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Biosensors
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FRET-Based Biosensors
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FRET-Based Biosensors

A special issue of Biosensors (ISSN 2079-6374).

Deadline for manuscript submissions: closed (1 December 2018) | Viewed by 65911

Special Issue Editor

Dr. Karl David Wegner

E-Mail Website
Guest Editor
Division Biophotonics (BAM-1.2), Federal Institute for Materials Research and Testing (BAM), 12489 Berlin, Germany
Interests: energy transfer; quantum dots; biosensing; bioimaging; nanoparticle synthesis
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

In the last few decades, Förster resonance energy transfer (FRET) has become an established method for the sensitive detection of various targets in numerous biosensing applications. FRET is a non-radiative energy transfer from an excited donor to an acceptor at a close distance (a few nanometres). The high distance sensitivity makes it a preferred tool for qualitative and quantitative analyses of biological interactions and processes. The utilization of new fluorescent materials, such as semiconductor nanocrystals, upconversion nanoparticles, fluorescent polymers, metal chelates, various noble metal and other nanoparticles, have greatly fostered advancements in the design of biosensors. FRET biosensors combining these robust fluorophores with new sensor designs enabled translation from the utilization of sophisticated benchtop fluorescent spectrometers to simple point-of-care devices for the assessment of biomarkers, drugs, environmental pollution, and for food quality analysis.

In this Special Issue, manuscripts are invited, which are devoted to the application of FRET for designing various types of sensors. Both reviews and original research articles will be published. Reviews should provide a critical overview of the current state-of-the-art in a particular application field, such as in vitro diagnostics, food safety and quality control or environmental pollution. Critical overviews about the use of a specific fluorophores, such as semiconductor nanocrystals or other nanoparticles in FRET-based biosensing applications, are also of interest. Original research papers that present new FRET-based sensor designs and/or fundamental studies with potential relevance to biosensing are also welcome.

Dr. Karl David Wegner
Guest Editor

Manuscript Submission Information

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. All submissions that pass pre-check are peer-reviewed. Accepted papers will be published continuously in the journal (as soon as accepted) and will be listed together on the special issue website. Research articles, review articles as well as short 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 thoroughly refereed through a single-blind peer-review process. A guide for authors and other relevant information for submission of manuscripts is available on the Instructions for Authors page. Biosensors 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 2700 CHF (Swiss Francs). Submitted papers should be well formatted and use good English. Authors may use MDPI's English editing service prior to publication or during author revisions.

Keywords

  • FRET
  • luminescence
  • nanotechnology
  • nanomaterials
  • fluorescent probes
  • diagnostics
  • bioanalysis
  • point-of-care
  • imaging
  • food safety
  • environmental pollution

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Published Papers (8 papers)

