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Clark JA, Robinson S, Espinoza EM, Bao D, Derr JB, Croft L, O'Mari O, Grover WH, Vullev VI. Poly(dimethylsiloxane) as a room-temperature solid solvent for photophysics and photochemistry. Phys Chem Chem Phys 2024; 26:8062-8076. [PMID: 38372740 DOI: 10.1039/d3cp05413f] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/20/2024]
Abstract
Medium viscosity strongly affects the dynamics of solvated species and can drastically alter the deactivation pathways of their excited states. This study demonstrates the utility of poly(dimethylsiloxane) (PDMS) as a room-temperature solid-state medium for optical spectroscopy. As a thermoset elastic polymer, PDMS is transparent in the near ultraviolet, visible, and near infrared spectral regions. It is easy to mould into any shape, forming surfaces with a pronounced smoothness. While PDMS is broadly used for the fabrication of microfluidic devices, it swells in organic solvents, presenting severe limitations for the utility of such devices for applications employing non-aqueous fluids. Nevertheless, this swelling is reversible, which proves immensely beneficial for loading samples into the PDMS solid matrix. Transferring molecular-rotor dyes (used for staining prokaryotic cells and amyloid proteins) from non-viscous solvents into PDMS induces orders-of-magnitude enhancement of their fluorescence quantum yield and excited-state lifetimes, providing mechanistic insights about their deactivation pathways. These findings demonstrate the unexplored potential of PDMS as a solid solvent for optical applications.
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Affiliation(s)
- John A Clark
- Department of Bioengineering, University of California, Riverside, CA 92521, USA.
| | - Samantha Robinson
- Department of Bioengineering, University of California, Riverside, CA 92521, USA.
| | - Eli M Espinoza
- Department of Chemistry, University of California, Riverside, CA 92521, USA
| | - Duoduo Bao
- Department of Bioengineering, University of California, Riverside, CA 92521, USA.
| | - James B Derr
- Department of Biochemistry, University of California, Riverside, CA 92521, USA
| | - Luca Croft
- Department of Bioengineering, University of California, Riverside, CA 92521, USA.
| | - Omar O'Mari
- Department of Bioengineering, University of California, Riverside, CA 92521, USA.
| | - William H Grover
- Department of Bioengineering, University of California, Riverside, CA 92521, USA.
| | - Valentine I Vullev
- Department of Bioengineering, University of California, Riverside, CA 92521, USA.
- Department of Chemistry, University of California, Riverside, CA 92521, USA
- Department of Biochemistry, University of California, Riverside, CA 92521, USA
- Materials Science and Engineering Program, University of California, Riverside, CA 92521, USA
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2
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Alia JD, Flack JA. Unspecified verticality of Franck–Condon transitions, absorption and emission spectra of cyanine dyes, and a classically inspired approximation. RSC Adv 2020; 10:43153-43167. [PMID: 35514896 PMCID: PMC9058138 DOI: 10.1039/d0ra06774a] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2020] [Accepted: 11/18/2020] [Indexed: 12/19/2022] Open
Abstract
The computed vertical energy, Ev,a/f, from the equilibrium geometry of the initial electronic state is frequently considered as representative of the experimental excitation/emission energy, Eabs/fl = hc/λmax. Application of the quantum mechanical version of the Franck–Condon principle does not involve precise specification of nuclear positions before, after, or during an electronic transition. Moreover, the duration of an electronic transition is not experimentally accessible in spectra with resolved vibrational structure. It is shown that computed vibronic spectra based on TDDFT methods and application of quantum mechanical FC analysis predict Eabs = hc/λmax with a 10-fold improvement in accuracy compared to Ev,a for nine cyanine dyes. It is argued that part of the reason for accuracy when this FC analysis is compared to experiment as opposed to Ev,a/f is the unspecified verticality of transitions in the context of the quantum version of the FC principle. Classical FC transitions that preserve nuclear kinetic energy before and after an electronic transition were previously found to occur at a weighted average of final and initial electronic state molecular geometries known as the r-centroid. Inspired by this approach a qualitative method using computed vertical and adiabatic energies and the harmonic approximation is developed and applied yielding a 5-fold improvement in accuracy compared to Ev,a. This improvement results from the dominance of low frequency vibronic transitions in the cyanine dye major band. The model gives insight into the nature of the redshift when qPCR dye EvaGreen is complexed to λDNA and is applicable to the low frequency band of similar non cyanine dyes such as curcumin. It is found that the computed vibronic cyanine dye spectra from time-dependent FC analysis at 0 K and 298 K show decreased intensity at higher temperature suggestive of increased intensity with restricted motion shown when cyanine dyes are used in biomedical imaging. A 2-layer ONIOM model of the DNA minor groove indicates restricted motion of the TC-1 dye excited state in this setting indicative of enhanced fluorescence. Insight into cyanine dye λmax from quantum and classical FC principle; high accuracy with classically inspired approach.![]()
