Survey of the 2009 commercial optical biosensor literature

Rich, Rebecca L.; Myszka, David G.

doi:10.1002/jmr.1138

Cited by 96 publications

(72 citation statements)

References 312 publications

(205 reference statements)

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“…In some cases, stoichiometry can also be determined (Teulade-Fichou et al 2003;Mistrik et al 2004;Di Primo and Lebars 2007;. SPR is widely used to investigate protein-protein, protein-small molecules, or protein-DNA interactions (for review, see Rich and Myszka 2011) but rarely for investigating RNA-RNA complexes, likely due to their susceptibility to hydrolysis. In previous studies, we have successfully investigated interactions between RNA oligonucleotides with structured RNA of human viruses or cells (Ducongé et al 2000;Aldaz-Carroll et al 2002;Lebars et al 2008;Dausse et al 2011).…”

Section: Introductionmentioning

confidence: 99%

Direct evidence for RNA–RNA interactions at the 3′ end of the Hepatitis C virus genome using surface plasmon resonance

Palau

Masante

Ventura

et al. 2013

RNA

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Surface plasmon resonance was used to investigate two previously described interactions analyzed by reverse genetics and complementation mutation experiments, involving 5BSL3.2, a stem-loop located in the NS5B coding region of HCV. 5BSL3.2 was immobilized on a sensor chip by streptavidin-biotin coupling, and its interaction either with the SL2 stem-loop of the 3 ′ end or with an upstream sequence centered on nucleotide 9110 (referred to as Seq9110) was monitored in real-time. In contrast with previous results obtained by NMR assays with the same short RNA sequences that we used or SHAPE analysis with longer RNAs, we demonstrate that recognition between 5BSL3.2 and SL2 can occur in solution through a kissing-loop interaction. We show that recognition between Seq9110 and the internal loop of 5BSL3.2 does not prevent binding of SL2 on the apical loop of 5BSL3.2 and does not influence the rate constants of the SL2-5BSL3.2 complex. Therefore, the two binding sites of 5BSL3.2, the apical and internal loops, are structurally independent and both interactions can coexist. We finally show that the stem-loop SL2 is a highly dynamic RNA motif that fluctuates between at least two conformations: One is able to hybridize with 5BSL3.2 through loop-loop interaction, and the other one is capable of self-associating in the absence of protein, reinforcing the hypothesis of SL2 being a dimerization sequence. This result suggests also that the conformational dynamics of SL2 could play a crucial role for controlling the destiny of the genomic RNA.

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Section: Introductionmentioning

confidence: 99%

Direct evidence for RNA–RNA interactions at the 3′ end of the Hepatitis C virus genome using surface plasmon resonance

Palau

Masante

Ventura

et al. 2013

RNA

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“…[36][37][38] Binding of an injected molecule (termed analyte in SPR terminology) to a molecule (termed ligand) immobilized on the surface of a thin Table 1. Advantages and disadvantages of some of the most commonly used biophysical methods for studying molecular interactions.…”

Section: Surface Plasmon Resonancementioning

confidence: 99%

How to Study Protein-protein Interactions

Podobnik¹,

Kraševec²,

Zavec³

et al. 2016

ACSi

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In memory of prof. dr. Janko Jamnik. AbstractPhysical and functional interactions between molecules in living systems are central to all biological processes. Identification of protein complexes therefore is becoming increasingly important to gain a molecular understanding of cells and organisms. Several powerful methodologies and techniques have been developed to study molecular interactions and thus help elucidate their nature and role in biology as well as potential ways how to interfere with them. All different techniques used in these studies have their strengths and weaknesses and since they are mostly employed in in vitro conditions, a single approach can hardly accurately reproduce interactions that happen under physiological conditions. However, complementary usage of as many as possible available techniques can lead to relatively realistic picture of the biological process. Here we describe several proteomic, biophysical and structural tools that help us understand the nature and mechanism of these interactions.

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“…Currently, the most common use of instruments performing label-free detection is for the characterization of specific molecular interactions or the screening of different compounds according to their interaction with molecular partners [10]. For these purposes, the use of instruments based on surface plasmon resonance (SPR) is widely consolidated, although several other techniques have been reported to enable high detection performance [11,12].…”

Section: Introductionmentioning

confidence: 99%

Emerging applications of label-free optical biosensors

et al. 2017

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Abstract:Innovative technical solutions to realize optical biosensors with improved performance are continuously proposed. Progress in material fabrication enables developing novel substrates with enhanced optical responses. At the same time, the increased spectrum of available biomolecular tools, ranging from highly specific receptors to engineered bioconjugated polymers, facilitates the preparation of sensing surfaces with controlled functionality. What remains often unclear is to which extent this continuous innovation provides effective breakthroughs for specific applications. In this review, we address this challenging question for the class of label-free optical biosensors, which can provide a direct signal upon molecular binding without using secondary probes. Label-free biosensors have become a consolidated approach for the characterization and screening of molecular interactions in research laboratories. However, in the last decade, several examples of other applications with high potential impact have been proposed. We review the recent advances in label-free optical biosensing technology by focusing on the potential competitive advantage provided in selected emerging applications, grouped on the basis of the target type. In particular, direct and real-time detection allows the development of simpler, compact, and rapid analytical methods for different kinds of targets, from proteins to DNA and viruses. The lack of secondary interactions facilitates the binding of small-molecule targets and minimizes the perturbation in single-molecule detection. Moreover, the intrinsic versatility of label-free sensing makes it an ideal platform to be integrated with biomolecular machinery with innovative functionality, as in case of the molecular tools provided by DNA nanotechnology.

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Survey of the 2009 commercial optical biosensor literature

Cited by 96 publications

References 312 publications

Direct evidence for RNA–RNA interactions at the 3′ end of the Hepatitis C virus genome using surface plasmon resonance

Direct evidence for RNA–RNA interactions at the 3′ end of the Hepatitis C virus genome using surface plasmon resonance

How to Study Protein-protein Interactions

Emerging applications of label-free optical biosensors

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