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High resolution DNA analysis with the,,,DNA 500 and DNA 1000 LabChip kits

a standard deviation of 10 % or less. The DNA 500 assay relies, like the other DNA assays, on an intercalating dye for fluorescence detection. The dye incorporation depends on the basepair composition and the secondary structure of the DNA fragments. For larger fragments such sequence differences are usually statistically evened out. For shorter fragments, however, the sequence can make a difference in dye incorporation. Therefore, deviations from the sizing and quantitative specifications can occur for individual fragments below 70 bp. The same samples shown in the chip-based electropherograms in figure 1 were compared to a slab gel separation using a commercially available 4- 20 % gradient gel (Novex, USA).

As shown in figure 2, the Agilent 2100 bioanalyzer performs with equal or better resolution than the slab gel, delivering a clearer image of the sample.

DNA 1000 LabChip kit
In the size range below 500 bp, the DNA 1000 LabChip kit shows a performance that is comparable to the DNA 500 LabChip kit. The operating range was extended to 1000 bp, to better match the size range, in which most PCR fragments fall. From 500 to 1000 bp the resolution of the DNA 1000 assay is 10 %, while the maximum error for quantitation remains at 30 % (this corresponds to a 95 % confidence level).
The DNA 1000 kit was used to optimize PCR conditions for a competitive RT-PCR reaction of two genes: GAPDH and the heat shock protein hsp721 . The goal of the experiment was to achieve a co-amplification of GAPDH (housekeeping gene) and hsp72. The hsp72 was the gene of interest, the expression of which can be influenced by various factors. For the experiment, RNA was isolated from HepG2-cells and reverse transcribed into cDNA. The cDNA was amp
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