Daniel:Notebook/HiResChrPaint/2013-5-1

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Probe Prep Test (Started 4/22/2013)[edit]

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TBU Gel Quantification[edit]

Purpose: Test quantification results from samples digested with lambda exonuclease at different time/concentrations.

Protocol[edit]

1. Set up gel according to following table; following Protocol 2
Lane 2 3 4 5 6 7 8 9
Sample 0.5 uL Low Mass ladder 1 uL LM ladder Control (10x exo, 1 hr) 1X lambda exo, 1 hr 10 x lambda exo, 30 min 10 x lambda exo, 2 hr V4S3 V6S3
Probe Set NA NA V6S3 V6S2 V6S4 V4S2 V4S3 V6S3

Results[edit]

Volume Report: File:TBUGel 050113.xls

File:TBUGel 050113.jpg

File:TBUGel 050113 analysis.jpg

Quantitation[edit]

Sample ng on gel ng/uL ng in 6 uL
V4S3 11.5 23.0 137.9
V6S3 10.9 21.9 131.2

Discussion[edit]

It would appear that too little DNA was left to quantify once everything was said and done.  Not surprising, since all of these reactions
started with very little DNA.  The V4S3 and V6S3 (from 4/27/2013) samples I was able to classify. Today's quantification showed around 
10 times the amount of DNA present as the 4/27 gel.  It would appear that this gel quantification is quite erroneous in many ways.  Not 
sure how Noi got such great results.
Looking at the gel qualitatively, I would say that the 2 hour digestion has almost no product left.  That being said, the 30 minute digest
should have more left than the 1 hour, but we do not see this response.  Another thing to remember is that all of these are different probe
sets, and may have very different behaviors.  In short, I don't know that I can draw any definite conclusions from this gel, other than the  
lambda exonuclease reaction, in general, is causing me to lose too much DNA.

TBE Gel[edit]

Purpose: I want to rerun the lambda digestion experiment (above) but using the same set of DNA.  I also want to keep a batch immediately after
digestion to make sure I'm not losing too much DNA in the ethanol precipitation.  I have identified two possible samples that have around 1 ug 
each, but I am unsure of which stage they are at.  This TBE gel should tell me.

Protocol[edit]

1. Loaded gel according to table: 
Lane 3 4 5
Sample 25 bp ladder V4S2 V4S3
uL sample 0.5 0.5 0.5
uL TBE 5.5 5.5 5.5
uL 6x dye 2 2 2
uL 7 7 7
2. Ran gel for 25 minutes at 200V
3. Stained with 3 uL SYBR gold for 2 minutes

Results[edit]

File:TBEgel 050113.jpg

Clearly, these are pre-DpnII digestion.  Proceeding to DpnII digest.

DpnII Digestion[edit]

1. Set up reaction according to table
  *DpnII-Lot 0091201; Buffer 0031105
Sample ng/uL uL ng uL 10x buffer uL DpnII (50 U/uL) uL nf H20 Total
V4S2 139.7 10 1397 5 1 34 50
V6S2 111.9 10 1119 5 1 34 50
2. Incubate 16 hours at 37 C followed by 20 minutes at 65 C for heat shock (continued on 5/2/2013)

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