RNAi Product Analysis / siRNA Purity

RNA interference (RNAi) is a rapidly emerging technology for controlling gene expression in biological systems. This process presents the opportunity to create entirely new classes of therapeutic drugs for the treatment of various diseases. A key component of RNAi is the use of small interfering RNA (siRNA) — short sequences of synthetic dsRNA that illicit the biological response and knockdown specific gene function. Production of RNAi–related reagents typically involves synthesis of specific ssRNA oligonucleotides (oligos) followed by annealing of complementary sense and antisense oligos to form the siRNA duplex. The quality of final product significantly affects the specificity and efficiency of the RNAi response and assessing that quality is a critical step in the process.

Advanced Analytical has developed a method for the quality control of siRNA purity and annealing efficiency using the Oligo PRO™ system. Compared to alternative methods, the Oligo PRO™ offers superior separation resolution, higher sample throughput, automation and improved quantification of impurities.

Key Benefits:

• Parallel 96-capillary gel electrophoresis with on-line UV absorbance detection (CGE-UV) provides unsurpassed throughput and automation;
• CGE-UV is the method of choice for assessing oligo purity, offering superior size-based resolution, nanoliter (nL) sampling volumes and direct quantification of impurities.
• Single nucleotide resolution as well as resolution of ssRNA and dsRNA species can be achieved across the size range of interest.
• Predefined separation and capillary conditioning methods, and an intuitive user interface help streamline instrument operation.
• Advanced data analysis software performs manual or automated peak integration and provides customized reports for individual samples or an entire 96-well sample plate.
• Single nucleotide resolution can be achieved for up to 100-mer lengths and higher using appropriate sample loading conditions.
• A unique, four position slide-out stage accommodates up to three 96-well sample plates allowing for unattended analysis of up to 288 samples.
• A full line of reagents, specifically optimized for use with the Oligo PRO™ system, provide a cost effective, “turn-key” solution for synthetic oligonucleotide purity analysis.

The above trace shows the separation of ssRNA from duplex siRNA using Native Oligel© on the Oligo PRO™ system. Single nucleotide resolution can be achieved across the size range of interest, providing a means for assessing the quality of RNAi reagents.