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 method, 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

• Agarose Gel Density (AGD) is arguably the most easily accessible as it does not require large expense (NGS) or project specific items (qPCR primers), or uncommon expertise (both NGS and qPCR).
• NGS and qPCR are much higher throughput, as they can both easily be done in plate format and with automated or semi automated analysis. AGD has an artistic flare requirement of getting good quality images, and using graphic user interfaces on a per sample/gel basis.
• NGS has the advantage of not requiring additional work if you already have plans/reasons to sequence the sample (though it should again be stressed decisions such as how to extract DNA and when to extract it can have large implications)
• qPCR allows semi automated computational analysis, but does require upfront design/test of plasmid specific primers that will likely vary from project to project.

Appropriately Culture Cells

Day 1: Reviving Strains

• 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.
• Biological replicates are recommended to be inoculated from separate ice scrapes at this stage.
• it is important to have a negative control that is the same strain without any plasmid grown in absence of antibiotic.

Day 2: Precondition Cultures

• This is important to remove effects of cryoprotectants which experience has shown can lead to oddities in the initial growth of the culture.
• Dilute at least 1:100 into 5 mL fresh media again with appropriate amount of antibiotic
• Incubate overnight with appropriate shaking and temperature.
  • Alternatively, cells can be cultured for less than 24 hours to measure differences in plasmid copy number in different cell phases. In that case, Day 3 work below should be done as soon as cells enter appropriate phase.

Agarose Gel Density

Day 3: Lyse cells and isolate DNA.

1. Centrifuge ~2x10^9 cells at 4000g for 5 minutes to generate cell pellet.
2. Carefully remove supernatant with suction/pipette.

1. resuspend cells by vortexing or aggressive pipetting in 200 µl of lysis buffer. Make sure to fully resuspend.
   • lysis buffer: 200 µg/mL RNaseA, 2 mg/mL lysozyme, 10 mM Tris-HCL, 20 mM Na2EDTA. pH 8.0
   • RNaseA and Lysozyme should be added fresh to lysis buffer on day of experiment as lysozyme is not stable for long term storage (ref).
2. incubate at room temperature for 15 minutes
3. lyse bacteria by adding 200 µl of 2% SDS (in water), vortex throughly.

Day 4: Gel electrophoresis.

1. load 20 µl of overnight lysate on 1% agarose gel (make sure all agarose is completely dissolved)

• • Note: gel must be made with TAE buffer which has very pure water (extra ions cause gel blurring). MillQ water works well

1. Run approximately 28 minutes on 130V in fresh TAE buffer

1. capture image

1. 1. only capture "1 gel" -- set intensity focus/adjustment for intense bands (as not to oversaturate these bands)

Day 6: data analysis

1. 1. Fiji

Batching samples -- Be sure to run each biological replicate on separate gel, unless number of samples so low as to fit all samples on single gel. -- When working with individual samples in other steps, order based on sample ID not based on replicate. Sample 1-12 replicate A sample 1-12 replicate B and so on.

Next Generation Sequencing

Day 3: DNA extraction

Day 4: Library prep

Day ?: Computational analysis

qPCR

Day 0: Design and Verify primers before isolating DNA

Day 1& 2: see Appropriately Culture Cells above

Day 3

separate page describing method candidate for consolidation

-- Main.DanielDeatherage - 11 Oct 2020

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

Comparison of methods

Day 1: Reviving Strains

• 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.
• Biological replicates are recommended to be inoculated from separate ice scrapes at this stage.

Day 2: Precondition Cultures

• This is important to remove effects of cryoprotectants which experience has shown can lead to oddities in the initial growth of the culture.
• Dilute at least 1:100 into 5 mL fresh media again with appropriate amount of antibiotic
• Incubate overnight with appropriate shaking and temperature.
  • Alternatively, cells can be cultured for less than 24 hours to measure differences in plasmid copy number in different cell phases. In that case, Day 3 work below should be done as soon as cells enter appropriate phase.

Day 3: Lyse cells and isolate DNA.

1. Centrifuge ~2x10^9 cells at 4000g for 5 minutes to generate cell pellet.
2. Carefully remove supernatant with suction/pipette.

• • lysis buffer: 200 µg/mL RNaseA, 2 mg/mL lysozyme, 10 mM Tris-HCL, 20 mM Na2EDTA. pH 8.0
  • RNaseA and Lysozyme should be added fresh to lysis buffer on day of experiment as lysozyme is not stable for long term storage (ref).

1. incubate at room temperature for 15 minutes
2. lyse bacteria by adding 200 µl of 2% SDS (in water), vortex throughly.

1. Transfer 75 µl to new tube containing 25 µl of loading solution
   • Post-lysis project expected to be slightly more viscus than water, and largely free of particulate/debris without need to centrifuge. Pay attention to tip to ensure absence of air bubble.
   • Brief vortex before pipetting 75µl may make pipetting easier.
   • loading solution: 60% sucrose 0.25% bromophenol blue, 2% SDS, 20% ethanol.
   • add note about dye band location not being relevant to current work but could be removed/changed if influencing other projects. example image?
2. Store overnight at room temp in the dark.

Day 4: Gel electrophoresis.

