Why a complementary analytical toolbox is essential for correct siRNA duplex content determination

Small interfering RNAs (siRNAs) have emerged as a highly promising class of therapeutics, capable of effectively treating a wide range of indications, including previously challenging targets. To correctly characterize the duplex content of siRNA therapeutics, a careful design of the analytical conditions is required. This is due to the weak interactions governing the duplex formation and thermal stability of these double-stranded oligonucleotides. In this study, we demonstrate that the reliability of duplex content analyses can be compromised by denaturation or hybridization artifacts caused by environmental factors related with sample preparation or with the 'non-denaturing' chromatographic analysis method. To address this issue, we propose to characterize the siRNA duplex in various analytical media with unbiased techniques such as circular dichroism spectrophotometry and use the results to evaluate potential artifacts in the 'non-denaturing' method, developed to determine the duplex content. Through this approach, one can optimize the sample preparation and develop 'non-denaturing' method conditions to minimize the influence of environmental factors on the duplex content, and thereby determine the assay of siRNA duplex with no bias.