1
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Fletcher M, Zhu J, Rubio-Sánchez R, Sandler SE, Nahas KA, Michele LD, Keyser UF, Tivony R. DNA-Based Optical Quantification of Ion Transport across Giant Vesicles. ACS NANO 2022; 16:17128-17138. [PMID: 36222833 PMCID: PMC9620405 DOI: 10.1021/acsnano.2c07496] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/27/2022] [Accepted: 10/06/2022] [Indexed: 06/16/2023]
Abstract
Accurate measurements of ion permeability through cellular membranes remains challenging due to the lack of suitable ion-selective probes. Here we use giant unilamellar vesicles (GUVs) as membrane models for the direct visualization of mass translocation at the single-vesicle level. Ion transport is indicated with a fluorescently adjustable DNA-based sensor that accurately detects sub-millimolar variations in K+ concentration. In combination with microfluidics, we employed our DNA-based K+ sensor for extraction of the permeation coefficient of potassium ions. We measured K+ permeability coefficients at least 1 order of magnitude larger than previously reported values from bulk experiments and show that permeation rates across the lipid bilayer increase in the presence of octanol. In addition, an analysis of the K+ flux in different concentration gradients allows us to estimate the complementary H+ flux that dissipates the charge imbalance across the GUV membrane. Subsequently, we show that our sensor can quantify the K+ transport across prototypical cation-selective ion channels, gramicidin A and OmpF, revealing their relative H+/K+ selectivity. Our results show that gramicidin A is much more selective to protons than OmpF with a H+/K+ permeability ratio of ∼104.
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Affiliation(s)
- Marcus Fletcher
- Cavendish
Laboratory, University of Cambridge, J.J. Thomson Avenue, CambridgeCB3 0HE, U.K.
| | - Jinbo Zhu
- Cavendish
Laboratory, University of Cambridge, J.J. Thomson Avenue, CambridgeCB3 0HE, U.K.
| | - Roger Rubio-Sánchez
- Department
of Chemistry, Molecular Sciences Research Hub, Imperial College London, LondonW12 0BZ, U.K.
- fabriCELL,
Molecular Sciences Research Hub, Imperial
College London, LondonW12 0BZ, U.K.
| | - Sarah E Sandler
- Cavendish
Laboratory, University of Cambridge, J.J. Thomson Avenue, CambridgeCB3 0HE, U.K.
| | - Kareem Al Nahas
- Cavendish
Laboratory, University of Cambridge, J.J. Thomson Avenue, CambridgeCB3 0HE, U.K.
| | - Lorenzo Di Michele
- Department
of Chemistry, Molecular Sciences Research Hub, Imperial College London, LondonW12 0BZ, U.K.
- fabriCELL,
Molecular Sciences Research Hub, Imperial
College London, LondonW12 0BZ, U.K.
| | - Ulrich F Keyser
- Cavendish
Laboratory, University of Cambridge, J.J. Thomson Avenue, CambridgeCB3 0HE, U.K.
| | - Ran Tivony
- Cavendish
Laboratory, University of Cambridge, J.J. Thomson Avenue, CambridgeCB3 0HE, U.K.
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2
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Meares A, Susumu K, Mathur D, Lee SH, Mass OA, Lee J, Pensack RD, Yurke B, Knowlton WB, Melinger JS, Medintz IL. Synthesis of Substituted Cy5 Phosphoramidite Derivatives and Their Incorporation into Oligonucleotides Using Automated DNA Synthesis. ACS OMEGA 2022; 7:11002-11016. [PMID: 35415341 PMCID: PMC8991898 DOI: 10.1021/acsomega.1c06921] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/07/2021] [Accepted: 02/14/2022] [Indexed: 05/03/2023]
Abstract
Cyanine dyes represent a family of organic fluorophores with widespread utility in biological-based applications ranging from real-time PCR probes to protein labeling. One burgeoning use currently being explored with indodicarbocyanine (Cy5) in particular is that of accessing exciton delocalization in designer DNA dye aggregate structures for potential development of light-harvesting devices and room-temperature quantum computers. Tuning the hydrophilicity/hydrophobicity of Cy5 dyes in such DNA structures should influence the strength of their excitonic coupling; however, the requisite commercial Cy5 derivatives available for direct incorporation into DNA are nonexistent. Here, we prepare a series of Cy5 derivatives that possess different 5,5'-substituents and detail their incorporation into a set of DNA sequences. In addition to varying dye hydrophobicity/hydrophilicity, the 5,5'-substituents, including hexyloxy, triethyleneglycol monomethyl ether, tert-butyl, and chloro groups were chosen so as to vary the inherent electron-donating/withdrawing character while also tuning their resulting absorption and emission properties. Following the synthesis of parent dyes, one of their pendant alkyl chains was functionalized with a monomethoxytrityl protective group with the remaining hydroxyl-terminated N-propyl linker permitting rapid, same-day phosphoramidite conversion and direct internal DNA incorporation into nascent oligonucleotides with moderate to good yields using a 1 μmole scale automated DNA synthesis. Labeled sequences were cleaved from the controlled pore glass matrix, purified by HPLC, and their photophysical properties were characterized. The DNA-labeled Cy5 derivatives displayed spectroscopic properties that paralleled the parent dyes, with either no change or an increase in fluorescence quantum yield depending upon sequence.
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Affiliation(s)
- Adam Meares
- Center
for Bio/Molecular Science and Engineering Code 6900, U. S. Naval Research Laboratory, Washington, D.C., Virginia 20375, United States
- College
of Science, George Mason University, Fairfax, Virginia 22030, United States
| | - Kimihiro Susumu
- Optical
Sciences Division Code 5600, U. S. Naval
Research Laboratory, Washington,
D.C., Virginia 20375, United States
- Jacobs
Corporation, Hanover, Maryland 21076, United
States
| | - Divita Mathur
- Center
for Bio/Molecular Science and Engineering Code 6900, U. S. Naval Research Laboratory, Washington, D.C., Virginia 20375, United States
- College
of Science, George Mason University, Fairfax, Virginia 22030, United States
| | - Sang Ho Lee
- Optical
Sciences Division Code 5600, U. S. Naval
Research Laboratory, Washington,
D.C., Virginia 20375, United States
- Jacobs
Corporation, Hanover, Maryland 21076, United
States
| | - Olga A. Mass
- Micron School
of Materials Science & Engineering, Boise State University, Boise, Idaho 83725, United States
| | - Jeunghoon Lee
- Micron School
of Materials Science & Engineering, Boise State University, Boise, Idaho 83725, United States
- Department
of Chemistry & Biochemistry, Boise State
University, Boise, Idaho 83725, United
States
| | - Ryan D. Pensack
- Micron School
of Materials Science & Engineering, Boise State University, Boise, Idaho 83725, United States
| | - Bernard Yurke
- Micron School
of Materials Science & Engineering, Boise State University, Boise, Idaho 83725, United States
- Department
of Electrical & Computer Engineering, Boise State University, Boise, Idaho 83725, United States
| | - William B. Knowlton
- Micron School
of Materials Science & Engineering, Boise State University, Boise, Idaho 83725, United States
- Department
of Electrical & Computer Engineering, Boise State University, Boise, Idaho 83725, United States
| | - Joseph S. Melinger
- Electronics
Science and Technology Division Code 6800, U.S. Naval Research Laboratory, Washington, D.C. 20375, United States
| | - Igor L. Medintz
- Center
for Bio/Molecular Science and Engineering Code 6900, U. S. Naval Research Laboratory, Washington, D.C., Virginia 20375, United States
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3
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Chiriboga M, Diaz SA, Mathur D, Hastman DA, Melinger JS, Veneziano R, Medintz IL. Understanding Self-Assembled Pseudoisocyanine Dye Aggregates in DNA Nanostructures and Their Exciton Relay Transfer Capabilities. J Phys Chem B 2021; 126:110-122. [PMID: 34962787 DOI: 10.1021/acs.jpcb.1c09048] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
Progress has been made using B-form DNA duplex strands to template chromophores in ordered molecular aggregates known as J-aggregates. These aggregates can exhibit strong electronic coupling, extended coherent lifetimes, and long-range exciton delocalization under appropriate conditions. Certain cyanine dyes such as pseudoisocyanine (PIC) dye have shown a proclivity to form aggregates in specific DNA sequences. In particular, DX-tiles containing nonalternating poly(dA)-poly(dT) dinucleotide tracks (AT-tracks), which template noncovalent PIC dye aggregates, have been demonstrated to exhibit interesting emergent photonic properties. These DNA-based aggregates are referred to as J-bits for their similarity to J-aggregates. Here, we assemble multifluorophore DX-tile scaffolds which template J-bits into both contiguous and noncontiguous linear arrays. Our goal is to understand the relay capability of noncontiguous J-bit arrays and probe the effects that orientation and position have on the energy transfer between them. We find that linearly contiguous J-bits can relay excitons from an initial AlexaFluor 405 donor to a terminal AlexaFluor 647 acceptor across a distance of up to 16.3 nm. We observed a maximum increase in energy transfer of 41% in the shortest scaffold and an 11% increase in energy transfer across the maximum distance. However, in nonlinear arrays, exciton transfer is not detectable, even when off-axis J-bit-to-J-bit transfer distances were <2 nm. These results, in conjunction with the previous work on PIC-DNA systems, suggest that PIC-DNA-based systems may currently be limited to simple 1-D designs, which prevent isolating J-bits for enhanced energy-transfer characteristics until further understanding and improvements to the system can be made.
