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

include competitive PCR and cleavage based applications such as RFLP. Also, the resolution in the lower range, i.e. below 100 bp, is significantly increased compared to the other two DNA LabChip kits, making it possible to distinguish between fragments that are very similar in size. Since the DNA 500 and the DNA 1000 LabChip kit show similar performance and are used for similar applications, they are presented jointly in this application note.
DNA 500 LabChip kit
The performance of the DNA 500 assay is demonstrated by the analysis of several mixtures of PCR products (figure 1). All chipbased separations were performed on the Agilent 2100 bioanalyzer according to the instructions provided with each kit. The conditions for the acrylamide gel separations are listed in the appropriate figure caption. Figure 1 shows the overlay of 3 different electropherograms acquired on the Agilent 2100 bioanalyzer that are mixtures of PCR samples ranging from 25 to 500 base pairs in size. The two closest eluting bands (50 bp and 53 bp) are partially separated and identified by the software as two separate peaks. The DNA 500 assay achieves a resolution of 5 base pairs from 25 to 100 base pairs and a 5 % resolution from 100 to 500 base pairs where the sizing error is less than 10 % over the entire size range. The digital data format allows accurate quantitation of the separated bands based on peak areas. A DNA mass ladder was used to verify quantitation accuracy. The ladder contains 3 fragments in the specified size range, with concentrations guaranteed by the supplier (Low DNA Mass ladder, Life Technologies, USA).

Table 1 lists the quantitative results obtained on the Agilent 2100 bioanalyzer. All separated bands were well within the specified margin of 70 % accuracy, with
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