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Molecules 2017, 22(11), 1991; doi:10.3390/molecules22111991

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

1
Faculty of Frontiers of Innovative Research in Science and Technology (FIRST), Konan University, 7-1-20 Minatojima-minamimachi, Chuo-ku, Kobe 650-0047, Japan
2
Institute of Advanced Energy, Kyoto University, Gokasho, Uji, Kyoto 611-0011, Japan
3
Graduate School of Energy Science, Kyoto University, Gokasho, Uji, Kyoto 611-0011, Japan
*
Author to whom correspondence should be addressed.
Received: 29 September 2017 / Revised: 27 October 2017 / Accepted: 3 November 2017 / Published: 16 November 2017
(This article belongs to the Special Issue Molecular Properties and the Applications of Peptide Nucleic Acids)
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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. View Full-Text
Keywords: designed peptide; G-wire; G-quadruplex; protease; peptide nucleic acid; PNA designed peptide; G-wire; G-quadruplex; protease; peptide nucleic acid; PNA
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This is an open access article distributed under the Creative Commons Attribution License which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. (CC BY 4.0).

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Usui, K.; Okada, A.; Sakashita, S.; Shimooka, M.; Tsuruoka, T.; Nakano, S.-I.; Miyoshi, D.; Mashima, T.; Katahira, M.; Hamada, Y. DNA G-Wire Formation Using an Artificial Peptide is Controlled by Protease Activity. Molecules 2017, 22, 1991.

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