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Special Issue "Fluorescent Biosensors"

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A special issue of Sensors (ISSN 1424-8220). This special issue belongs to the section "Biosensors".

Deadline for manuscript submissions: closed (31 October 2013)

Special Issue Editor

Guest Editor
Dr. Hui-Wang Ai (Website)

Department of Chemistry, 501 Big Springs Road, University of California, Riverside, CA 92521, USA
Interests: fluorescent sensors; environmental chemical biology; protein engineering and protein chemistry

Special Issue Information

Dear Colleagues,

The past a few decades have witnessed extraordinary advances in fluorescent biosensors that have revolutionized the way how biology could be studied. Fluorescent biosensors are molecules and devices that measure the concentrations, locations and other dynamics of biomolecules and bioactivities by means of fluorescence. Often these probes are coupled with state-of-the-art instruments including various microscopes and macroscopes to enable the imaging of cells, tissues, and intact multicellular organisms (e.g., plants, animals and human beings).

Fluorescent biosensors are usually based on fluorescent organic molecules, nanoparticles, proteins, or combinations of organic molecules, nanoparticles and proteins. They are designed and engineered to change their fluorescent colors or intensities in response to external stimuli or physiological changes including pH fluctuations, metal ion homeostasis, cell signaling, membrane potential differences, phosphorylation, ubiquitination, redox reactions, and apoptosis. In particular, the 2008 Nobel Prize in Chemistry was awarded to three scientists who discovered and developed fluorescent proteins, which have now been developed into a very large group of biosensors.

The aim of this special issue is to highlight high-quality results (including original research articles and reviews) in the field of fluorescent biosensor. Articles that focus on or propose new ideas and new directions are particularly welcome.

Dr. Huiwang Ai
Guest Editor

Submission

Manuscripts should be submitted online at www.mdpi.com by registering and logging in to this website. Once you are registered, click here to go to the submission form. Manuscripts can be submitted until the deadline. Papers will be published continuously (as soon as accepted) and will be listed together on the special issue website. Research articles, review articles as well as communications are invited. For planned papers, a title and short abstract (about 100 words) can be sent to the Editorial Office for announcement on this website.

Submitted manuscripts should not have been published previously, nor be under consideration for publication elsewhere (except conference proceedings papers). All manuscripts are refereed through a peer-review process. A guide for authors and other relevant information for submission of manuscripts is available on the Instructions for Authors page. Sensors is an international peer-reviewed Open Access monthly journal published by MDPI.

Please visit the Instructions for Authors page before submitting a manuscript. The Article Processing Charge (APC) for publication in this open access journal is 1800 CHF (Swiss Francs).


Keywords

  • fluorescent sensor
  • ratiometric sensor
  • intensiometric sensor
  • fluorescent protein
  • synthetic probe
  • quantum dot
  • optogenetic reporter
  • genetically encoded probe
  • reaction-based fluorescent sensor

Published Papers (10 papers)

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Editorial

Jump to: Research, Review

Open AccessEditorial Fluorescent Sensors for Biological Applications
Sensors 2014, 14(9), 17829-17831; doi:10.3390/s140917829
Received: 19 September 2014 / Accepted: 24 September 2014 / Published: 25 September 2014
PDF Full-text (608 KB) | HTML Full-text | XML Full-text
Abstract
Fluorescence is one of the most important analytical methods used in biological studies. In the past decade or two, instrumentation in this field has greatly advanced, and now it is possible to detect single photons or fluorescent molecules [1,2], or break the [...] Read more.
Fluorescence is one of the most important analytical methods used in biological studies. In the past decade or two, instrumentation in this field has greatly advanced, and now it is possible to detect single photons or fluorescent molecules [1,2], or break the Abbe diffraction limit to distinguish two points spaced less than 50 nm apart [3]. Concurrently, the development of improved fluorescent probes, which can be coupled with state-of-the-art instruments, has been equally important. This special issue on “fluorescent biosensors” in Sensors reports recent results from eight research groups in the field of sensor development. It includes three review articles, and six research articles reporting original results. [...] Full article
(This article belongs to the Special Issue Fluorescent Biosensors)