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Research

Jump to: Review

9 pages, 2507 KiB  
Article
Graphene Oxide-Based Nanostructured DNA Sensor
by Aditya Balaji, Songlin Yang, Jeslyn Wang and Jin Zhang
Biosensors 2019, 9(2), 74; https://doi.org/10.3390/bios9020074 - 30 May 2019
Cited by 35 | Viewed by 7948
Abstract
Quick detection of DNA sequence is vital for many fields, especially, early-stage diagnosis. Here, we develop a graphene oxide-based fluorescence quenching sensor to quickly and accurately detect small amounts of a single strand of DNA. In this paper, fluorescent magnetic nanoparticles (FMNPs) modified [...] Read more.
Quick detection of DNA sequence is vital for many fields, especially, early-stage diagnosis. Here, we develop a graphene oxide-based fluorescence quenching sensor to quickly and accurately detect small amounts of a single strand of DNA. In this paper, fluorescent magnetic nanoparticles (FMNPs) modified with target DNA sequence (DNA-t) were bound onto the modified graphene oxide acting as the fluorescence quenching element. FMNPs are made of iron oxide (Fe3O4) core and fluorescent silica (SiO2) shell. The average particle size of FMNPs was 74 ± 6 nm and the average thickness of the silica shell, estimated from TEM results, was 30 ± 4 nm. The photoluminescence and magnetic properties of FMNPs have been investigated. Target oligonucleotide (DNA-t) was conjugated onto FMNPs through glutaraldehyde crosslinking. Meanwhile, graphene oxide (GO) nanosheets were produced by a modified Hummers method. A complementary oligonucleotide (DNA-c) was designed to interact with GO. In the presence of GO-modified with DNA-c, the fluorescence intensity of FMNPs modified with DNA-t was quenched through a FRET quenching mechanism. Our study indicates that FMNPs can not only act as a FRET donor, but also enhance the sensor accuracy by magnetically separating the sensing system from free DNA and non-hybridized GO. Results indicate that this sensing system is ideal to detect small amounts of DNA-t with limitation detection at 0.12 µM. Full article
(This article belongs to the Special Issue FRET-Based Biosensors)
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12 pages, 3444 KiB  
Article
In-Vitro Characterization of mCerulean3_mRuby3 as a Novel FRET Pair with Favorable Bleed-Through Characteristics
by Kira Erismann-Ebner, Anne Marowsky and Michael Arand
Biosensors 2019, 9(1), 33; https://doi.org/10.3390/bios9010033 - 28 Feb 2019
Cited by 3 | Viewed by 6451
Abstract
In previous studies, we encountered substantial problems using the CFP_YFP Förster resonance energy transfer (FRET) pair to analyze protein proximity in the endoplasmic reticulum of live cells. Bleed-through of the donor emission into the FRET channel and overlap of the FRET emission wavelength [...] Read more.
In previous studies, we encountered substantial problems using the CFP_YFP Förster resonance energy transfer (FRET) pair to analyze protein proximity in the endoplasmic reticulum of live cells. Bleed-through of the donor emission into the FRET channel and overlap of the FRET emission wavelength with highly variable cellular autofluorescence significantly compromised the sensitivity of our analyses. Here, we propose mCerulean3 and mRuby3 as a new FRET pair to potentially overcome these problems. Fusion of the two partners with a trypsin-cleavable linker allowed the direct comparison of the FRET signal characteristics of the associated partners with those of the completely dissociated partners. We compared our new FRET pair with the canonical CFP_YFP and the more recent mClover3_mRuby3 pairs and found that, despite a lower total FRET signal intensity, the novel pair had a significantly better signal to noise ratio due to lower donor emission bleed-through. This and the fact that the mRuby3 emission spectrum did not overlap with that of common cellular autofluorescence renders the mCerulean3_mRuby3 FRET pair a promising alternative to the common CFP_YFP FRET pair for the interaction analysis of membrane proteins in living cells. Full article
(This article belongs to the Special Issue FRET-Based Biosensors)
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17 pages, 5252 KiB  
Article
Energy Transfer between Tm-Doped Upconverting Nanoparticles and a Small Organic Dye with Large Stokes Shift
by Anna López de Guereñu, Philipp Bastian, Pablo Wessig, Leonard John and Michael U. Kumke
Biosensors 2019, 9(1), 9; https://doi.org/10.3390/bios9010009 - 8 Jan 2019
Cited by 18 | Viewed by 5825
Abstract
Lanthanide-doped upconverting nanoparticles (UCNP) are being extensively studied for bioapplications due to their unique photoluminescence properties and low toxicity. Interest in RET applications involving UCNP is also increasing, but due to factors such as large sizes, ion emission distributions within the particles, and [...] Read more.
