Welcome to the Home of Vesicle Trafficking

A small repository of synaptic protein information

Caution! In converting these protocols to HTML, some units have been scrambled.
Specifically, microliters (ul) often appear as milliliters (ml). Think first!

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1. Cut DNA with 5'- and 3'- overhangs, gel check, phenol-Sevag extract and NaOAc/EtOH ppt.

2. Prepare one S1 nuclease tube (on ice) for each time point: 15ml S1 Buffer + 0.25U S1/ml (5U).

3. Use 5ml (=0.5mg) digested plasmid (in EB) per time point. Add 4U Exonuclease III/ml reaction mix and incubate @ 37oC (‰400 digested/min).

4. Remove 5ml aliquots into the S1 nuclease tubes (on ice) at various times. When all time points have been collected, incubate the tubes 30' @ RT.

5. Add 2ml STOP Buffer/tube and incubate 10' @ 70oC.

6. Add: 2.0ml 10X Klenow Mix
+2.0ml 0.125mM dNTPs
+0.5ml Klenow
Incubate 10' @ 37oC.

7. Analyze 10ml on a gel. To the remainder in each tube, add 40ml Ligation Mix + 1ml T4 DNA Ligase. Incubate overnight @ 15oC (or 2-3h @ RT).

8. Transform 100ml competent cells with 10ml ligation reaction; freeze remainder.

EB
66mM Tris-HCl, pH 8
0.66mM MgCl2

10X Klenow Mix
20mM Tris-HCl, pH 8
100mM MgCl2

S1B
40mM KOAc
300mM NaCl
1.3mM ZnS04
7% Glycerol

Ligation Mix
50mM Tris-HCl, pH7.6
1mM MgCl2
1mM ATP
1mM DTT
5% PEG 6000

S1 STOP 300mM Trizma base
50mM EDTA