The bio-barcode assay for the detection of protein and nucleic acid targets using DTT-induced ligand exchange

Hill, Haley D.; Mirkin, Chad A.

doi:10.1038/nprot.2006.51

Cited by 558 publications

(480 citation statements)

References 16 publications

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“…37. Before AuNP conjugation, 5Ј-thiol terminated oligonucleotides (DNA sequence 1) were reduced with DTT (obtained from Sigma-Aldrich), then purified using a NAP5 column (Amersham Pharmacia).…”

Section: Methodsmentioning

confidence: 99%

Assembly and organization processes in DNA-directed colloidal crystallization

Macfarlane

Lee

Hill

et al. 2009

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

146

143

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We present an analysis of the key steps involved in the DNAdirected assembly of nanoparticles into crystallites and polycrystalline aggregates. Additionally, the rate of crystal growth as a function of increased DNA linker length, solution temperature, and self-complementary versus non-self-complementary DNA linker strands (1-versus 2-component systems) has been studied. The data show that the crystals grow via a 3-step process: an initial ''random binding'' phase resulting in disordered DNA-AuNP aggregates, followed by localized reorganization and subsequent growth of crystalline domain size, where the resulting crystals are well-ordered at all subsequent stages of growth.DNA materials ͉ SAXS ͉ self assembly T he chemical and physical properties of most materials are determined by the placement of individual atoms relative to one another (1-4). These atom-atom interactions include forces such as covalent and ionic bonds, Van der Waals forces and London dispersion forces. However, in the field of nanomaterials, the length scales of particle assembly are significantly larger and the assembly process is governed by a more complicated set of interactions (5-7). The tailorable arrangement of nanoscale materials through directed-mechanisms has proven to be the most practical method to create ordered arrangements of nanoparticles in solution (8-15); crystalline nanoparticle aggregates have potential implications for the development of materials with unique plasmonic (16, 17), photonic (18, 19), electrical (20), and magnetic properties (21). Previous strategies developed to create well-ordered nanoscale assemblies have used electrostatic interactions (11, 12), hydrogen bonding networks (10, 13), and peptide recognition properties (9). Over a decade ago, we introduced the concept of synthetically programmable particle assembly through the use of DNA and polyvalent oligonucleotide nanoparticle conjugates (22). Recently, we (23,24) and the Gang group (25) independently used these principles to construct highly-ordered nanoparticle crystallites via DNA hybridization, where crystal type and lattice parameters can be programmed through design of DNA linker.The formation of these crystals involves multiple types of molecular interactions that are highly dependent and predictable based on the DNA base sequence (22,(26)(27)(28), where the hybridization of the DNA linkers drives the crystallization process. Moreover, the ultimate structure formed is typically the one that maximizes the number of hybridization events, and therefore, if enough thermal energy is provided, the system will typically equilibrate to this structure (23,25,29,30). Indeed, only highly-ordered crystalline aggregates present the thermodynamically most stable arrangement of nanoparticles, because they allow for a maximum of nearestneighbor complementary DNA interactions.Previous work has shown that the complexity of the nanoparticle systems studied thus far necessitates significant thermal annealing to create the thermodynamically favorable crystal structu...

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Section: Methodsmentioning

confidence: 99%

Assembly and organization processes in DNA-directed colloidal crystallization

Macfarlane

Lee

Hill

et al. 2009

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

146

143

View full text Add to dashboard Cite

show abstract

“…Indeed, it takes 3 days to execute all the steps; of that time, approximately 14 h is active and the rest is incubation time (Hill and Mirkin, 2006). Other versions of the assay have been reported with an assay time of 90 minutes but with a lower sensitivity (around 300 aM) (Oh et al, 2006).…”

Section: Technology Commercializationmentioning

confidence: 99%

“…One of the technologies currently in market is the BioBarcode technology (Hill and Mirkin, 2006). This is considered to be the most sensitive biological assay capable of detecting proteins and oligonucleotides in the attomolar concentration range.…”

