What is the doubling time of Drosophila S2 cells?

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Answer

When grown at the optimal temperature of 27-28ºC, Drosophila S2 cells grow very quickly, with an approximate 14-16 hr doubling time. The cells can also be grown at 22-25ºC with doubling time of 24hrs. Humidity is an issue, so a shallow pan of water can be left in the incubator, but the incubator does not need to be turned on.

Growth medium is also a factor in doubling time - the doubling times listed here are for Sf900 II medium.

The cells can reach maximum densities of 1 to 2.5 x 10E7 cells/ml in shake flask cultures.

Answer Id: E3312

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e21fa135f9e701e441d88b89f900b471_FAQ

How can I tell whether or not a reagent bottle is pressurizing correctly when using the Procise™ System?

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Answer

You can backflush the bottle's pickup line in manual control (there is a specific function for each bottle position on the Procise™ System) and observe its bubbling, which should slow and then stop within a short period (depending upon how full the bottle is) as it pressurizes with argon. If it continues to bubble, either the cap assembly is leaking or the pressurizing or venting valves for the bottle are.

Answer Id: E1261

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9ca71b74fe0c5b11318526bdf6ffc1ce_FAQ

Why is the conductivity so high in my peptide synthesis (monitored during deprotection)?

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Answer

The meter detects any ionic species. A common cause of higher than expected values is a leak of a small amount of resin from the RV into the lines and up to the in-line filters. The use of old or poor quality piperidine or NMP may also give a high background. Standard conductivity measured in micro Siemens/cm is much higher than the sensitivity of this cell. A very small amount of ionic material caused a large change in the reading. Occasionally, Fmoc amino acids have ionic contaminants which give high readings. In-line filters may also be contaminated.

Answer Id: E1313

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cd091005917e115be909607d8970a3e3_FAQ

Which PCR polymerases do you recommend for TA/Blunt/D-TOPO cloning and why?

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Answer

A. TA Cloning:
- This cloning method was designed for pure Taq polymerases (native, recombinant, hot start); however, High Fidelity or Taq blends generally work well with TA cloning. A 10:1 of 15:1 ratio of Taq to proofreader polymerase will still generate enough 3’ A overhangs for TA cloning
- The recommended Life Technologies® polymerases include Platinum® Taq, AccuPrime™ Taq, Platinum® or AccuPrime™ Taq High Fidelity, AmpliTaq®, AmpliTaq Gold®, or AmpliTaq Gold® 360.

B. Blunt cloning:
- Use proofreading enzymes such as Pfx50, Platinum® or AccuPrime™ Pfx.

C. Directional TOPO cloning:
- Pfx50 or AccuPrime Pfx work well.

Answer Id: E6651

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c282cdd6154484d04bb8b2ce3e2275db_FAQ

Can I use TOPO®TA pCR2.1 or pCR II or pCR4 for my protein expression experiments?

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Answer

No, these vectors do not contain a functional promoter to express your gene of interest. These vectors are typically for subcloning or sequencing.

Answer Id: E6661

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68e8de1e920dec09a9ab5dd783827991_FAQ

How does blue/white screening work?

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Answer

If working with a vector that contains the lac promoter and the LacZ alpha fragment (for α complementation), blue/white screening can be used as a tool to select for presence of the insert. X-gal is added to the plate as a substrate for the LacZ enzyme and must always be present for blue/white screening. The minimum insert size needed to completely disrupt the lacZ gene is >400 bp. If the LacIq repressor is present (either provided by the host cells, for example TOP10F’, or expressed from the plasmid) it will repress expression from the lac promoter, thus preventing blue/white screening. Hence in the presence of the LacIq repressor, IPTG must be provided to inhibit the LacIq. Inhibition of LacIq permits expression from the lac promoter for blue/white screening. X-gal (also known as 5-bromo-4-chloro-3-indolyl β-D-glucopyranoside) is soluble in DMSO or DMF, and can be stored in solution in the freezer for up to 6 months. Protect the solution from light. Final concentration of X-gal and IPTG in agar plates: Prior to pouring plates, add X-gal to 20 mg/mL and IPTG to 0.1 mM to the medium. When adding directly on the surface of the plate, add 40 μl X-gal (20 mg/mL stock) and 4 μl IPTG (200 mg/mL stock).

