Analysis of Single Stranded DNA on the Fragment Analyzer

Answer

This Information Applies To: Agilent 5200/5300/5400 Fragment Analyzer systems, RNA kit (15 nt) (p/n DNF-471-0500/1000), HS RNA kit (15 nt) (p/n DNF-472-0500/1000), Small RNA kit (p/n DNF-470-0275)

Issue

Which kit should be used to analyze single stranded DNA (ssDNA) on the Agilent Fragment Analyzer?

Resolution 

Agilent does not offer any kit dedicated or validated for ssDNA analysis. However, given that RNA assays are validated for RNA, which is a single stranded nucleic acid, RNA kits can be considered. However, please note that the migration profile might be different for DNA versus the validated RNA, so data for ssDNA may not be accurate. Therefore, Agilent cannot guarantee data obtained for ssDNA using RNA kits. If users do decide to use RNA kits for the analysis of ssDNA, then it would be recommended to include ssDNA fragments of known sizes to use as internal standards.

Check this application note, which discusses the analysis of ssDNA molecules for use in CRISPR/Cas HDR.

Learn how to effectively maintain and operate your Fragment Analyzer: 5200, 5300, and 5400 Fragment Analyzer System Manual ProSize Data Analysis Software User Manual Agilent DNF-471 RNA kit (15 nt) Quick Guide for Fragment Analyzer Systems Agilent DNF-472 HS RNA (15 nt) Kit Quick Guide for Fragment Analyzer Systems Agilent DNF-470 Small RNA kit Quick Guide for Fragment Analyzer Systems user manuals on Agilent.com

For Research Use only. Not for diagnostic purposes.

PR7000-8636