Properties of short double-stranded RNAs carrying randomized base pairs: toward better controls for RNAi experiments.

ABSTRACT: Short interfering RNAs (siRNAs) are mediators of RNA interference (RNAi), a commonly used technique for selective down-regulation of target gene expression. Using an equimolar mixture of A, G, C, and U phosphoramidites during solid-phase synthesis, we introduced degenerate positions into RNA guide and passenger strands so that, when annealed, a large pool of distinct siRNA duplexes with randomized base pairs at defined sites was created. We assessed the randomization efficiency by deep sequencing one of the RNAs. All possible individual sequences were present in the pool with generally an excellent distribution of bases. Melting temperature analyses suggested that pools of randomized guide and passenger strands RNAs with up to eight degenerate positions annealed so that mismatched base-pai

SUBMITTER: Zagalak JA 

PROVIDER: S-EPMC4647466 | biostudies-literature | 2015 Dec

REPOSITORIES: biostudies-literature