Answer Id: E6664

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467e1a97574e4e4d9e5ce269a7d4d16d_FAQ

How does ccdB selection work?

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Answer

TOPO® vectors containing the LacZ-ccdB cassette allow direct selection of recombinants via disruption of the lethal E. coli gene, ccdB. Ligation of a PCR product disrupts expression of the LacZ-ccdB gene fusion permitting growth of only positive recombinants upon transformation. Cells that contain non-recombinant vector are killed upon plating. Therefore, blue/white screening is not required. When doing blue/white color screening of clones in TOPO® vectors containing the LacZ-ccdB cassette, colonies showing different shades of blue may be observed. It is our experience that those colonies that are light blue as well as those that are white generally contain inserts. The light blue is most likely due to some transcription initiation in the presence of the insert for the production of the lacZ alpha without enough ccdB expressed to kill the cells and is insert dependent. To completely interrupt the lacZ gene, inserts must be >400 bp; therefore an insert of 300 bp can produce a light blue colony. A white colony that does not contain an insert is generally due to a spontaneous mutation in the ccdB gene.
A minimum insertion of 150 bp is needed in order to ensure disruption of the ccdB gene and prevent cell death. (Reference: Bernard et al., 1994. Positive-selection vectors using the F plasmid ccdB killer gene. Gene 148: 71-74.) Strains that contain an F plasmid, such as TOP10F’, are not recommended for transformation and selection of recombinant clones in any TOPO® vector containing the ccdB gene. The F plasmid encodes the CcdA protein, which acts as an inhibitor of the CcdB gyrase-toxin protein. The ccdB gene is also found in the ccd (control of cell death) locus on the F plasmid. This locus contains two genes, ccdA and ccdB, which encode proteins of 72 and 101 amino acids respectively. The ccd locus participates in stable maintenance of F plasmid by post-segregational killing of cells that do not contain the F plasmid. The CcdB protein is a potent cell-killing protein when the CcdA protein does not inhibit its action.

Answer Id: E6665

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897dd8f2419e66e253ac03d76aea4d67_FAQ

How does selection with the LacZ gene work?

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Answer

If working with a vector that contains the lac promoter and the LacZ α fragment (for α complementation), blue/white screening can be used as a tool to select for presence of the insert. X-gal is added to the plate as a substrate for the LacZ enzyme and must always be present for blue/white screening. The minimum insert size needed to completely disrupt the lacZ gene is >400 bp. If the LacIq repressor is present (either provided by the host cells, for example TOP10F’, or expressed from the plasmid), it will repress expression from the lac promoter thus preventing blue/white screening. Hence, in the presence of the LacIq repressor, IPTG must be provided to inhibit the LacIq. Inhibition of LacIq permits expression from the lac promoter for blue/white screening.

Answer Id: E6666

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fbaab7c272d5a4edaa00f9a77bd23036_FAQ

I’m getting low to no colonies after transformation. Why?

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Answer

Some possible causes and remedies are:
- Ligase function is poor. Check the age of the ligase and function of the buffer.
- Competent cells are not transforming. Test the efficiency of the cells with a control supercoiled vector, such as puc19.
- Both molecules were de-phosphorylated.
- Inhibition of ligation by restriction enzymes and residual buffer. Try transformation of uncut vector, clean up restriction with phenol, or carry out PCR cleanup/gel extraction before ligation.
- Incorrect antibiotic selection used. Check the plasmid and plates and make sure concentration of antibiotic used is correct.

