Functional Nucleic Acid Sensors
About: This article is published in Chemical Reviews.The article was published on 2009-03-20 and is currently open access. It has received 1915 citations till now. The article focuses on the topics: Nucleic acid methods & Nucleic acid.
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TL;DR: A single-layer MoS2 nanosheet exhibits high fluorescence quenching ability and different affinity toward ssDNA versus dsDNA and has been successfully used as a sensing platform for the detection of DNA and small molecules.
Abstract: A single-layer MoS2 nanosheet exhibits high fluorescence quenching ability and different affinity toward ssDNA versus dsDNA. As a proof of concept, the MoS2 nanosheet has been successfully used as a sensing platform for the detection of DNA and small molecules.
961 citations
TL;DR: This critical review presents the active and/or emerging areas of ECL research as well as new applications and phenomena of ECR, such as light-emitting electrochemical cell, wireless electrochemical microarray, and single molecule detection.
Abstract: Electrochemiluminescence (ECL) is chemiluminescence triggered by electrochemical techniques. More than 150 ECL assays with remarkably high sensitivity and extremely wide dynamic range are currently available, and accounts for hundreds of millions of dollars in sales per year. The recent development of ECL is particularly rapid. After a brief introduction to ECL, this critical review presents the active and/or emerging areas of ECL research as well as new applications and phenomena of ECL, such as light-emitting electrochemical cell, wireless electrochemical microarray using ECL as photonic reporter, high throughput analysis, aptasensors, immunoassays and DNA analysis, ECL of nanoclusters and carbon nanomaterials, ECL imaging techniques, scanning ECL microscopy, colorimetric ECL sensor, surface plasmon-coupled ECL, electrostatic chemiluminescence, soliton-like ECL waves, ECL investigation of molecular interaction, and single molecule detection. Finally, some perspectives on this rapidly developing field are discussed (322 references).
901 citations
TL;DR: This review presents the working principles and reaction mechanism of paper-based diagnostics, including dipstick assays, lateral flow assays (LFAs), and microfluidic paper- based analytical devices (μPADs), as well as the selection of substrates and fabrication methods.
796 citations
Cites background from "Functional Nucleic Acid Sensors"
...Functional nucleic acids, including DNAzymes, aptamers and aptazymes, are nucleic acids which have functions not limited to nucleic acid hybridization (Liu et al., 2009)....
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TL;DR: In this paper, the authors focus on recent advances on controllable synthesis and fuel cell and sensing applications of noble metal nanomaterials (NMNs) and present diversified approaches to different types of NMNs-based nanoelectrocatalysts with the aim to enhance their activity and durability for fuel cell reactions.
709 citations
TL;DR: A series of electrochemical and optical nucleic acid sensors that use target-responsive DNA structures that monitor target-induced structural switching of DNA or aptamer-specific small molecule probes by measuring electrochemical currents that are directly associated with the distance between the redox label and the electrode surface.
Abstract: Interest in the development of sensitive, selective, rapid, and cost-effective biosensors for biomedical analysis, environmental monitoring, and the detection of bioterrorism agents is rapidly increasing. A classic biosensor directly transduces ligand−target binding events into a measurable physical readout. More recently, researchers have proposed novel biosensing strategies that couple ligand-induced structural switching of biomolecules with advanced optical and electronic transducers. This approach has proven to be a highly general platform for the development of new biosensors. In this Account, we describe a series of electrochemical and optical nucleic acid sensors that use target-responsive DNA structures. By employing surface-confined DNA structures with appropriate redox labels, we can monitor target-induced structural switching of DNA or aptamer-specific small molecule probes by measuring electrochemical currents that are directly associated with the distance between the redox label and the elect...
681 citations
References
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TL;DR: The objective of this web server is to provide easy access to RNA and DNA folding and hybridization software to the scientific community at large by making use of universally available web GUIs (Graphical User Interfaces).
