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Simisi Clovis N, Alam P, Kumar Chand A, Sardana D, Firoz Khan M, Sen S. Molecular Crowders Modulate Ligand Binding Affinity to G-Quadruplex DNA by Decelerating Ligand Association. J Photochem Photobiol A Chem 2022. [DOI: 10.1016/j.jphotochem.2022.114432] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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2
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Clovis NS, Sen S. G-Tetrad-Selective Ligand Binding Kinetics in G-Quadruplex DNA Probed with Fluorescence Correlation Spectroscopy. J Phys Chem B 2022; 126:6007-6015. [PMID: 35939531 DOI: 10.1021/acs.jpcb.2c04181] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Probing the kinetics of ligand binding to biomolecules is of paramount interest in biology and pharmacology. Measurements of such kinetic processes provide information on the rate-determining steps that control the binding affinity of ligands to biomolecules, thereby predicting the mechanism of the molecular interaction. In this context, ligand binding to G-quadruplex DNA (GqDNA) structures has attracted tremendous attention primarily because of their use in possible anticancer therapy. Although a large number of G-quadruplex-specific ligands have been proposed, probing the kinetics of G-tetrad-selective binding of (multiple) ligands within a G-quadruplex DNA (GqDNA) structure remains challenging. Most of the earlier studies focused on the thermodynamics of ligand binding; however, the kinetics of ligand association and dissociation with GqDNA, particularly binding of multiple ligands within a GqDNA structure, have not been explored. Here, we propose a simple fluorescence correlation spectroscopy-based method that measures the G-tetrad-selective association and dissociation rates of ligands within a GqDNA structure by correlating the fluorescence fluctuations of a site-specific (5' or 3' end-labeled) fluorophore (Cy3) in GqDNA due to quenching of Cy3 fluorescence, induced by the ligand binding to the G-tetrads. We show that well-known GqDNA ligands, BRACO19, TMPyP4, Hoechst 33258, and Hoechst 33342, have G-tetrad-selective association and dissociation rates, which suggest site-dependent variation of free energy barriers for binding/unbinding of the ligands with GqDNA. We also show that the measured kinetic rates depend not only on the G-tetrad site (5' vs 3' end) but also on the ligand and GqDNA structures.
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Affiliation(s)
- Ndege Simisi Clovis
- Spectroscopy Laboratory, School of Physical Sciences, Jawaharlal Nehru University, New Delhi 110067, India
| | - Sobhan Sen
- Spectroscopy Laboratory, School of Physical Sciences, Jawaharlal Nehru University, New Delhi 110067, India
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3
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Tang X, Chen T, Chen H, Yu S, Cao S, Liu C, Ma Y, Sun F, Pan Q, Zhu X. Sperm-like nanocarriers for ultrafast delivery of antisense DNA. NANOSCALE 2022; 14:10844-10850. [PMID: 35838371 DOI: 10.1039/d2nr02050e] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Although various nanomaterials have been designed as intracellular delivery tools, the following aspects have become obstacles to limit their development, like a complex and time-consuming synthesis process, as well as relatively limited application areas (i.e. biosensing or cell imaging). Here, we developed a novel nano-delivery system called "nano-sperm" with low cytotoxicity and high biocompatibility. In this system, we used DNA oligonucleotides as a backbone to synthesize a nanostructure with silver nanoclusters in the head and functional fragments in the tail, which is shaped like a sperm, to achieve dual functions of ultrafast delivery and imaging/therapy. As a model, we analyzed the possibility of the "nano-sperm" carrying DNA with different structures for imaging or survivin-asDNA for tumor therapy. Therefore, this work reports a novel bifunctional high-speed delivery vehicle, which successfully fills the gap in the field of tumor therapy using DNA-templated nanoclusters as a delivery vehicle.
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Affiliation(s)
- Xiaochen Tang
- Department of Clinical Laboratory Medicine, Shanghai Children's Medical Center, School of Medicine, Shanghai Jiao Tong University, Shanghai 200127, P. R. China.
- Shanghai Key Laboratory of Clinical Molecular Diagnostics for Pediatrics, Shanghai 200127, P. R. China
| | - Tianshu Chen
- Department of Clinical Laboratory Medicine, Shanghai Children's Medical Center, School of Medicine, Shanghai Jiao Tong University, Shanghai 200127, P. R. China.