Research

Jump to: Editorial, Review

Open AccessArticle Coumarin-Based Fluorescent Probes for Dual Recognition of Copper(II) and Iron(III) Ions and Their Application in Bio-Imaging
Sensors 2014, 14(1), 1358-1371; doi:10.3390/s140101358
Received: 31 October 2013 / Revised: 18 December 2013 / Accepted: 18 December 2013 / Published: 13 January 2014
Cited by 16 | PDF Full-text (722 KB) | HTML Full-text | XML Full-text | Supplementary Files
Abstract
Two new coumarin-based “turn-off” fluorescent probes, (E)-3-((3,4-dihydroxybenzylidene)amino)-7-hydroxy-2H-chromen-2-one (BS1) and (E)-3-((2,4-dihydroxybenzylidene)amino)-7-hydroxy-2H-chromen-2-one (BS2), were synthesized and their detection of copper(II) and iron(III) ions was studied. Results show that both compounds are highly [...] Read more.
Two new coumarin-based “turn-off” fluorescent probes, (E)-3-((3,4-dihydroxybenzylidene)amino)-7-hydroxy-2H-chromen-2-one (BS1) and (E)-3-((2,4-dihydroxybenzylidene)amino)-7-hydroxy-2H-chromen-2-one (BS2), were synthesized and their detection of copper(II) and iron(III) ions was studied. Results show that both compounds are highly selective for Cu2+ and Fe3+ ions over other metal ions. However, BS2 is detected directly, while detection of BS1 involves a hydrolysis reaction to regenerate 3-amino-7-hydroxycoumarin (3) and 3,4-dihydroxybenzaldehyde, of which 3 is able to react with copper(II) or iron(III) ions. The interaction between the tested compounds and copper or iron ions is associated with a large fluorescence decrease, showing detection limits of ca. 10−5 M. Preliminary studies employing epifluorescence microscopy demonstrate that Cu2+ and Fe3+ ions can be imaged in human neuroblastoma SH-SY5Y cells treated with the tested probes. Full article
(This article belongs to the Special Issue Fluorescent Biosensors)
Open AccessArticle Optimization of ERK Activity Biosensors for both Ratiometric and Lifetime FRET Measurements
Sensors 2014, 14(1), 1140-1154; doi:10.3390/s140101140
Received: 8 November 2013 / Revised: 6 December 2013 / Accepted: 19 December 2013 / Published: 10 January 2014
Cited by 6 | PDF Full-text (351 KB) | HTML Full-text | XML Full-text
Abstract
Among biosensors, genetically-encoded FRET-based biosensors are widely used to localize and measure enzymatic activities. Kinases activities are of particular interest as their spatiotemporal regulation has become crucial for the deep understanding of cell fate decisions. This is especially the case for ERK, [...] Read more.
Among biosensors, genetically-encoded FRET-based biosensors are widely used to localize and measure enzymatic activities. Kinases activities are of particular interest as their spatiotemporal regulation has become crucial for the deep understanding of cell fate decisions. This is especially the case for ERK, whose activity is a key node in signal transduction pathways and can direct the cell into various processes. There is a constant need for better tools to analyze kinases in vivo, and to detect even the slightest variations of their activities. Here we report the optimization of the previous ERK activity reporters, EKAR and EKAREV. Those tools are constituted by two fluorophores adapted for FRET experiments, which are flanking a specific substrate of ERK, and a domain able to recognize and bind this substrate when phosphorylated. The latter phosphorylation allows a conformational change of the biosensor and thus a FRET signal. We improved those biosensors with modifications of: (i) fluorophores and (ii) linkers between substrate and binding domain, resulting in new versions that exhibit broader dynamic ranges upon EGF stimulation when FRET experiments are carried out by fluorescence lifetime and ratiometric measurements. Herein, we characterize those new biosensors and discuss their observed differences that depend on their fluorescence properties. Full article
(This article belongs to the Special Issue Fluorescent Biosensors)
