(1095-D) Applying the right reference standard for high throughput ssDNA size analysis
Tuesday, February 6, 2024
2:00 PM – 3:00 PM EST
Location: Exhibit Halls AB
Abstract: For research use only. Not for use in diagnostic procedures.
A molecular-weight size marker, also referred to as a protein ladder, DNA ladder, or RNA ladder, is a set of size standards, which are a prerequisite for estimating the quality, size, and quantity of a molecule in electrophoresis systems. We recently developed a novel, large-size single-stranded DNA (ssDNA) 7K Ladder ranging from 1.1kb to 7.2kb (P/N CLS157950). This ssDNA 7K Ladder is a great reference material for evaluating critical quality attributes (CQAs) of biotherapeutical products such as CRISPR Homology-Directed Repair (HDR) mediated long ssDNA genetic templates. In this report, we investigated its migration behavior and size resolutions in four electrophoresis systems: a) Revvity ssDNA 7K assay system on LabChip® GX TouchTM I or II (P/N CLS158169); b) agarose electrophoresis; c) Agilent Bioanalyzer 2100 and d) Agilent Tape station 4200. Overall, Revvity ssDNA 7K assay high throughput system produces the best resolution for ssDNA fragments at sizes from 1kb to 7.2kb. Furthermore, by comparing migrations of ssDNA to double-stranded DNA (dsDNA) and RNA fragments, we raised concerns of using dsDNA ladder or RNA ladder as reference for ssDNA analysis. Finally, we summarized ssDNA/dsDNA/RNA size migration patterns on these four electrophoresis platforms. Our data presented here provides a great resource and reference for researchers who are looking for reference standards and electrophoresis platforms for ssDNA size analysis.