- Shanghai Key Laboratory of Clinical Molecular Diagnostics for Pediatrics, Shanghai 200127, P. R. China
| | - Huinan Chen
- School of Life Sciences, Shanghai University, Shanghai 200444, P. R. China
| | - Sinuo Yu
- School of Life Sciences, Shanghai University, Shanghai 200444, P. R. China
| | - Siyu Cao
- School of Life Sciences, Shanghai University, Shanghai 200444, P. R. China
| | - Chenbin Liu
- Department of Clinical Laboratory Medicine, Shanghai Tenth People's Hospital of Tongji University, Shanghai 200072, P. R. China.
| | - Yonggeng Ma
- School of Life Sciences, Shanghai University, Shanghai 200444, P. R. China
| | - Fenyong Sun
- Department of Clinical Laboratory Medicine, Shanghai Tenth People's Hospital of Tongji University, Shanghai 200072, P. R. China.
| | - Qiuhui Pan
- Department of Clinical Laboratory Medicine, Shanghai Children's Medical Center, School of Medicine, Shanghai Jiao Tong University, Shanghai 200127, P. R. China.
- Shanghai Key Laboratory of Clinical Molecular Diagnostics for Pediatrics, Shanghai 200127, P. R. China
| | - Xiaoli Zhu
- Department of Clinical Laboratory Medicine, Shanghai Tenth People's Hospital of Tongji University, Shanghai 200072, P. R. China.
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4
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Development of fluorescence-xBased nucleic acid blot hybridization method using Cy5.5 labeled DNA probes. J Microbiol Methods 2022; 197:106479. [DOI: 10.1016/j.mimet.2022.106479] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2022] [Revised: 04/26/2022] [Accepted: 04/26/2022] [Indexed: 12/27/2022]
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5
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Pace NA, Hennelly SP, Goodwin PM. Immobilization of Cyanines in DNA Produces Systematic Increases in Fluorescence Intensity. J Phys Chem Lett 2021; 12:8963-8971. [PMID: 34506152 DOI: 10.1021/acs.jpclett.1c02022] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
Cyanines are useful fluorophores for a myriad of biological labeling applications, but their interactions with biomolecules are unpredictable. Cyanine fluorescence intensity can be highly variable due to complex photoisomerization kinetics, which are exceedingly sensitive to the surrounding environment. This introduces large errors in Förster resonance energy transfer (FRET)-based experiments where fluorescence intensity is the output parameter. However, this environmental sensitivity is a strength from a biological sensing point of view if specific relationships between biomolecular structure and cyanine photophysics can be identified. We describe a set of DNA structures that modulate cyanine fluorescence intensity through the insertion of adenine or thymine bases. These structures simultaneously provide photophysical predictability and tunability. We characterize these structures using steady-state fluorescence measurements, fluorescence correlation spectroscopy (FCS), and time-resolved photoluminescence (TRPL). We find that the photoisomerization rate decreases over an order of magnitude across the adenine series, which is consistent with increasing immobilization of the cyanine moiety by the surrounding DNA structure.