Lanthanide-doped upconverting nanoparticles (UCNP) are being extensively studied for bioapplications due to their unique photoluminescence properties and low toxicity. Interest in RET applications involving UCNP is also increasing, but due to factors such as large sizes, ion emission distributions within the particles, and complicated energy transfer processes within the UCNP, there are still many questions to be answered. In this study, four types of core and core-shell NaYF4-based UCNP co-doped with Yb3+ and Tm3+ as sensitizer and activator, respectively, were investigated as donors for the Methyl 5-(8-decanoylbenzo[1,2-d:4,5-d′]bis([1,3]dioxole)-4-yl)-5-oxopentanoate (DBD-6) dye. The possibility of resonance energy transfer (RET) between UCNP and the DBD-6 attached to their surface was demonstrated based on the comparison of luminescence intensities, band ratios, and decay kinetics. The architecture of UCNP influenced both the luminescence properties and the energy transfer to the dye: UCNP with an inert shell were the brightest, but their RET efficiency was the lowest (17%). Nanoparticles with Tm3+ only in the shell have revealed the highest RET efficiencies (up to 51%) despite the compromised luminescence due to surface quenching. Full article
(This article belongs to the Special Issue FRET-Based Biosensors)
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13 pages, 1081 KiB  
Article
Development of DNA Pair Biosensor for Quantization of Nuclear Factor Kappa B
by Zhaohui Wang and Pak Kin Wong
Biosensors 2018, 8(4), 126; https://doi.org/10.3390/bios8040126 - 10 Dec 2018
Cited by 1 | Viewed by 4673
Abstract
Nuclear factor kappa B (NF-κB), regulating the expression of several genes that mediate the inflammatory responses and cell proliferation, is one of the therapeutic targets for chronic inflammatory disease and cancer. A novel molecular binding scheme for the detection of NF-κB was investigated [...] Read more.
Nuclear factor kappa B (NF-κB), regulating the expression of several genes that mediate the inflammatory responses and cell proliferation, is one of the therapeutic targets for chronic inflammatory disease and cancer. A novel molecular binding scheme for the detection of NF-κB was investigated for its affinity to Ig-κB DNA composed by dye and quencher fluorophores, and this specificity is confirmed by competing with the DNA sequence that is complementary to the Ig-κB DNA. We create a normalization equation to remove the negative effects from the various initial fluorophore concentrations and the background noise. We also found that a periodic shaking at a frequency could help to stabilize the DNA–protein binding. The calibration experiment, using purified p50 (NF-κB), shows that this molecular probe biosensor has a detection limit on the order of nanomolar. The limit of detection is determined by the binding performance of dye and quencher oligonucleotides, and only a small portion of probes are stabilized by DNA-binding protein NF-κB. The specificity experiment also shows that p50/p65 heterodimer has the highest affinity for Ig-κB DNA; p65 homodimer binds with intermediate affinity, whereas p50 shows the lowest binding affinity, and Ig-κB DNA is not sensitive to BSA (bovine albumin serum). The experiment of HeLa nuclear extract shows that TNF-α stimulated HeLa nuclear extract has higher affinity to Ig-κB DNA than non-TNF-stimulated HeLa nuclear extract (4-h serum response). Therefore, the molecular binding scheme provides a rapid, quantitative, high throughput, and automated measurement of the DNA-binding protein NF-κB at low cost, which is beneficial for automated drug screening systems. Full article
(This article belongs to the Special Issue FRET-Based Biosensors)
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12 pages, 3840 KiB  
Article
A DNA-Based Assay for Digoxin Detection
by Michael V. Kjelstrup, Line D. F. Nielsen, Malthe Hansen-Bruhn and Kurt V. Gothelf
Biosensors 2018, 8(1), 19; https://doi.org/10.3390/bios8010019 - 6 Mar 2018
Cited by 7 | Viewed by 8284
Abstract
The most common method for quantifying small-molecule drugs in blood samples is by liquid chromatography in combination with mass spectrometry. Few immuno-based assays are available for the detection of small-molecule drugs in blood. Here we report on a homogeneous assay that enables detection [...] Read more.
The most common method for quantifying small-molecule drugs in blood samples is by liquid chromatography in combination with mass spectrometry. Few immuno-based assays are available for the detection of small-molecule drugs in blood. Here we report on a homogeneous assay that enables detection of the concentration of digoxin spiked into in a plasma sample. The assay is based on a shift in the equilibrium of a DNA strand displacement competition reaction, and can be performed in 30 min for concentrations above 10 nM. The equilibrium shift occurs upon binding of anti-digoxigenin antibody. As a model, the assay provides a potential alternative to current small-molecule detection methods used for therapeutic drug monitoring. Full article
(This article belongs to the Special Issue FRET-Based Biosensors)
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Review