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Affiliation(s)
- Joseph D. Alia
- Division of Science and Mathematics
- University of Minnesota Morris
- USA
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3
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Magana JR, Solans C, Salonen LM, Carbó-Argibay E, Gallo J, Tiddy GJ, Rodríguez-Abreu C. Chromonic self-assemblies in a series of dialkyl-thiacarbocyanine dyes and generalization of a facile route for the synthesis of fluorescent nanostructured silica fibers. J Taiwan Inst Chem Eng 2018. [DOI: 10.1016/j.jtice.2018.03.027] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
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4
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Espinoza EM, Larsen-Clinton JM, Krzeszewski M, Darabedian N, Gryko DT, Vullev VI. Bioinspired approach toward molecular electrets: synthetic proteome for materials. PURE APPL CHEM 2017. [DOI: 10.1515/pac-2017-0309] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
AbstractMolecular-level control of charge transfer (CT) is essential for both, organic electronics and solar-energy conversion, as well as for a wide range of biological processes. This article provides an overview of the utility of local electric fields originating from molecular dipoles for directing CT processes. Systems with ordered dipoles, i.e. molecular electrets, are the centerpiece of the discussion. The conceptual evolution from biomimicry to biomimesis, and then to biological inspiration, paves the roads leading from testing the understanding of how natural living systems function to implementing these lessons into optimal paradigms for specific applications. This progression of the evolving structure-function relationships allows for the development of bioinspired electrets composed of non-native aromatic amino acids. A set of such non-native residues that are electron-rich can be viewed as a synthetic proteome for hole-transfer electrets. Detailed considerations of the electronic structure of an individual residue prove of key importance for designating the points for optimal injection of holes (i.e. extraction of electrons) in electret oligomers. This multifaceted bioinspired approach for the design of CT molecular systems provides unexplored paradigms for electronic and energy science and engineering.
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Affiliation(s)
- Eli M. Espinoza
- Department of Chemistry, University of California, Riverside, CA 92521, USA
| | | | - Maciej Krzeszewski
- Department of Bioengineering, University of California, Riverside, CA 92521, USA
- Institute of Organic Chemistry, Polish Academy of Sciences, Kasprzaka 44-52, 01-224 Warsaw, Poland
| | - Narek Darabedian
- Department of Bioengineering, University of California, Riverside, CA 92521, USA
| | - Daniel T. Gryko
- Institute of Organic Chemistry, Polish Academy of Sciences, Kasprzaka 44-52, 01-224 Warsaw, Poland
| | - Valentine I. Vullev
- Department of Chemistry, University of California, Riverside, CA 92521, USA
- Department of Bioengineering, University of California, Riverside, CA 92521, USA
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5
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Yao H, Enseki T. Organic Ion-Pair Charge-Transfer (IPCT) Nanoparticles: Synthesis and Photoinduced Electrochromism. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2017; 33:219-227. [PMID: 27960059 DOI: 10.1021/acs.langmuir.6b03618] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
We report fabrication of photoinduced-electrochromic (or photochromic) organic nanoparticles that can be regarded as a new class of photoswitchable nanomaterials. Ion association between dicationic benzyl viologen (BzV2+) and tetraphenylborate anion (TPB-) in water produces organic ion-pair charge-transfer-type (IPCT) nanoparticles with a mean diameter of 15-20 nm. Electrostatic binding of BzV2+ with TPB- results in the prominent appearance of a new broad absorption band at 400-550 nm, which can be assign to the CT transition between these species. The IPCT nanoparticles show an interesting photoinduced electrochromic behavior caused by the electron transfer (ET) from TPB- to BzV2+, giving an intense blue-color dispersion. The feed charge stoichiometry (= [TPB-]/(2 × [BzV2+])) does not influence the kinetics of the photoinduced electrochromism, but it remarkably controls the reverse ET reaction (or retention time) in the nanoparticles; in the case of neutral stoichiometry, a very long-lived ET state can be observed, which is mainly due to decomposition of the oxidized TPB (sacrificial donor) and the resultant absence of the counterpart of benzyl viologen radical cations (BzV+•) for back ET reaction. On the other hand, the excess presence of TPB- does not cause the decomposition of oxidized TPB in the nanoparticle, making the reverse ET reaction faster, but a moderately long-lived ET state is still observable, which is probably originated from efficient electron diffusion or transport between molecules inside the nanoparticle.