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Affiliation(s)
- Matthew Chiriboga
- Center for Bio/Molecular Science & Engineering Code 6900, U.S. Naval Research Laboratory, 4555 Overlook Avenue S.W., Washington, District of Columbia 20375, United States.,Volgenau School of Engineering, Department of Bioengineering, Institute for Advanced Biomedical Research George Mason University, Manassas, Virginia 22030, United States
| | - Sebastian A Diaz
- Center for Bio/Molecular Science & Engineering Code 6900, U.S. Naval Research Laboratory, 4555 Overlook Avenue S.W., Washington, District of Columbia 20375, United States
| | - Divita Mathur
- Center for Bio/Molecular Science & Engineering Code 6900, U.S. Naval Research Laboratory, 4555 Overlook Avenue S.W., Washington, District of Columbia 20375, United States.,College of Science, George Mason University, Fairfax, Virginia 22030, United States
| | - David A Hastman
- Center for Bio/Molecular Science & Engineering Code 6900, U.S. Naval Research Laboratory, 4555 Overlook Avenue S.W., Washington, District of Columbia 20375, United States.,A. James Clark School of Engineering, Fischell Department of Bioengineering, University of Maryland College Park, College Park, Maryland 20742, United States
| | - Joseph S Melinger
- Electronics Science and Technology Division Code 6800, U.S. Naval Research Laboratory, 4555 Overlook Avenue S.W., Washington, District of Columbia 20375, United States
| | - Remi Veneziano
- Volgenau School of Engineering, Department of Bioengineering, Institute for Advanced Biomedical Research George Mason University, Manassas, Virginia 22030, United States
| | - Igor L Medintz
- Center for Bio/Molecular Science & Engineering Code 6900, U.S. Naval Research Laboratory, 4555 Overlook Avenue S.W., Washington, District of Columbia 20375, United States
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4
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Dillen A, Vandezande W, Daems D, Lammertyn J. Unraveling the effect of the aptamer complementary element on the performance of duplexed aptamers: a thermodynamic study. Anal Bioanal Chem 2021; 413:4739-4750. [PMID: 34109445 DOI: 10.1007/s00216-021-03444-y] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2021] [Revised: 05/25/2021] [Accepted: 05/28/2021] [Indexed: 12/24/2022]
Abstract
Duplexed aptamers (DAs) are widespread aptasensor formats that simultaneously recognize and signal the concentration of target molecules. They are composed of an aptamer and aptamer complementary element (ACE) which consists of a short oligonucleotide that partially inhibits the aptamer sequence. Although the design principles to engineer DAs are straightforward, the tailored development of DAs for a particular target is currently based on trial and error due to limited knowledge of how the ACE sequence affects the final performance of DA biosensors. Therefore, we have established a thermodynamic model describing the influence of the ACE on the performance of DAs applied in equilibrium assays and demonstrated that this relationship can be described by the binding strength between the aptamer and ACE. To validate our theoretical findings, the model was applied to the 29-mer anti-thrombin aptamer as a case study, and an experimental relation between the aptamer-ACE binding strength and performance of DAs was established. The obtained results indicated that our proposed model could accurately describe the effect of the ACE sequence on the performance of the established DAs for thrombin detection, applied for equilibrium assays. Furthermore, to characterize the binding strength between the aptamer and ACEs evaluated in this work, a set of fitting equations was derived which enables thermodynamic characterization of DNA-based interactions through thermal denaturation experiments, thereby overcoming the limitations of current predictive software and chemical denaturation experiments. Altogether, this work encourages the development, characterization, and use of DAs in the field of biosensing.
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Affiliation(s)
- Annelies Dillen
- Department of Biosystems - Biosensors Group, KU Leuven, Willem de Croylaan 42, Box 2428, 3001, Leuven, Belgium
| | - Wouter Vandezande
- Department of Microbial and Molecular Systems - Centre for Membrane Separations, Adsorption, Catalysis and Spectroscopy for Sustainable Solutions, KU Leuven, Celestijnenlaan 200F, Box 2454, 3001, Leuven, Belgium
| | - Devin Daems
- Department of Chemistry - AXES research group, University of Antwerp, Groenenborgerlaan 171, 2010, Antwerpen, Belgium
| | - Jeroen Lammertyn
- Department of Biosystems - Biosensors Group, KU Leuven, Willem de Croylaan 42, Box 2428, 3001, Leuven, Belgium.
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5
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Feng S, Pei F, Wu Y, Lv J, Hao Q, Yang T, Tong Z, Lei W. A ratiometric fluorescent sensor based on g-CNQDs@Zn-MOF for the sensitive detection of riboflavin via FRET. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2021; 246:119004. [PMID: 33070014 DOI: 10.1016/j.saa.2020.119004] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/02/2020] [Revised: 09/16/2020] [Accepted: 09/22/2020] [Indexed: 05/03/2023]
Abstract
A novel ratiometric fluorescent sensor based on Förster resonance energy transfer (FRET) platform was designed for riboflavin (RF) detection. The graphitic carbon nitrides quantum dots - Zn-MOF composite (g-CNQDs@Zn-MOF) was used as the fluorescent probe. In the FRET system, g-CNQDs@Zn-MOF and RF acted as donor and acceptor, respectively. The probe exhibited high sensitivity and good selectivity to RF, and had been successfully used for the detection of RF in milk and vitamin B2 tablets. The detection limit of the sensor was 15 nM. The strategy expanded the application of MOF in sensing filed and provided a new method for the detection of RF.
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Affiliation(s)
- Shasha Feng
- School of Chemical Engineering, Nanjing University of Science and Technology, Nanjing 210094, China
| | - Fubin Pei
- School of Chemical Engineering, Nanjing University of Science and Technology, Nanjing 210094, China
| | - Yi Wu
- School of Chemical Engineering, Nanjing University of Science and Technology, Nanjing 210094, China
| | - Jingjing Lv
- School of Chemical Engineering, Nanjing University of Science and Technology, Nanjing 210094, China
| | - Qingli Hao
- School of Chemical Engineering, Nanjing University of Science and Technology, Nanjing 210094, China
| | - Tinghai Yang
- School of Chemistry & Environmental Engineering, Jiangsu University of Technology, Changzhou 213001, China
| | - Zhaoyang Tong
- State Key Laboratory of NBC Protection for Civilian, Beijing 102205, China.
| | - Wu Lei
- School of Chemical Engineering, Nanjing University of Science and Technology, Nanjing 210094, China.
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6
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Antibody engineering-driven controllable chemiluminescence resonance energy transfer for immunoassay with tunable dynamic range. Anal Chim Acta 2021; 1152:338231. [PMID: 33648650 DOI: 10.1016/j.aca.2021.338231] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2020] [Revised: 12/10/2020] [Accepted: 01/15/2021] [Indexed: 11/22/2022]
Abstract
The donor-acceptor distance is a critical factor for the occurrence of chemiluminescent resonance energy transfer (CRET). We herein evaluate the donor-acceptor distance and transfer efficiency of CRET immunoassays of a series of donors which contain different sized antibody fragments, intact monoclonal antibody (IgG), antigen binding fragment (Fab), and single chain fragment antibody (scFv). Core/multishell quantum dots were used as the acceptor in three CRET systems. IgG is the maximum antibody fragment, leading to the longest donor-acceptor distance and the lowest transfer efficiency. Donors with Fab and scFv show significantly decreased distance and increased transfer efficiency. These results suggest an inverse correlation between donor size and transfer efficiency and can be used to provide guidance for the construction of controllable CRET. By combining the controllable CRET with immunoassay, we further develop a tunable sulfamethazine analytical system. Three different sized donors based CRET immunoassay show a markedly different sensitivity and dynamic range. Such adjustable detection provides greater flexibility for contaminant detection in different foodstuffs with different residue limits. This work not only illustrates the effect of donor-acceptor distance on regulating the energy transfer efficiency of CRET system, but also provides a guideline for the construction of a tunable immunoassay.
