Reagent Kits

Our capillary electrophoresis instruments utilize specially designed reagent kits to analyze diverse nucleic acid samples, from small RNA to genomic DNA, and NGS library quality control.

Reagent Kit Box

Genomic DNA 50kb Kit

The Genomic DNA 50kb Kit (DNF-467) is employed in the automated quality assessment of genomic DNA. Able to accurately size samples from 75 bp through 60 Kb, it is commonly employed as a quality check prior to downstream applications, such as whole genome sequencing. To simplify sample handling and preparation, a single 200X dilution of your sample is all that is required, further improving laboratory workflow.

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Components

500 Sample Kit
Genomic DNA Separation Gel240 mL (DNF-270-0500)
Intercalating Dye30 µL (DNF-600-U030)
5X 930 dsDNA Inlet Buffer125 mL (DNF-355-0300)
5X Capillary Conditioning Solution50 mL (DNF-475-0050)
HS Genomic DNA Diluent Marker Solution120 mL (DNF-375-0120)
Extended Genomic DNA Ladder50 µL (DNF-367-U050)
0.25X TE Rinse Buffer125 mL (DNF-497-0125)
BF-25 Blank Solution8 mL (DNF-300-0008)
Eppendorf LoBind 0.5 mL TubesPackage of 50

Specifications

SpecificationsDescription
Sample Volume Required1 µL
Diluent Marker Volume Required199 µL
DNA Sizing Range75 bp – 60,000 bp
gDNA Concentration Range25 ng/µL - 250 ng/µL input gDNA
(0.125 – 1.25 ng/µL final concentration after dilution)
gDNA Quantification Accuracy± 30%
gDNA Quantification Precision25% CV
Maximum gDNA Concentration250 ng/µL
Total Electrophoresis Run Time 50 min (Ultra-Short Array, 22-47); 60 min (Short Array, 33-55)

Examples

The capability of the Genomic DNA 50kb Kit to accurately quantify and size genomic DNA samples is directly related to the Extended Genomic DNA Ladder. Accurate sizing and quantification is accomplished by the inclusion of a 48.5 Kb DNA fragment in the DNA ladder. Figure 1 shows a standard separation of the Extended Genomic DNA Ladder.

Figure 1
Figure 1. Extended Genomic DNA Ladder (DNF-367) separated on a Fragment Analyzer equipped with a Short Capillary Array (33-55) using the Genomic DNA 50kb Kit (DNF-467).

A separation of a standard genomic DNA sample is shown in Figure 2. An important feature in PROSize® for the rapid and efficient analysis of sample quality is the Genomic Quality Number (GQN). The GQN provides users with an adaptable measurement for sample quality. By manually setting a threshold for genomic DNA quality, users are able to define what good quality DNA is for their specific application. Genomic preparations vary in quality – based on myriad factors ranging from technique employed to source material – to a point that a fixed quality metric is limited in scope. In Figure 2, a threshold of 10 Kb (indicated by the dotted blue line) was set with a resulting GQN of 7.9. Allowing users to define, what they believe is, good quality DNA for their application enhances the versatility of this analysis.

Figure 1
Figure 2. A typical genomic DNA sample separated on a Fragment Analyzer equipped with a Short Capillary Array (33-55) using the Genomic DNA 50kb Kit (DNF-467). The sample had a GQN of 7.9 with a user-defined threshold of 10 Kb.

Additionally, the Genomic DNA 50kb Kit can be used to evaluate degraded samples, such as FFPE genomic DNA. The quality of FFPE samples are dependent on numerous factors including amount of time the sample was incubated in formalin and the physical size of the tissue sample. Figure 3 provides two examples of an FFPE genomic DNA sample. As the factors influencing DNA quality vary sample to sample, a common degradation pattern is not typical.

Figure 3a
Figure 3b
Figure 3. Two examples of an FFPE genomic DNA sample separated using the Genomic DNA 50kb Kit on a Fragment Analyzer fitted with a standard short capillary array (33-55).

The quantification precision and accuracy of the Genomic DNA 50Kb Kit is shown in Figure 4. Samples were measured by a fluorometric instrument and Fragment Analyzer using this kit, with the measured concentrations for each instrument then plotted against each other. The graph clearly shows a near perfect one to one ratio, indicating that both methods produce equivalent measurements.

Figure 5
Figure 4. Fluorometric instrument concentration plotted against Fragment Analyzer concentration. The concentration values were obtained from the same samples.

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