Exonuclease III-Assisted Upconversion Resonance Energy Transfer in a Wash-Free Suspension DNA Assay

Chen, Y; Duong, HTT; Wen, S; Mi, C; Zhou, Y; Shimoni, O; Valenzuela, SM; Jin, D

Exonuclease III-Assisted Upconversion Resonance Energy Transfer in a Wash-Free Suspension DNA Assay

Chen, Y

Duong, HTT

Wen, S

Mi, C Zhou, Y Shimoni, O

Valenzuela, SM

Jin, D

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Publication Type:: Journal Article
Citation:: Analytical Chemistry, 2018, 90 (1), pp. 663 - 668
Issue Date:: 2018-01-02

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Field	Value	Language
dc.contributor.author	Chen, Y https://orcid.org/0000-0002-7886-7144	en_US
dc.contributor.author	Duong, HTT https://orcid.org/0000-0003-2224-2046	en_US
dc.contributor.author	Wen, S https://orcid.org/0000-0002-4670-4658	en_US
dc.contributor.author	Mi, C	en_US
dc.contributor.author	Zhou, Y	en_US
dc.contributor.author	Shimoni, O https://orcid.org/0000-0001-8822-1024	en_US
dc.contributor.author	Valenzuela, SM https://orcid.org/0000-0001-5934-6047	en_US
dc.contributor.author	Jin, D https://orcid.org/0000-0003-1046-2666	en_US
dc.date.available	2020-05-25T19:10:11Z
dc.date.issued	2018-01-02	en_US
dc.identifier.citation	Analytical Chemistry, 2018, 90 (1), pp. 663 - 668	en_US
dc.identifier.issn	0003-2700	en_US
dc.identifier.uri	http://hdl.handle.net/10453/124672
dc.description.abstract	© 2017 American Chemical Society. Sensitivity is the key in optical detection of low-abundant analytes, such as circulating RNA or DNA. The enzyme Exonuclease III (Exo III) is a useful tool in this regard; its ability to recycle target DNA molecules results in markedly improved detection sensitivity. Lower limits of detection may be further achieved if the detection background of autofluorescence can be removed. Here we report an ultrasensitive and specific method to quantify trace amounts of DNA analytes in a wash-free suspension assay. In the presence of target DNA, the Exo III recycles the target DNA by selectively digesting the dye-tagged sequence-matched probe DNA strand only, so that the amount of free dye removed from the probe DNA is proportional to the number of target DNAs. Remaining intact probe DNAs are then bound onto upconversion nanoparticles (energy donor), which allows for upconversion luminescence resonance energy transfer (LRET) that can be used to quantify the difference between the free dye and tagged dye (energy acceptor). This scheme simply avoids both autofluorescence under infrared excitation and many tedious washing steps, as the free dye molecules are physically located away from the nanoparticle surface, and as such they remain "dark" in suspension. Compared to alternative approaches requiring enzyme-assisted amplification on the nanoparticle surface, introduction of probe DNAs onto nanoparticles only after DNA hybridization and signal amplification steps effectively avoids steric hindrance. Via this approach, we have achieved a detection limit of 15 pM in LRET assays of human immunodeficiency viral DNA.	en_US
dc.relation	http://purl.org/au-research/grants/nhmrc/APP1101258
dc.relation	http://purl.org/au-research/grants/arc/IH150100028
dc.relation	http://purl.org/au-research/grants/arc/FT130100517
dc.relation.ispartof	Analytical Chemistry	en_US
dc.relation.isbasedon	10.1021/acs.analchem.7b04240	en_US
dc.subject.classification	Analytical Chemistry	en_US
dc.subject.mesh	HIV	en_US
dc.subject.mesh	Rhodamines	en_US
dc.subject.mesh	Exodeoxyribonucleases	en_US
dc.subject.mesh	DNA, Viral	en_US
dc.subject.mesh	Fluorescent Dyes	en_US
dc.subject.mesh	Biological Assay	en_US
dc.subject.mesh	Nucleic Acid Amplification Techniques	en_US
dc.subject.mesh	Nucleic Acid Hybridization	en_US
dc.subject.mesh	Light	en_US
dc.subject.mesh	Metal Nanoparticles	en_US
dc.subject.mesh	Limit of Detection	en_US
dc.title	Exonuclease III-Assisted Upconversion Resonance Energy Transfer in a Wash-Free Suspension DNA Assay	en_US
dc.type	Journal Article
utslib.citation.volume	1	en_US
utslib.citation.volume	90	en_US
utslib.for	0301 Analytical Chemistry	en_US
utslib.for	0904 Chemical Engineering	en_US
utslib.for	0399 Other Chemical Sciences	en_US
pubs.embargo.period	Not known	en_US
pubs.organisational-group	/University of Technology Sydney
pubs.organisational-group	/University of Technology Sydney/Faculty of Science
pubs.organisational-group	/University of Technology Sydney/Faculty of Science/School of Life Sciences
pubs.organisational-group	/University of Technology Sydney/Faculty of Science/School of Mathematical and Physical Sciences
pubs.organisational-group	/University of Technology Sydney/Strength - CHT - Health Technologies
pubs.organisational-group	/University of Technology Sydney/Strength - IBMD - Initiative for Biomedical Devices
pubs.organisational-group	/University of Technology Sydney/Students
utslib.copyright.status	open_access
pubs.issue	1	en_US
pubs.publication-status	Published	en_US
pubs.volume	90	en_US

Abstract:

© 2017 American Chemical Society. Sensitivity is the key in optical detection of low-abundant analytes, such as circulating RNA or DNA. The enzyme Exonuclease III (Exo III) is a useful tool in this regard; its ability to recycle target DNA molecules results in markedly improved detection sensitivity. Lower limits of detection may be further achieved if the detection background of autofluorescence can be removed. Here we report an ultrasensitive and specific method to quantify trace amounts of DNA analytes in a wash-free suspension assay. In the presence of target DNA, the Exo III recycles the target DNA by selectively digesting the dye-tagged sequence-matched probe DNA strand only, so that the amount of free dye removed from the probe DNA is proportional to the number of target DNAs. Remaining intact probe DNAs are then bound onto upconversion nanoparticles (energy donor), which allows for upconversion luminescence resonance energy transfer (LRET) that can be used to quantify the difference between the free dye and tagged dye (energy acceptor). This scheme simply avoids both autofluorescence under infrared excitation and many tedious washing steps, as the free dye molecules are physically located away from the nanoparticle surface, and as such they remain "dark" in suspension. Compared to alternative approaches requiring enzyme-assisted amplification on the nanoparticle surface, introduction of probe DNAs onto nanoparticles only after DNA hybridization and signal amplification steps effectively avoids steric hindrance. Via this approach, we have achieved a detection limit of 15 pM in LRET assays of human immunodeficiency viral DNA.

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http://hdl.handle.net/10453/124672