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

Abstract

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 Ca2+, 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.

Polymorphism of G4 associates: from stacks to wires via interlocks

“…Programming head-to-tail interlocking, which is analogous to strand arrangement in ‘classical’ G-wires ( 20 , 21 ), seems to be more challenging than head-to-head dimerization. We use the term ‘classical’ here to distinguish such well-known vertically interlocked structures (scheme (e) in Figure 1 ) from ‘lego’ G4s ( 22 , 23 ) which are characterized by side-by-side interlocking (scheme (f) in Figure 1 ).…”

Special Issue: Molecular Properties and the Applications of Peptide Nucleic Acids

“…Nanoassembly, molecular machines, switches and logic gates can be designed using PNAs as components or as switching stimuli. A good example of this is reported by Kenji Usui and co-workers in this issue, where a DNA G-quadruplex secondary structure and nanostructural shape were shown to be affected by PNA switching segments [ 16 ].…”

Effect of tryptophan residues on gold mineralization by a gold reducing peptide

“…[10][11][12][13][14][15][16][17][18][19][20][21][22][23][24][25] (2) Peptides can be conjugated with articial amino acids and functional molecules. 19,[26][27][28] (3) Peptides are easier to design and handle than proteins. However, clear guidelines for the relationships between peptide sequences and inorganic precipitation ability have not been established.…”