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Digitally encoded DNA nanostructures for multiplexed, single-molecule protein sensing with nanopores.

Accepted version
Peer-reviewed

Repository DOI


Type

Article

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Authors

Bell, Nicholas AW 
Keyser, Ulrich F 

Abstract

The simultaneous detection of a large number of different analytes is important in bionanotechnology research and in diagnostic applications. Nanopore sensing is an attractive method in this regard as the approach can be integrated into small, portable device architectures, and there is significant potential for detecting multiple sub-populations in a sample. Here, we show that highly multiplexed sensing of single molecules can be achieved with solid-state nanopores by using digitally encoded DNA nanostructures. Based on the principles of DNA origami, we designed a library of DNA nanostructures in which each member contains a unique barcode; each bit in the barcode is signalled by the presence or absence of multiple DNA dumbbell hairpins. We show that a 3-bit barcode can be assigned with 94% accuracy by electrophoretically driving the DNA structures through a solid-state nanopore. Select members of the library were then functionalized to detect a single, specific antibody through antigen presentation at designed positions on the DNA. This allows us to simultaneously detect four different antibodies of the same isotype at nanomolar concentration levels.

Description

Keywords

Binding Sites, DNA, Nanopores, Nanostructures, Nanotechnology, Proteins

Journal Title

Nat Nanotechnol

Conference Name

Journal ISSN

1748-3387
1748-3395

Volume Title

11

Publisher

Springer Science and Business Media LLC
Sponsorship
European Research Council (647144)
European Research Council (261101)
N.A.W.B. and U.F.K. acknowledge funding from an ERC starting grant (Passmembrane 261101) and an ERC consolidator grant (Designerpores 647144). N.A.W.B. also acknowledges funding from an EPSRC doctoral prize award.