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)
Which kit should be used to analyze single stranded DNA (ssDNA) on the Agilent Fragment Analyzer?
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:
Agilent DNF-470 Small RNA kit Quick Guide for Fragment Analyzer Systems user manuals on Agilent.com