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Affiliation(s)
- Hiroshi Yao
- Graduate School of Material Science, University of Hyogo , 3-2-1 Koto, Kamigori-cho, Ako-gun, Hyogo 678-1297, Japan
| | - Tomoki Enseki
- Graduate School of Material Science, University of Hyogo , 3-2-1 Koto, Kamigori-cho, Ako-gun, Hyogo 678-1297, Japan
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6
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Upadhyayula S, Nuñez V, Espinoza EM, Larsen JM, Bao D, Shi D, Mac JT, Anvari B, Vullev VI. Photoinduced dynamics of a cyanine dye: parallel pathways of non-radiative deactivation involving multiple excited-state twisted transients. Chem Sci 2015; 6:2237-2251. [PMID: 29449923 PMCID: PMC5701728 DOI: 10.1039/c4sc02881c] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2014] [Accepted: 02/09/2015] [Indexed: 12/11/2022] Open
Abstract
Cyanine dyes are broadly used for fluorescence imaging and other photonic applications. 3,3'-Diethylthiacyanine (THIA) is a cyanine dye composed of two identical aromatic heterocyclic moieties linked with a single methine, -CH[double bond, length as m-dash]. The torsional degrees of freedom around the methine bonds provide routes for non-radiative decay, responsible for the inherently low fluorescence quantum yields. Using transient absorption spectroscopy, we determined that upon photoexcitation, the excited state relaxes along two parallel pathways producing three excited-state transients that undergo internal conversion to the ground state. The media viscosity impedes the molecular modes of ring rotation and preferentially affects one of the pathways of non-radiative decay, exerting a dominant effect on the emission properties of THIA. Concurrently, the polarity affects the energy of the transients involved in the decay pathways and further modulates the kinetics of non-radiative deactivation.
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Affiliation(s)
- Srigokul Upadhyayula
- Department of Bioengineering , University of California , Riverside , CA 92521 , USA .
- Department of Biochemistry , University of California , Riverside , CA 92521 , USA
| | - Vicente Nuñez
- Department of Bioengineering , University of California , Riverside , CA 92521 , USA .
| | - Eli M Espinoza
- Department of Chemistry , University of California , Riverside , CA 92521 , USA
| | - Jillian M Larsen
- Department of Bioengineering , University of California , Riverside , CA 92521 , USA .
| | - Duoduo Bao
- Department of Bioengineering , University of California , Riverside , CA 92521 , USA .
| | - Dewen Shi
- Department of Bioengineering , University of California , Riverside , CA 92521 , USA .
| | - Jenny T Mac
- Department of Biochemistry , University of California , Riverside , CA 92521 , USA
| | - Bahman Anvari
- Department of Bioengineering , University of California , Riverside , CA 92521 , USA .
| | - Valentine I Vullev
- Department of Bioengineering , University of California , Riverside , CA 92521 , USA .
- Department of Biochemistry , University of California , Riverside , CA 92521 , USA
- Department of Chemistry , University of California , Riverside , CA 92521 , USA
- Materials Science and Engineering Program , University of California , Riverside , CA 92521 , USA
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7
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Abstract
This chapter describes an experimental layout for time and spectrally resolved fluorescence measurements with femtosecond time resolution based on Kerr gating. The combination of data recorded using different Kerr media allows a temporal dynamic range from ~100 fs to several nanoseconds. Simultaneous analysis of multiple datasets is described.
