An autonomously self-assembling dendritic DNA nanostructure for target DNA detection

Journal Article

There is a growing need for sensitive and reliable nucleic acid detection methods that are convenient and inexpensive. Responsive and programmable DNA nanostructures have shown great promise as chemical detection systems. Here, we describe a DNA detection system employing the triggered self-assembly of a novel DNA dendritic nanostructure. The detection protocol is executed autonomously without external intervention. Detection begins when a specific, single-stranded target DNA strand (T) triggers a hybridization chain reaction (HCR) between two, distinct DNA hairpins (α and β). Each hairpin opens and hybridizes up to two copies of the other. In the absence of T, α and β are stable and remain in their poised, closed-hairpin form. In the presence of T, α hairpins are opened by toe-hold mediated strand-displacement, each of which then opens and hybridizes two β hairpins. Likewise, each opened β hairpin can open and hybridize two α hairpins. Hence, each layer of the growing dendritic nanostructure can in principle accommodate an exponentially increasing number of cognate molecules, generating a high molecular weight nanostructure. This HCR system has minimal sequence constraints, allowing reconfiguration for the detection of arbitrary target sequences. Here, we demonstrate detection of unique sequence identifiers of HIV and Chlamydia pathogens. Responsive and programmable DNA nanostructures have shown great promise as chemical detection systems. In this study, the authors describe a DNA detection system by using a metastable mixture of DNA hairpins (α and β) to detect the target DNA strand (T1). The target binds to and opens the first hairpin which then exponentially binds and opens the other hairpins, thus triggering a dendrimer formation. The system was further tested with HIV and Chlamydia trachomatis pathogens with positive results. This method offers an inexpensive and convenient method for detecting pathogenic DNA. Copyright © 2013 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Full Text

Duke Authors

Cited Authors

  • Chandran, H; Rangnekar, A; Shetty, G; Schultes, EA; Reif, JH; Labean, TH

Published Date

  • 2013

Published In

Volume / Issue

  • 8 / 2

Start / End Page

  • 221 - 227

International Standard Serial Number (ISSN)

  • 1860-6768

Digital Object Identifier (DOI)

  • 10.1002/biot.201100499