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7
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Advances in oligonucleotide-based detection coupled with fluorescence resonance energy transfer. Trends Analyt Chem 2020. [DOI: 10.1016/j.trac.2019.115756] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
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8
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Yoshioka K, Kunieda T, Asami Y, Guo H, Miyata H, Yoshida-Tanaka K, Sujino Y, Piao W, Kuwahara H, Nishina K, Hara RI, Nagata T, Wada T, Obika S, Yokota T. Highly efficient silencing of microRNA by heteroduplex oligonucleotides. Nucleic Acids Res 2019; 47:7321-7332. [PMID: 31214713 PMCID: PMC6698647 DOI: 10.1093/nar/gkz492] [Citation(s) in RCA: 32] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2018] [Revised: 05/21/2019] [Accepted: 05/28/2019] [Indexed: 12/11/2022] Open
Abstract
AntimiR is an antisense oligonucleotide that has been developed to silence microRNA (miRNA) for the treatment of intractable diseases. Enhancement of its in vivo efficacy and improvement of its toxicity are highly desirable but remain challenging. We here design heteroduplex oligonucleotide (HDO)-antimiR as a new technology comprising an antimiR and its complementary RNA. HDO-antimiR binds targeted miRNA in vivo more efficiently by 12-fold than the parent single-stranded antimiR. HDO-antimiR also produced enhanced phenotypic effects in mice with upregulated expression of miRNA-targeting messenger RNAs. In addition, we demonstrated that the enhanced potency of HDO-antimiR was not explained by its bio-stability or delivery to the targeted cell, but reflected an improved intracellular potency. Our findings provide new insights into biology of miRNA silencing by double-stranded oligonucleotides and support the in vivo potential of this technology based on a new class of for the treatment of miRNA-related diseases.
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Affiliation(s)
- Kotaro Yoshioka
- Department of Neurology and Neurological Science, Graduate School of Medical and Dental Sciences and Center for Brain Integration Research, Tokyo Medical and Dental University (TMDU), 1-5-45 Yushima, Bunkyo-Ku, Tokyo, 113-8519, Japan.,Section of Molecular Technology, Core Research for Evolutional Science and Technology (CREST), Japan Science and Technology Agency (JST), 4-1-8 Honcho, Kawaguchi-shi, Saitama 332-0012, Japan
| | - Taiki Kunieda
- Department of Neurology and Neurological Science, Graduate School of Medical and Dental Sciences and Center for Brain Integration Research, Tokyo Medical and Dental University (TMDU), 1-5-45 Yushima, Bunkyo-Ku, Tokyo, 113-8519, Japan.,Section of Molecular Technology, Core Research for Evolutional Science and Technology (CREST), Japan Science and Technology Agency (JST), 4-1-8 Honcho, Kawaguchi-shi, Saitama 332-0012, Japan
| | - Yutaro Asami
- Department of Neurology and Neurological Science, Graduate School of Medical and Dental Sciences and Center for Brain Integration Research, Tokyo Medical and Dental University (TMDU), 1-5-45 Yushima, Bunkyo-Ku, Tokyo, 113-8519, Japan.,Section of Molecular Technology, Core Research for Evolutional Science and Technology (CREST), Japan Science and Technology Agency (JST), 4-1-8 Honcho, Kawaguchi-shi, Saitama 332-0012, Japan
| | - Huijia Guo
- Department of Neurology and Neurological Science, Graduate School of Medical and Dental Sciences and Center for Brain Integration Research, Tokyo Medical and Dental University (TMDU), 1-5-45 Yushima, Bunkyo-Ku, Tokyo, 113-8519, Japan
| | - Haruka Miyata
- Department of Neurology and Neurological Science, Graduate School of Medical and Dental Sciences and Center for Brain Integration Research, Tokyo Medical and Dental University (TMDU), 1-5-45 Yushima, Bunkyo-Ku, Tokyo, 113-8519, Japan.,Section of Molecular Technology, Core Research for Evolutional Science and Technology (CREST), Japan Science and Technology Agency (JST), 4-1-8 Honcho, Kawaguchi-shi, Saitama 332-0012, Japan
| | - Kie Yoshida-Tanaka
- Department of Neurology and Neurological Science, Graduate School of Medical and Dental Sciences and Center for Brain Integration Research, Tokyo Medical and Dental University (TMDU), 1-5-45 Yushima, Bunkyo-Ku, Tokyo, 113-8519, Japan.,Section of Molecular Technology, Core Research for Evolutional Science and Technology (CREST), Japan Science and Technology Agency (JST), 4-1-8 Honcho, Kawaguchi-shi, Saitama 332-0012, Japan
| | - Yumiko Sujino
- Department of Neurology and Neurological Science, Graduate School of Medical and Dental Sciences and Center for Brain Integration Research, Tokyo Medical and Dental University (TMDU), 1-5-45 Yushima, Bunkyo-Ku, Tokyo, 113-8519, Japan.,Section of Molecular Technology, Core Research for Evolutional Science and Technology (CREST), Japan Science and Technology Agency (JST), 4-1-8 Honcho, Kawaguchi-shi, Saitama 332-0012, Japan
| | - Wenying Piao
- Department of Neurology and Neurological Science, Graduate School of Medical and Dental Sciences and Center for Brain Integration Research, Tokyo Medical and Dental University (TMDU), 1-5-45 Yushima, Bunkyo-Ku, Tokyo, 113-8519, Japan.,Section of Molecular Technology, Core Research for Evolutional Science and Technology (CREST), Japan Science and Technology Agency (JST), 4-1-8 Honcho, Kawaguchi-shi, Saitama 332-0012, Japan
| | - Hiroya Kuwahara
- Department of Neurology and Neurological Science, Graduate School of Medical and Dental Sciences and Center for Brain Integration Research, Tokyo Medical and Dental University (TMDU), 1-5-45 Yushima, Bunkyo-Ku, Tokyo, 113-8519, Japan.,Section of Molecular Technology, Core Research for Evolutional Science and Technology (CREST), Japan Science and Technology Agency (JST), 4-1-8 Honcho, Kawaguchi-shi, Saitama 332-0012, Japan
| | - Kazutaka Nishina
- Department of Neurology and Neurological Science, Graduate School of Medical and Dental Sciences and Center for Brain Integration Research, Tokyo Medical and Dental University (TMDU), 1-5-45 Yushima, Bunkyo-Ku, Tokyo, 113-8519, Japan.,Section of Molecular Technology, Core Research for Evolutional Science and Technology (CREST), Japan Science and Technology Agency (JST), 4-1-8 Honcho, Kawaguchi-shi, Saitama 332-0012, Japan
| | - Rintaro Iwata Hara
- Section of Molecular Technology, Core Research for Evolutional Science and Technology (CREST), Japan Science and Technology Agency (JST), 4-1-8 Honcho, Kawaguchi-shi, Saitama 332-0012, Japan.,Faculty of Pharmaceutical Sciences, Tokyo University of Science, 2641 Yamazaki, Noda, Chiba, 278-8510, Japan
| | - Tetsuya Nagata
- Department of Neurology and Neurological Science, Graduate School of Medical and Dental Sciences and Center for Brain Integration Research, Tokyo Medical and Dental University (TMDU), 1-5-45 Yushima, Bunkyo-Ku, Tokyo, 113-8519, Japan.,Section of Molecular Technology, Core Research for Evolutional Science and Technology (CREST), Japan Science and Technology Agency (JST), 4-1-8 Honcho, Kawaguchi-shi, Saitama 332-0012, Japan
| | - Takeshi Wada
- Section of Molecular Technology, Core Research for Evolutional Science and Technology (CREST), Japan Science and Technology Agency (JST), 4-1-8 Honcho, Kawaguchi-shi, Saitama 332-0012, Japan.,Faculty of Pharmaceutical Sciences, Tokyo University of Science, 2641 Yamazaki, Noda, Chiba, 278-8510, Japan
| | - Satoshi Obika
- Section of Molecular Technology, Core Research for Evolutional Science and Technology (CREST), Japan Science and Technology Agency (JST), 4-1-8 Honcho, Kawaguchi-shi, Saitama 332-0012, Japan.,Graduate School of Pharmaceutical Sciences, Osaka University, 1-6 Yamadaoka, Suita, Osaka, 565-0871, Japan
| | - Takanori Yokota
- Department of Neurology and Neurological Science, Graduate School of Medical and Dental Sciences and Center for Brain Integration Research, Tokyo Medical and Dental University (TMDU), 1-5-45 Yushima, Bunkyo-Ku, Tokyo, 113-8519, Japan.,Section of Molecular Technology, Core Research for Evolutional Science and Technology (CREST), Japan Science and Technology Agency (JST), 4-1-8 Honcho, Kawaguchi-shi, Saitama 332-0012, Japan
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9
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Aloisi A, Della Torre A, De Benedetto A, Rinaldi R. Bio-Recognition in Spectroscopy-Based Biosensors for *Heavy Metals-Water and Waterborne Contamination Analysis. BIOSENSORS 2019; 9:E96. [PMID: 31366137 PMCID: PMC6784378 DOI: 10.3390/bios9030096] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/12/2019] [Revised: 07/23/2019] [Accepted: 07/25/2019] [Indexed: 02/07/2023]
Abstract
: Microsystems and biomolecules integration as well multiplexing determinations are key aspects of sensing devices in the field of heavy metal contamination monitoring. The present review collects the most relevant information about optical biosensors development in the last decade. Focus is put on analytical characteristics and applications that are dependent on: (i) Signal transduction method (luminescence, colorimetry, evanescent wave (EW), surface-enhanced Raman spectroscopy (SERS), Förster resonance energy transfer (FRET), surface plasmon resonance (SPR)); (ii) biorecognition molecules employed (proteins, nucleic acids, aptamers, and enzymes). The biosensing systems applied (or applicable) to water and milk samples will be considered for a comparative analysis, with an emphasis on water as the primary source of possible contamination along the food chain.