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Affiliation(s)
- Sergey P Laptenok
- Laboratoire d'Optique et Biosciences, INSERM U696-CNRS UMR7645, Ecole Polytechnique, Palaiseau, France
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8
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Nuñez V, Upadhyayula S, Millare B, Larsen JM, Hadian A, Shin S, Vandrangi P, Gupta S, Xu H, Lin AP, Georgiev GY, Vullev VI. Microfluidic Space-Domain Time-Resolved Emission Spectroscopy of Terbium(III) and Europium(III) Chelates with Pyridine-2,6-Dicarboxylate. Anal Chem 2013; 85:4567-77. [DOI: 10.1021/ac400200x] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Affiliation(s)
- Vicente Nuñez
- Department of Bioengineering
and Center for Bioengineering Research, University of California, Riverside, California 92521, United States
| | - Srigokul Upadhyayula
- Department of Bioengineering
and Center for Bioengineering Research, University of California, Riverside, California 92521, United States
- Department of Biochemistry, University of California, Riverside, California 92521,
United States
| | - Brent Millare
- Department of Bioengineering
and Center for Bioengineering Research, University of California, Riverside, California 92521, United States
| | - Jillian M. Larsen
- Department of Bioengineering
and Center for Bioengineering Research, University of California, Riverside, California 92521, United States
| | - Ali Hadian
- Department of Bioengineering
and Center for Bioengineering Research, University of California, Riverside, California 92521, United States
| | - Sanghoon Shin
- Department of Bioengineering
and Center for Bioengineering Research, University of California, Riverside, California 92521, United States
| | - Prashanthi Vandrangi
- Department of Bioengineering
and Center for Bioengineering Research, University of California, Riverside, California 92521, United States
| | - Sharad Gupta
- Department of Bioengineering
and Center for Bioengineering Research, University of California, Riverside, California 92521, United States
| | - Hong Xu
- Department of Bioengineering
and Center for Bioengineering Research, University of California, Riverside, California 92521, United States
| | - Adam P. Lin
- Department of Bioengineering
and Center for Bioengineering Research, University of California, Riverside, California 92521, United States
| | - Georgi Y. Georgiev
- Department of Bioengineering
and Center for Bioengineering Research, University of California, Riverside, California 92521, United States
| | - Valentine I. Vullev
- Department of Bioengineering
and Center for Bioengineering Research, University of California, Riverside, California 92521, United States
- Department of Biochemistry, University of California, Riverside, California 92521,
United States
- Department
of Chemistry, University of California,
Riverside, California 92521,
United States
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9
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Upadhyayula S, Lam S, Ha A, Malik-Chaudhry HK, Vullev VI. Dynamic staining of Bacillus endospores with Thioflavin T. ANNUAL INTERNATIONAL CONFERENCE OF THE IEEE ENGINEERING IN MEDICINE AND BIOLOGY SOCIETY. IEEE ENGINEERING IN MEDICINE AND BIOLOGY SOCIETY. ANNUAL INTERNATIONAL CONFERENCE 2013; 2012:499-502. [PMID: 23365938 DOI: 10.1109/embc.2012.6345977] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
Rapid detection and identification of endospores presents a range of complex challenges. Dynamic staining approach, developed in our lab, utilizes the time-course fluorescence enhancement of an amyloid-staining dye, Thioflavin T (ThT), after mixing with intact endospores. We examined the kinetics of staining Bacillus atrophaeus and Bacillus thuringiensis endospores, and the rates of staining were different for the two bacilli when intact endospores were treated with ThT. This finding demonstrates an avenue for attaining information about the sporulated bacterial species without lysing, germinating or other pretreatment steps.
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Affiliation(s)
- Srigokul Upadhyayula
- Department of Biochemistry, Department of Bioengineering and Center for Bioengineering Research, University of California, Riverside, CA 92521, USA.
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10
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Xia B, Bao D, Upadhyayula S, Jones G, Vullev VI. Anthranilamides as bioinspired molecular electrets: experimental evidence for a permanent ground-state electric dipole moment. J Org Chem 2013; 78:1994-2004. [PMID: 23270467 DOI: 10.1021/jo301942g] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
As electrostatic equivalents of magnets, organic electrets offer unparalleled properties for impacting energy conversion and electronic applications. While biological systems have evolved to efficiently utilize protein α-helices as molecular electrets, the synthetic counterparts of these conjugates still remain largely unexplored. This paper describes a study of the electronic properties of anthranilamide oligomers, which proved to be electrets based on their intrinsic dipole moments as evident from their spectral and dielectric properties. NMR studies provided the means for estimating the direction of the intrinsic electric dipoles of these conjugates. This study sets the foundation for the development of a class of organic materials that are de novo designed from biomolecular motifs and possess unexplored electronic properties.
