12,761 research outputs found
Electrically Guided DNA Immobilization and Multiplexed DNA Detection with Nanoporous Gold Electrodes.
Molecular diagnostics have significantly advanced the early detection of diseases, where the electrochemical sensing of biomarkers (e.g., DNA, RNA, proteins) using multiple electrode arrays (MEAs) has shown considerable promise. Nanostructuring the electrode surface results in higher surface coverage of capture probes and more favorable orientation, as well as transport phenomena unique to nanoscale, ultimately leading to enhanced sensor performance. The central goal of this study is to investigate the influence of electrode nanostructure on electrically-guided immobilization of DNA probes for nucleic acid detection in a multiplexed format. To that end, we used nanoporous gold (np-Au) electrodes that reduced the limit of detection (LOD) for DNA targets by two orders of magnitude compared to their planar counterparts, where the LOD was further improved by an additional order of magnitude after reducing the electrode diameter. The reduced electrode diameter also made it possible to create a np-Au MEA encapsulated in a microfluidic channel. The electro-grafting reduced the necessary incubation time to immobilize DNA probes into the porous electrodes down to 10 min (25-fold reduction compared to passive immobilization) and allowed for grafting a different DNA probe sequence onto each electrode in the array. The resulting platform was successfully used for the multiplexed detection of three different biomarker genes relevant to breast cancer diagnosis
An ultrasensitive photoelectrochemical nucleic acid biosensor
A simple and ultrasensitive procedure for non-labeling detection of nucleic acids is described in this study. It is based on the photoelectrochemical detection of target nucleic acids by forming a nucleic acid/photoreporter adduct layer on an ITO electrode. The target nucleic acids were hybridized with immobilized oligonucleotide capture probes on the ITO electrode. A subsequent binding of a photoreporter—a photoactive threading bis-intercalator consisting of two N,N′-bis(3-propyl-imidazole)-1,4,5,8-naphthalene diimides (PIND) linked by a [Formula: see text] (bpy = 2,2′-bipyridine) complex (PIND–Ru–PIND)—allowed for photoelectrochemical detection of the target nucleic acids. The extremely low dissociation rate of the adduct and the highly reversible photoelectrochemical response under visible light illumination (490 nm) make it possible to conduct nucleic acid detection, with a sensitivity enhancement of four orders of magnitude over voltammetry. These results demonstrate for the first time the potential of photoelectrochemical biosensors for PCR-free ultrasensitive detection of nucleic acids
A novel cassette method for probe evaluation in the designed biochips
A critical step in biochip design is the selection of probes with identical hybridisation characteristics. In this article we describe a novel method for evaluating DNA hybridisation probes, allowing the fine-tuning of biochips, that uses cassettes with multiple probes. Each cassette contains probes in equimolar proportions so that their hybridisation performance can be assessed in a single reaction. The model used to demonstrate this method was a series of probes developed to detect TORCH pathogens. DNA probes were designed for Toxoplasma gondii, Chlamidia trachomatis, Rubella, Cytomegalovirus, and Herpes virus and these were used to construct the DNA cassettes. Five cassettes were constructed to detect TORCH pathogens using a variety of genes coding for membrane proteins, viral matrix protein, an early expressed viral protein, viral DNA polymerase and the repetitive gene B1 of Toxoplasma gondii. All of these probes, except that for the B1 gene, exhibited similar profiles under the same hybridisation conditions. The failure of the B1 gene probe to hybridise was not due to a position effect, and this indicated that the probe was unsuitable for inclusion in the biochip. The redesigned probe for the B1 gene exhibited identical hybridisation properties to the other probes, suitable for inclusion in a biochip
Nanostructured luminescently labeled nucleic acids
Important and emerging trends at the interface of luminescence, nucleic acids and nanotechnology
are: (i) the conventional luminescence labeling of nucleic acid nanostructures (e.g. DNA tetrahedron);
(ii) the labeling of bulk nucleic acids (e.g. single‐stranded DNA, double‐stranded DNA) with
nanostructured luminescent labels (e.g. copper nanoclusters); and (iii) the labeling of nucleic acid
nanostructures (e.g. origami DNA) with nanostructured luminescent labels (e.g. silver
nanoclusters). This review surveys recent advances in these three different approaches to the
generation of nanostructured luminescently labeled nucleic acids, and includes both direct and
indirect labeling methods
A cellulose-based bioassay for the colorimetric detection of pathogen DNA
Cellulose-paper-based colorimetric bioassays may be used at the point of sampling without sophisticated equipment. This study reports the development of a colorimetric bioassay based on cellulose that can detect pathogen DNA. The detection was based on covalently attached single-stranded DNA probes and visual analysis. A cellulose surface functionalized with tosyl groups was prepared by the N,N-dimethylacetamide-lithium chloride method. Tosylation of cellulose was confirmed by scanning electron microscopy, Fourier transform infrared spectroscopy and elemental analysis. Sulfhydryl-modified oligonucleotide probes complementary to a segment of the DNA sequence IS6110 of Mycobacterium tuberculosis were covalently immobilized on the tosylated cellulose. On hybridization of biotin-labelled DNA oligonucleotides with these probes, a colorimetric signal was obtained with streptavidin-conjugated horseradish peroxidase catalysing the oxidation of tetramethylbenzamidine by H2O2. The colour intensity was significantly reduced when the bioassay was subjected to DNA oligonucleotide of randomized base composition. Initial experiments have shown a sensitivity of 0.1 μM. A high probe immobilization efficiency (more than 90 %) was observed with a detection limit of 0.1 μM, corresponding to an absolute amount of 10 pmol. The detection of M. tuberculosis DNA was demonstrated using this technique coupled with PCR for biotinylation of the DNA. This work shows the potential use of tosylated cellulose as the basis for point-of-sampling bioassays.Peer reviewedFinal Accepted Versio
