic amino acids.	+	* '''Thus phosphohistidine based phosphoramidates can be classified as purine analogues; the substance (Purines) was formally discovered by Emil Fischer during WW1 as a fundamental group of heterocyclic amino acids.'''
		+	** see also [[http://en.wikipedia.org/wiki/Piperidine Piperidine]]

	== References ==		== References ==

Etienne Robillard: /* Orthogonal DNA shell/therapy with Benzyl-derived phosphotriester protecting groups */

Etienne Robillard — Thu, 22 Nov 2012 00:28:12 GMT

Orthogonal DNA shell/therapy with Benzyl-derived phosphotriester protecting groups

←Older revision		Revision as of 00:28, 22 November 2012
Line 24:		Line 24:
	* amino-acid sequence signature (Myc epitope tag) = EQKLISEEDL		* amino-acid sequence signature (Myc epitope tag) = EQKLISEEDL

-	=== Orthogonal DNA ~~shell/therapy~~ with ~~Benzyl~~-derived phosphotriester protecting groups ===	+	=== Orthogonal DNA synthesis with Benzoyl-derived phosphotriester protecting groups (dA) ===

	* note! note! Important: Can you elucidate the reasoning of using an carboxilic acid as protecting group for DNA assembly?		* note! note! Important: Can you elucidate the reasoning of using an carboxilic acid as protecting group for DNA assembly?
-	** FIRST PROBABLE PROTECTION GROUP (~~A STRONG PROMOTER~~):	+	** FIRST PROBABLE PROTECTION GROUP (dA):
	*** Bz = Benzoyl (Bz, benzoic acid ester) : 2nd step in the catalysis of Benzilic acid from oxidation of Benzoic acid. See "benzoic acid". A very common [reagent] for site-directed oligonucleotide synthesis.		*** Bz = Benzoyl (Bz, benzoic acid ester) : 2nd step in the catalysis of Benzilic acid from oxidation of Benzoic acid. See "benzoic acid". A very common [reagent] for site-directed oligonucleotide synthesis.
	*** Note: Consensus promoter sequences are by definition strong promoters!		*** Note: Consensus promoter sequences are by definition strong promoters!
-	** 2ND HIGHLY PROBABLE PROTECTION GROUP (~~A WEAK PROMOTER~~):	+	** 2ND HIGHLY PROBABLE PROTECTION GROUP (araBAD):
	*** 2-cyanoethyl : for protecting phosphoramidites based nucleosides? XXX		*** 2-cyanoethyl : for protecting phosphoramidites based nucleosides? XXX
	*** araBAD XXX		*** araBAD XXX
	*** phospho'''tri'''ester = a '''tri'''cyclic N-derived nitrogenous base bound to a Histidine residue made for '''DNA''' synthesis.		*** phospho'''tri'''ester = a '''tri'''cyclic N-derived nitrogenous base bound to a Histidine residue made for '''DNA''' synthesis.
-	**** Thus phosphohistidine based phosphoramidates can be classified as purine analogues; the substance (Purines) was formally discovered by Emil Fischer during WW1 as a fundamental group of heterocyclic amino acids.	+	**** Thus phosphohistidine based phosphoramidates can be classified as purine analogues; the substance (Purines) was formally discovered by Emil Fischer during WW1 as a fundamental group of heterocyclic amino acids.

	== References ==		== References ==

Etienne Robillard: /* References */

Etienne Robillard — Thu, 15 Nov 2012 08:32:12 GMT

References

←Older revision		Revision as of 08:32, 15 November 2012
Line 41:		Line 41:
	* http://en.wikipedia.org/wiki/Protecting_group#Carboxylic_acid_protecting_groups protecting groups		* http://en.wikipedia.org/wiki/Protecting_group#Carboxylic_acid_protecting_groups protecting groups
	* http://en.wikipedia.org/wiki/Oligonucleotide_synthesis#Nucleoside_phosphoramidites		* http://en.wikipedia.org/wiki/Oligonucleotide_synthesis#Nucleoside_phosphoramidites
		+	* http://en.wikibooks.org/wiki/Structural_Biochemistry/Nucleic_Acid/Nitrogenous_Bases/Purines

Etienne Robillard at 08:30, 15 November 2012

Etienne Robillard — Thu, 15 Nov 2012 08:30:29 GMT

←Older revision		Revision as of 08:30, 15 November 2012
Line 24:		Line 24:
	* amino-acid sequence signature (Myc epitope tag) = EQKLISEEDL		* amino-acid sequence signature (Myc epitope tag) = EQKLISEEDL

-	=== Orthogonal DNA shell with Benzyl-derived phosphotriester protecting groups ===	+	=== Orthogonal DNA shell/therapy with Benzyl-derived phosphotriester protecting groups ===

	* note! note! Important: Can you elucidate the reasoning of using an carboxilic acid as protecting group for DNA assembly?		* note! note! Important: Can you elucidate the reasoning of using an carboxilic acid as protecting group for DNA assembly?
Line 33:		Line 33:
	*** 2-cyanoethyl : for protecting phosphoramidites based nucleosides? XXX		*** 2-cyanoethyl : for protecting phosphoramidites based nucleosides? XXX
	*** araBAD XXX		*** araBAD XXX
		+	*** phospho'''tri'''ester = a '''tri'''cyclic N-derived nitrogenous base bound to a Histidine residue made for '''DNA''' synthesis.
		+	**** Thus phosphohistidine based phosphoramidates can be classified as purine analogues; the substance (Purines) was formally discovered by Emil Fischer during WW1 as a fundamental group of heterocyclic amino acids.

	== References ==		== References ==