Alice:LabNotes/2008-7-21

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circularization of cosmic 3760 using CircleHelper[edit]

The concentration of Cosmic 3760 probe purified from previous step is 16.1 ng/ul. refer to LabNotes on 
[1]
The length of the probe is approximately 100 base (single strand oligoDNA). Since 1base = 330Da, the concentration of probe 
is 16.1 ng/ul /(100x330) = 488 nM. There are 30ul of probe, so it is 14640 x 10^-15 mol.
The volume of CircleHelper(10uM) needed is 1.464ul.
The PCR reaction system setup is as follows:
 template                        30ul
10x Ampligase Buffer             5ul
Circlehelper(10uM)             1.5ul
dNTP(10mM)                     0.5ul
  Stoffel fragment(10U/ul)       0.5ul
Ampligase                        1ul
ddH2O                         11.5ul
94C 3min -> 5 cycles X (94C 30sec -> 60C 10mins) -> 4C .
check product on TBU gel and do PAGE purification of digested product

gel result:
File:2008-07-24 after circularization Cosmic.jpg

CES22K probe preparation using Jumpstart Taq[edit]

PCR reaction system setup:                                         x96        
H2O                                                 80.5ul      7647.5ul  
10x Stoffel buffer                                    10ul         960ul
MgCl2(25mM)                                            6ul         576ul    
dNTP(10mM each, NEB)                                   2ul         192ul
primer mix                                           0.4ul        38.4ul
50x SYBG I                                           0.4ul        38.4ul  
template(CES22K #4)                                  0.1ul         9.6ul
Jumpstart Taq                                        0.6ul        57.6ul
94c 2min -> 94c 30sec -> 60C 2min -> 72C 1min-> Plate read -> (94c 30sec -> 60C 2min -> 72C 1min)x 20 cycles -> 72C 5min -> 15C hold
Result:
File:7-21-08 22K w jumpstart.jpg
Step 2: Probe purification with ethanol precipitation
1. pool the 24 reactions into one 16 mL tube, add 240 uL 3M NaOAC, 8 uL GlycoBlue, 
   6 mL 100% Ethanol.
2. Store at -70C for more than 20 min.
3. Spin at 4000rpm for 15 min at 4C.
4. Remove all liqid, you should see a blue pallette at the bottom of the tube.
5. Add 750 uL cold 75% Ethanol, piette well and transfer to a 1.6 mL tube.
6. Spin at 10000 rpm for 5 min at 4C.
7. Remove all liquid, let the pallette dry for 5 min, resuspend the DNA with 250 uL dH2O. Transfer the
liquid to two 0.2ml 
tube.
Step 3: Exonuclease treatment
1. Add 15 uL 10X Exo buffer and 8 uL Lambdo Exonuclease (5K/ml) for total volume of 150uL(each tube).
2. Incubate at 37C for 2 hours followed by 90C for 10 min, and leave it at 4C forever.
Step 4: Purify the reaction with Qiaquick columns
1. for each 150ul tube, add 750 uL of PBI buffer, mix well, load 450 ul each time to column (twice with
total of 900 uL)
2. Spin at top speed (14000 rpm) for 1 min
3. Empty the collection tube, add 750 uL wash buffer (PE buffer) to the column
4. Spin at top speed for 1 min
5. Empty the collection tube, spin at top speed for 1 min
6. Carefully transfer the columns to clean 1.6 mL tubes
7. Place the column/tube assemblies to 37C incubator, incubate for 5 min
8. Add 45 uL ddH2O to each column, wait for 1 min, spin at top speed for 1 min.
9. Pool DNAs from the two tubes into one, measure the concentration with Nanodrop.
NanoDrop result:
tube 1: 69.3 ng/ul * 45ul =3118.5ng tube 2: 57.7 ng/ul * 45ul =2596.5ng tube 3: 70.0 ng/ul * 45ul =3150ng tube 4: 81.3 ng/ul * 45ul =3658.5ng
