Difference between revisions of "User:Etienne Robillard/Notebook/Agent Ecoli:SolidPhasePeptideSynthesisReagentEvidencesInAgentScoobyDoo"

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== Measuring the amplitude of the synthetic reagent lysis TE buffer on NMDA receptor ==
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* Date: 2012/12/03 10:29 AM EDT 
 
* Organism: E. coli (K-12 substr.)
 
* Strain: [http://cgsc2.biology.yale.edu/Strain.php?ID=65553 BW26434]
 
 
 
 
 
=== Hypothesis ===
 
 
 
* Amine protection groups (piperidine based) undergo chiral nucleophilic substitution on Histidine based autophosphorylation.
 
* Cosmid like recombinase system for -35 lacl+ (LacZ) transcription, thus no infection produced; (no lacY)
 
* orthogonal oligo/peptide protection using methylamino (methyltransferase) agents; 
 
* methylamino buffering agents used as intermediates for orthogonal protection; (probably a side-effect of Magnesium chelation with EDTA?)
 
* artificial cos-mid size is 30-45 bp length => reduced genome ?
 
* The NMDA receptor is voltage gated: [http://www.physicsforums.com/showthread.php?t=632781 The addition of EDTA (mg2+) ions to the reaction may act as '''NMDA receptor antagonist''' by binding to the NMDA ligand...]
 
* [[IPTG]] induction is a chemical reaction which may be neutralized with 1mL NaHC03... (Sodium bicarbonate, 2.99$) [[http://en.wikipedia.org/wiki/Sodium_bicarbonate#Neutralization_of_acids_and_bases 1]] [[http://bioserv.fiu.edu/~biolab/labs/genetics/lac%20operon.htm 2]] [[http://www.openwetware.org/wiki/BE.109:Protein_engineering/Assessing_beta-galactosidase 3]] [[http://www.openwetware.org/wiki/Beta-Galactosidase_Assay_(A_better_Miller) 4]]
 
 
 
=== Experiment ===
 
 
 
==== Material ====
 
 
 
* 1 x 10ml TE = TAE -> 10x buffer (Tris-HCl) (see [TE]
 
 
 
==== Expected results ====
 
 
 
* '''Amine''' protection groups = piperidine derived compound (NH2 undergo nucleophilic substitution on Histidine based autophosphorylation)
 
* a heterocyclic base-labile group (NHC?)
 
* [[IPTG]] inducible promoter: DNA lambda prophage induction (Transformation or mutation from lytic lacZ-repressed state to lysogenic!)
 
** in that case a matching E. coli genotype is "HB101 lacIq, lacY+" (ie [http://partsregistry.org/Part:BBa_V1003 laclq])
 
** From [http://www.sigmaaldrich.com/life-science/molecular-biology/cloning-and-expression/learning-center/genotypes-of-e-coli.html Sigma], the expected genotype matching the laclq strain is:
 
*** HB101 F– Δ(gpt-proA)62 leuB6 glnV44 ara-14 galK2 lacY1 Δ(mcrC-mrr) rpsL20 (Strr) xyl-5 mtl-1 recA13h
 
* (2R)-2-(methylamino)succinic acid - An orthogonal N-methyltransferase/NH2 base labile compound; exogenous NMDA receptor antagonist compound (Ketamine-like); synthetically recombined oligonucleotide protection group (dA-dT) for solid-phase peptide synthesis (SPPS), etc (see also [[PHP]], [[Succinic_acid]], and BW26434.)
 
** important: N-methyl-D-asparte receptor is a "sensory" neurotransmitter with analogous functions to the TRPV neurotransmitter but for brain functions including learning and memory.
 
 
 
==== References ====
 
 
 
* [https://www.openwetware.org/wiki/TE TE]
 
* [http://cgsc.biology.yale.edu/Strain.php?ID=9130 AB266]
 
* [http://cgsc.biology.yale.edu/Strain.php?ID=11958 E.coli B]: WOOP WOOP
 
* [[IPTG]]
 
* [[EDTA]]
 

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