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Affiliation(s)
- Natalie A Pace
- Center for Integrated Nanotechnologies, Los Alamos National Laboratory, Los Alamos, New Mexico 87545, United States
| | - Scott P Hennelly
- Bioenergy and Biome Sciences Group, Los Alamos National Laboratory, Los Alamos, New Mexico 87545, United States
| | - Peter M Goodwin
- Center for Integrated Nanotechnologies, Los Alamos National Laboratory, Los Alamos, New Mexico 87545, United States
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6
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Kawai K, Maruyama A. Kinetics of Photoinduced Reactions at the Single‐Molecule Level: The KACB Method. Chemistry 2020; 26:7740-7746. [DOI: 10.1002/chem.202000439] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2020] [Revised: 02/20/2020] [Indexed: 01/08/2023]
Affiliation(s)
- Kiyohiko Kawai
- The Institute of Scientific and Industrial Research (SANKEN)Osaka University Mihogaoka 8-1 Ibaraki, Osaka 567-0047 Japan
| | - Atsushi Maruyama
- Department of Life Science and TechnologyTokyo Institute of Technology 4259 B-57 Nagatsuta Midori-ku, Yokohama, Kanagawa 226-8501 Japan
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7
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Larkey NE, Phillips JL, Jang HS, Kolluri SK, Burrows SM. Small RNA Biosensor Design Strategy To Mitigate Off-Analyte Response. ACS Sens 2020; 5:377-384. [PMID: 31942801 DOI: 10.1021/acssensors.9b01968] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
Abstract
Several bottlenecks in the design of current sensor technologies for small noncoding RNA must be addressed. The small size of the sensors and the large number of other nucleotides that may have sequence similarity makes selectivity a real concern. Many of the current sensors have one strand with an exposed region called a toehold. The toehold serves as a place for the analyte nucleic acid strand to bind and initiate competitive displacement of sensors' secondary strands. Since the toehold region is not protected, any endogenous oligonucleotide sequences that are similar or only different by a few nucleic acids will interact with the toehold and cause false signals. To address sensor selectivity, we investigated how the toehold location in the sensor impacts the sensitivity and selectivity for the analyte of interest. We will discuss the differences in sensitivity and selectivity for a miR-146a-5p biosensor in the presence of different naturally occurring mismatch sequences. We found that altering the toehold location lowered the rate of the false signal from off-analyte microRNA by upward of 20 percentage points. Detection limits as low as 56 pM were observed when the sensor concentration was 5 nM. The findings herein are broadly applicable to other small and large RNAs as well as other types of sensing platforms.
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Affiliation(s)
- Nicholas E. Larkey
- Department of Chemistry, Oregon State University, 153 Gilbert Hall, Corvallis, Oregon 97331, United States
| | - Jessica L. Phillips
- Department of Environmental and Molecular Toxicology, Cancer Research Laboratory, Oregon State University, Corvallis, Oregon 97331, United States
| | - Hyo Sang Jang
- Department of Environmental and Molecular Toxicology, Cancer Research Laboratory, Oregon State University, Corvallis, Oregon 97331, United States
| | - Siva K. Kolluri
- Department of Environmental and Molecular Toxicology, Cancer Research Laboratory, Oregon State University, Corvallis, Oregon 97331, United States
| | - Sean M. Burrows
- Department of Chemistry, Oregon State University, 153 Gilbert Hall, Corvallis, Oregon 97331, United States
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8
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Lee SY, Fazlina N, Tye GJ. DNA-templated silver nanocluster for live-intracellular FOXP3 detection. Anal Biochem 2019; 581:113352. [DOI: 10.1016/j.ab.2019.113352] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2018] [Revised: 06/10/2019] [Accepted: 06/27/2019] [Indexed: 01/23/2023]
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9
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Kohle FFE, Hinckley JA, Wiesner UB. Dye Encapsulation in Fluorescent Core-Shell Silica Nanoparticles as Probed by Fluorescence Correlation Spectroscopy. THE JOURNAL OF PHYSICAL CHEMISTRY. C, NANOMATERIALS AND INTERFACES 2019; 123:9813-9823. [PMID: 31819780 PMCID: PMC6901343 DOI: 10.1021/acs.jpcc.9b00297] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/22/2023]
Abstract
Synthetic advances in the formation of ultrasmall (<10 nm) fluorescent poly(ethylene glycol)-coated (PEGylated) core-shell silica nanoparticles (SNPs), enabling improved particle size and surface chemical property control have led to successful clinical translation of SNPs as diagnostic probes in oncology. Despite the success of such probes, details of the dye incorporation and resulting silica architecture are still poorly understood. Here, we employ afterpulse-corrected fluorescence correlation spectroscopy (FCS) to monitor fast fluorescence fluctuations (lag times <10-5 s) of the negatively charged cyanine dye Cy5 as a probe to study such details for dye encapsulation in 5 nm silica cores of PEGylated core-shell SNPs (C dots). Upon deposition of additional silica shells over the silica core we find that the amplitude of photo-induced cis-trans isomerization decreases, suggesting that the Cy5 dyes are located near or on the surface of the original SNP cores. In combination with time correlated fluorescence decay measurements we deduce radiative and non-radiative rates of the Cy5 dye in these particles. Results demonstrate that FCS is a well-suited tool to investigate aspects of the photophysics of fluorescent nanoparticles, and that conformational changes of cyanine dyes like Cy5 are excellent indicators for the local dye environment within ultrasmall SNPs.