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Affiliation(s)
- Alessandra Aloisi
- Institute for Microelectronics and Microsystems (IMM), CNR, Via Monteroni, 73100 Lecce, Italy
| | - Antonio Della Torre
- Institute for Microelectronics and Microsystems (IMM), CNR, Via Monteroni, 73100 Lecce, Italy
| | - Angelantonio De Benedetto
- Mathematics and Physics "E. De Giorgi" Department, University of Salento, Via Monteroni, 73100 Lecce, Italy
| | - Rosaria Rinaldi
- Institute for Microelectronics and Microsystems (IMM), CNR, Via Monteroni, 73100 Lecce, Italy.
- Mathematics and Physics "E. De Giorgi" Department, University of Salento, Via Monteroni, 73100 Lecce, Italy.
- ISUFI, University of Salento, Via Monteroni, 73100 Lecce, Italy.
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10
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Hu J, Xiao K, Jin B, Zheng X, Ji F, Bai D. Paper-based point-of-care test with xeno nucleic acid probes. Biotechnol Bioeng 2019; 116:2764-2777. [PMID: 31282991 DOI: 10.1002/bit.27106] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2019] [Revised: 06/20/2019] [Accepted: 06/24/2019] [Indexed: 01/09/2023]
Abstract
Bridging the unmet need of efficient point-of-care testing (POCT) in biomedical engineering research and practice with the emerging development in artificial synthetic xeno nucleic acids (XNAs), this review summarized the recent development in paper-based POCT using XNAs as sensing probes. Alongside the signal transducing mode and immobilization methods of XNA probes, a detailed evaluation of probe performance was disclosed. With these new aspects, both researchers in synthetic chemistry / biomedical engineering and physicians in clinical practice could gain new insights in designing, manufacturing and choosing suitable reagents and techniques for POCT.
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Affiliation(s)
- Jie Hu
- Singapore Institute of Manufacturing Technology, Agency for Science, Technology and Research (A*STAR), Singapore, Singapore
| | - Kang Xiao
- Chinese Center for Disease Control and Prevention, National Institute for Viral Disease Control and Prevention, Beijing, P. R. China.,Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Zhejiang University, Hangzhou, P. R. China
| | - Birui Jin
- School of Materials and Chemical Engineering, Xi'an Technological University, Xi'an, P. R. China
| | - Xuyang Zheng
- Department of Infectious Diseases, Tangdu Hospital, The Fourth Military Medical University, Xi'an, Shaanxi, P. R. China
| | - Fanpu Ji
- Department of Infectious Diseases, The Second Affiliated Hospital of Xi'an Jiaotong University, Xi'an, Shaanxi, P. R. China
| | - Dan Bai
- Xi'an Institute of Flexible Electronics (IFE) & Xi'an Key Laboratory of Flexible Electronics (KLoFE), MIIT Key Laboratory of Flexible Electronics (KLoFE), Shaanxi Key Laboratory of Flexible Electronics (KLoFE), Northwestern Polytechnical University (NPU), Xi'an, Shaanxi, P. R. China.,Xi'an Institute of Biomedical Materials and Engineering (IBME) & Xi'an Key Laboratory of Biomedical Materials and Engineering (KLBME), Northwestern Polytechnical University (NPU), Xi'an, Shaanxi, P. R. China
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11
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Xiong Y, McQuistan TJ, Stanek JW, Summerton JE, Mata JE, Squier TC. Detection of unique Ebola virus oligonucleotides using fluorescently-labeled phosphorodiamidate morpholino oligonucleotide probe pairs. Anal Biochem 2018; 557:84-90. [PMID: 30030994 DOI: 10.1016/j.ab.2018.07.006] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2018] [Accepted: 07/12/2018] [Indexed: 12/22/2022]
Abstract
Here we identify a low-cost diagnostic platform using fluorescently-labeled phosphorodiamidate morpholino oligonucleotide (PMO) probe pairs, which upon binding target oligonucleotides undergo fluorescence resonance energy transfer (FRET). Using a target oligonucleotide derived from the Ebola virus (EBOV), we have derivatized PMO probes with either Alexa Fluor488 (donor) or tetramethylrhodamine (acceptor). Upon EBOV target oligonulceotide binding, observed changes in FRET between PMO probe pairs permit a 25 pM lower limit of detection; there is no off-target binding within a complex mixture of nucleic acids and other biomolecules present in human saliva. Equivalent levels of FRET occur using PMO probe pairs for single or double stranded oligonucleotide targets. High-affinity binding is retained under low-ionic strength conditions that disrupt oligonucleotide secondary structures (e.g., stem-loop structures), ensuring reliable target detection. Under these low-ionic strength conditions, rates of PMO probe binding to target oligonucleotides are increased 3-fold relative to conventional high-ionic strength conditions used for nucleic acid hybridization, with half-maximal binding occurring within 10 min. Our results indicate an ability to use PMO probe pairs to detect clinically relevant levels of EBOV and other oligonucleotide targets in complex biological samples without the need for nucleic acid amplification, and open the possibility of population screening that includes assays for the genomic integration of DNA based copies of viral RNA.
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Affiliation(s)
- Yijia Xiong
- Department of Basic Medical Sciences, Western University of Health Sciences, 200 Mullins Drive, Lebanon, OR, 97355, United States
| | - Tammie J McQuistan
- Department of Basic Medical Sciences, Western University of Health Sciences, 200 Mullins Drive, Lebanon, OR, 97355, United States
| | - James W Stanek
- Department of Basic Medical Sciences, Western University of Health Sciences, 200 Mullins Drive, Lebanon, OR, 97355, United States
| | - James E Summerton
- Gene Tools, LLC, One Summerton Way, Philomath, OR, 97370, United States
| | - John E Mata
- Department of Basic Medical Sciences, Western University of Health Sciences, 200 Mullins Drive, Lebanon, OR, 97355, United States; Takena Technologies Inc, 405 West First Street, Albany, OR, 97321, United States
| | - Thomas C Squier
- Department of Basic Medical Sciences, Western University of Health Sciences, 200 Mullins Drive, Lebanon, OR, 97355, United States.
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12
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Jalalian SH, Karimabadi N, Ramezani M, Abnous K, Taghdisi SM. Electrochemical and optical aptamer-based sensors for detection of tetracyclines. Trends Food Sci Technol 2018. [DOI: 10.1016/j.tifs.2018.01.009] [Citation(s) in RCA: 77] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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13
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Joseph J, Baumann KN, Koehler P, Zuehlsdorff TJ, Cole DJ, Weber J, Bohndiek SE, Hernández-Ainsa S. Distance dependent photoacoustics revealed through DNA nanostructures. NANOSCALE 2017; 9:16193-16199. [PMID: 29043366 DOI: 10.1039/c7nr05353c] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
Molecular rulers that rely on the Förster resonance energy transfer (FRET) mechanism are widely used to investigate dynamic molecular processes that occur on the nanometer scale. However, the capabilities of these fluorescence molecular rulers are fundamentally limited to shallow imaging depths by light scattering in biological samples. Photoacoustic tomography (PAT) has recently emerged as a high resolution modality for in vivo imaging, coupling optical excitation with ultrasound detection. In this paper, we report the capability of PAT to probe distance-dependent FRET at centimeter depths. Using DNA nanotechnology we created several nanostructures with precisely positioned fluorophore-quencher pairs over a range of nanoscale separation distances. PAT of the DNA nanostructures showed distance-dependent photoacoustic signal enhancement and demonstrated the ability of PAT to reveal the FRET process deep within tissue mimicking phantoms. Further, we experimentally validated these DNA nanostructures as a novel and biocompatible strategy to augment the intrinsic photoacoustic signal generation capabilities of small molecule fluorescent dyes.
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Affiliation(s)
- James Joseph
- Cavendish Laboratory, Department of Physics, University of Cambridge, Cambridge, UK.
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14
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Marukhyan SS, Gasparyan VK. Fluorometric immunoassay for human serum albumin based on its inhibitory effect on the immunoaggregation of quantum dots with silver nanoparticles. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2017; 173:34-38. [PMID: 27591512 DOI: 10.1016/j.saa.2016.08.029] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/01/2016] [Revised: 08/01/2016] [Accepted: 08/16/2016] [Indexed: 06/06/2023]
Abstract
Quantitative determination of HSA was conducted by competitive immunoassay. Inhibition of aggregation of antibody conjugated quantum dots (QD) with albumin conjugated silver nanoparticles (AgNPs) in the presence of HSA was conducted. If antibody-loaded CdSe QDs aggregate with HSA-coated silver nanoparticles the distance between the two kinds of nanoparticles will be reduced enough to cause fluorescence resonance energy transfer (FRET). In this case the yellow fluorescence of the Ab-QDs is quenched. However if HSA (antigen) is added to the Ab-QDs their surface will be blocked and they cannot aggregate any longer with the HSA-AgNPs. Hence, fluorescence will not be quenched. The drop of the intensity of fluorescence (peaking at 570nm) is inversely correlated with the concentration of HSA in the sample. The method allows to determine HSA in the 30-600ng·mL-1 concentration range.
