Multiplexed detection of pathogen DNA with DNA-based fluorescence nanobarcodes

Li, Yougen; Cu, Yen; Luo, Dan

doi:10.1038/nbt1106

Cited by 475 publications

(348 citation statements)

References 30 publications

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“…Currently available methods for the detection of microbiological threats utilize specific enrichment media to separate, identify and count bacterial cells 26 . Alternatively, PCR 34 and DNA-based nanobarcode 35 detection strategies have proven to be fast and highly sensitive, but such methods require pretreatment and cell lysis to extract DNA. An alternative strategy is the development of methods that allow for direct and sensitive detection of whole microbial cells or endotoxins.…”

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confidence: 99%

Graphene-based wireless bacteria detection on tooth enamel

et al. 2012

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Direct interfacing of nanosensors onto biomaterials could impact health quality monitoring and adaptive threat detection. Graphene is capable of highly sensitive analyte detection due to its nanoscale nature. Here we show that graphene can be printed onto water-soluble silk. This in turn permits intimate biotransfer of graphene nanosensors onto biomaterials, including tooth enamel. The result is a fully biointerfaced sensing platform, which can be tuned to detect target analytes. For example, via self-assembly of antimicrobial peptides onto graphene, we show bioselective detection of bacteria at single-cell levels. Incorporation of a resonant coil eliminates the need for onboard power and external connections. Combining these elements yields two-tiered interfacing of peptide-graphene nanosensors with biomaterials. In particular, we demonstrate integration onto a tooth for remote monitoring of respiration and bacteria detection in saliva. overall, this strategy of interfacing graphene nanosensors with biomaterials represents a versatile approach for ubiquitous detection of biochemical targets.

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confidence: 99%

Graphene-based wireless bacteria detection on tooth enamel

et al. 2012

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“…DNA was identified with DAPI (blue for A-C and E; gray for D Importantly, the primer sequences retained in the probe provide general strategies for coupling a wide variety of functionalities to bioinformatically designed oligo libraries, thereby extending the potential usefulness of Oligopaints. Functionalities can be attached directly to primers and incorporated into the probe during amplification, or they can be brought in by the hybridization of a secondary oligo (48,50,51) that is homologous to the primer sequence; either way, significant cost savings can be achieved by bulk orders of modified oligos that can then be applied to any number of libraries. The availability of primer sequences further opens opportunities for bringing in functionalities via DNA binding factors or assembling DNA structures, such as those used in branched signal amplification (11,27).…”

Section: Discussionmentioning

confidence: 99%

Versatile design and synthesis platform for visualizing genomes with Oligopaint FISH probes

Beliveau

Joyce

Apostolopoulos

et al. 2012

Proc. Natl. Acad. Sci. U.S.A.

410

472

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A host of observations demonstrating the relationship between nuclear architecture and processes such as gene expression have led to a number of new technologies for interrogating chromosome positioning. Whereas some of these technologies reconstruct intermolecular interactions, others have enhanced our ability to visualize chromosomes in situ. Here, we describe an oligonucleotide-and PCR-based strategy for fluorescence in situ hybridization (FISH) and a bioinformatic platform that enables this technology to be extended to any organism whose genome has been sequenced. The oligonucleotide probes are renewable, highly efficient, and able to robustly label chromosomes in cell culture, fixed tissues, and metaphase spreads. Our method gives researchers precise control over the sequences they target and allows for single and multicolor imaging of regions ranging from tens of kilobases to megabases with the same basic protocol. We anticipate this technology will lead to an enhanced ability to visualize interphase and metaphase chromosomes.T he role of chromosome positioning in gene regulation and chromosome stability is fueling a growing interest in technologies that reveal the in situ organization of the genome. Among these technologies are chromosome conformation capture (3C) (1) and its several iterations, such as Hi-C (2), which are applied to populations of nuclei to identify chromosomal regions that are in close proximity to each other (3, 4). Another technology is fluorescence in situ hybridization (FISH), wherein nucleic acids are targeted by fluorescently labeled probes and then visualized via microscopy; this technology is an extension of methods that once used radioactive probes and autoradiography but have since been adapted to use nonradioactive labels (5-11). FISH is a single-cell assay, making it especially powerful for the detection of rare events that might otherwise be lost in mixed or asynchronous populations of cells. In addition, because FISH is applied to fixed cells, it can reveal the positioning of chromosomes relative to nuclear, cytoplasmic, and even tissue structures. FISH can also be used to visualize RNA, permitting the simultaneous assessment of gene expression, chromosome position, and protein localization.FISH probes are typically derived from cloned genomic regions or flow-sorted chromosomes, which are labeled directly via nick translation or PCR in the presence of fluorophore-conjugated nucleotides or labeled indirectly with nucleotide-conjugated haptens, such as biotin and digoxigenin, and then visualized with secondary detection reagents. Probe DNA is often fragmented into ∼150-to 250-bp pieces to facilitate its penetration into fixed cells (12) and, as many genomic clones contain repetitive sequences that occur abundantly in the genome, hybridization is typically performed in the presence of unlabeled repetitive DNA (13). Another limitation to clone-based probes is that the genomic regions that can be visualized with them are restricted by the availability of clones and the size of ...

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“…Optical multiplexing has applications in broad areas including information technologies 1,2 , high-throughput clinical diagnostics [3][4][5] , multichannel bioimaging 6 and anti-counterfeitng 7 , as it enables high data-storage capacity, simultaneous identification and quantification of multiple species, multiple target registration, improved encryption, and so on. In optical multiplexing techniques, the optical encoding dimensions play a fundamental role, in which multiple unique codes are generated.…”

Section: Introductionmentioning

confidence: 99%

Phase angle encoded upconversion luminescent nanocrystals for multiplexing applications

et al. 2017

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Lanthanide-doped upconversion nanoparticles (UCNPs) are increasingly used as luminescent candidates in multiplexed applications due to their excellent optical properties. Inthepast,several encodingidentities havebeen proposedforUCNPs,includingemissioncolour,intensity ratio between different emissionbands, colourspatial distribution, and luminescencelifetime.In this paper, a new optical encoding dimension for upconversion nanomaterials is developed by exploring their luminescence kinetics, i.e., the phase angle of upconversion luminescence in response to a harmonic-wave excitation. Our theoretical derivation shows that the phase angle is governed jointly by the rise and decay times, characterizing the upconversion luminescence kinetics. Experimentally, a full set of methods are developed to manage the upconversion luminescence kinetics, through which the rise and decay times can be manipulated dependently or independently. Furthermore,a large phase-angle space is achieved in which tens of unique codes can be potentially generated in the same colour channel. Our work greatly extends the multiplexing capacity of UCNPs,and offers newopportunities for their applicationsin a wide range such as microarray assays, bioimaging, anti-counterfeiting, deep tissue multiplexed labelling/detectionand high-density data storage.In addition, the development of thisluminescence kinetics-based optical encoding strategy is also instructive for developing multiplexing techniques using other cascade luminescent systems that inherently lack multi-spectral channels, such as triplet-triplet annihilation molecule pairs.

QC 20170330

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Multiplexed detection of pathogen DNA with DNA-based fluorescence nanobarcodes

Cited by 475 publications

References 30 publications

Graphene-based wireless bacteria detection on tooth enamel

Graphene-based wireless bacteria detection on tooth enamel

Versatile design and synthesis platform for visualizing genomes with Oligopaint FISH probes

Phase angle encoded upconversion luminescent nanocrystals for multiplexing applications

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