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Biosensors, Volume 3, Issue 2 (June 2013), Pages 185-237

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Review

Open AccessReview DNA/RNA Detection Using DNA-Templated Few-Atom Silver Nanoclusters
Biosensors 2013, 3(2), 185-200; doi:10.3390/bios3020185
Received: 11 March 2013 / Revised: 10 April 2013 / Accepted: 11 April 2013 / Published: 23 April 2013
Cited by 31 | PDF Full-text (350 KB) | HTML Full-text | XML Full-text
Abstract
DNA-templated few-atom silver nanoclusters (DNA/Ag NCs) are a new class of organic/inorganic composite nanomaterials whose fluorescence emission can be tuned throughout the visible and near-IR range by simply programming the template sequences. Compared to organic dyes, DNA/Ag NCs can be brighter and [...] Read more.
DNA-templated few-atom silver nanoclusters (DNA/Ag NCs) are a new class of organic/inorganic composite nanomaterials whose fluorescence emission can be tuned throughout the visible and near-IR range by simply programming the template sequences. Compared to organic dyes, DNA/Ag NCs can be brighter and more photostable. Compared to quantum dots, DNA/Ag NCs are smaller, less prone to blinking on long timescales, and do not have a toxic core. The preparation of DNA/Ag NCs is simple and there is no need to remove excess precursors as these precursors are non-fluorescent. Our recent discovery of the fluorogenic and color switching properties of DNA/Ag NCs have led to the invention of new molecular probes, termed NanoCluster Beacons (NCBs), for DNA detection, with the capability to differentiate single-nucleotide polymorphisms by emission colors. NCBs are inexpensive, easy to prepare, and compatible with commercial DNA synthesizers. Many other groups have also explored and taken advantage of the environment sensitivities of DNA/Ag NCs in creating new tools for DNA/RNA detection and single-nucleotide polymorphism identification. In this review, we summarize the recent trends in the use of DNA/Ag NCs for developing DNA/RNA sensors. Full article
(This article belongs to the Special Issue Nano and Micro DNA/RNA Sensors)
Open AccessReview Miniaturized Quantum Semiconductor Surface Plasmon Resonance Platform for Detection of Biological Molecules
Biosensors 2013, 3(2), 201-210; doi:10.3390/bios3020201
Received: 28 April 2013 / Revised: 22 May 2013 / Accepted: 24 May 2013 / Published: 7 June 2013
Cited by 1 | PDF Full-text (545 KB) | HTML Full-text | XML Full-text
Abstract
The concept of a portable, inexpensive and semi-automated biosensing platform, or lab-on-a-chip, is a vision shared by many researchers and venture industries. Under this scope, we have investigated the application of optical emission from quantum well (QW) microstructures for monitoring surface phenomena [...] Read more.
The concept of a portable, inexpensive and semi-automated biosensing platform, or lab-on-a-chip, is a vision shared by many researchers and venture industries. Under this scope, we have investigated the application of optical emission from quantum well (QW) microstructures for monitoring surface phenomena on gold layers remaining in proximity (<300 nm) with QW microstructures. The uncollimated QW radiation excites surface plasmons (SP) and through the surface plasmon resonance (SPR) effect allows for detection of small perturbation in the density surface adsorbates. The SPR technology is already commonly used for biochemical characterization in pharmaceutical industries, but the reduction of the distance between the SP exciting source and the biosensing platform to a few hundreds of nanometers is an innovative approach enabling us to achieve an ultimate miniaturization of the device. We evaluate the signal quality of this nanophotonic QW-SPR device using hyperspectral-imaging technology, and we compare its performance with that of a standard prism-based commercial system. Two standard biochemical agents are employed for this characterization study: bovine serum albumin and inactivated influenza A virus. With an innovative conical method of SPR data collection, we demonstrate that individually collected SPR scan, each in less than 2.2 s, yield a resolution of the detection at 1.5 × 10−6 RIU. Full article
Figures

Open AccessReview The Heme-Based Oxygen-Sensor Phosphodiesterase Ec DOS (DosP): Structure-Function Relationships
Biosensors 2013, 3(2), 211-237; doi:10.3390/bios3020211
Received: 24 April 2013 / Revised: 24 May 2013 / Accepted: 13 June 2013 / Published: 17 June 2013
Cited by 8 | PDF Full-text (699 KB) | HTML Full-text | XML Full-text
Abstract
Escherichia coli Direct Oxygen Sensor (Ec DOS, also known as Ec DosP) is a heme-based O2-sensing phosphodiesterase from Escherichia coli that catalyzes the conversion of cyclic-di-GMP to linear di-GMP. Cyclic-di-GMP is an important second messenger in bacteria, highlighting the [...] Read more.
Escherichia coli Direct Oxygen Sensor (Ec DOS, also known as Ec DosP) is a heme-based O2-sensing phosphodiesterase from Escherichia coli that catalyzes the conversion of cyclic-di-GMP to linear di-GMP. Cyclic-di-GMP is an important second messenger in bacteria, highlighting the importance of understanding structure-function relationships of Ec DOS. Ec DOS is composed of an N-terminal heme-bound O2-sensing PAS domain and a C-terminal phosphodiesterase catalytic domain. Notably, its activity is markedly enhanced by O2 binding to the heme Fe(II) complex in the PAS sensor domain. X-ray crystal structures and spectroscopic and catalytic characterization of the wild-type and mutant proteins have provided important structural and functional clues to understanding the molecular mechanism of intramolecular catalytic regulation by O2 binding. This review summarizes the intriguing findings that have obtained for Ec DOS. Full article
(This article belongs to the Special Issue Physiological Sensors of Gases, Light, Redox State and Hypoxia)

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