Agilent DNF-920 Quick Start Guide

Analytical specifications

dsDNA 920 assay

DNA Sizing Range

75 bp – 15,000 bp

DNA Sizing Accuracy1

+ 5% or better

DNA Fragment Concentration Range1

DNA Sizing Precision1

2% CV

Physical Specifications

22cm2: 27 minutes, 33cm: 50 minutes, 55cm: 80 minutes

Samples per run

12, 48 or 96; depending on the instrument type

Sample volume required

2 µL (adjustable depending on sample concentration)

Kit stability

4 months

Agilent DNF-920 Reagent Kit (75 – 15000 bp) Quick Guide for Fragment Analyzer Systems

The Agilent Fragment Analyzer systems are automated capillary electrophoresis platforms for scalable, flexible, fast, and reliable electrophoresis of nucleic acids.

This Quick Guide is intended for use with the Agilent 5200, 5300, and 5400 Fragment Analyzer systems only. The DNF-920 Reagent kit from Agilent is for the analysis of dsDNA fragments between 75 bp and 15 kb. Sizing and relative quantification between samples can be obtained using this kit. Example applications include PCR fragment sizing, and restriction digest analysis.

Specifications

0.5 ng/µL – 50 ng/µL input DNA (adjustable by dilution sample)

Separation Resolution

Total electrophoresis run time

Results using DNA Ladder of DNA Fragment standards initially prepared in 1x TE buffer.

The 22 cm effective, 47 cm total length capillary is only available for 12-capillary Fragment Analyzer instruments

75 bp – 1,500 bp ≤ 5% (33-55 array) 1,500 bp – 15,000 bp ≤ 10% (33-55 array)

DNF-920 dsDNA Reagent Kit (75-15000 bp) Quick Guide for Fragment

WARNING

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Kit Components – 500 Sample Kit

Kit Component Number

Part Number (Re-order Number)

Description Quantity Per Kit

5191-6598*

DNF-920-0240 dsDNA 920 Gel, 240 mL 1

DNF-355-0125 5x 930 dsDNA Inlet Buffer, 125 mL

DNF-495-0060 Dilution Buffer 1X TE, 60mL

DNF-920-FR*

DNF-600-U030

FS-SLR920-U100

FS-SMK920-0003

5191-6614* Qualitative DNA, 500, RT

FS-SMO15 Mineral Oil Dropper Bottle, 15mL 1

DNF-475-0050 5x Capillary Conditioning Soln, 50 mL 1

dsDNA 920, 500, 4oC

• Dilute with sub-micron filtered water prior to use

dsDNA 920, FR

Intercalating Dye, 30 μL

1 kb DNA Ladder, 100 µL

Markers, 75bp & 15kb, 3.2 mL

*not orderable

Refer to product safety data sheets for further information

When working with the Fragment Analyzer kit components follow the appropriate safety procedures such as wearing goggles, safety gloves and protective clothing.

DNF-920 dsDNA Reagent Kit (75-15000 bp) Quick Guide for Fragment

Additional Material Required for Analysis with the Fragment Analyzer Systems

• Fragment Analyzer systems with LED fluorescence detection:

• 5200 Fragment Analyzer system (p/n M5310AA)

• FA 12-Capillary Array Ultrashort, 22 cm (p/n A2300-1250-2247) OR

• FA 12-Capillary Array Short, 33 cm (p/n A2300-1250-3355) OR

• FA 12-Capillary Array Long, 55 cm (p/n A2300-1250-5580)

• 5300 Fragment Analyzer system (p/n M5311AA)

• FA 48-Capillary Array Short, 33 cm (p/n A2300-4850-3355) OR

• FA/ZAG 96-Capillary Array Short, 33 cm (p/n A2300-9650-3355) OR

• FA/ZAG 96-Capillary Array Long, 55 cm (p/n A2300-9650-5580)

• 5400 Fragment Analyzer system (p/n M5312AA)

• FA 48-Capillary Array Short, 33 cm (p/n A2300-4850-3355) OR

• FA/ZAG 96-Capillary Array Short, 33 cm (p/n A2300-9650-3355) OR

• FA/ZAG 96-Capillary Array Long, 55 cm (p/n A2300-9650-5580):

• Agilent Fragment Analyzer controller software (Version 1.1.0.11 or higher)

• Agilent ProSize data analysis software (Version 2.0.0.61 or higher)

Additional equipment/reagents required (not supplied)

• 96-well PCR sample plates. Please refer to Appendix – Fragment Analyzer Compatible Plates and Tubes in the Fragment Analyzer System User Manual for a complete approved sample plate list

• Multichannel pipettor(s) and/or liquid handling device capable of dispensing 1 – 100 µL volumes (sample plates) and 1,000 µL volumes (inlet buffer plate)

• Pipette tips

• 96-well plate centrifuge (for spinning down bubbles from sample plates)

• Sub-micron filtered DI water system (for diluting the 5x 930 dsDNA Inlet Buffer and 5x Capillary Conditioning Solution)

• 96-deepwell 1mL plate: Fisher Scientific #12-566-120 (inlet buffer and/or waste plate)

• Reagent reservoir, 50 mL (VWR #89094-680 or similar) (for use in pipetting inlet buffer plates/sample trays)

• Conical centrifuge tubes for prepared separation gel/dye mixture and/or 1x Capillary Conditioning Solution

• 50 mL (for 5200 Fragment Analyzer system or 50 mL volumes): BD Falcon #352070, available from Fisher

Scientific #14-432-22 or VWR #21008-940

• 250 mL (for 5300 and 5400 Fragment Analyzer systems or larger volumes): Corning #430776, available from Fisher Scientific #05-538-53 or VWR #21008-771

• Vortexer (for mixing of samples, ladders, and/or markers in tubes and/or plates)

Capillary Storage Solution (p/n GP-440-0100)

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