IGEM:University of Chicago/2009/Notebook/Paraoxon Biosensor/2009/07/01

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=July 1, 2009=
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PCR

 * ran a gel of yesterday's PCR (62°C, magnesium gradient)
 * Gel is mostly blank except for 035
 * Looks like we didn't add polymerase and primers, but we certainly did
 * Possibly the change in temperature messed things up?
 * Will use 035C(2) in restriction digest to try to determine nature of the band

Restriction Digest

 * BstBI/BglII double digest
 * Should have 1 fragment at 333bp if we have GFP - AHI construct OR kan-ADH construct
 * Ran a gel of product. Weird: No apparent digest.

Gel Purification
Top: Ladder, -DNA, -Pol, 035, -, 49, 213, -, 236, 346. At 55C 41(0), 49(1), 49(2), 49(4) Bottom: Ladder, -, -, 035, 49, 186, 213, 236, 346
 * PCR. Used purified product as template.
 * 2 MgCl gradients (0 and 2) at 58°C annealing
 * for 49, will try all 4 gradients (0, 1, 2, 4) at 55°C annealing
 * After running PCR, realized we mixed up primers/templates for 139 and 186; they were discarded.
 * Ran a gel; only got funky bands at 850kb; no actual product


 * [[Image:2009-07-01.FragmentPcrAll.jpg]]
 * must be a mispriming error, which is weird because they are supposedly no redundancies according to the sequence

PCR

 * Realized (after running out of polymerase) that we've been doing our reactions all wrong. Correct recipe is below. Will have to order more polymerase and/or use another kind.
 * Correct PCR recipe using Accusure polymerase (20μL RXN)

10μL of reaction mix 10X NEB buffer.. 2μL dNTPs..........0.5μL DNA............0.5μL Primer 1(5μM)... 2μL Primer 2(5μM)... 2μL ddH2O........... 2μL Polymerase.......1μL '''10μL of H2O/MgCl mix (concentrations of MgCl at 0, 1, 2 4). Use 20mM MgCl''' MgCl......ddH2O 0: 0.......10μL 1: 1........9μL 2: 2........8μL 4: 4........6μL

*Add reaction mix to H2O/MgCl mix at whatever MgCl concentration you desire. Total will be 20μL


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