1. load 20 µl of overnight lysate on 1% agarose gel (make sure all agarose is completely dissolved)
   • 8 well comb, 2 rows/gel, 40 mL volume, 2 uL SYBR safe (50% concentration), first lane ladder (control)
   • Note: gel must be made with TAE buffer which has very pure water (extra ions cause gel blurring). MillQ water works well
2. Run approximately 28 minutes on 130V in fresh TAE buffer
3. capture image
   1. only capture "1 gel" -- set intensity focus/adjustment for intense bands (as not to oversaturate these bands)

Day 6: data analysis

1. 1. Fiji

Batching samples -- Be sure to run each biological replicate on separate gel, unless number of samples so low as to fit all samples on single gel. -- When working with individual samples in other steps, order based on sample ID not based on replicate. Sample 1-12 replicate A sample 1-12 replicate B and so on.

Next Generation Sequencing

qPCR

-- Main.DanielDeatherage - 11 Oct 2020

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. 1. Fiji

Batching samples -- Be sure to run each biological replicate on separate gel, unless number of samples so low as to fit all samples on single gel. -- When working with individual samples in other steps, order based on sample ID not based on replicate. Sample 1-12 replicate A sample 1-12 replicate B and so on.

Next Generation Sequencing

qPCR

-- Main.DanielDeatherage - 11 Oct 2020

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. Recommend the use of saline intermediate if doing 10,000 fold dilution
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.
   • Alternatively, cells can be cultured for less than 24 hours to measure differences in plasmid copy number in different cell phases. In that case, Day 4 work should be done on Day 3 as soon as cells enter appropriate phase
4. Day 4: Lyse cells and isolate DNA.
   1. Centrifuge ~2x10^9 cells at 4000g for 5 minutes to generate cell pellet.
   2. Carefully remove supernatant with suction/pipette.
   3. resuspend cells by vortexing or agressive pipetting in 200 µl of lysis buffer. Make sure to fully resuspend.
      • lysis buffer: 200 µg/mL RNase, 2 mg/mL lysozyme, 10 mM Tris-HCL, 20 mM Na2EDTA. pH 8.0
      • fresh? how should it be stored?
   4. incubate at room temperature for 15 minutes
   5. lyse bacteria by adding 200 µl of 2% SDS (in water), vortex throughly.
   6. incubate in 65 C water bath for 30 minutes mix lightly at 15 minutes
   7. Transfer 75 µl to new tube containing 25 µl of loading solution
      • post-lysis project expected to be slightly more viscus than water, and free of particulate/debris without need to centrifuge.
      • loading solution: 60% sucrose 0.25% bromophenol blue, 2% SDS, 20% ethanol.
      • add note about dye band location not being relevant to current work but could be removed/changed if influencing other projects. example image?
   8. Store overnight at room temp in the dark.
5. Day 5: Gel electrophoresis.

1. 1. capture image

1. Day 6: data analysis

Next Generation Sequencing

qPCR

-- Main.DanielDeatherage - 11 Oct 2020

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.

1. 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.

1. Day 4: Lyse cells and isolate DNA.
   1. Centrifuge ~2x10^9 cells at 4000g for 5 minutes to generate cell pellet.
   2. Carefully remove supernatant with suction/pipette.

• • • lysis buffer: 200 µg/mL RNase, 2 mg/mL lysozyme, 10 mM Tris-HCL, 20 mM Na2EDTA. pH 8.0
    • fresh? how should it be stored?
  1. incubate at room temperature for 15 minutes
  2. lyse bacteria by adding 200 µl of 2% SDS (in water), vortex throughly.
  3. incubate in 65 C water bath for 30 minutes mix lightly at 15 minutes

1. 1. Transfer 75 µl to new tube containing 25 µl of loading solution

• • • loading solution: 60% sucrose 0.25% bromophenol blue, 2% SDS, 20% ethanol.

1. 1. Store overnight at room temp in the dark.
2. Day 5: Gel electrophoresis.
   1. load 20 µl of overnight lysate on 1% agarose gel

1. 1. Run approximately 28 minutes on 130V fresh TAE

1. 1. capture image
      1. conditions/considerations
2. Day 6: data analysis

Batching samples -- Be sure to run each biological replicate on separate gel, unless number of samples so low as to fit all samples on single gel. -- When working with individual samples in other steps, order based on sample ID not based on replicate. Sample 1-12 replicate A sample 1-12 replicate B and so on.

Next Generation Sequencing

qPCR

-- Main.DanielDeatherage - 11 Oct 2020

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.

• • • lysis buffer: 200 µg/mL RNase, 2 mg/mL lysozyme, 10 mM Tris-HCL, 20 mM Na2EDTA. pH 8.0

1. 1. incubate at room temperature for 15 minutes

1. 1. Transfer 75 µl to new tube containing 25 µl of loading solution
      • loading solution: 60% sucrose 0.25% bromophenol blue, 2% SDS, 20% ethanol.

1. Day 5: Gel electrophoresis.
   1. load 20 µl of overnight lysate on 1% agarose gel

1. 1. capture image
      1. conditions/considerations
2. Day 6: data analysis

Next Generation Sequencing

qPCR

-- Main.DanielDeatherage - 11 Oct 2020

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.

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?

Comparison of methods

in progress

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.

%warn% 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; )

Comparison of methods

in progress

-- Main.DanielDeatherage - 11 Oct 2020