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Affiliation(s)
- Seda S Marukhyan
- Institute of Biochemistry, National Academy of Science, Republic of Armenia, P. Sevak str. 5/1, Yerevan 0014, Armenia
| | - Vardan K Gasparyan
- Institute of Biochemistry, National Academy of Science, Republic of Armenia, P. Sevak str. 5/1, Yerevan 0014, Armenia.
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15
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Shamsipur M, Nasirian V, Mansouri K, Barati A, Veisi-Raygani A, Kashanian S. A highly sensitive quantum dots-DNA nanobiosensor based on fluorescence resonance energy transfer for rapid detection of nanomolar amounts of human papillomavirus 18. J Pharm Biomed Anal 2017; 136:140-147. [PMID: 28081500 DOI: 10.1016/j.jpba.2017.01.002] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2016] [Revised: 12/23/2016] [Accepted: 01/02/2017] [Indexed: 11/30/2022]
Abstract
A very sensitive and convenient nanobiosensor based on fluorescence resonance energy transfer (FRET) was developed for the detection of a 22-mer oligonucleotides sequence in Human Papillomavirus 18 virus (HPV18) gene. For this purpose, water-soluble CdTe quantum dots (QDs) were synthesized and, subsequently, amino-modified 11-mer oligonucleotide as one of the two necessary probes was attached to QDs surface to form functional QDs-DNA conjugates. Right after addition of the QDs-DNA and a second Cyanine5 (Cy5)-labeled 11-mer oligonucleotide probe to the DNA target solution, the sandwiched hybrids were formed. The resulting hybridization brings the Cy5 fluorophore as the acceptor to close proximity of the QDs as donor, so that an effective transfer of energy from the excited QDs to the Cy5 probe would occur via FRET processing. The fluorescence intensity of Cy5 found to linearly enhance by increasing the DNA target concentration from 1.0 to 50.0nM, with a detection limit of 0.2nM. This homogeneous DNA detection method does not require excessive washing and separation steps of un-hybridized DNA, due to the fact that no FRET can be observed when the probes are not ligated. Finally, feasibility and selectivity of the proposed one-spot DNA detection nanobiosensor were investigated by analysis of derived nucleotides from HPV18 and mismatched sequences.
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Affiliation(s)
| | - Vahid Nasirian
- Department of Chemistry, Razi University, Kermanshah, Iran
| | - Kamran Mansouri
- Medical Biology Research Center, Kermanshah University of Medical Sciences, Kermanshah, Iran
| | - Ali Barati
- Department of Chemistry, Razi University, Kermanshah, Iran
| | - Asad Veisi-Raygani
- Department of Biochemistry, School of Medicine, Kermanshah University of Medical Sciences, Kermanshah, Iran
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16
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Oh T, Kim S, Choi JY, Chang H, Heller MJ. Enhancement of fluorescent resonant energy transfer and the antenna effect in DNA structures with multiple fluorescent dyes. RSC Adv 2017. [DOI: 10.1039/c7ra01470h] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
This study examines the use of surfactants and metal cations to enhance the long range fluorescent resonant energy transfer (FRET) and the antenna effect from three TAMRA donor dyes to one Texas Red acceptor dye conjugated in dsDNA structure.
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Affiliation(s)
- Taeseok Oh
- Materials Science and Engineering Program
- University of California
- San Diego
- USA
- Department of NanoEngineering
| | - Sejung Kim
- Department of NanoEngineering
- University of California
- San Diego
- USA
| | - Jae-Young Choi
- Department of NanoEngineering
- University of California
- San Diego
- USA
| | - Haeun Chang
- Department of NanoEngineering
- University of California
- San Diego
- USA
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17
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Algar WR, Khachatrian A, Melinger JS, Huston AL, Stewart MH, Susumu K, Blanco-Canosa JB, Oh E, Dawson PE, Medintz IL. Concurrent Modulation of Quantum Dot Photoluminescence Using a Combination of Charge Transfer and Förster Resonance Energy Transfer: Competitive Quenching and Multiplexed Biosensing Modality. J Am Chem Soc 2016; 139:363-372. [DOI: 10.1021/jacs.6b11042] [Citation(s) in RCA: 55] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Affiliation(s)
- W. Russ Algar
- Department
of Chemistry, University of British Columbia, Vancouver, BC, V6T 1Z1, Canada
| | - Ani Khachatrian
- Sotera Defense Solutions, Columbia, Maryland 21046, United States
| | | | | | | | - Kimihiro Susumu
- Sotera Defense Solutions, Columbia, Maryland 21046, United States
| | - Juan B. Blanco-Canosa
- Departments
of Chemistry and Cell Biology, The Scripps Research Institute, La Jolla, California 92037, United States
| | - Eunkeu Oh
- Sotera Defense Solutions, Columbia, Maryland 21046, United States
| | - Philip E. Dawson
- Departments
of Chemistry and Cell Biology, The Scripps Research Institute, La Jolla, California 92037, United States
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18
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Mei Z, Tang L. Surface-Plasmon-Coupled Fluorescence Enhancement Based on Ordered Gold Nanorod Array Biochip for Ultrasensitive DNA Analysis. Anal Chem 2016; 89:633-639. [PMID: 27991768 DOI: 10.1021/acs.analchem.6b02797] [Citation(s) in RCA: 76] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Abstract
An innovative gold nanorod (GNR) array biochip was developed to systematically investigate the localized surface plasmon resonance (LSPR)-coupled fluorescence enhancement for signal amplification in molecular beacon detection. An ordered GNR assembly in vertical standing array on a glass surface was fabricated as plasmonic substrates, resulting in dramatically intensified LSPR between adjacent nanoparticles as compared to that from an ensemble of random nanorods. We have shown that the plasmonic response of the nanoarray can be tuned by the proper choice of GNR size to overlap the fluorophore excitation and emission wavelengths greater than 600 nm. Plasmon-induced fluorescence enhancement was found to be distance-dependent with the competition between quenching and enhancement by the metal nanostructures. The augmented fluorescence enhancement by the GNR array can efficiently overcome the quenching effect of the gold nanoparticle even at close proximity. The enhancement correlates with the spectral overlap between the fluorophore excitation/emission and the plasmonic resonance of the GNR array, indicating a surface-plasmon-enhanced excitation and radiative mechanism for the amplification. From these results, the applicability of the ordered GNR array chip was extended to molecular fluorescence enhancement for practical use as a highly functional and ultrasensitive plasmonic DNA biochip in molecular beacon fashion.
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Affiliation(s)
- Zhong Mei
- Department of Biomedical Engineering, University of Texas at San Antonio , San Antonio, Texas 78249, United States
| | - Liang Tang
- Department of Biomedical Engineering, University of Texas at San Antonio , San Antonio, Texas 78249, United States
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19
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Araujo JV, Rifaie-Graham O, Apebende EA, Bruns N. Self-reporting Polymeric Materials with Mechanochromic Properties. BIO-INSPIRED POLYMERS 2016. [DOI: 10.1039/9781782626664-00354] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Abstract
The mechanical transduction of force onto molecules is an essential feature of many biological processes that results in the senses of touch and hearing, gives important cues for cellular interactions and can lead to optically detectable signals, such as a change in colour, fluorescence or chemoluminescence. Polymeric materials that are able to visually indicate deformation, stress, strain or the occurrence of microdamage draw inspiration from these biological events. The field of self-reporting (or self-assessing) materials is reviewed. First, mechanochromic events in nature are discussed, such as the formation of bruises on skin, the bleeding of a wound, or marine glow caused by dinoflagellates. Then, materials based on force-responsive mechanophores, such as spiropyrans, cyclobutanes, cyclooctanes, Diels–Alder adducts, diarylbibenzofuranone and bis(adamantyl)-1,2-dioxetane are reviewed, followed by mechanochromic blends, chromophores stabilised by hydrogen bonds, and pressure sensors based on ionic interactions between fluorescent dyes and polyelectrolyte brushes. Mechanobiochemistry is introduced as an important tool to create self-reporting hybrid materials that combine polymers with the force-responsive properties of fluorescent proteins, protein FRET pairs, and other biomacromolecules. Finally, dye-filled microcapsules, microvascular networks, and hollow fibres are demonstrated to be important technologies to create damage-indicating coatings, self-reporting fibre-reinforced composites and self-healing materials.
