Plasmid copy number determination

Plasmid copy number is known to vary depending on origin of replication and culture conditions [refs]. Typically, plasmids are referred to in qualitative terms such as "High" "Low" "Single" copy yet the quantitative value can be altered with only slight/single bp changes in the origin of replication [refs] and dramatically alter both the per cell and population yield of other products coded on the plasmid [refs]. Here we describe 3 methods used in our lab and discuss advantages and disadvantages of each.

note, this page is in progress, and requires additional information .

Overview

Regardless of what method of is used to evaluate the plasmid copy number, all methods are limited by the DNA extraction, and biological relevance of the sample when the DNA is extracted.

To minimize bias in DNA extraction we recommend: never using a "plasmid prep" kit as these kits strongly favor isolation of plasmid DNA over genomic DNA, more?

To maximize biological relevance we recommend isolating DNA under the same conditions as you are interested in or expect there to be a difference (stationary vs exponential growth; media choice; maintain antibiotic concentration; precondition cultures if reviving from frozen; do not grow/transfer more than required)

Comparison of methods

in progress

Agarose Gel Density

1. Day 1: Revive from freezer using small scrape of frozen culture to inoculate 5 mL of media with appropriate amount of antibiotic. Incubate overnight with appropriate shaking and temperature.
2. Day 2: Precondition culture by diluting 1:1,000 or 1:10,000 into 5-10 mL fresh media containing appropriate amount of antibiotic and culturing over night at the appropriate temperature/shaking conditions. This is important to remove effects of cryoprotectants.
3. Day 3: Inoculate up to 3 independent cultures from each preconditioned culture by diluting 1:100 or 1:1000. Fresh media and appropriate antibiotic should again be used, 24 hours of growth at appropriate temperature and shaking conditions.
4. Day 4: Lyse cells and isolate DNA.
   1. Centrifuge ~2x10^9 cells at ?SPEED? for ?TIME? to generate cell pellet
   2. Carefully remove supernatant with ?pipette/suction/decantation?.
   3. resuspend cells by ?VORTEX/PIPET/INVERSION? in 200 µl of lysis buffer
      • lysis buffer: 200 µg/mL RNase, 2 mg/mL lysozyme, 10 mM Tris-HCL, 20 mM Na2EDTA. pH 8.0
   4. incubate at room temperature for 15 minutes
   5. lyse bacteria by adding 200 µl of 2% SDS, vortex throughly.
   6. incubate in 65 C water bath for 30 minutes ?vortex/invert at some point(s)?
   7. ?centrifuge?
   8. Transfer 75 µl to new tube containing 25 µl of loading solution
      • loading solution: 60% sucrose 0.25% bromophenol blue, 2% SDS, 20% ethanol.
   9. Store overnight at ?TEMP?
5. Day 5: Gel electrophoresis.
   1. load 20 µl of overnight lysate on 1% agarose gel
      • Comb size, volume, gel size
   2. Run approximately ?TIME?
   3. capture image
      1. conditions/considerations
6. Day 6: data analysis

Next Generation Sequencing

qPCR

-- Main.DanielDeatherage - 11 Oct 2020