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Affiliation(s)
- Bing Xia
- Department of Bioengineering, University of California, Riverside, California 92521, United States
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11
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Yao H, Ashiba K. Efficient Excitation-Energy Transfer in Ion-Based Organic Nanoparticles with Versatile Tunability of the Fluorescence Colours. Chemphyschem 2012; 13:2703-10. [DOI: 10.1002/cphc.201200191] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2012] [Revised: 04/19/2012] [Indexed: 11/06/2022]
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12
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Upadhyayula S, Quinata T, Bishop S, Gupta S, Johnson NR, Bahmani B, Bozhilov K, Stubbs J, Jreij P, Nallagatla P, Vullev VI. Coatings of polyethylene glycol for suppressing adhesion between solid microspheres and flat surfaces. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2012; 28:5059-69. [PMID: 22364506 DOI: 10.1021/la300545v] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/23/2023]
Abstract
This article describes the development and the examination of surface coatings that suppress the adhesion between glass surfaces and polymer microspheres. Superparamagnetic doping allowed for exerting magnetic forces on the microbeads. The carboxyl functionalization of the polymer provided the means for coating the beads with polyethylene glycol (PEG) with different molecular weight. Under gravitational force, the microbeads settled on glass surfaces with similar polymer coatings. We examined the efficacy of removing the beads from the glass surfaces by applying a pulling force of ~1.2 pN. The percent beads remaining on the surface after applying the pulling force for approximately 5 s served as an indication of the adhesion propensity. Coating of PEG with molecular weight ranging between 3 and 10 kDa was essential for suppressing the adhesion. For the particular substrates, surface chemistry and aqueous media we used, coatings of 5 kDa manifested optimal suppression of adhesion: that is, only 3% of the microbeads remained on the surface after applying the pulling magnetic force. When either the glass or the beads were not PEGylated, the adhesion between them was substantial. Addition of a noncharged surfactant, TWEEN, above its critical micelle concentrations (CMCs) suppressed the adhesion between noncoated substrates. The extent of this surfactant-induced improvement of the adhesion suppression, however, did not exceed the quality of preventing the adhesion that we attained by PEGylating both substrates. In addition, the use of surfactants did not significantly improve the suppression of bead-surface adhesion when both substrates were PEGylated. These findings suggest that such surfactant additives tend to be redundant and that covalently grafted coatings of PEGs with selected chain lengths provide sufficient suppression of nonspecific interfacial interactions.
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Affiliation(s)
- Srigokul Upadhyayula
- Department of Bioengineering, University of California, Riverside, California 91521, United States
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13
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Abstract
Bacterial endospores are some of the most resilient forms of life known to us, with their persistent survival capability resulting from a complex and effective structural organization. The outer membrane of endospores is surrounded by the densely packed endospore coat and exosporium, containing amyloid or amyloid-like proteins. In fact, it is the impenetrable composition of the endospore coat and the exosporium that makes staining methodologies for endospore detection complex and challenging. Therefore, a plausible strategy for facile and expedient staining would be to target components of the protective surface layers of the endospores. Instead of targeting endogenous markers encapsulated in the spores, here we demonstrated staining of these dormant life entities that targets the amyloid domains, i.e., the very surface components that make the coats of these species impenetrable. Using an amyloid staining dye, thioflavin T (ThT), we examined this strategy. A short incubation of bacillus endospore suspensions with ThT, under ambient conditions, resulted in (i) an enhancement of the fluorescence of ThT and (ii) the accumulation of ThT in the endospores, affording fluorescence images with excellent contrast ratios. Fluorescence images revealed that ThT tends to accumulate in the surface regions of the endospores. The observed fluorescence enhancement and dye accumulation, coupled with the sensitivity of emission techniques, provide an effective and rapid means of staining endospores without the inconvenience of pre- or posttreatment of samples.
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14
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Yao H, Ashiba K. Highly fluorescent organic nanoparticles of thiacyanine dye: A synergetic effect of intermolecular H-aggregation and restricted intramolecular rotation. RSC Adv 2011. [DOI: 10.1039/c1ra00497b] [Citation(s) in RCA: 54] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023] Open
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