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De Novo Design of a Nanopore for DNA Detection Incorporating a β-hairpin Peptide

preprint
revised on 11.06.2020, 03:33 and posted on 12.06.2020, 09:51 by Keisuke Shimizu, Batsaikhan Mijiddorj, Shuhei Yoshida, Shiori Akayama, Yoshio Hamada, akifumi ohyama, Kenji Usui, Izuru Kawamura, Ryuji Kawano
The amino acid sequence of a protein encodes information on its three-dimensional structure and specific functionality. De novo protein design has emerged as a method to manipulate the primary structure for the development of artificial proteins and peptides with desired functionality. This paper describes the de novo design of a pore-forming peptide that has a β-hairpin structure and assembles to form a stable nanopore in a bilayer lipid membrane. This large synthetic nanopore is an entirely artificial device with practical applications. This peptide, named SV28, forms nanopore structures ranging from 1.6 to 6.2 nm in diameter assembled from 7 to 18 monomers. The nanopore formed with a diameter of 5 nm is able to detect long double-stranded DNA (dsDNA) with 1 kbp length, and measurement of current signals allowed us to investigate the translocation behavior of dsDNA at the single molecule level. Such de novo design of peptide sequences has the potential to create assembled structure in lipid membrane such as novel nanopores, which would also be applicable in molecular transporter between inside and outside of lipid membrane.

Funding

KAKENHI (grant nos. 19H05382 and 19H00901) from MEXT.

History

Email Address of Submitting Author

rjkawano@cc.tuat.ac.jp

Institution

Tokyo University of Agriculture and Technology

Country

Japan

ORCID For Submitting Author

https://orcid.org/0000-0001-6523-0649

Declaration of Conflict of Interest

No conflict of interest.

Version Notes

Version 2.

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