If nothing above applies, low to no colonies may be due to instability of the insert DNA in your competent cells. In this case, E. coli strains such as Stbl2™, Stbl3™, or Stbl4™ have been shown to support the propagation of DNA with multiple repeats, retroviral sequences, and DNA with high GC content better than other strains.

Answer Id: E6667

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dc47d8ce8525ad4ff9cd2ada6c505a88_FAQ

The clones I’m selecting show deleted inserts. Why?

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Answer

This may be caused by the instability of the insert DNA in TOP10 E. Coli. In this case, E.coli strains such as Stbl2™, Stbl3™, or Stbl4™ have been shown to support the propagation of DNA with multiple repeats, retroviral sequences, and DNA with high GC content better than other strains.

Answer Id: E6668

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4a55e164f4a31cccd5e2141ea6947d1a_FAQ

I’m able to see colonies on a plate, but when I pick them for liquid culture, no growth is observed. Why?

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Answer

One possible explanation could be toxicity associated with the insert. This toxicity does not affect slow growing cells on solid medium but is much stronger in faster growth conditions like liquid medium.

Suggestions:
1. Use TOP10F’ or any other strain with the LacIq repressor
2. Try using any other strain appropriate for cloning.
3. Lower growth temperature to 27 - 30 degrees C and grow the culture longer
4. Another possibility to explain lack of growth is possible phage contamination. In this situation we recommend using an E. coli strain that is T1 phage resistant like DH5alpha-T1R.

Answer Id: E6669

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afc1ca9447653f880ceedc5d25b633d9_FAQ

I see small satellite colonies on my LB+Amp plates. Why is this?

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Answer

These small colonies are most likely caused by degradation of the Ampicillin. The colonies are just untransformed cells that grow on LB with degraded Amp. In order to circumvent this scenario, you can try to:
1. Plate cells at a lower density
2. Use fresh LB-Amp plates or replace Ampicillin with carbenicillin.
3. The plates should not be incubated for more than 20 hours at 37 degrees C. Beta-lactamase, the enzyme produced from the Ampicillin-resistance gene, is secreted from the Amp-resistant transformants and inactivates the antibiotic in the area surrounding the transformant colony. This inactivation of the selection agent allows satellite colonies (which are not truly Amp-resistant) to grow. This is also true if carbenicillin is being used.

Answer Id: E6670

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f9466fc63ebea23cccde2e28544b2068_FAQ

I’m trying to decide between the TOP10, DH5α™, and Mach1™ strains you have for my TOPO® TA Cloning® reactions. Can you explain the significant differences between these strains?

Product FAQ

Answer

DH5α™ cells are commonly used for routine cloning, but are mcr/mrr+, and therefore not recommended for genomic cloning. The TOP10 competent cells, on the other hand, contain mutated mcr/mrr, and therefore are a good choice for routine cloning and can be used for cloning of methylated DNA, such as eukaryotic genomic DNA. Our Mach1™ strain is the fastest growing cloning strain that is T1 phage resistant.

Answer Id: E6704

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aa3bb3779254c68e40fc7f711474f757_FAQ

What are some tips you can give me to obtain the highest transformation efficiency?

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Answer

Some suggestions that will help you to obtain the highest transformation efficiency are:
- Thaw competent cells on ice instead of room temperature; do not vortex cells.
- Add DNA to competent cells once thawed.
- Ensure that the incubation times are followed as outlined in the competent cell protocol for the strain you are working with; changes in the length of time can decrease efficiency.
- Remove salts and other contaminants from your DNA sample; DNA can be purified before transformation using a spin column, or phenol/chloroform extraction and ethanol precipitation can be employed.

Answer Id: E6709

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b64491a31cb52f2fa0c475749a4240e6_FAQ

How is competent cell efficiency measured? How is it calculated?

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Answer

Competent cell efficiency is measured by transformation efficiency. Transformation efficiency is equal to the number of transformants, or colony forming units, per microgram of plasmid DNA (cfu/microgram).

Answer Id: E6710

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072c8dceb71ef354b20f7566886ce7c4_FAQ