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Article ; Online: Optofluidic Accumulation of Silica Beads on Gel-Based Three-Dimensional SERS Substrate To Enhance Sensitivity Using Multiple Photonic Nanojets.

Xie, Cheng-Zhe / Li, Cheng-Han / Chang, You-Chia / Chen, Yih-Fan

ACS applied materials & interfaces

2023 Volume 15, Issue 26, Page(s) 31703–31710

Abstract: This paper presents a gel-based three-dimensional (3D) substrate for surface-enhanced Raman spectroscopy (SERS) mediated by photonic nanojets (PNJs) to enhance the sensitivity of SERS detection. The porous structure of the gel-based substrate allowed ... ...

Abstract	This paper presents a gel-based three-dimensional (3D) substrate for surface-enhanced Raman spectroscopy (SERS) mediated by photonic nanojets (PNJs) to enhance the sensitivity of SERS detection. The porous structure of the gel-based substrate allowed small molecules to diffuse into the substrate, while the placement of silica beads on the substrate surface resulted in the generation of photonic nanojets during SERS measurements. Because the gel-based SERS substrate had electromagnetic (EM) hot spots along the
Language	English
Publishing date	2023-06-21
Publishing country	United States
Document type	Journal Article
ISSN	1944-8252
ISSN (online)	1944-8252
DOI	10.1021/acsami.3c04569
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Article: Comparison of Hydrogen Peroxide Secretion From Living Cells Cultured in Different Formats Using Hydrogel-Based LSPR Substrates.

Siao, Yang-Jyun / Peng, Chien-Chung / Tung, Yi-Chung / Chen, Yih-Fan

Frontiers in bioengineering and biotechnology

2022 Volume 10, Page(s) 869184

Abstract: Reactive oxygen species (ROS), a number of reactive molecules and free radicals derived from molecular oxygen, are generated as by-products during mitochondrial electron transport within cells. Physiologically, cells are capable of metabolizing the ROS ... ...

Abstract	Reactive oxygen species (ROS), a number of reactive molecules and free radicals derived from molecular oxygen, are generated as by-products during mitochondrial electron transport within cells. Physiologically, cells are capable of metabolizing the ROS exploiting specific mechanisms. However, if excessive ROS accumulate inside the cells, it will cause the cells apoptosis or necrosis. Hydrogen peroxide (H
Language	English
Publishing date	2022-04-08
Publishing country	Switzerland
Document type	Journal Article
ZDB-ID	2719493-0
ISSN	2296-4185
ISSN	2296-4185
DOI	10.3389/fbioe.2022.869184
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Article ; Online: High temporal resolution and polarization resolved fluorescence lifetime measurements through stimulated emission.

Rehman, Khalil Ur / Das, Subir / Chen, Yih-Fan / Kao, Fu-Jen

Methods and applications in fluorescence

2020 Volume 8, Issue 2, Page(s) 24008

Abstract: We have implemented polarization-resolved fluorescence lifetime measurement through stimulated emission based pump-probe technique, which promises much higher temporal resolution (∼4 ps) than conventional time-correlated single-photon counting (TCSPC). ... ...

Abstract	We have implemented polarization-resolved fluorescence lifetime measurement through stimulated emission based pump-probe technique, which promises much higher temporal resolution (∼4 ps) than conventional time-correlated single-photon counting (TCSPC). The depolarization of ATTO 647N fluorescent dye is resolved through anisotropy fluorescence lifetime measurements, with variable time delay introduced between the pump and the probe beams. Importantly, the polarization anisotropy measurement and the corresponding rotational correlation time characterization of the fluorescent dye are carried out at various temperatures. We have also demonstrated the need of high temporal resolution via hetero Förster energy transfer (Hetero-FRET) through the interaction between the gold nanorods (GNRs) and the fluorescent dye ATTO 647N. Notably, our results compare highly favorably with conventional TCSPC method, which is rather limited in temporal resolution, for the above characterization. Additionally, this technique is applicable even under ambient light while being very cost-effective and robust.
Language	English
Publishing date	2020-03-23
Publishing country	England
Document type	Journal Article
ISSN	2050-6120
ISSN (online)	2050-6120
DOI	10.1088/2050-6120/ab7c36
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Article: Rapid Formation of Nanoclusters for Detection of Drugs in Urine Using Surface-Enhanced Raman Spectroscopy.

Chen, Yun-Chu / Hong, Shang-Wen / Wu, Huang-Hesin / Wang, Yuh-Lin / Chen, Yih-Fan

Nanomaterials (Basel, Switzerland)

2021 Volume 11, Issue 7

Abstract: We developed a method based on surface-enhanced Raman spectroscopy (SERS) and a sample pretreatment process for rapid, sensitive, reproducible, multiplexed, and low-cost detection of illegal drugs in urine. The abuse of new psychoactive substances (NPS) ... ...