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Affiliation(s)
- Jose V. Araujo
- Adolphe Merkle Institute, University of Fribourg Chemin des Verdiers 4 1700 Fribourg Switzerland
| | - Omar Rifaie-Graham
- Adolphe Merkle Institute, University of Fribourg Chemin des Verdiers 4 1700 Fribourg Switzerland
| | - Edward A. Apebende
- Adolphe Merkle Institute, University of Fribourg Chemin des Verdiers 4 1700 Fribourg Switzerland
| | - Nico Bruns
- Adolphe Merkle Institute, University of Fribourg Chemin des Verdiers 4 1700 Fribourg Switzerland
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20
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Highly specific quantification of microRNA by coupling probe–rolling circle amplification and Förster resonance energy transfer. Anal Biochem 2016; 502:16-23. [DOI: 10.1016/j.ab.2016.03.001] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2015] [Revised: 03/01/2016] [Accepted: 03/02/2016] [Indexed: 12/17/2022]
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21
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Wasin T, Enomoto K, Sakurai T, Padalkar VS, Cheng HL, Tang MT, Horio A, Sakamaki D, Omichi M, Saeki A, Kikuchi K, Hori Y, Chiba A, Saito Y, Kamiya T, Sugimoto M, Seki S. Fabrication of “Clickable” Polyfluorene Nanowires with High Aspect Ratio as Biological Sensing Platforms. ACS Sens 2016. [DOI: 10.1021/acssensors.6b00070] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Affiliation(s)
- Tuchinda Wasin
- Department
of Molecular Engineering, Graduate School of Engineering, Kyoto University, Nishikyo-ku, Kyoto 615-8510, Japan
- International
College, Osaka University, Toyonaka, Osaka 560-0043, Japan
| | - Kazuyuki Enomoto
- International
College, Osaka University, Toyonaka, Osaka 560-0043, Japan
| | - Tsuneaki Sakurai
- Department
of Molecular Engineering, Graduate School of Engineering, Kyoto University, Nishikyo-ku, Kyoto 615-8510, Japan
| | - Vikas S. Padalkar
- Department
of Molecular Engineering, Graduate School of Engineering, Kyoto University, Nishikyo-ku, Kyoto 615-8510, Japan
| | - Hoi Lok Cheng
- International
College, Osaka University, Toyonaka, Osaka 560-0043, Japan
| | - Michael T. Tang
- International
College, Osaka University, Toyonaka, Osaka 560-0043, Japan
| | - Akifumi Horio
- Department
of Molecular Engineering, Graduate School of Engineering, Kyoto University, Nishikyo-ku, Kyoto 615-8510, Japan
| | - Daisuke Sakamaki
- Department
of Molecular Engineering, Graduate School of Engineering, Kyoto University, Nishikyo-ku, Kyoto 615-8510, Japan
| | - Masaaki Omichi
- Department
of Applied Chemistry, Graduate School of Engineering, Osaka University, Suita 565-0871, Japan
| | - Akinori Saeki
- Department
of Applied Chemistry, Graduate School of Engineering, Osaka University, Suita 565-0871, Japan
| | - Kazuya Kikuchi
- Department
of Applied Chemistry, Graduate School of Engineering, Osaka University, Suita 565-0871, Japan
- Department
of Material and Life Science, Graduate School of Engineering, Osaka University, Suita 565-0871, Japan
| | - Yuichiro Hori
- Department
of Applied Chemistry, Graduate School of Engineering, Osaka University, Suita 565-0871, Japan
- Department
of Material and Life Science, Graduate School of Engineering, Osaka University, Suita 565-0871, Japan
| | - Atsuya Chiba
- Quantum
Beam Science
Research Directorate (QuBS), National Institutes for Quantum and Radiological
Science and Technology (QST), 1233,
Watanuki-machi, Takasaki, Gunma 370-1292, Japan
| | - Yuichi Saito
- Quantum
Beam Science
Research Directorate (QuBS), National Institutes for Quantum and Radiological
Science and Technology (QST), 1233,
Watanuki-machi, Takasaki, Gunma 370-1292, Japan
| | - Tomihiro Kamiya
- Quantum
Beam Science
Research Directorate (QuBS), National Institutes for Quantum and Radiological
Science and Technology (QST), 1233,
Watanuki-machi, Takasaki, Gunma 370-1292, Japan
| | - Masaki Sugimoto
- Quantum
Beam Science
Research Directorate (QuBS), National Institutes for Quantum and Radiological
Science and Technology (QST), 1233,
Watanuki-machi, Takasaki, Gunma 370-1292, Japan
| | - Shu Seki
- Department
of Molecular Engineering, Graduate School of Engineering, Kyoto University, Nishikyo-ku, Kyoto 615-8510, Japan
- International
College, Osaka University, Toyonaka, Osaka 560-0043, Japan
- Department
of Applied Chemistry, Graduate School of Engineering, Osaka University, Suita 565-0871, Japan
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22
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Oh T, Choi JY, Heller MJ. Enhanced fluorescent resonant energy transfer of DNA conjugates complexed with surfactants and divalent metal ions. Analyst 2016; 141:2371-5. [PMID: 26985458 DOI: 10.1039/c5an02516h] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Dimerization and resultant quenching of donor and acceptor dyes conjugated on DNA causes loss of fluorescent resonant energy transfer (FRET) efficiency. However, when complexed with surfactants and divalent metal ions, sheathing effects insulate and shield the DNA structures, reducing dimerization and quenching which leads to significant enhancement of FRET efficiency.
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Affiliation(s)
- Taeseok Oh
- Materials Science and Engineering, University of California, San Diego, 9500 Gilman Dr., La Jolla, CA 92093, USA
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23
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Yu X, Wen K, Wang Z, Zhang X, Li C, Zhang S, Shen J. General Bioluminescence Resonance Energy Transfer Homogeneous Immunoassay for Small Molecules Based on Quantum Dots. Anal Chem 2016; 88:3512-20. [PMID: 26948147 DOI: 10.1021/acs.analchem.5b03581] [Citation(s) in RCA: 44] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
Here, we describe a general bioluminescence resonance energy transfer (BRET) homogeneous immunoassay based on quantum dots (QDs) as the acceptor and Renilla luciferase (Rluc) as the donor (QD-BRET) for the determination of small molecules. The ratio of the donor-acceptor that could produce energy transfer varied in the presence of different concentrations of free enrofloxacin (ENR), an important small molecule in food safety. The calculated Förster distance (R0) was 7.86 nm. Under optimized conditions, the half-maximal inhibitory concentration (IC50) for ENR was less than 1 ng/mL and the linear range covered 4 orders of magnitude (0.023 to 25.60 ng/mL). The cross-reactivities (CRs) of seven representative fluoroquinolones (FQs) were similar to the data obtained by an enzyme-linked immunosorbent assay (ELISA). The average intra- and interassay recoveries from spiked milk of were 79.8-118.0%, and the relative standard deviations (RSDs) were less than 10%, meeting the requirement of residue detection, which was a satisfactory result. Furthermore, we compared the influence of different luciferase substrates on the performance of the assay. Considering sensitivity and stability, coelenterazine-h was the most appropriate substrate. The results from this study will enable better-informed decisions on the choice of Rluc substrate for QD-BRET systems. For the future, the QD-BRET immunosensor could easily be extended to other small molecules and thus represents a versatile strategy in food safety, the environment, clinical diagnosis, and other fields.