Open AccessArticle Noninvasive High-Throughput Single-Cell Analysis of HIV Protease Activity Using Ratiometric Flow Cytometry
Sensors 2013, 13(12), 16330-16346; doi:10.3390/s131216330
Received: 18 October 2013 / Revised: 11 November 2013 / Accepted: 13 November 2013 / Published: 28 November 2013
Cited by 2 | PDF Full-text (1081 KB) | HTML Full-text | XML Full-text
Abstract
To effectively fight against the human immunodeficiency virus infection/ acquired immunodeficiency syndrome (HIV/AIDS) epidemic, ongoing development of novel HIV protease inhibitors is required. Inexpensive high-throughput screening assays are needed to quickly scan large sets of chemicals for potential inhibitors. We have developed [...] Read more.
To effectively fight against the human immunodeficiency virus infection/ acquired immunodeficiency syndrome (HIV/AIDS) epidemic, ongoing development of novel HIV protease inhibitors is required. Inexpensive high-throughput screening assays are needed to quickly scan large sets of chemicals for potential inhibitors. We have developed a Förster resonance energy transfer (FRET)-based, HIV protease-sensitive sensor using a combination of a fluorescent protein pair, namely mCerulean and mCitrine. Through extensive in vitro characterization, we show that the FRET-HIV sensor can be used in HIV protease screening assays. Furthermore, we have used the FRET-HIV sensor for intracellular quantitative detection of HIV protease activity in living cells, which more closely resembles an actual viral infection than an in vitro assay. We have developed a high-throughput method that employs a ratiometric flow cytometry for analyzing large populations of cells that express the FRET-HIV sensor. The method enables FRET measurement of single cells with high sensitivity and speed and should be used when subpopulation-specific intracellular activity of HIV protease needs to be estimated. In addition, we have used a confocal microscopy sensitized emission FRET technique to evaluate the usefulness of the FRET-HIV sensor for spatiotemporal detection of intracellular HIV protease activity. Full article
(This article belongs to the Special Issue Fluorescent Biosensors)
Open AccessArticle Temporal and Spatial Properties of a Yeast Multi-Cellular Amplification System Based on Signal Molecule Diffusion
Sensors 2013, 13(11), 14511-14522; doi:10.3390/s131114511
Received: 22 August 2013 / Revised: 11 October 2013 / Accepted: 18 October 2013 / Published: 25 October 2013
Cited by 3 | PDF Full-text (817 KB) | HTML Full-text | XML Full-text | Supplementary Files
Abstract
We report on the spatial and temporal signaling properties of a yeast pheromone-based cell communication and amplifier system. It utilizes the Saccharomyces cerevisiae mating response pathway and relies on diffusion of the pheromone α–factor as key signaling molecule between two cell types. [...] Read more.
We report on the spatial and temporal signaling properties of a yeast pheromone-based cell communication and amplifier system. It utilizes the Saccharomyces cerevisiae mating response pathway and relies on diffusion of the pheromone α–factor as key signaling molecule between two cell types. One cell type represents the α–factor secreting sensor part and the other the reporter part emitting fluorescence upon activation. Although multi-cellular signaling systems promise higher specificity and modularity, the complex interaction of the cells makes prediction of sensor performance difficult. To test the maximum distance and response time between sensor and reporter cells, the two cell types were spatially separated in defined compartments of agarose hydrogel (5 ´ 5 mm) and reconnected by diffusion of the yeast pheromone. Different ratios of sensor to reporter cells were tested to evaluate the minimum amount of sensor cells required for signal transduction. Even the smallest ratio, one α–factor-secreting cell to twenty reporter cells, generated a distinct fluorescence signal. When using a 1:1 ratio, the secreted pheromone induced fluorescence in a distance of up to four millimeters after six hours. We conclude from both our experimental results and a mathematical diffusion model that in our approach: (1) the maximum dimension of separated compartments should not exceed five millimeters in gradient direction; and (2) the time-limiting step is not diffusion of the signaling molecule but production of the reporter protein. Full article
