We use Applied Biosystems 3730 and 3730XL DNA analyzers to generate the best possible data for our customers.
We utilise commercial DNA purification kits (Promega, Wizard SV 96(TM)) combined with robotic extraction (Qiagen, Bio-Robot 9600(TM)). This approach consistently produces high purity plasmid DNA that is suitable for use in the DNA sequencing reaction. For isolation of larger amounts of plasmid DNA, we perform plasmid maxi-preps using Invitrogen Pure-link HiPure(TM) kits and plasmid midi-preps using Promega PureYield(TM) kits. This DNA is routinely used by customers for various research purposes, including mammalian cell transfection (the DNA isolated via the midi-prep kits is endotoxin free, making it especially suitable for this), but can, of course, also be sequenced.
Analysis of DNA Fragments
Though we do not perform the PCR reactions that produce the fluorescent fragments, we do undertake all subsequent steps in the preparation and analysis of genotyping or fragment analysis using our in-house technology.
Our range of instruments includes those outlined below, all of which facilitates rapid turnaround of samples:
- Two Applied Biosystems 3730 DNA analyzers
- One Applied Biosystems 3730XL DNA analyzer
- Four Qiagen Biorobot 9600s
- Two KingFisher Flex 96 Robots
- One nanodrop spectrophotometer
- Other Equipment
Applied Biosystems 3730 DNA analyzers
These machines are both equipped with a 50cm, 48 capillary array and can process 48 samples simultaneously. Within each, the plate stacker allows uninterrupted processing of multiple plates and is capable of processing about 500 standard sequencing samples per 24 hours.
High quality templates can easily achieve >1 kb reads with Q20 Phred scores. Both instruments are equipped with Genemapper generic software so that they can be used for DNA fragment sizing applications such as analysing STRs, SNP analysis, etc.
Applied Biosystems 3730XL DNA analyser
Our newest sequencer, obtained in 2010, is equipped with a 50cm 96 capillary array, allowing us to run and analyse 96 samples in the same time as the our other machines run and analyse 48 samples. This instrument is also equipped with Genemapper software so that it can be used for DNA fragment sizing applications such as analysing STRs, SNP analysis, etc.
Qiagen Biorobot 9600s
We routinely use the Qiagen Biorobot 9600s for preparing plasmid mini-prep DNA from small scale (5ml) E. coli cultures. The robots can prepare up to 96 DNA samples at a time in about 2 hours.
The resultant DNA can be used for DNA sequencing or any other standard molecular biology application without the need for additional purification steps. These robots are used for our standard mini-prep service and also for preparing mini-prep DNA that will then be sequenced directly by us for customers.
KingFisher Flex 96 Robots
Magnetic bead clean-up of DNA sequencing samples is great at generating high purity samples, but it is time-consuming to do by hand. The KingFisher Flex(TM) Robots are routinely used for automating the magnetic bead clean-up of DNA sequencing reactions before the samples are loaded onto the 3730 DNA analysers. These machines will purify 96 samples in parallel and do this in just over ten minutes and ensure very high reproducibility of purification across a run. Moreover, the manner in which the robot performs the cleanup (by moving the beads and not the liquids) results in an increased purity of products going onto the sequencers, which means cleaner results for customers.
The Nanodrop spectrophotometer allows our team to quickly and accurately measure quantity and quality of DNA samples. The primary advantages of this spectrophotometer over others are its speed, ability to work with very small volumes of sample (2µl) and the ability to recover the sample after measurement. We use this piece of equipment daily for checking yield and quality of maxi-preps and other samples. If you have a problem with your sequencing, often the first thing we will do is check your sample(s) on our nanodrop.
As can be expected from a facility handling such varied services, we are well-stocked with equipment critical for carrying out these tasks including but not limited to: shakers, centrifuges, PCR machines, and multi-channel pipettes.