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17 pages, 1866 KiB  
Review
FRET Microscopy in Yeast
by Michal Skruzny, Emma Pohl and Marc Abella
Biosensors 2019, 9(4), 122; https://doi.org/10.3390/bios9040122 - 11 Oct 2019
Cited by 15 | Viewed by 12577
Abstract
Förster resonance energy transfer (FRET) microscopy is a powerful fluorescence microscopy method to study the nanoscale organization of multiprotein assemblies in vivo. Moreover, many biochemical and biophysical processes can be followed by employing sophisticated FRET biosensors directly in living cells. Here, we summarize [...] Read more.
Förster resonance energy transfer (FRET) microscopy is a powerful fluorescence microscopy method to study the nanoscale organization of multiprotein assemblies in vivo. Moreover, many biochemical and biophysical processes can be followed by employing sophisticated FRET biosensors directly in living cells. Here, we summarize existing FRET experiments and biosensors applied in yeasts Saccharomyces cerevisiae and Schizosaccharomyces pombe, two important models of fundamental biomedical research and efficient platforms for analyses of bioactive molecules. We aim to provide a practical guide on suitable FRET techniques, fluorescent proteins, and experimental setups available for successful FRET experiments in yeasts. Full article
(This article belongs to the Special Issue FRET-Based Biosensors)
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35 pages, 21221 KiB  
Review
In Vivo Biosensing Using Resonance Energy Transfer
by Shashi Bhuckory, Joshua C. Kays and Allison M. Dennis
Biosensors 2019, 9(2), 76; https://doi.org/10.3390/bios9020076 - 3 Jun 2019
Cited by 35 | Viewed by 11973
Abstract
Solution-phase and intracellular biosensing has substantially enhanced our understanding of molecular processes foundational to biology and pathology. Optical methods are favored because of the low cost of probes and instrumentation. While chromatographic methods are helpful, fluorescent biosensing further increases sensitivity and can be [...] Read more.
Solution-phase and intracellular biosensing has substantially enhanced our understanding of molecular processes foundational to biology and pathology. Optical methods are favored because of the low cost of probes and instrumentation. While chromatographic methods are helpful, fluorescent biosensing further increases sensitivity and can be more effective in complex media. Resonance energy transfer (RET)-based sensors have been developed to use fluorescence, bioluminescence, or chemiluminescence (FRET, BRET, or CRET, respectively) as an energy donor, yielding changes in emission spectra, lifetime, or intensity in response to a molecular or environmental change. These methods hold great promise for expanding our understanding of molecular processes not just in solution and in vitro studies, but also in vivo, generating information about complex activities in a natural, organismal setting. In this review, we focus on dyes, fluorescent proteins, and nanoparticles used as energy transfer-based optical transducers in vivo in mice; there are examples of optical sensing using FRET, BRET, and in this mammalian model system. After a description of the energy transfer mechanisms and their contribution to in vivo imaging, we give a short perspective of RET-based in vivo sensors and the importance of imaging in the infrared for reduced tissue autofluorescence and improved sensitivity. Full article
(This article belongs to the Special Issue FRET-Based Biosensors)
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14 pages, 853 KiB  
Review
Homotransfer FRET Reporters for Live Cell Imaging
by Nicole E. Snell, Vishnu P. Rao, Kendra M. Seckinger, Junyi Liang, Jenna Leser, Allison E. Mancini and M. A. Rizzo
Biosensors 2018, 8(4), 89; https://doi.org/10.3390/bios8040089 - 11 Oct 2018
Cited by 16 | Viewed by 6481
Abstract
Förster resonance energy transfer (FRET) between fluorophores of the same species was recognized in the early to mid-1900s, well before modern heterotransfer applications. Recently, homotransfer FRET principles have re-emerged in biosensors that incorporate genetically encoded fluorescent proteins. Homotransfer offers distinct advantages over the [...] Read more.
Förster resonance energy transfer (FRET) between fluorophores of the same species was recognized in the early to mid-1900s, well before modern heterotransfer applications. Recently, homotransfer FRET principles have re-emerged in biosensors that incorporate genetically encoded fluorescent proteins. Homotransfer offers distinct advantages over the standard heterotransfer FRET method, some of which are related to the use of fluorescence polarization microscopy to quantify FRET between two fluorophores of identical color. These include enhanced signal-to-noise, greater compatibility with other optical sensors and modulators, and new design strategies based upon the clustering or dimerization of singly-labeled sensors. Here, we discuss the theoretical basis for measuring homotransfer using polarization microscopy, procedures for data collection and processing, and we review the existing genetically-encoded homotransfer biosensors. Full article
(This article belongs to the Special Issue FRET-Based Biosensors)
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