(This article belongs to the Special Issue Fluorescent Biosensors)
Open AccessArticle Mutational Analysis of a Red Fluorescent Protein-Based Calcium Ion Indicator
Sensors 2013, 13(9), 11507-11521; doi:10.3390/s130911507
Received: 11 August 2013 / Revised: 27 August 2013 / Accepted: 29 August 2013 / Published: 2 September 2013
Cited by 3 | PDF Full-text (1888 KB) | HTML Full-text | XML Full-text | Supplementary Files
Abstract
As part of an ongoing effort to develop genetically encoded calcium ion (Ca2+) indicators we recently described a new variant, designated CH-GECO2.1, that is a genetic chimera of the red fluorescent protein (FP) mCherry, calmodulin (CaM), and a peptide that [...] Read more.
As part of an ongoing effort to develop genetically encoded calcium ion (Ca2+) indicators we recently described a new variant, designated CH-GECO2.1, that is a genetic chimera of the red fluorescent protein (FP) mCherry, calmodulin (CaM), and a peptide that binds to Ca2+-bound CaM. In contrast to the closely related Ca2+ indicator R-GECO1, CH-GECO2.1 is characterized by a much higher affinity for Ca2+ and a sensing mechanism that does not involve direct modulation of the chromophore pKa. To probe the structural basis underlying the differences between CH-GECO2.1 and R-GECO1, and to gain a better understanding of the mechanism of CH-GECO2.1, we have constructed, purified, and characterized a large number of variants with strategic amino acid substitutions. This effort led us to identify Gln163 as the key residue involved in the conformational change that transduces the Ca2+ binding event into a change in the chromophore environment. In addition, we demonstrate that many of the substitutions that differentiate CH-GECO2.1 and R-GECO1 have little influence on both the Kd for Ca2+ and the sensing mechanism, and that the interdomain linkers and interfaces play important roles. Full article
(This article belongs to the Special Issue Fluorescent Biosensors)
Open AccessArticle DNA Hairpins as Temperature Switches, Thermometers and Ionic Detectors
Sensors 2013, 13(5), 5937-5944; doi:10.3390/s130505937
Received: 28 March 2013 / Revised: 25 April 2013 / Accepted: 5 May 2013 / Published: 10 May 2013
Cited by 7 | PDF Full-text (430 KB) | HTML Full-text | XML Full-text
Abstract
Temperature is of major importance in most branches of science and technology as well as in everyday life, and with the miniaturization of electronic devices and the increasing ability to make research into small-scale systems, a specific need for very small thermostats [...] Read more.
Temperature is of major importance in most branches of science and technology as well as in everyday life, and with the miniaturization of electronic devices and the increasing ability to make research into small-scale systems, a specific need for very small thermostats and thermometers has been created. Here we describe how DNA molecules can be used as nanoscale sensors to meet these requirements. We illustrate how the hybridization kinetics between bases in DNA molecules combined with conformational changes of the DNA backbone can be exploited in the construction of simple but versatile temperature switches and thermometers, which can be built into electronic systems. DNA based sensors are at the same time applicable as ion detectors to monitor the chemical environment of a specific system. Full article
(This article belongs to the Special Issue Fluorescent Biosensors)
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Review

