Charge modulation of peptide/nucleic acid complexes: an anionic additive enhances gene silencing and CRISPR/Cas9 editing by promoting intracellular nucleic acid release

Abstract

Small interfering RNA (siRNA) and Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR)/CRISPR-associated Protein 9 (Cas9) complexes are effective approaches to temporarily downregulate protein expression via post-transcription RNA interference or permanently altering protein expression via editing genomic DNA, respectively. However, the efficient delivery of these mediators to targeted cells has been challenging, largely due to their anionic and hydrophilic nature, which hinders their interaction with the cell membrane and cellular internalization. Cell-penetrating peptides (CPPs) exhibit dual characteristics as a carrier for nucleic acid delivery, where positively charged components bind to the negatively charged nucleic acid, and the hydrophobic components enhance interactions with the cell membranes. Arginine/tryptophan-containing peptides provide both characteristics and have been shown to be efficient in delivering nucleic acids. In this project, we evaluated a library of novel linear and hybrid (cyclic/linear) peptides with increasing molecular weight for their physical characteristics, interaction with nucleic acids, cytotoxicity, internalization into different breast cancer cell lines, and their ability to promote and enhance silencing efficiency. The majority of the peptides included in this study demonstrated strong binding affinity to siRNA; however, despite effective cellular internalization, they did not show expected silencing/transfection efficiency, which we hypothesized to be due to the strong bonding between the carrier and cargo and, therefore, poor intracellular release of delivered nucleic acids. The addition of a negatively charged component to the peptide/siRNA and peptide/ribonucleoprotein complexes enhanced the efficiency of the delivered nucleic acid. These data emphasize the importance of the balance between stability of the carrier/cargo complex and timely intracellular release in the efficiency of this approach.