Crowding-induced hybridization of single DNA hairpins
It is clear that a crowded environment influences the structure, dynamics, and interactions of biological molecules, but the complexity of this phenomenon demands the development of new experimental and theoretical approaches. Here we use two complementary single-molecule FRET techniques to show that the kinetics of DNA base pairing and unpairing, which are fundamental to both the biological role of DNA and its technological applications, are strongly modulated by a crowded environment. We directly observed single DNA hairpins, which are excellent model systems for studying hybridization, either freely diffusing in solution or immobilized on a surface under crowding conditions. The hairpins followed two-state folding dynamics with a closing rate increasing by 4-fold and the opening rate decreasing 2-fold, for only modest concentrations of crowder [10% (w/w) polyethylene glycol (PEG)]. These experiments serve both to unambiguously highlight the impact of a crowded environment on a fundamental biological process, DNA base pairing, and to illustrate the benefits of single-molecule approaches to probing the structure and dynamics of complex biomolecular systems
Nanophotonic waveguide enhanced Raman spectroscopy of biological submonolayers
Characterizing a monolayer of biological molecules has been a major
challenge. We demonstrate nanophotonic wave-guide enhanced Raman spectroscopy
(NWERS) of monolayers in the near-infrared region, enabling real-time
measurements of the hybridization of DNA strands and the density of
sub-monolayers of biotin-streptavidin complex immobilized on top of a photonics
chip. NWERS is based on enhanced evanescent excitation and collection of
spontaneous Raman scattering near nanophotonic waveguides, which for a one
centimeter silicon nitride waveguide delivers a signal that is more than four
orders of magnitude higher in comparison to a confocal Raman microscope. The
reduced acquisition time and specificity of the signal allows for a
quantitative and real-time characterization of surface species, hitherto not
possible using Raman spectroscopy. NWERS provides a direct analytic tool for
monolayer research and also opens a route to compact microscope-less
lab-on-a-chip devices with integrated sources, spectrometers and detectors
fabricated using a mass-producible CMOS technology platform
Physico-chemical foundations underpinning microarray and next-generation sequencing experiments
Hybridization of nucleic acids on solid surfaces is a key process involved in high-throughput technologies such as microarrays and, in some cases, next-generation sequencing (NGS). A physical understanding of the hybridization process helps to determine the accuracy of these technologies. The goal of a widespread research program is to develop reliable transformations between the raw signals reported by the technologies and individual molecular concentrations from an ensemble of nucleic acids. This research has inputs from many areas, from bioinformatics and biostatistics, to theoretical and experimental biochemistry and biophysics, to computer simulations. A group of leading researchers met in Ploen Germany in 2011 to discuss present knowledge and limitations of our physico-chemical understanding of high-throughput nucleic acid technologies. This meeting inspired us to write this summary, which provides an overview of the state-of-the-art approaches based on physico-chemical foundation to modeling of the nucleic acids hybridization process on solid surfaces. In addition, practical application of current knowledge is emphasized
Nucleic acids and protein synthesis in cancer cell mitochondria. I. Nucleic acids in rat hepatoma mitochondria
The contents of nucleic acids in rat liver and hepatoma mitochondria and the physico-chemical properties on DNA's isolated from these mitochondria were comparatively investigated. The results are briefly summarized as follows. 1. The contents of DNA and RNA per mg protein of the hepatoma cell mitochondria were about 10 and 2 to 4 times higher than those of rat liver mitochondria, respectively. 2. The λ max. and λmin. values of DNA isolated from the hepatoma mitochondria were 257 mμ and 231 mμ, respectively and those of DNA isolated
from the nuclei were 259 mμ and 233 mμ, respectively, in saline-citrate, pH 7.0. 3. Three fractions of mitochondrial DNA were obtained by the sucrose
density gradient and these DNA fractions corresponded, probably, to about 30 S, and 20 S and 14 S DNA's. 4. There was little difference in base compositions between nuclear and mitochondrial DNA's of the hepatoma cells.
5. The degree of hybridization between the nuclear and mitochondrial DNA's of the hepatoma cells was almost the same as that between the nuclear and nuclear DNA's of the hepatoma cells, and somewhat higher than that between
the nuclear DNA of rat liver and the nuclear DNA of hepatoma cells. 6. "Highly twisted" circular, "open" circular and linear forms were observed in the DNA preparations of the hepatoma mitochondria. The average
values of contour lengths of rat liver and the hepatoma DNA's observed at high frequency were 5.3 μ and 4.5 μ. 7. A discussion was made on the relation between the genetic informations of mitochondrial DNA and the formation of a mitochondrion in rat liver and
the hepatoma cells.</p
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