DNA G-Wire Formation Using an Artificial Peptide is Controlled by Protease Activity

• Published in: Molecules (Basel, Switzerland) Vol. 22; no. 11; p. 1991
• Main Authors: Usui, Kenji, Okada, Arisa, Sakashita, Shungo, Shimooka, Masayuki, Tsuruoka, Takaaki, Nakano, Shu-Ichi, Miyoshi, Daisuke, Mashima, Tsukasa, Katahira, Masato, Hamada, Yoshio
• Format: Journal Article
• Language: English
• Published: Switzerland MDPI AG 16.11.2017; MDPI
• Subjects: Atomic force microscopy; Calcium; Deoxyribonucleic acid; designed peptide; DNA; DNA - chemistry; DNA structure; Electronic circuits; G-quadruplex; G-Quadruplexes; G-wire; Gel filtration; Guanine; Nanotechnology; Nanowires; Nanowires - chemistry; Nucleotide sequence; Particle Size; Peptide Hydrolases - chemistry; peptide nucleic acid; Peptide nucleic acids; Peptide Nucleic Acids - chemistry; Peptides; Peptides - chemistry; PNA; Protease; Proteases; Protein structure; Proteinase; Secondary structure; Substrates; Surface Properties; Wire; Zeta potential; protease; designed peptide; G-wire; PNA; G-quadruplex; peptide nucleic acid
• ISSN: 1420-3049; 1420-3049
• DOI: 10.3390/molecules22111991

The development of a switching system for guanine nanowire (G-wire) formation by external signals is important for nanobiotechnological applications. Here, we demonstrate a DNA nanostructural switch (G-wire <--> particles) using a designed peptide and a protease. The peptide consists of a PNA sequence for inducing DNA to form DNA-PNA hybrid G-quadruplex structures, and a protease substrate sequence acting as a switching module that is dependent on the activity of a particular protease. Micro-scale analyses via TEM and AFM showed that G-rich DNA alone forms G-wires in the presence of Ca , and that the peptide disrupted this formation, resulting in the formation of particles. The addition of the protease and digestion of the peptide regenerated the G-wires. Macro-scale analyses by DLS, zeta potential, CD, and gel filtration were in agreement with the microscopic observations. These results imply that the secondary structure change (DNA G-quadruplex <--> DNA/PNA hybrid structure) induces a change in the well-formed nanostructure (G-wire <--> particles). Our findings demonstrate a control system for forming DNA G-wire structures dependent on protease activity using designed peptides. Such systems hold promise for regulating the formation of nanowire for various applications, including electronic circuits for use in nanobiotechnologies.