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Affiliation(s)
- Ferdinand F. E. Kohle
- Materials Science and Engineering, Cornell University, Ithaca, NY 14853
- Chemistry and Chemical Biology, Cornell University, Ithaca, NY 14853
| | - Joshua A. Hinckley
- Materials Science and Engineering, Cornell University, Ithaca, NY 14853
- Chemistry and Chemical Biology, Cornell University, Ithaca, NY 14853
| | - Ulrich B. Wiesner
- Materials Science and Engineering, Cornell University, Ithaca, NY 14853
- Department of Materials Science and Engineering, Cornell University, 330 Bard Hall, Ithaca, NY 14853. Fax: 607-255-2365
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10
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Kawai K, Maruyama A. Triple helix conformation-specific blinking of Cy3 in DNA. Chem Commun (Camb) 2015; 51:4861-4. [PMID: 25697775 DOI: 10.1039/c5cc00607d] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
We report that Cy3 undergoes triple helix conformation-specific blinking in DNA. Blinking patterns were affected by the stabilization of the Hoogsteen base-pair, suggesting that not only the presence but also the fluctuating behaviour of the triple helix can be monitored by the changes in the Cy3 blinking patterns.
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Affiliation(s)
- Kiyohiko Kawai
- The Institute of Scientific and Industrial Research, Osaka University, Mihogaoka 8-1, Ibaraki, Osaka 5670047, Japan.
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11
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Abstract
Fluorescent silver nanoclusters (few atoms, quantum sized) have attracted much attention as promising substitutes for conventional fluorophores. Due to their unique environmental sensitivities, new fluorescent probes have been developed based on silver nanoclusters for the sensitive and specific detection of DNA. In this review we present the recent discoveries of activatable and color-switchable properties of DNA-templated silver nanoclusters and discuss the strategies to use these new properties in DNA sensing.
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Affiliation(s)
- Judy M Obliosca
- Department of Biomedical Engineering, University of Texas at Austin, Austin, TX 78712, USA
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12
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Shin HS, Okamoto A, Sako Y, Kim SW, Kim SY, Pack CG. Characterization of the triplet state of hybridization-sensitive DNA probe by using fluorescence correlation spectroscopy. J Phys Chem A 2012; 117:27-33. [PMID: 23210598 DOI: 10.1021/jp307018k] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
The nonradiative relaxation mechanism of the newly synthesized hybridized-sensitive DNA probe has not been fully understood until now. In this study, the transient dark state of the probe, which is a double fluorescent dye attached to a specific DNA sequence, was investigated using a fluorescence correlation spectroscopy (FCS). The transient dark state was measured in various solvents that are known to affect the intersystem crossing or photoisomerization of the DNA probe. On the basis of the experimental results, a simplified two energy state model of the probe was constructed, and this model provides an insight into the nonradiative relaxation mechanism of the fluorophore and the applications for DNA and RNA detection. The transient dark state that was measured in a time scale of a few microseconds is a triplet state and is related to photoisomerization, viscosity, oxygen concentration, and hybridization, all of which are important parameters for cellular microscopy. The transient dark state in a time scale of a sub-microseconds is sensitively changed after the addition of target DNA. The characterization can improve the probe's capability to identify target DNA/RNA by using FCS since the triplet state that occurred after hybridization is distinctive in the time scale with that occurred before hybridization.
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Affiliation(s)
- Hyo-Sup Shin
- Department of Physics, Korea Advanced Institute of Science and Technology, Daejeon 305-701, South Korea
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13
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Yeh HC, Sharma J, Shih IM, Vu DM, Martinez JS, Werner JH. A fluorescence light-up Ag nanocluster probe that discriminates single-nucleotide variants by emission color. J Am Chem Soc 2012; 134:11550-8. [PMID: 22775452 DOI: 10.1021/ja3024737] [Citation(s) in RCA: 214] [Impact Index Per Article: 17.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Rapid and precise screening of small genetic variations, such as single-nucleotide polymorphisms (SNPs), among an individual's genome is still an unmet challenge at point-of-care settings. One crucial step toward this goal is the development of discrimination probes that require no enzymatic reaction and are easy to use. Here we report a new type of fluorescent molecular probe, termed a chameleon NanoCluster Beacon (cNCB), that lights up into different colors upon binding SNP targets. NanoCluster Beacons (NCBs) are collections of a small number of Ag atoms templated on single-stranded DNA that fluoresce strongly when placed in proximity to particular DNA sequences, termed enhancers. Here we show the fluorescence emission color of a NCB can change substantially (a shift of 60-70 nm in the emission maximum) depending upon the alignment between the silver nanocluster and the DNA enhancer sequence. Chameleon NCBs exploit this color shift to directly detect SNPs, based on the fact that different SNPs produce a different alignment between the Ag nanocluster and the enhancer. This SNP detection method has been validated on all single-nucleotide substitution scenarios in three synthetic DNA targets, in six disease-related SNP targets, and in two clinical samples taken from patients with ovarian serous borderline tumors. Samples with single-nucleotide variations can be easily identified by the naked eye under UV excitation, making this method a reliable and low-cost assay with a simple readout format.