Abstract: The abbreviated name,‘mfold web server’,describes a number of closely related software applications available on the World Wide Web (WWW) for the prediction of the secondary structure of single stranded nucleic acids. The objective of this web server is to provide easy access to RNA and DNA folding and hybridization software to the scientific community at large. By making use of universally available web GUIs (Graphical User Interfaces),the server circumvents the problem of portability of this software. Detailed output,in the form of structure plots with or without reliability information,single strand frequency plots and ‘energy dot plots’, are available for the folding of single sequences. A variety of ‘bulk’ servers give less information,but in a shorter time and for up to hundreds of sequences at once. The portal for the mfold web server is http://www.bioinfo.rpi.edu/applications/ mfold. This URL will be referred to as ‘MFOLDROOT’.
12,535 citations
TL;DR: High-affinity nucleic acid ligands for a protein were isolated by a procedure that depends on alternate cycles of ligand selection from pools of variant sequences and amplification of the bound species.
Abstract: High-affinity nucleic acid ligands for a protein were isolated by a procedure that depends on alternate cycles of ligand selection from pools of variant sequences and amplification of the bound species. Multiple rounds exponentially enrich the population for the highest affinity species that can be clonally isolated and characterized. In particular one eight-base region of an RNA that interacts with the T4 DNA polymerase was chosen and randomized. Two different sequences were selected by this procedure from the calculated pool of 65,536 species. One is the wild-type sequence found in the bacteriophage mRNA; one is varied from wild type at four positions. The binding constants of these two RNA's to T4 DNA polymerase are equivalent. These protocols with minimal modification can yield high-affinity ligands for any protein that binds nucleic acids as part of its function; high-affinity ligands could conceivably be developed for any target molecule.
9,367 citations
TL;DR: Subpopulations of RNA molecules that bind specifically to a variety of organic dyes have been isolated from a population of random sequence RNA molecules.
Abstract: Subpopulations of RNA molecules that bind specifically to a variety of organic dyes have been isolated from a population of random sequence RNA molecules. Roughly one in 10(10) random sequence RNA molecules folds in such a way as to create a specific binding site for small ligands.
8,781 citations
TL;DR: A method for assembling colloidal gold nanoparticles rationally and reversibly into macroscopic aggregates by using the specificity of DNA interactions to direct the interactions between particles of different size and composition is described.
Abstract: COLLOIDAL particles of metals and semiconductors have potentially useful optical, optoelectronic and material properties1–4 that derive from their small (nanoscopic) size. These properties might lead to applications including chemical sensors, spectro-scopic enhancers, quantum dot and nanostructure fabrication, and microimaging methods2–4. A great deal of control can now be exercised over the chemical composition, size and polydis-persity1,2 of colloidal particles, and many methods have been developed for assembling them into useful aggregates and materials. Here we describe a method for assembling colloidal gold nanoparticles rationally and reversibly into macroscopic aggregates. The method involves attaching to the surfaces of two batches of 13-nm gold particles non-complementary DNA oligo-nucleotides capped with thiol groups, which bind to gold. When we add to the solution an oligonucleotide duplex with 'sticky ends' that are complementary to the two grafted sequences, the nanoparticles self-assemble into aggregates. This assembly process can be reversed by thermal denaturation. This strategy should now make it possible to tailor the optical, electronic and structural properties of the colloidal aggregates by using the specificity of DNA interactions to direct the interactions between particles of different size and composition.
6,188 citations
TL;DR: The small size and capability of these semiconductor nanowires for sensitive, label-free, real-time detection of a wide range of chemical and biological species could be exploited in array-based screening and in vivo diagnostics.
Abstract: Boron-doped silicon nanowires (SiNWs) were used to create highly sensitive, real-time electrically based sensors for biological and chemical species. Amine- and oxide-functionalized SiNWs exhibit pH-dependent conductance that was linear over a large dynamic range and could be understood in terms of the change in surface charge during protonation and deprotonation. Biotin-modified SiNWs were used to detect streptavidin down to at least a picomolar concentration range. In addition, antigen-functionalized SiNWs show reversible antibody binding and concentration-dependent detection in real time. Lastly, detection of the reversible binding of the metabolic indicator Ca2+ was demonstrated. The small size and capability of these semiconductor nanowires for sensitive, label-free, real-time detection of a wide range of chemical and biological species could be exploited in array-based screening and in vivo diagnostics.
5,841 citations