Effects of N–1-Mer Impurities in Antisense Oligonucleotides on the Target RNA Suppression

In this study, we focused on N-1 impurities in antisense oligonucleotides. We evaluated their binding affinity to the therapeutic target RNA, which had the complementary sequence to the full-length N-mer desired product (DP), and their ability to recruit ribonuclease H (RNase H) using cell-free <i>in vitro</i> assays. The binding affinity of each N-1-mer to the target RNA was extremely low, with binding constants <1: 100 of that of the DP/RNA duplex. However, the degree of destabilization varied significantly depending on the position of the nucleotide defect within the N-1-mer, with differences of up to 5.1 kcal/mol (a 4,000-fold difference in binding constant). This weak binding capability to the target RNA suggests that the presence of the N-1-mer has little effect on DP activity. This study provides essential information for the dissemination of oligonucleotide therapeutics by providing a basis for considering the effect of N-1-mer impurities.