Abstract	We developed a method based on surface-enhanced Raman spectroscopy (SERS) and a sample pretreatment process for rapid, sensitive, reproducible, multiplexed, and low-cost detection of illegal drugs in urine. The abuse of new psychoactive substances (NPS) has become an increasingly serious problem in many countries. However, immunoassay-based screening kits for NPS are usually not available because of the lack of corresponding antibodies. SERS has a great potential for rapid detection of NPS because it can simultaneously detect multiple kinds of drugs without the use of antibodies. To achieve highly sensitive SERS detection of drugs, sodium bromide was first employed to induce the rapid formation of Ag nanoclusters by aggregating silver nanoparticles (AgNPs) in the extracted sample solution. SERS measurements were performed immediately after the sample pretreatment without incubation. The three-dimensional SERS hot spots were believed to form significantly within the nanoclusters, providing strong SERS enhancement effects. The displacement of citrate molecules on the surfaces of the AgNPs by bromide ions helped increase the adsorption of drug molecules, increasing their areal density. We demonstrated the simultaneous detection of two kinds of NPS, methcathinone and 4-methylmethcathinone, in urine at a concentration as low as 0.01 ppm.
Language	English
Publishing date	2021-07-09
Publishing country	Switzerland
Document type	Journal Article
ZDB-ID	2662255-5
ISSN	2079-4991
ISSN	2079-4991
DOI	10.3390/nano11071789
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Article ; Online: Concentration-dependent thermophoretic accumulation for the detection of DNA using DNA-functionalized nanoparticles.

Yu, Li-Hsien / Chen, Yih-Fan

Analytical chemistry

2015 Volume 87, Issue 5, Page(s) 2845–2851

Abstract: Thermophoresis is a phenomenon about the migration of particles along a temperature gradient and is sensitive to the properties of particles and the surrounding medium. While a few studies have investigated its mechanisms and effects on particle motion ... ...

Abstract	Thermophoresis is a phenomenon about the migration of particles along a temperature gradient and is sensitive to the properties of particles and the surrounding medium. While a few studies have investigated its mechanisms and effects on particle motion in recent years, the applications of thermophoresis in biosensing has not been well explored. In this study, we demonstrate a thermophoresis-based method for detecting DNA. We use DNA-functionalized gold nanoparticles and fluorescent DNA probes to capture target DNA in free solution, and we demonstrate that the hybridization between the specially designed capture probes and the target DNA significantly changes the thermophoretic properties of the fluorescent probes. As a result, the target DNA can be specifically detected in serum-containing buffers based on the spatial distribution of the fluorescent probes in a laser-induced temperature gradient. The optical setup consists of only a laser and an epifluorescence microscope, and the detection does not rely on any micro- or nanofabricated devices. In addition, because the detection is based on the thermophoretic motion of molecules in free solution, no capture probes need to be immobilized on a fixed surface before detection, and no channels or pumps are needed for washing away unbound molecules. The thermophoresis-based biosensing method is found to be simple and effective for detecting DNA.
MeSH term(s)	Biosensing Techniques/methods ; DNA/analysis ; DNA/chemistry ; Fluorescent Dyes/chemistry ; Gold/chemistry ; Humans ; Metal Nanoparticles/chemistry ; Temperature
Chemical Substances	Fluorescent Dyes ; Gold (7440-57-5) ; DNA (9007-49-2)
Language	English
Publishing date	2015-03-03
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	1508-8
ISSN	1520-6882 ; 0003-2700
ISSN (online)	1520-6882
ISSN	0003-2700
DOI	10.1021/ac504296e
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Article: Concentration-Dependent Thermophoretic Accumulation for the Detection of DNA Using DNA-Functionalized Nanoparticles