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Affiliation(s)
- Hsin-Chih Yeh
- Center of Integrated Nanotechnologies, Los Alamos National Laboratory, Mail Stop K771, Los Alamos, New Mexico 87545, USA.
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14
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15
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Yeh HC, Sharma J, Han JJ, Martinez JS, Werner JH. A DNA--silver nanocluster probe that fluoresces upon hybridization. NANO LETTERS 2010; 10:3106-10. [PMID: 20698624 DOI: 10.1021/nl101773c] [Citation(s) in RCA: 477] [Impact Index Per Article: 34.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/08/2023]
Abstract
DNA-templated silver nanoclusters (DNA/Ag NCs) are an emerging set of fluorophores that are smaller than semiconductor quantum dots and can have better photostability and brightness than commonly used organic dyes. Here we find the red fluorescence of DNA/Ag NCs can be enhanced 500-fold when placed in proximity to guanine-rich DNA sequences. On the basis of this new phenomenon, we have designed a DNA detection probe (NanoCluster Beacon, NCB) that "lights up" upon target binding. Since NCBs do not rely on Forster energy transfer for quenching, they can easily reach high (>100) signal-to-background ratios (S/B ratios) upon target binding. Here, in a separation-free assay, we demonstrate NCB detection of an influenza target with a S/B ratio of 175, a factor of 5 better than a conventional molecular beacon probe. Since the observed fluorescence enhancement is caused by intrinsic nucleobases, our detection technique is simple, inexpensive, and compatible with commercial DNA synthesizers.
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Affiliation(s)
- Hsin-Chih Yeh
- Center for Integrated Nanotechnologies, Los Alamos National Laboratory, Los Alamos, New Mexico 87545, USA
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16
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Richards CI, Hsiang JC, Khalil AM, Hull NP, Dickson RM. FRET-enabled optical modulation for high sensitivity fluorescence imaging. J Am Chem Soc 2010; 132:6318-23. [PMID: 20397664 PMCID: PMC2874320 DOI: 10.1021/ja100175r] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Fluorescence resonance energy transfer is utilized to engineer donor photophysics for facile signal amplification and selective fluorescence recovery from high background. This is generalized such that many different fluorophores can be used in optical modulation schemes to drastically improve fluorescence imaging sensitivity. Dynamic, simultaneous, and direct excitation of the acceptor brightens and optically modulates higher energy donor emission. The externally imposed modulation waveform enables selective donor fluorescence extraction through demodulation. By incorporating an acceptor with significant, spectrally shifted, dark-state population, necessary excitation intensities are quite low and agree well with simulated enhancements. Enhancement versus modulation frequency directly yields dark-state lifetimes in a simple ensemble measurement. Using the long-lived Cy5 dark state in conjunction with Cy3 donors, we demonstrate image extraction from a large background to yield >>10-fold sensitivity improvements through synchronously amplified fluorescence image recovery (SAFIRe).
