The right answers to frequently asked questions
Find the answers to all our products and services by clicking the links below.
How should I send my sequencing samples?
You will find all information about sample format, template and primer concentration as well as shipping information for each of our sequencing services in the respective "Sample Submission" tab.
How should I determine the concentration of my samples?
Please measure the OD with a spectrophotometer at 260 nm and 280 nm. The OD 260 values should be in the range of 0.05 to 0.8 to give reproducible and reliable results. The OD 260/280 ratio should be about 1.8. Values lower than 1.6 and higher than 2.0 indicate contaminants in the sample that interfere with the determination of the concentration and might inhibit the sequencing reaction.
If possible, we recommend measuring the ODs at 230 nm and 320 nm, too. A high value at OD 320 indicates a contaminant. This should be ideally 0.0. The OD 230/260 ratio should be lower than 0.6.
We also recommend ensuring the quality of your DNA by running your sample on an agarose gel.
Which purification method should I use?
For plasmids, we recommend the use of commercially available
plasmid mini scale preparation kits employing spin columns. From
our experience, repeating the washing step will improve the quality
of the DNA and therefore improve the sequencing results. Please do
not send DNA prepared with alkaline lysis methods or with the
boiling method (Holmes and Quigley, 1981) without column
purification. For PCR products please use commercially available
PCR purification spin column kits.
Can I send my DNA samples in Tris-EDTA (TE)?
No, please don't.
EDTA binds bivalent cations such as Mg2+ that are essential for the Taq polymerase. Your DNA is stable in double distilled water or Tris-HCl at room temperature for several days or even longer if it is dried down.
Should I submit my DNA samples cooled?
This is not necessary; DNA is stable in water at room
temperature for several days. Just send your samples either in
Tris-HCl, distilled water or air dried. Please, do not use EDTA as
this will inhibit the Taq polymerase.
Can I send unpurified PCR products or clones?
Yes, for all sequencing services we offer template preparation and PCR product purification as an additional service.
Which E.coli strain should I use?
Successful isolation of plasmid DNA is possible from most E.coli
strains, though the strain which is used can have a significant
influence on the quality of the purified DNA. Host strains such as
DH10b, DH5 alpha, XL10 Gold and TOP10 normally result in high
quality DNA in combination with many commercially available plasmid
DNA isolation kits and are therefore ideal for the propagation of
plasmids to be sequenced. Lower quality DNA is derived from strains
producing large amounts of carbohydrates, which are released during
lysis and inhibit enzyme activity. Examples are HB101 and its
derivatives such as TG1 and the JM100 series. Also strains with
medium or high levels of endonuclease activity like HB101, JM101 or
BL21 generate DNA of lower quality, hence a proteinase K treatment
should be considered.
Do I need to clean up my PCR product if there is only one band visible?
Yes, primers and dNTPs must be removed from the product. The primers would produce a mixed sequence (5% contamination with a primer results in unreadable mixed sequences!) and the dNTPs would interfere with the dNTP/ddNTP concentration in the sequencing reaction. We recommend purification by using commercially available PCR spin column kits. Alternatively we can perform the PCR product purification for you as additional service.
I see unspecific bands in my PCR reaction. Do I need to gel
purify my product?
If you want to employ one of the PCR primers in the sequencing
reaction you must elute the product of interest from an agarose
gel. Otherwise, a mixed sequence will be produced as the primer is
most likely to bind both the specific and unspecific products. If
you employ a specific nested primer in the sequencing reaction, it
might work. However, producing only one product in the PCR reaction
is the best guarantee for a good sequence. In almost all cases,
improving the PCR conditions (specific primer design, higher
annealing temperature and/or lower primer concentration) helps to
avoid unspecific products.