User:Etienne Robillard/Notebook/Agent Ecoli:Plasmid cloning vectors for gene therapy with phosphohistidine based oligos

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(Orthogonal DNA synthesis with Benzoyl-derived phosphotriester protecting groups (dA))
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= Plasmid cloning vectors for gene therapy with phosphohistidine-based oligos =
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__TOC__
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== Eukariotic DNA Promoters ==
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cDNA:
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* N-6-benzoyl-deoxyadenosine phosphoramidite - Notice the P-N bound indicating the linkage of a phosphonate diester to a benzoyl atom :)
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* N-3-oxo-hexanoyl-L-homoserine lactone - A light-inducible phosphohistidine-bound AHL ? A(denosine)TP/cAMP dependent.
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* Reminder:
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** NHC = (N heterocycle carbene) - Chemical compounds with a N chiral prodrug switch - highly enantioselective molecules
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** N = indicates a Nitrogen atom
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** P = a Phosphonate (inorganic state) - a compound for oligo synthesis using the [http://en.wikipedia.org/wiki/Oligonucleotide_synthesis#Nucleoside_phosphoramidites nucleoside phosphoramidite] method. 
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** P-N = phosphoramidate (a Nitrogen atom bound to a Phosphonate ester in nucleophilic substitution).
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deoxynucleotide synthesis:
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* cDNA synthesis building block = deoxynucleoside + 3'-phosphonate = synthetic nucleotide analog (dATP) [http://dwb4.unl.edu/Teacher/NSF/C08/C08Links/www.dur.ac.uk/~dbl0www/Staff/Croy/cDNAfigs.htm 1]
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oligodeoxyribonucleotide synthesis:
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* short 50-200(?) bp restriction endonucleases enzymes for cDNA catalysis/plasmid vector cloning in ''E. coli''
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* building blocks for oligonucleotides assembly with phosphoramidites method [http://en.wikipedia.org/wiki/Oligonucleotide 1]
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* see also [http://openwetware.org/wiki/CH391L/S12/GeneandGenomeSynthesis#Oligonucleotide_Synthesis Oligonucleotide Synthesis]
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* 1 mutation, 1 oligo assay (phosphoramidite-based oligo synthesis): [http://openwetware.org/wiki/Reviews/Directed_evolution/Library_construction#Directing_diversity:_Oligonucleotide-based_methods]
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[http://openwetware.org/wiki/20.109(S07):Start-up_genome_engineering#Part_3:_Digest_M13K07 M13K07] cloning in ''E. coli'':
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* amino-acid sequence signature (Myc epitope tag) = EQKLISEEDL
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=== Orthogonal DNA synthesis with Benzoyl-derived phosphotriester protecting groups (dA) ===
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* note! note! Important: Can you elucidate the reasoning of using an carboxilic acid as protecting group for DNA assembly?
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** FIRST PROBABLE PROTECTION GROUP (dA):
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*** 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.
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*** Note: Consensus promoter sequences are by definition strong promoters!
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** 2ND HIGHLY PROBABLE PROTECTION GROUP (araBAD):
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*** 2-cyanoethyl : for protecting phosphoramidites based nucleosides?  XXX
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*** araBAD XXX
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*** phospho'''tri'''ester = a '''tri'''cyclic N-derived nitrogenous base bound to a Histidine residue made for '''DNA''' synthesis.
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* '''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.'''
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** see also [http://en.wikipedia.org/wiki/Piperidine Piperidine]
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== References ==
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* http://openwetware.org/images/1/1c/TheBacterialPromoter.pdf
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* http://en.wikipedia.org/wiki/Protecting_group#Carboxylic_acid_protecting_groups protecting groups
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* http://en.wikipedia.org/wiki/Oligonucleotide_synthesis#Nucleoside_phosphoramidites
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* http://en.wikibooks.org/wiki/Structural_Biochemistry/Nucleic_Acid/Nitrogenous_Bases/Purines
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