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Affiliation(s)
- Chris I. Richards
- School of Chemistry and Biochemistry and Petit Institute for Biosciences and Bioengineering, Georgia Institute of Technology Atlanta, GA 30332-0400
| | - Jung-Cheng Hsiang
- School of Chemistry and Biochemistry and Petit Institute for Biosciences and Bioengineering, Georgia Institute of Technology Atlanta, GA 30332-0400
| | - Andrew M. Khalil
- School of Chemistry and Biochemistry and Petit Institute for Biosciences and Bioengineering, Georgia Institute of Technology Atlanta, GA 30332-0400
| | - Nathan P. Hull
- School of Chemistry and Biochemistry and Petit Institute for Biosciences and Bioengineering, Georgia Institute of Technology Atlanta, GA 30332-0400
| | - Robert M. Dickson
- School of Chemistry and Biochemistry and Petit Institute for Biosciences and Bioengineering, Georgia Institute of Technology Atlanta, GA 30332-0400
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17
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Kalinin S, Sisamakis E, Magennis SW, Felekyan S, Seidel CAM. On the Origin of Broadening of Single-Molecule FRET Efficiency Distributions beyond Shot Noise Limits. J Phys Chem B 2010; 114:6197-206. [DOI: 10.1021/jp100025v] [Citation(s) in RCA: 88] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Affiliation(s)
- Stanislav Kalinin
- Institut für Physikalische Chemie, Lehrstuhl für Molekulare Physikalische Chemie, Heinrich-Heine-Universität, Universitätsstrasse 1, Geb 26.32, 40225 Düsseldorf, Germany, and Department of Applied Physics, Group of Experimental Biomolecular Physics, The Royal Institute of Technology, Albanova University Center, SE-106 91 Stockholm, Sweden
| | - Evangelos Sisamakis
- Institut für Physikalische Chemie, Lehrstuhl für Molekulare Physikalische Chemie, Heinrich-Heine-Universität, Universitätsstrasse 1, Geb 26.32, 40225 Düsseldorf, Germany, and Department of Applied Physics, Group of Experimental Biomolecular Physics, The Royal Institute of Technology, Albanova University Center, SE-106 91 Stockholm, Sweden
| | - Steven W. Magennis
- Institut für Physikalische Chemie, Lehrstuhl für Molekulare Physikalische Chemie, Heinrich-Heine-Universität, Universitätsstrasse 1, Geb 26.32, 40225 Düsseldorf, Germany, and Department of Applied Physics, Group of Experimental Biomolecular Physics, The Royal Institute of Technology, Albanova University Center, SE-106 91 Stockholm, Sweden
| | - Suren Felekyan
- Institut für Physikalische Chemie, Lehrstuhl für Molekulare Physikalische Chemie, Heinrich-Heine-Universität, Universitätsstrasse 1, Geb 26.32, 40225 Düsseldorf, Germany, and Department of Applied Physics, Group of Experimental Biomolecular Physics, The Royal Institute of Technology, Albanova University Center, SE-106 91 Stockholm, Sweden
| | - Claus A. M. Seidel
- Institut für Physikalische Chemie, Lehrstuhl für Molekulare Physikalische Chemie, Heinrich-Heine-Universität, Universitätsstrasse 1, Geb 26.32, 40225 Düsseldorf, Germany, and Department of Applied Physics, Group of Experimental Biomolecular Physics, The Royal Institute of Technology, Albanova University Center, SE-106 91 Stockholm, Sweden
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18
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Abstract
Fluorescence intermittency severely limits brightness in both single molecule and bulk fluorescence. Herein, we demonstrate that optical depopulation of organic fluorophore triplet states opens a path to significantly increased sensitivity by simultaneously increasing brightness and greatly reducing background through synchronously detected fluorescence modulation. Image recovery is achieved through selective fluorescence enhancement via modulating a secondary laser excitation at much lower energy than the observed emission in order to depopulate the long-lived triplet states. A series of xanthene dyes that exhibit efficient triplet-state formation demonstrate that this method of selective signal extraction can be achieved at moderate primary and secondary excitation intensities through tailoring dye photophysics and imaging conditions. Up to 5-fold increases in solution-based fluorescence over primary laser excitation alone was achieved upon secondary laser excitation, and dynamic control of signal modulation was demonstrated over a wide time range simply by varying the modulation frequency of the laser used for depopulation of the triplet state. We identify the photophysical characteristics that enable existing or to-be-designed fluorophores to be used in synchronously amplified fluorescence image recovery (SAFIRe) microscopy.