Step 5: Incubation with USER enzyme:
add 6 uL of 10X DpnII reaction buffer and 10 uL of USER (1K/ml)enzyme and last 8 hour on 37C. 
Take 4ul out to run gel later. 
Step 6: Annealing of DpnII oligo and incubation with DpnII.
1. Add 1uL of 10X DpnII reaction buffer and 10 uL of 100 uM RE_RE_DpnII_n2S guide oligo. Denature at 95C in 
PCR machine for 10 min. Turn off the machine and wait for 20 min.
2. Wait until th machine cool to 37C then add 2 uL of DpnII restriction enzyme (50K/ml) to reaction, 
incubate for about 4 hours at 37C.
Step 7: Page Denaturing Gel
1. Add TBE-Urea sample buffer (2x) in each tube.
2. Mix 0.5 uL Invitrogen 10bp ladder with 4.5 uL dH2O, 5 uL 2x TBE-Urea sample buffer.
3. Denature at 75C for 8 min, then quickly transfer to ice, wait for 1 min.
4. Use a 2D well denaturing gel, add 0.5x TBE buffer. Flush the wells very well to remove all urea. 
6. Pre-run the gel for 10 min at 200V, load the samples into the wells, run at 200V for 30 min.
7. Stain gel with 5uL SYBR Gold in ~100 mL of TBE in clean tray. Place tray on an orbital shaker for ~5 min.
Results:
File:ZhangLab 2 2008-07-24 16hr 09min.jpg File:ZhangLab 2 2008-07-24 16hr 11min.jpg
File:ZhangLab 2 2008-07-24 17hr 27min.jpg File:ZhangLab 2 2008-07-24 17hr 28min.jpg
Step 8: Purify the product from the gel
1. Prepare two gel shearing assemblies by placing a 0.5 mL tube within another 1.5 mL Non-Stick tube. Use
G20 needle to punch a small hole at the bottom of the 0.5 mL tube. You need two assemblies for each PAGE
gel. 
2.Cut out the correct band (85-92 nt in this case), chop the band into small slices, split into two half
and transfer each half to one shearing assembly.
3. Centrifuge at top speed > 12000 rpm for 2 min to sheer the gel, remove the 0.5 mL tube.
4. Add 400 uL clean 1x TE buffer in the 1.5 mL tube. Tape the tubes on a vortexer, place the vortexer in 50C
incubator, shake the tubes at low speed for 1 hour. Alternatively, can keep the tubes in 4C fridge overnight.
5. In the PCR hood, transfer the gel mix to Nanosep columns, spin for 3 min at top speed (15,000 rpm),
and then transfer supernatant to 1.5mL tube.
Step 9: Precipitation
1. Add 0.1x of 3M sodium acetate and 2.5x 100% ethanol.
2. Add 1uL Glycoblue so that one can precipitate better and see the DNA.
3. Freeze in -70C for 20 min, spin at 14,000 rpm for 15 min at 4C, discard supernatant with pipette.
4. Add 500 uL of 75% ethanol to wash DNA, spin at 8000 rpm for 5 min at 4C, discard supernatant with 
   first large tip and then small tip to remove as much liquid as possible.
5. Let dry in hood ~ 10 min.
6. Add 20 uL of water(totally) to the tube to resolve the DNA in, leave at least 15 min.
Step 10: Quantification of DNA using denaturing gel and a quantitative ladder
1. Add 4uL of 5ng/uL 90-mer, 4ul of H2O and 8 uL of 2x TBE-Urea buffer
2. Dilute sample 10x (1uL sample + 9 uL of water) so total is 10uL of sample, and add 10 uL of 2x TBE-Urea
buffer.
3. Denature the DNA with loading dye on thermalcycler 75C for 15 min, then quickly transfer to ice, wait for
1 min.
4. Use 6% 10 well TBU gel, add 0.5x TBE buffer, flush the wells very well to remove all urea.
5. Pre-run the gel at 200V for 10 min, then load the samples into the wells, run at 200V for 30 min. 
Load the ladder as 8, 4, 2, 1 uL, and load the samples as 10, 5, 2.5 uL.
6. Stain the gel with 5 uL SYBR gold in ~100 mL of TBE in clean tray. Place the tray on an orbital shaker
for 5 min. Then quantify the gel to calculate the % yield.

result: 7.34 ng/ul * 80 ul= 587ng