Jump to: Editorial, Research

Open AccessReview Applications of Delayed Fluorescence from Photosystem II
Sensors 2013, 13(12), 17332-17345; doi:10.3390/s131217332
Received: 1 November 2013 / Revised: 9 December 2013 / Accepted: 11 December 2013 / Published: 16 December 2013
Cited by 7 | PDF Full-text (219 KB) | HTML Full-text | XML Full-text
Abstract
While photosystem II (PSII) of plants utilizes light for photosynthesis, part of the absorbed energy may be reverted back and dissipated as long-term fluorescence (delayed fluorescence or DF). Because the generation of DF is coupled with the processes of forward photosynthetic activities, [...] Read more.
While photosystem II (PSII) of plants utilizes light for photosynthesis, part of the absorbed energy may be reverted back and dissipated as long-term fluorescence (delayed fluorescence or DF). Because the generation of DF is coupled with the processes of forward photosynthetic activities, DF contains the information about plant physiological states and plant-environment interactions. This makes DF a potentially powerful biosensing mechanism to measure plant photosynthetic activities and environmental conditions. While DF has attracted the interest of many researchers, some aspects of it are still unknown because of the complexity of photosynthetic system. In order to provide a holistic picture about the usefulness of DF, it is meaningful to summarize the research on DF applications. In this short review, available literature on applications of DF from PSII is summarized. Full article
(This article belongs to the Special Issue Fluorescent Biosensors)
Open AccessReview Illumination of the Spatial Order of Intracellular pH by Genetically Encoded pH-Sensitive Sensors
Sensors 2013, 13(12), 16736-16758; doi:10.3390/s131216736
Received: 12 November 2013 / Revised: 27 November 2013 / Accepted: 27 November 2013 / Published: 5 December 2013
Cited by 17 | PDF Full-text (857 KB) | HTML Full-text | XML Full-text
Abstract
Fluorescent proteins have been extensively used for engineering genetically encoded sensors that can monitor levels of ions, enzyme activities, redox potential, and metabolites. Certain fluorescent proteins possess specific pH-dependent spectroscopic features, and thus can be used as indicators of intracellular pH. Moreover, [...] Read more.
Fluorescent proteins have been extensively used for engineering genetically encoded sensors that can monitor levels of ions, enzyme activities, redox potential, and metabolites. Certain fluorescent proteins possess specific pH-dependent spectroscopic features, and thus can be used as indicators of intracellular pH. Moreover, concatenated pH-sensitive proteins with target proteins pin the pH sensors to a definite location within the cell, compartment, or tissue. This study provides an overview of the continually expanding family of pH-sensitive fluorescent proteins that have become essential tools for studies of pH homeostasis and cell physiology. We describe and discuss the design of intensity-based and ratiometric pH sensors, their spectral properties and pH-dependency, as well as their performance. Finally, we illustrate some examples of the applications of pH sensors targeted at different subcellular compartments. Full article
(This article belongs to the Special Issue Fluorescent Biosensors)
Open AccessReview Genetically Encoded Fluorescent Redox Probes
Sensors 2013, 13(11), 15422-15433; doi:10.3390/s131115422
Received: 19 October 2013 / Revised: 2 November 2013 / Accepted: 5 November 2013 / Published: 11 November 2013
Cited by 7 | PDF Full-text (593 KB) | HTML Full-text | XML Full-text
Abstract
Redox processes are involved in almost every cell of the body as a consequence of aerobic life. In the past decades, redox biology has been increasingly recognized as one of the key themes in cell signaling. The progress has been accelerated by [...] Read more.
Redox processes are involved in almost every cell of the body as a consequence of aerobic life. In the past decades, redox biology has been increasingly recognized as one of the key themes in cell signaling. The progress has been accelerated by development of fluorescent probes that can monitor redox conditions and dynamics in cells and cell compartments. This short paper focuses on fluorescent redox probes that are genetically encoded, and discusses their properties, molecular mechanism, advantages and pitfalls. Our recent work on reaction-based encoded probes that are responsive to particular redox signaling molecules is also reviewed. Future challenges and directions are also commented. Full article
(This article belongs to the Special Issue Fluorescent Biosensors)
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