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Affiliation(s)
- Chris I Richards
- School of Chemistry and Biochemistry and Petit Institute for Biosciences and Bioengineering, Georgia Institute of Technology, Atlanta, Georgia 30332-0400, USA
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19
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Mitigating unwanted photophysical processes for improved single-molecule fluorescence imaging. Biophys J 2009; 96:2371-81. [PMID: 19289062 DOI: 10.1016/j.bpj.2008.11.061] [Citation(s) in RCA: 169] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2008] [Revised: 11/12/2008] [Accepted: 11/17/2008] [Indexed: 01/12/2023] Open
Abstract
Organic fluorophores common to fluorescence-based investigations suffer from unwanted photophysical properties, including blinking and photobleaching, which limit their overall experimental performance. Methods to control such processes are particularly important for single-molecule fluorescence and fluorescence resonance energy transfer imaging where uninterrupted, stable fluorescence is paramount. Fluorescence and FRET-based assays have been carried out on dye-labeled DNA and RNA-based systems to quantify the effect of including small-molecule solution additives on the fluorescence and FRET behaviors of both cyanine and Alexa fluorophores. A detailed dwell time analysis of the fluorescence and FRET trajectories of more than 200,000 individual molecules showed that two compounds identified previously as triplet state quenchers, cyclooctatetraene, and Trolox, as well as 4-nitrobenzyl alcohol, act to favorably attenuate blinking, photobleaching, and influence the rate of photoresurrection in a concentration-dependent and context-dependent manner. In both biochemical systems examined, a unique cocktail of compounds was shown to be optimal for imaging performance. By simultaneously providing the most rapid and direct access to multiple photophysical kinetic parameters, smFRET imaging provides a powerful avenue for future investigations aimed at discovering new compounds, and effective combinations thereof. These efforts may ultimately facilitate tuning organic dye molecule performance according to each specific experimental demand.
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20
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Puleo CM, Wang TH. Microfluidic means of achieving attomolar detection limits with molecular beacon probes. LAB ON A CHIP 2009; 9:1065-72. [PMID: 19350088 PMCID: PMC3000354 DOI: 10.1039/b819605b] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/02/2023]
Abstract
We used inline, micro-evaporators to concentrate and transport DNA targets to a nanoliter single molecule fluorescence detection chamber for subsequent molecular beacon probe hybridization and analysis. This use of solvent removal as a unique means of target transport in a microanalytical platform led to a greater than 5000-fold concentration enhancement and detection limits that pushed below the femtomolar barrier commonly reported using confocal fluorescence detection. This simple microliter-to-nanoliter interconnect for single molecule counting analysis resolved several common limitations, including the need for excessive fluorescent probe concentrations at low target levels and inefficiencies in direct handling of highly dilute biological samples. In this report, the hundreds of bacteria-specific DNA molecules contained in approximately 25 microliters of a 50 aM sample were shuttled to a four nanoliter detection chamber through micro-evaporation. Here, the previously undetectable targets were enhanced to the pM regime and underwent probe hybridization and highly-efficient fluorescent event analysis via microfluidic recirculation through the confocal detection volume. This use of microfluidics in a single molecule detection (SMD) platform delivered unmatched sensitivity and introduced compliment technologies that may serve to bring SMD to more widespread use in replacing conventional methodologies for detecting rare target biomolecules in both research and clinical labs.
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Affiliation(s)
- Christopher M. Puleo
- Johns Hopkins University, Department of Biomedical Engineering, 3400 N. Charles St., Clark Hall Rm. 123, Baltimore, MD, USA. Fax: 410-516-4771; Tel: 410-516-7576;
| | - Tza-Huei Wang
- Johns Hopkins University, Department of Biomedical Engineering, 3400 N. Charles St., Clark Hall Rm. 123, Baltimore, MD, USA. Fax: 410-516-4771; Tel: 410-516-7576;
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FUJIWARA K, HIROKAWA S, AOKI M. Comparison of Fluorescence Correlation Spectrometry with the Ordinary Fluorescence Optical Configuration with Flow Cytometry as a Tool for Micrometer-level Size Determination. ANAL SCI 2008; 24:1623-7. [DOI: 10.2116/analsci.24.1623] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Affiliation(s)
- Kitao FUJIWARA
- School of Life Sciences, Tokyo University of Pharmacy and Life Sciences
| | - Shun HIROKAWA
- School of Life Sciences, Tokyo University of Pharmacy and Life Sciences
| | - Motohide AOKI
- School of Life Sciences, Tokyo University of Pharmacy and Life Sciences
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Wang Z, Gidwani V, Zhang DD, Wong PK. Separation-free detection of nuclear factor kappa B with double-stranded molecular probes. Analyst 2008; 133:998-1000. [DOI: 10.1039/b809113g] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
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