Peptide nanostructures-based delivery of DNA nanomaterial therapeutics for regulating gene expression

Bineeth Baral; Bijayananda Panigrahi; Avishek Kar; Kiran D Tulsiyan; Uday Suryakant; Dindyal Mandal; Umakanta Subudhi

doi:10.1016/j.omtn.2023.07.017

Peptide nanostructures-based delivery of DNA nanomaterial therapeutics for regulating gene expression

Mol Ther Nucleic Acids. 2023 Jul 18:33:493-510. doi: 10.1016/j.omtn.2023.07.017. eCollection 2023 Sep 12.

Authors

Bineeth Baral^{1

2}, Bijayananda Panigrahi^{3

4}, Avishek Kar^{1

2}, Kiran D Tulsiyan^{5

6}, Uday Suryakant³, Dindyal Mandal³, Umakanta Subudhi^{1

2}

Affiliations

¹ DNA Nanotechnology & Application Laboratory, Environment & Sustainability Department, CSIR-Institute of Minerals & Materials Technology, Bhubaneswar 751013, Odisha, India.
² Academy of Scientific & Innovative Research (AcSIR), Ghaziabad 201002, India.
³ School of Biotechnology, Kalinga Institute of Industrial Technology Deemed to be University, Bhubaneswar 751024, Odisha, India.
⁴ Biopioneer Private Limited, Bhubaneswar 751024, Odisha, India.
⁵ School of Chemical Sciences, National Institute of Science Education & Research, Bhubaneswar 752050, India.
⁶ Homi Bhaba National Institute, Mumbai 400094, India.

Abstract

Self-assembled branched DNA (bDNA) nanomaterials have exhibited their functionality in various biomedical and diagnostic applications. However, the anionic cellular membrane has restricted the movement of bDNA nanostructures. Recently, amphiphilic peptides have been investigated as cationic delivery agents for nucleic acids. Herein, we demonstrate a strategy for delivering functional bDNA nanomaterials into mammalian cells using self-assembled linear peptides. In this study, antisense oligonucleotides of vascular endothelial growth factor (VEGF) were inserted in the overhangs of bDNAs. Novel linear peptides have been synthesized and the peptide-bound bDNA complex formation was examined using various biophysical experiments. Interestingly, the W4R4-bound bDNAs were found to be exceptionally stable against DNase I compared to other complexes. The delivery of fluorescent-labeled bDNAs into the mammalian cells confirmed the potential of peptide transporters. Furthermore, the functional efficacy of the peptide-bound bDNAs has been examined through RT-PCR and western blot analysis. The observed results revealed that W4R4 peptides exhibited excellent internalization of antisense bDNAs and significantly suppressed (3- to 4-fold) the transcripts and translated product of VEGF compared to the control. In summary, the results highlight the potential use of peptide-based nanocarrier for delivering bDNA nanostructures to regulate the gene expression in cell lines.

Keywords: DNA nanostructures; DNA nanotechnology; MT: Oligonucleotides: Therapies and Applications; VEGF; delivery; nucleic acid therapeutics; peptide; self-assembly.