Yu, Li-Hsien / Chen Yih-Fan

Analytical chemistry. 2015 Mar. 03, v. 87, no. 5

2015

Abstract	Thermophoresis is a phenomenon about the migration of particles along a temperature gradient and is sensitive to the properties of particles and the surrounding medium. While a few studies have investigated its mechanisms and effects on particle motion in recent years, the applications of thermophoresis in biosensing has not been well explored. In this study, we demonstrate a thermophoresis-based method for detecting DNA. We use DNA-functionalized gold nanoparticles and fluorescent DNA probes to capture target DNA in free solution, and we demonstrate that the hybridization between the specially designed capture probes and the target DNA significantly changes the thermophoretic properties of the fluorescent probes. As a result, the target DNA can be specifically detected in serum-containing buffers based on the spatial distribution of the fluorescent probes in a laser-induced temperature gradient. The optical setup consists of only a laser and an epifluorescence microscope, and the detection does not rely on any micro- or nanofabricated devices. In addition, because the detection is based on the thermophoretic motion of molecules in free solution, no capture probes need to be immobilized on a fixed surface before detection, and no channels or pumps are needed for washing away unbound molecules. The thermophoresis-based biosensing method is found to be simple and effective for detecting DNA.
Keywords	buffers ; DNA ; DNA probes ; fluorescence ; fluorescent dyes ; nanogold ; nanoparticles ; nucleic acid hybridization ; temperature ; washing
Language	English
Dates of publication	2015-0303
Size	p. 2845-2851.
Publishing place	American Chemical Society
Document type	Article
ZDB-ID	1508-8
ISSN	1520-6882 ; 0003-2700
ISSN (online)	1520-6882
ISSN	0003-2700
DOI	10.1021%2Fac504296e
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Article ; Online: Three-Dimensional SERS Substrates Formed with Plasmonic Core-Satellite Nanostructures.

Wu, Li-An / Li, Wei-En / Lin, Ding-Zheng / Chen, Yih-Fan

Scientific reports

2017 Volume 7, Issue 1, Page(s) 13066

Abstract: We demonstrate three-dimensional surface-enhanced Raman spectroscopy (SERS) substrates formed by accumulating plasmonic nanostructures that are synthesized using a DNA-assisted assembly method. We densely immobilize Au nanoparticles (AuNPs) on polymer ... ...

Abstract	We demonstrate three-dimensional surface-enhanced Raman spectroscopy (SERS) substrates formed by accumulating plasmonic nanostructures that are synthesized using a DNA-assisted assembly method. We densely immobilize Au nanoparticles (AuNPs) on polymer beads to form core-satellite nanostructures for detecting molecules by SERS. The experimental parameters affecting the AuNP immobilization, including salt concentration and the number ratio of the AuNPs to the polymer beads, are tested to achieve a high density of the immobilized AuNPs. To create electromagnetic hot spots for sensitive SERS sensing, we add a Ag shell to the AuNPs to reduce the interparticle distance further, and we carefully adjust the thickness of the shell to optimize the SERS effects. In addition, to obtain sensitive and reproducible SERS results, instead of using the core-satellite nanostructures dispersed in solution directly, we prepare SERS substrates consisting of closely packed nanostructures by drying nanostructure-containing droplets on hydrophobic surfaces. The densely distributed small and well-controlled nanogaps on the accumulated nanostructures function as three-dimensional SERS hot spots. Our results show that the SERS spectra obtained using the substrates are much stronger and more reproducible than that obtained using the nanostructures dispersed in solution. Sensitive detection of melamine and sodium thiocyanate (NaSCN) are achieved using the SERS substrates.
Language	English
Publishing date	2017-10-12
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2615211-3
ISSN	2045-2322 ; 2045-2322
ISSN (online)	2045-2322
ISSN	2045-2322
DOI	10.1038/s41598-017-13577-9
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Article ; Online: Increasing the spectral shifts in LSPR biosensing using DNA-functionalized gold nanorods in a competitive assay format for the detection of interferon-γ.

Lin, Ding-Zheng / Chuang, Po-Chun / Liao, Pei-Chen / Chen, Jung-Po / Chen, Yih-Fan

Biosensors & bioelectronics

2016 Volume 81, Page(s) 221–228

Abstract: We demonstrate an approach that utilizes DNA-functionalized gold nanorods (AuNRs) in an indirect competitive assay format to increase the spectra shift in localized surface plasmon resonance (LSPR) biosensing. We use interferon gamma (IFN-γ) as a model ... ...