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Affiliation(s)
- Xuezhi Yu
- Beijing Advanced Innovation Center for Food Nutrition and Human Health, College of Veterinary Medicine, China Agricultural University , No. 2 Yuanmingyuan West Road, Beijing 100193, China
| | - Kai Wen
- Beijing Advanced Innovation Center for Food Nutrition and Human Health, College of Veterinary Medicine, China Agricultural University , No. 2 Yuanmingyuan West Road, Beijing 100193, China
| | - Zhanhui Wang
- Beijing Advanced Innovation Center for Food Nutrition and Human Health, College of Veterinary Medicine, China Agricultural University , No. 2 Yuanmingyuan West Road, Beijing 100193, China
| | - Xiya Zhang
- Beijing Advanced Innovation Center for Food Nutrition and Human Health, College of Veterinary Medicine, China Agricultural University , No. 2 Yuanmingyuan West Road, Beijing 100193, China
| | - Chenglong Li
- Beijing Advanced Innovation Center for Food Nutrition and Human Health, College of Veterinary Medicine, China Agricultural University , No. 2 Yuanmingyuan West Road, Beijing 100193, China
| | - Suxia Zhang
- Beijing Advanced Innovation Center for Food Nutrition and Human Health, College of Veterinary Medicine, China Agricultural University , No. 2 Yuanmingyuan West Road, Beijing 100193, China.,Beijing Laboratory for Food Quality and Safety and Beijing Key Laboratory of Detection Technology for Animal-Derived Food Safety , No. 2 Yuanmingyuan West Road, Beijing 100193, China
| | - Jianzhong Shen
- Beijing Advanced Innovation Center for Food Nutrition and Human Health, College of Veterinary Medicine, China Agricultural University , No. 2 Yuanmingyuan West Road, Beijing 100193, China.,Beijing Laboratory for Food Quality and Safety and Beijing Key Laboratory of Detection Technology for Animal-Derived Food Safety , No. 2 Yuanmingyuan West Road, Beijing 100193, China
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24
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Larkey NE, Brucks CN, Lansing SS, Le SD, Smith NM, Tran V, Zhang L, Burrows SM. Molecular structure and thermodynamic predictions to create highly sensitive microRNA biosensors. Anal Chim Acta 2016; 909:109-20. [DOI: 10.1016/j.aca.2015.12.040] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2015] [Revised: 12/24/2015] [Accepted: 12/30/2015] [Indexed: 01/04/2023]
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25
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Oh T, Takahashi T, Kim S, Heller MJ. CTAB enhancement of FRET in DNA structures. JOURNAL OF BIOPHOTONICS 2016; 9:49-54. [PMID: 26530400 DOI: 10.1002/jbio.201500221] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/16/2015] [Revised: 09/20/2015] [Accepted: 10/13/2015] [Indexed: 06/05/2023]
Abstract
The effect of cetyl-trimethylammonium bromide (CTAB) on enhancing the fluorescence resonance energy transfer (FRET) between two dye-conjugated DNA strands was studied using fluorescence emission spectroscopy and dynamic light scattering (DLS). For hybridized DNA where one strand is conjugated with a TAMRA donor and the other with a TexasRed acceptor, increasing the concentration of CTAB changes the fluorescence emission properties and improves the FRET transfer efficiency through changes in the polarity of the solvent, neutralization of the DNA backbone and micelle formation. For the DNA FRET system without CTAB, the DNA hybridization leads to contact quenching between TAMRA donor and TexasRed acceptor producing reduced donor emission and only a small increase in acceptor emission. At 50 µM CTAB, however, the sheathing and neutralization of the dye-conjugated dsDNA structure significantly reduces quenching by DNA bases and dye interactions, producing a large increase in FRET efficiency, which is almost four fold higher than without CTAB.
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Affiliation(s)
- Taeseok Oh
- Materials Science and Engineering Program, University of California, San Diego, 9500, Gilman Dr., La Jolla, CA 92093, USA
| | - Tsukasa Takahashi
- Department of Mechanical and Aerospace Engineering, University of California, San Diego, 9500, Gilman Dr., La Jolla, CA 92093, USA
| | - Sejung Kim
- Materials Science and Engineering Program, University of California, San Diego, 9500, Gilman Dr., La Jolla, CA 92093, USA
| | - Michael J Heller
- Department of NanoEngineering, University of California, San Diego, 9500, Gilman Dr., La Jolla, CA 92093, USA.
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26
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HAGIHARA K, TSUKAGOSHI K, NAKAJIMA C, ESAKI S, HASHIMOTO M. Improvement of the Mutation-Discrimination Threshold for Rare Point Mutations by a Separation-Free Ligase Detection Reaction Assay Based on Fluorescence Resonance Energy Transfer. ANAL SCI 2016; 32:367-70. [DOI: 10.2116/analsci.32.367] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Affiliation(s)
- Kenta HAGIHARA
- Department of Chemical Engineering and Materials Science, Faculty of Science and Engineering, Doshisha University
| | - Kazuhiko TSUKAGOSHI
- Department of Chemical Engineering and Materials Science, Faculty of Science and Engineering, Doshisha University
| | - Chinami NAKAJIMA
- Department of Chemical Engineering and Materials Science, Faculty of Science and Engineering, Doshisha University
| | - Shinsuke ESAKI
- Department of Chemical Engineering and Materials Science, Faculty of Science and Engineering, Doshisha University
| | - Masahiko HASHIMOTO
- Department of Chemical Engineering and Materials Science, Faculty of Science and Engineering, Doshisha University
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27
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Li H, Wang M, Wang C, Li W, Qiang W, Xu D. Silver nanoparticle-enhanced fluorescence resonance energy transfer sensor for human platelet-derived growth factor-BB detection. Anal Chem 2013; 85:4492-9. [PMID: 23531211 DOI: 10.1021/ac400047d] [Citation(s) in RCA: 66] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
A silver nanoparticle (AgNP)-enhanced fluorescence resonance energy transfer (FRET) sensing system is designed for the sensitive detection of human platelet-derived growth factor-BB (PDGF-BB). Fluorophore-functionalized aptamers and quencher-carrying strands hybridized in duplex are coupled with streptavidin (SA)-functionalized nanoparticles to form a AgNP-enhanced FRET sensor. The resulting sensor shows lower background fluorescence intensity in the duplex state due to the FRET effect between fluorophores and quenchers. Upon the addition of PDGF-BB, the quencher-carrying strands (BHQ-2) of the duplex are displaced leading to the disruption of the FRET effect. As a result, the fluorescent intensity of the fluorophore-aptamer within the proximity of the AgNP is increased. When compared to the gold nanoparticle (AuNP)-based FRET and bare FRET sensors, the AgNP-based FRET sensor showed remarkable increase in fluorescence intensity, target specificity, and sensitivity. Results also show versatility of the AgNP in the enhancement of sensitivity and selectivity of the FRET sensor. In addition, a good linear response was obtained when the PDGF-BB concentrations are in the ranges of 100-500 and 6.2-50 ng/mL with the detection limit of 0.8 ng/mL.
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Affiliation(s)
- Hui Li
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, China
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28
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Rao AN, Vandencasteele N, Gamble LJ, Grainger DW. High-resolution epifluorescence and time-of-flight secondary ion mass spectrometry chemical imaging comparisons of single DNA microarray spots. Anal Chem 2012; 84:10628-36. [PMID: 23150996 DOI: 10.1021/ac3019334] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
DNA microarray assay performance is commonly compromised by spot-spot probe and signal variations as well as heterogeneity within printed microspots. Accurate metrics for captured DNA target signal rely upon uniform spot distribution of both probe and target DNA to yield reliable hybridized signal. While often presumed, this is neither easily achieved nor often proven experimentally. High-resolution imaging techniques were used to determine spot heterogeneity in identical DNA array microspots comprising varied ratios of unlabeled and dye-labeled DNA probes contact-printed onto commercial arraying surfaces. Epifluorescence imaging data for individual array microspots were correlated with time-of-flight secondary ion mass spectrometry (TOF-SIMS) chemical state imaging of the same spots. Epifluorescence imaging intensity distinguished varying DNA density distributed both within a given spot and from spot to spot. TOF-SIMS chemical analysis confirmed these heterogeneous printed DNA distributions by tracking bound Cy3 dye, DNA base, and phosphate specific ion fragments often correlating to fluorescence patterns within identical spots. TOF-SIMS ion fragments originating from probe DNA and Cy3 dye are enriched in microspot centers, correlating with high fluorescence intensity regions. Both TOF-SIMS and epifluorescence support Marangoni flow effects on spot drying, with high-density DNA-Cy3 located in spot centers and nonhomogeneous DNA distribution within printed spots. Microspot image dimensional analysis results for DNA droplet spreading show differing DNA densities across printed spots. The study directly supports different DNA probe chemical and spatial microenvironments within spots that yield spot-spot signal variations known to affect DNA target hybridization efficiencies and kinetics. These variations critically affect probe-target duplex formation and DNA array signal generation.
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Affiliation(s)
- Archana N Rao
- Department of Pharmaceutics and Pharmaceutical Chemistry, University of Utah, Salt Lake City, Utah 84112-5820, USA
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29
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Astakhova IK, Wengel J. Interfacing click chemistry with automated oligonucleotide synthesis for the preparation of fluorescent DNA probes containing internal xanthene and cyanine dyes. Chemistry 2012. [PMID: 23180379 DOI: 10.1002/chem.201202621] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
Double-labeled oligonucleotide probes containing fluorophores interacting by energy-transfer mechanisms are essential for modern bioanalysis, molecular diagnostics, and in vivo imaging techniques. Although bright xanthene and cyanine dyes are gaining increased prominence within these fields, little attention has thus far been paid to probes containing these dyes internally attached, a fact which is mainly due to the quite challenging synthesis of such oligonucleotide probes. Herein, by using 2'-O-propargyl uridine phosphoramidite and a series of xanthenes and cyanine azide derivatives, we have for the first time performed solid-phase copper(I)-catalyzed azide-alkyne cycloaddition (CuAAC) click labeling during the automated phosphoramidite oligonucleotide synthesis followed by postsynthetic click reactions in solution. We demonstrate that our novel strategy is rapid and efficient for the preparation of novel oligonucleotide probes containing internally positioned xanthene and cyanine dye pairs and thus represents a significant step forward for the preparation of advanced fluorescent oligonucleotide probes. Furthermore, we demonstrate that the novel xanthene and cyanine labeled probes display unusual and very promising photophysical properties resulting from energy-transfer interactions between the fluorophores controlled by nucleic acid assembly. Potential benefits of using these novel fluorescent probes within, for example, molecular diagnostics and fluorescence microscopy include: Considerable Stokes shifts (40-110 nm), quenched fluorescence of single-stranded probes accompanied by up to 7.7-fold light-up effect of emission upon target DNA/RNA binding, remarkable sensitivity to single-nucleotide mismatches, generally high fluorescence brightness values (FB up to 26), and hence low limit of target detection values (LOD down to <5 nM).
