Bait-and-Switch Molecular Recognition in Nucleic Acid Sensors

Mira K. Y. Nishimura; Colin D. McGuinness; David Keszenman-Pereyra; Paul Dickinson; Cohn J. Campbell; Till T. Bachmann; Peter Ghazal; Jason Crain; Colin Campbell

Bait-and-Switch Molecular Recognition in Nucleic Acid Sensors

Mira K. Y. Nishimura, Colin D. McGuinness, David Keszenman-Pereyra, Paul Dickinson, Cohn J. Campbell, Till T. Bachmann, Peter Ghazal, Jason Crain, Colin Campbell

Research output: Chapter in Book/Report/Conference proceeding › Conference contribution

Abstract / Description of output

We investigate the properties of a simple DNA-based nanodevice capable of detecting single nucleotide polymorphisms (SNPs) in unlabelled nucleic acid target sequences. Detection is achieved by a two-stage bait-and-switch process combining complementary-base hybridization and switching as molecular recognition criteria. A probe molecule is constructed from a single DNA strand designed to adopt a partial cruciform structure with a pair of exposed (unhybridized) strands. Upon target binding, a switchable cloverleaf construct (similar to a Holliday junction) is formed where the states are the open and closed junction conformations. Switching between these occurs by junction folding in the presence of divalent ions. A combination of steady-state and time-resolved fluorescence spectroscopy is used to measure Forster resonance energy transfer.

Original language	English
Title of host publication	2009 SYMPOSIUM ON PHOTONICS AND OPTOELECTRONICS (SOPO 2009)
Place of Publication	NEW YORK
Publisher	Institute of Electrical and Electronics Engineers
Pages	915-920
Number of pages	6
ISBN (Print)	978-1-4244-4411-3
Publication status	Published - 2009

Keywords / Materials (for Non-textual outputs)

Biosensor
FRET
single nucleotide polymorphisms
fluorescence lifetime
DNA
JUNCTION

Cite this

@inproceedings{7145091a2be24ffc991b5eed5d4176b6,

title = "Bait-and-Switch Molecular Recognition in Nucleic Acid Sensors",

abstract = "We investigate the properties of a simple DNA-based nanodevice capable of detecting single nucleotide polymorphisms (SNPs) in unlabelled nucleic acid target sequences. Detection is achieved by a two-stage bait-and-switch process combining complementary-base hybridization and switching as molecular recognition criteria. A probe molecule is constructed from a single DNA strand designed to adopt a partial cruciform structure with a pair of exposed (unhybridized) strands. Upon target binding, a switchable cloverleaf construct (similar to a Holliday junction) is formed where the states are the open and closed junction conformations. Switching between these occurs by junction folding in the presence of divalent ions. A combination of steady-state and time-resolved fluorescence spectroscopy is used to measure Forster resonance energy transfer.",

keywords = "Biosensor, FRET, single nucleotide polymorphisms, fluorescence lifetime, DNA, JUNCTION",

author = "Nishimura, {Mira K. Y.} and McGuinness, {Colin D.} and David Keszenman-Pereyra and Paul Dickinson and Campbell, {Cohn J.} and Bachmann, {Till T.} and Peter Ghazal and Jason Crain and Colin Campbell",

year = "2009",

language = "English",

isbn = "978-1-4244-4411-3",

pages = "915--920",

booktitle = "2009 SYMPOSIUM ON PHOTONICS AND OPTOELECTRONICS (SOPO 2009)",

publisher = "Institute of Electrical and Electronics Engineers",

address = "United States",

}

Bait-and-Switch Molecular Recognition in Nucleic Acid Sensors. / Nishimura, Mira K. Y.; McGuinness, Colin D.; Keszenman-Pereyra, David et al.
2009 SYMPOSIUM ON PHOTONICS AND OPTOELECTRONICS (SOPO 2009). NEW YORK: Institute of Electrical and Electronics Engineers, 2009. p. 915-920.

Research output: Chapter in Book/Report/Conference proceeding › Conference contribution

TY - GEN

T1 - Bait-and-Switch Molecular Recognition in Nucleic Acid Sensors

AU - Nishimura, Mira K. Y.

AU - McGuinness, Colin D.

AU - Keszenman-Pereyra, David

AU - Dickinson, Paul

AU - Campbell, Cohn J.

AU - Bachmann, Till T.

AU - Ghazal, Peter

AU - Crain, Jason

AU - Campbell, Colin

PY - 2009

Y1 - 2009

N2 - We investigate the properties of a simple DNA-based nanodevice capable of detecting single nucleotide polymorphisms (SNPs) in unlabelled nucleic acid target sequences. Detection is achieved by a two-stage bait-and-switch process combining complementary-base hybridization and switching as molecular recognition criteria. A probe molecule is constructed from a single DNA strand designed to adopt a partial cruciform structure with a pair of exposed (unhybridized) strands. Upon target binding, a switchable cloverleaf construct (similar to a Holliday junction) is formed where the states are the open and closed junction conformations. Switching between these occurs by junction folding in the presence of divalent ions. A combination of steady-state and time-resolved fluorescence spectroscopy is used to measure Forster resonance energy transfer.

AB - We investigate the properties of a simple DNA-based nanodevice capable of detecting single nucleotide polymorphisms (SNPs) in unlabelled nucleic acid target sequences. Detection is achieved by a two-stage bait-and-switch process combining complementary-base hybridization and switching as molecular recognition criteria. A probe molecule is constructed from a single DNA strand designed to adopt a partial cruciform structure with a pair of exposed (unhybridized) strands. Upon target binding, a switchable cloverleaf construct (similar to a Holliday junction) is formed where the states are the open and closed junction conformations. Switching between these occurs by junction folding in the presence of divalent ions. A combination of steady-state and time-resolved fluorescence spectroscopy is used to measure Forster resonance energy transfer.

KW - Biosensor

KW - FRET

KW - single nucleotide polymorphisms

KW - fluorescence lifetime

KW - DNA

KW - JUNCTION

UR - http://www.scopus.com/inward/record.url?scp=70350520865&partnerID=8YFLogxK

M3 - Conference contribution

SN - 978-1-4244-4411-3

SP - 915

EP - 920

BT - 2009 SYMPOSIUM ON PHOTONICS AND OPTOELECTRONICS (SOPO 2009)

PB - Institute of Electrical and Electronics Engineers

CY - NEW YORK

ER -

Bait-and-Switch Molecular Recognition in Nucleic Acid Sensors

Abstract / Description of output

Keywords / Materials (for Non-textual outputs)

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