Abstract	We demonstrate an approach that utilizes DNA-functionalized gold nanorods (AuNRs) in an indirect competitive assay format to increase the spectra shift in localized surface plasmon resonance (LSPR) biosensing. We use interferon gamma (IFN-γ) as a model analyte to demonstrate the feasibility of our detection method. The LSPR chips with periodic gold nanodot arrays are fabricated using a thermal lithography process and are functionalized with IFN-γ aptamers for detection. The DNA-functionalized AuNRs and IFN-γ compete with each other to bind to the aptamers during detection, and the spectra shifts are mainly caused by the AuNRs rather than IFN-γ. When using our approach, the target molecules do not need to be captured by two capture ligands simultaneously during detection and thus do not require multiple binding sites. Both experiments and finite-difference time-domain (FDTD) simulations show that making the AuNRs as close to the chip surface as possible is very critical for increasing LSPR shifts, and the simulated results also show that the orientation of the AuNR affects the plasmon coupling between the gold nanodots on the chip surface and the nearby AuNRs. Although only the detection of IFN-γ is demonstrated in this study, we expect that the LSPR biosensing method can be applied to label-free detection of a variety of molecules as long as suitable aptamers are available.
MeSH term(s)	Aptamers, Nucleotide/chemistry ; Equipment Design ; Gold/chemistry ; Interferon-gamma/analysis ; Nanotubes/chemistry ; Surface Plasmon Resonance/instrumentation ; Surface Plasmon Resonance/methods
Chemical Substances	Aptamers, Nucleotide ; Gold (7440-57-5) ; Interferon-gamma (82115-62-6)
Language	English
Publishing date	2016-07-15
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	1011023-9
ISSN	1873-4235 ; 0956-5663
ISSN (online)	1873-4235
ISSN	0956-5663
DOI	10.1016/j.bios.2016.02.071
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Article ; Online: Femtonewton entropic forces can control the formation of protein-mediated DNA loops.

Chen, Yih-Fan / Milstein, J N / Meiners, Jens-Christian

Physical review letters

2010 Volume 104, Issue 4, Page(s) 48301

Abstract: We show that minuscule entropic forces, on the order of 100 fN, can prevent the formation of DNA loops-a ubiquitous means of regulating the expression of genes. We observe a tenfold decrease in the rate of LacI-mediated DNA loop formation when a tension ... ...

Abstract	We show that minuscule entropic forces, on the order of 100 fN, can prevent the formation of DNA loops-a ubiquitous means of regulating the expression of genes. We observe a tenfold decrease in the rate of LacI-mediated DNA loop formation when a tension of 200 fN is applied to the substrate DNA, biasing the thermal fluctuations that drive loop formation and breakdown events. Conversely, once looped, the DNA-protein complex is insensitive to applied force. Our measurements are in excellent agreement with a simple polymer model of loop formation in DNA, and show that an antiparallel topology is the preferred LacI-DNA loop conformation for a generic loop-forming construct.
MeSH term(s)	DNA, Bacterial/chemistry ; DNA, Bacterial/metabolism ; Entropy ; Escherichia coli/metabolism ; Kinetics ; Lac Repressors/metabolism ; Nucleic Acid Conformation ; Operator Regions, Genetic
Chemical Substances	DNA, Bacterial ; Lac Repressors
Language	English
Publishing date	2010-01-29
Publishing country	United States
Document type	Journal Article ; Research Support, N.I.H., Extramural ; Research Support, U.S. Gov't, Non-P.H.S.
ZDB-ID	208853-8
ISSN	1079-7114 ; 0031-9007
ISSN (online)	1079-7114
ISSN	0031-9007
DOI	10.1103/PhysRevLett.104.048301
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Article ; Online: Protein-mediated DNA loop formation and breakdown in a fluctuating environment.

Chen, Yih-Fan / Milstein, J N / Meiners, Jens-Christian

Physical review letters

2010 Volume 104, Issue 25, Page(s) 258103

Abstract: Living cells provide a fluctuating, out-of-equilibrium environment in which genes must coordinate cellular function. DNA looping, which is a common means of regulating transcription, is very much a stochastic process; the loops arise from the thermal ... ...

Abstract	Living cells provide a fluctuating, out-of-equilibrium environment in which genes must coordinate cellular function. DNA looping, which is a common means of regulating transcription, is very much a stochastic process; the loops arise from the thermal motion of the DNA and other fluctuations of the cellular environment. We present single-molecule measurements of DNA loop formation and breakdown when an artificial fluctuating force, applied to mimic a fluctuating cellular environment, is imposed on the DNA. We show that loop formation is greatly enhanced in the presence of noise of only a fraction of k_{B}T, yet find that hypothetical regulatory schemes that employ mechanical tension in the DNA-as a sensitive switch to control transcription-can be surprisingly robust due to a fortuitous cancellation of noise effects.
MeSH term(s)	Biomechanical Phenomena ; DNA/chemistry ; DNA/metabolism ; DNA/physiology ; Gene Expression Regulation ; Models, Biological ; Motion ; Nucleic Acid Conformation ; Proteins/metabolism ; Stochastic Processes ; Temperature ; Thermodynamics
Chemical Substances	Proteins ; DNA (9007-49-2)
Language	English
Publishing date	2010-06-25
Publishing country	United States
Document type	Journal Article ; Research Support, N.I.H., Extramural ; Research Support, U.S. Gov't, Non-P.H.S.
ZDB-ID	208853-8
ISSN	1079-7114 ; 0031-9007
ISSN (online)	1079-7114
ISSN	0031-9007
DOI	10.1103/PhysRevLett.104.258103
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