Section: Technology Commercializationmentioning

confidence: 99%

Post-Genomics Nanotechnology Is Gaining Momentum: Nanoproteomics and Applications in Life Sciences

Kobeissy

Gülbakan

Alawieh

et al. 2014

OMICS: A Journal of Integrative Biology

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The post-genomics era has brought about new Omics biotechnologies, such as proteomics and metabolomics, as well as their novel applications to personal genomics and the quantified self. These advances are now also catalyzing other and newer post-genomics innovations, leading to convergences between Omics and nanotechnology. In this work, we systematically contextualize and exemplify an emerging strand of post-genomics life sciences, namely, nanoproteomics and its applications in health and integrative biological systems. Nanotechnology has been utilized as a complementary component to revolutionize proteomics through different kinds of nanotechnology applications, including nanoporous structures, functionalized nanoparticles, quantum dots, and polymeric nanostructures. Those applications, though still in their infancy, have led to several highly sensitive diagnostics and new methods of drug delivery and targeted therapy for clinical use. The present article differs from previous analyses of nanoproteomics in that it offers an in-depth and comparative evaluation of the attendant biotechnology portfolio and their applications as seen through the lens of post-genomics life sciences and biomedicine. These include: (1) immunosensors for inflammatory, pathogenic, and autoimmune markers for infectious and autoimmune diseases, (2) amplified immunoassays for detection of cancer biomarkers, and (3) methods for targeted therapy and automatically adjusted drug delivery such as in experimental stroke and brain injury studies. As nanoproteomics becomes available both to the clinician at the bedside and the citizens who are increasingly interested in access to novel post-genomics diagnostics through initiatives such as the quantified self, we anticipate further breakthroughs in personalized and targeted medicine.

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“…39 Briefly, 4 nanomoles of freshly reduced thiolated DNA was added to 1 mL of 13 ± 2 nm gold nanoparticles and shaken gently overnight. The system was buffered to a phosphate concentration of 10 mM (pH 7.0) including 0.01 percent sodium dodecyl sulfate (SDS).…”

Section: Gold Nanoparticle Functionalization With Dnamentioning

confidence: 99%

“…17,39 Briefly, 2.8 μm amine-functionalized magnetic microparticles (Dynal Corp/Invitrogen) were coupled to thiolated oligonucleotide strands using the hetero-bi-functional crosslinker sulfo-SMPB (Pierce Biotechnology). Unreacted amine sites were passivated with sulfo-NHS acetate (Pierce Biotechnology).…”

Section: Magnetic Particle Functionalization With Dnamentioning

confidence: 99%

Nonenzymatic Detection of Bacterial Genomic DNA Using the Bio Bar Code Assay

2007

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The detection of bacterial genomic DNA through a non-enzymatic nanomaterials based amplification method, the bio-barcode assay, is reported. The assay utilizes oligonucleotide functionalized magnetic microparticles to capture the target of interest from the sample. A critical step in the new assay involves the use of blocking oligonucleotides during heat denaturation of the double stranded DNA. These blockers bind to specific regions of the target DNA upon cooling, and prevent the duplex DNA from re-hybridizing, which allows the particle probes to bind. Following target isolation using the magnetic particles, oligonucleotide functionalized gold nanoparticles act as target recognition agents. The oligonucleotides on the nanoparticle (barcodes) act as amplification surrogates. The barcodes are then detected using the Scanometric method. The limit of detection for this assay was determined to be 2.5 femtomolar, and this is the first demonstration of a barcode type assay for the detection of double stranded, genomic DNA.

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The bio-barcode assay for the detection of protein and nucleic acid targets using DTT-induced ligand exchange

Cited by 558 publications

References 16 publications

Assembly and organization processes in DNA-directed colloidal crystallization

Assembly and organization processes in DNA-directed colloidal crystallization

Post-Genomics Nanotechnology Is Gaining Momentum: Nanoproteomics and Applications in Life Sciences

Nonenzymatic Detection of Bacterial Genomic DNA Using the Bio Bar Code Assay

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