Gene-silencing potency of symmetric and asymmetric lipid-conjugated siRNAs and its correlation with dicer recognition

Bioconjug Chem. 2013 Dec 18;24(12):2045-57. doi: 10.1021/bc400391n. Epub 2013 Dec 9.

Abstract

Three types of siRNAs and three types of left-overhang siRNAs (LoRNAs) were synthesized along with their conjugations with palmitic acid (C16) to investigate the correlation between Dicer recognition and gene-silencing potency. The siRNA types were composed of 21-nucleotide (nt), 23-nt, and 25-nt lengths of sense and antisense strands with a 2-nt overhang at each 3'-end. The three LoRNA types were composed of a 21-nt, a 23-nt, and a 25-nt length of sense strand with a 2-nt DNA at the 3'-blunt-end and a 23-nt, a 25-nt, and a 27-nt length of antisense strand with a 2-nt overhang at the 3'-end. Additionally, each of these siRNAs and LoRNAs was modified with a C16 at the 5'- or 3'-end of the sense strand; these were named C16-siRNAs and C16-LoRNAs, respectively. The siRNAs and C16-siRNAs were barely cleaved by Dicer, and their gene-silencing efficacies were not excellent, contrary to our expectations. In contrast, most of the LoRNAs and C16-LoRNAs became substrates of Dicer, and they showed both strong gene-silencing efficacies and high nuclease resistance. Among the LoRNAs, the 25D-C16/27-nt LoRNA, which is composed of a 25-nt sense strand with a 2-nt DNA conjugated with C16 at the 3'-end and a 27-nt antisense strand with a 2-nt overhang at the 3'-end, showed an excellent gene-silencing effect with high cell membrane permeability and strong resistance against nuclease degradation. Additionally, the Lo25D-C16/27RNA excelled in all three aspects, nuclease resistance, cell membrane permeability, and RNAi efficacy, compared with the cholesterol conjugation. We are certain that Lo25D-C16/27RNA can be useful as a new generation of RNAi molecules with which to overcome some of the limitations of RNAi technology.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Animals
  • Base Sequence
  • Cholesterol / metabolism*
  • DNA / genetics
  • HeLa Cells
  • Humans
  • Intracellular Space / metabolism
  • Palmitic Acid / metabolism*
  • RNA Interference*
  • RNA, Antisense / genetics
  • RNA, Small Interfering / genetics*
  • RNA, Small Interfering / metabolism*
  • Ribonuclease III / metabolism*

Substances

  • RNA, Antisense
  • RNA, Small Interfering
  • Palmitic Acid
  • DNA
  • Cholesterol
  • Ribonuclease III