Reagent Kits

AATI's 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

High Sensitivity Small DNA Fragment Analysis Kit

High Sensitivity Small DNA Fragment Analysis Kit
500 Sample High Sensitivity Small DNA Fragment Analysis Kit

The High Sensitivity Small DNA Fragment Analysis Kit was designed for the automated analysis of small, low concentration DNA samples. Able to size DNA fragments and smears from 50 bp – 1,500 bp with unparalleled accuracy, the kit is ideal for the evaluation of small RNA NGS libraries. Other applications include genotyping, the quantitative analysis of PCR amplicons, and microsatellites.

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Components

Components 500 Sample Kit 1,000 Sample Kit
Small Fragment Separation Gel 240 mL (DNF-230-0240) 500 mL (DNF-230-0500)
Intercalating Dye 30 µL (DNF-600-U030) 30 µL x 2 (DNF-600-U030)
5X 930 dsDNA Inlet Buffer 125 mL (DNF-355-0125) 300 mL (DNF-355-0300)
5X Capillary Conditioning Solution 50 mL (DNF-475-0050) 100 mL (DNF-475-0100)
HS Small Fragment Diluent Marker Solution 2.4 mL x 5 vials (DNF-371-0003) 2.4 mL x 10 vials (DNF-371-0003)
HS Small Fragment DNA Ladder 100 µL (DNF-372-U100) 100 µL x 2 (DNF-372-U100)
0.25X TE Rinse Buffer 125 mL (DNF-497-0125) 125 mL (DNF-497-0125)
BF-25 Blank Solution 8 mL (DNF-300-0008) 8 mL (DNF-300-0008)

Specifications

Specifications Description
Sample Volume Required 2 µL
Diluent Marker Volume Required 22 µL
DNA Sizing Range 50 bp – 1,500 bp
Separation Resolution Ultra-Short Array: 50 bp – 700 bp ≤ 5%; 700 bp – 1500 bp ≤ 10%
Short Array: 50 bp – 900 bp ≤ 5%; 900 bp – 1500 bp ≤ 10%
DNA Sizing Accuracy ± 5% or better
DNA Sizing Precision 2% CV
DNA Fragment Concentration Range 5 pg/µL – 500 pg/µL input DNA
DNA Smear Concentration Range 200 pg/µL – 5000 pg/µL input DNA
DNA Quantification Accuracy ± 25 %
DNA Quantification Precision 15 % CV
Maximum DNA Concentration 500 pg/µL per fragment; 5000 pg/µL total
Total Electrophoresis Run Time 33 min (Ultra-Short Array, 22-47); 40 min (Short Array, 33-55)

Examples

Sizing and quantification of small DNA fragments necessitates the use of a DNA ladder with precise, well selected fragments provided at a proper molarity. Figure 1 depicts a typical separation of the High Sensitivity Small Fragment DNA Ladder (DNF-372) using the High Sensitivity Small DNA Fragment Analysis Kit (DNF-477). Electrophoresis was performed on a Fragment Analyzer equipped with a Short Capillary Array (33-55), providing an excellent separation of the ladder fragments.

Figure 1
Figure 1. A typical separation of the High Sensitivity Small Fragment DNA Ladder (DNF-372) performed on a Fragment Analyzer equipped with a Short Capillary Array (33-55) with the High Sensitivity Small DNA Fragment Analysis Kit (DNF-477).

Small RNA NGS libraries are accurately assessed using the HS Small DNA Fragment Analysis Kit, promoting quality sequencing results. A small RNA NGS library is shown in Figure 2. Prior to electrophoresis the library was size selected, removing the appearance of a traditional library smear.

Figure 2
Figure 2. Size selected small RNA library run on a Fragment Analyzer equipped with a Short Capillary Array (33-55) using the High Sensitivity Small Fragment DNA Analysis Kit (DNF-477).

The High Sensitivity Small Fragment DNA Analysis Kit (DNF-477) is suited to any application that requires accurate and precise sizing and quantification of small DNA fragments and smears. Sheared DNA smears are sized and quantified with the same level of accuracy and precision as DNA fragments. The Smear Analysis function in PROSize® provides enhanced measurements over the default fragment analysis function. In Figure 3, the Smear Analysis region is bounded by the dotted red lines and the average size of the smear is listed in red numbers.

Figure 3
Figure 3. Separation of sheared gDNA performed on a Fragment Analyzer equipped with a Short Capillary Array (33-55) using the High Sensitivity Small Fragment Analysis Kit (DNF-477). Smear Analysis region within the dotted red lines with the size of the smear centered in red numbers.

In addition to excellent sizing, the High Sensitivity Small Fragment Analysis Kit (DNF-477) also provides accurate and precise quantification. Figure 4 shows the results of measuring the same samples via two methods, a fluorometric instrument and the Fragment Analyzer. The measured concentrations were plotted against each other revealing a one-to-one linear relationship between the methods with a high coefficient of determination, indicating equivalent measurements by both instruments.

Figure 4
Figure 4. Fragment Analyzer concentrations were plotted against concentrations measured via a fluorometric instrument. The same samples were measured revealing a one-to-one relationship between quantification methods.
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