Hypothesis 2: Gene L is necessary for phage propagation.
- Last time, I verified the final WP-PCR protocol.
- Now, I want to see if DpnI digestion works or not on the methylated ΦX174 template genomic DNA in the PCR conditions.
- For there to be 0.5 μg of DNA to digest in 10 μL, which is enough to see on a gel, I'll need 50 ng/μL ~ 15 nM final concentration DNA.
- 50 μL WP-PCR reaction w/o primers:
- 36 μL H2O
- 7.5 μL 100 nM ΦX174 template (~15 nM final)
- 5 μL 10X reaction buffer
- 0.5 μL 25 mM dNTPs mix
- 1 μL PfuUltra I DNA polymerase
- WP-PCR Cycling parameters:
- 95 °C 2 m
- 95 °C 30 s
- 58° C 30 s
- 72 °C 15 m
- Repeat 2-4 an additional 29 times for 30 total cycles
- 72 °C 30 m
- I prepared this today (Fri) and placed in the Chromato. Vincent will run the WP-PCR Mon. morning.
- Used up the rest of the PfuUltra I DNAP making 225 μL 90% ΦX174 WP-PCR mix
- 185 μL H2O
- 25 μL 10X reaction buffer
- 7.5 μL 3.2 nM ΦX174 template (~0.1 nM final)
- 2.5 μL 25 mM dNTPs mix
- 5 μL PfuUltra I DNA polymerase
- Next on the list:
- Topisomerase IV / Gyrase (preceded by PCR purification) - how to assay linking number?
- Final experiment is planned to be WP-PCR of 0.1 nM ΦX174 at optimized conditions (primer concentration, Ta, elongation time, N), + PFU ligase
- experimental 1 = +template, +primer 4, +DNAP
- experimental 2 = +template. +primer 4 T3585A, +DNAP
- control 1: -template, +primer 4, +DNAP
- control 2: -template, +primer 4 T3485, +DNAP
- control 3: +template, +primer 4, +DNAP
Characterization B-C: Expression of PHIX174 promoters/UTRs fused to PX-UTR1-deGFP and PX-UTRX-deGFP.
- Experiment specified yesterday was actually run today, with the modification that reads happen every minute for 12 h, with continuous fast double-orbital shaking between read times.