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Affiliation(s)
- I Kira Astakhova
- Nucleic Acid Center, Department of Physics, Chemistry and Pharmacy, University of Southern Denmark, Campusvej 55, 5230 Odense M, Denmark.
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30
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Preus S, Wilhelmsson LM. Advances in quantitative FRET-based methods for studying nucleic acids. Chembiochem 2012; 13:1990-2001. [PMID: 22936620 DOI: 10.1002/cbic.201200400] [Citation(s) in RCA: 98] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2012] [Indexed: 01/02/2023]
Abstract
Förster resonance energy transfer (FRET) is a powerful tool for monitoring molecular distances and interactions at the nanoscale level. The strong dependence of transfer efficiency on probe separation makes FRET perfectly suited for "on/off" experiments. To use FRET to obtain quantitative distances and three-dimensional structures, however, is more challenging. This review summarises recent studies and technological advances that have improved FRET as a quantitative molecular ruler in nucleic acid systems, both at the ensemble and at the single-molecule levels.
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Affiliation(s)
- Søren Preus
- Department of Chemistry, University of Copenhagen, Universitetsparken 5, 2100 Copenhagen, Denmark
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31
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White AG, Gray BD, Pak KY, Smith BD. Deep-red fluorescent imaging probe for bacteria. Bioorg Med Chem Lett 2012; 22:2833-6. [PMID: 22424976 PMCID: PMC3321076 DOI: 10.1016/j.bmcl.2012.02.078] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2011] [Revised: 02/17/2012] [Accepted: 02/23/2012] [Indexed: 12/01/2022]
Abstract
A versatile deep-red fluorescent imaging probe is described that is comprised of a bis(zinc(II)-dipicolylamine) targeting unit covalently attached to a pentamethine carbocyanine fluorophore with Cy5-like spectroscopic properties. A titration assay based on fluorescence resonance energy transfer is used to prove that the probe selectively associates with anionic vesicle membranes whose composition mimics bacterial cell membranes. Whole-body optical imaging experiments show that the probe associates with the surfaces of both Gram-positive and Gram-negative bacteria cells, and it can target the site of bacterial infection in a living mouse. In vivo accumulation at the infection site and subsequent clearance occurs more quickly than a structurally related near-infrared bis(zinc(II)-dipicolylamine) probe. The fact that the same deep-red probe molecule can be used for spectroscopic assays, cell microscopy, and in vivo imaging studies, is an important and attractive technical feature.
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Affiliation(s)
- Alexander G. White
- Department of Chemistry and Biochemistry, 236 Nieuwland Science Hall, University of Notre Dame, Notre Dame, IN 46556, USA
| | - Brian D. Gray
- Molecular Targeting Technologies Incorporated, 833 Lincoln Ave., Unit 9, West Chester, PA 19380, USA
| | - Koon Yan Pak
- Molecular Targeting Technologies Incorporated, 833 Lincoln Ave., Unit 9, West Chester, PA 19380, USA
| | - Bradley D. Smith
- Department of Chemistry and Biochemistry, 236 Nieuwland Science Hall, University of Notre Dame, Notre Dame, IN 46556, USA
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32
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Graugnard E, Kellis DL, Bui H, Barnes S, Kuang W, Lee J, Hughes WL, Knowlton WB, Yurke B. DNA-controlled excitonic switches. NANO LETTERS 2012; 12:2117-22. [PMID: 22401838 PMCID: PMC3324986 DOI: 10.1021/nl3004336] [Citation(s) in RCA: 50] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/02/2012] [Revised: 02/27/2012] [Indexed: 05/19/2023]
Abstract
Fluorescence resonance energy transfer (FRET) is a promising means of enabling information processing in nanoscale devices, but dynamic control over exciton pathways is required. Here, we demonstrate the operation of two complementary switches consisting of diffusive FRET transmission lines in which exciton flow is controlled by DNA. Repeatable switching is accomplished by the removal or addition of fluorophores through toehold-mediated strand invasion. In principle, these switches can be networked to implement any Boolean function.
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Affiliation(s)
- Elton Graugnard
- Department of Materials Science and Engineering, Boise State University, Boise, Idaho 83725, USA.
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33
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Juskowiak B. Nucleic acid-based fluorescent probes and their analytical potential. Anal Bioanal Chem 2011; 399:3157-76. [PMID: 21046088 PMCID: PMC3044240 DOI: 10.1007/s00216-010-4304-5] [Citation(s) in RCA: 160] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2010] [Revised: 10/04/2010] [Accepted: 10/05/2010] [Indexed: 12/21/2022]
Abstract
It is well known that nucleic acids play an essential role in living organisms because they store and transmit genetic information and use that information to direct the synthesis of proteins. However, less is known about the ability of nucleic acids to bind specific ligands and the application of oligonucleotides as molecular probes or biosensors. Oligonucleotide probes are single-stranded nucleic acid fragments that can be tailored to have high specificity and affinity for different targets including nucleic acids, proteins, small molecules, and ions. One can divide oligonucleotide-based probes into two main categories: hybridization probes that are based on the formation of complementary base-pairs, and aptamer probes that exploit selective recognition of nonnucleic acid analytes and may be compared with immunosensors. Design and construction of hybridization and aptamer probes are similar. Typically, oligonucleotide (DNA, RNA) with predefined base sequence and length is modified by covalent attachment of reporter groups (one or more fluorophores in fluorescence-based probes). The fluorescent labels act as transducers that transform biorecognition (hybridization, ligand binding) into a fluorescence signal. Fluorescent labels have several advantages, for example high sensitivity and multiple transduction approaches (fluorescence quenching or enhancement, fluorescence anisotropy, fluorescence lifetime, fluorescence resonance energy transfer (FRET), and excimer-monomer light switching). These multiple signaling options combined with the design flexibility of the recognition element (DNA, RNA, PNA, LNA) and various labeling strategies contribute to development of numerous selective and sensitive bioassays. This review covers fundamentals of the design and engineering of oligonucleotide probes, describes typical construction approaches, and discusses examples of probes used both in hybridization studies and in aptamer-based assays.
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Affiliation(s)
- Bernard Juskowiak
- Faculty of Chemistry, A. Mickiewicz University, Grunwaldzka 6, 60-780 Poznan, Poland.
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34
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Cyanine dyes in biophysical research: the photophysics of polymethine fluorescent dyes in biomolecular environments. Q Rev Biophys 2010; 44:123-51. [DOI: 10.1017/s0033583510000247] [Citation(s) in RCA: 294] [Impact Index Per Article: 21.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
AbstractThe breakthroughs in single molecule spectroscopy of the last decade and the recent advances in super resolution microscopy have boosted the popularity of cyanine dyes in biophysical research. These applications have motivated the investigation of the reactions and relaxation processes that cyanines undergo in their electronically excited states. Studies show that the triplet state is a key intermediate in the photochemical reactions that limit the photostability of cyanine dyes. The removal of oxygen greatly reduces photobleaching, but induces rapid intensity fluctuations (blinking). The existence of non-fluorescent states lasting from milliseconds to seconds was early identified as a limitation in single-molecule spectroscopy and a potential source of artifacts. Recent studies demonstrate that a combination of oxidizing and reducing agents is the most efficient way of guaranteeing that the ground state is recovered rapidly and efficiently. Thiol-containing reducing agents have been identified as the source of long-lived dark states in some cyanines that can be photochemically switched back to the emissive state. The mechanism of this process is the reversible addition of the thiol-containing compound to a double bond in the polymethine chain resulting in a non-fluorescent molecule. This process can be reverted by irradiation at shorter wavelengths. Another mechanism that leads to non-fluorescent states in cyanine dyes is cis–trans isomerization from the singlet-excited state. This process, which competes with fluorescence, involves the rotation of one-half of the molecule with respect to the other with an efficiency that depends strongly on steric effects. The efficiency of fluorescence of most cyanine dyes has been shown to depend dramatically on their molecular environment within the biomolecule. For example, the fluorescence quantum yield of Cy3 linked covalently to DNA depends on the type of linkage used for attachment, DNA sequence and secondary structure. Cyanines linked to the DNA termini have been shown to be mostly stacked at the end of the helix, while cyanines linked to the DNA internally are believed to partially bind to the minor or major grooves. These interactions not only affect the photophysical properties of the probes but also create a large uncertainty in their orientation.
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35
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Markarian MZ, Schlenoff JB. Effect of molecular crowding and ionic strength on the isothermal hybridization of oligonucleotides. J Phys Chem B 2010; 114:10620-7. [PMID: 20701389 DOI: 10.1021/jp103213w] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The isothermal hybridization of complementary oligonucleotides, 15-mer, 25-mer, 35-mer, and a molecular beacon, was investigated under varying conditions of molecular crowding and ionic strength, using hypochromicity to follow strand pairing and polyethylene glycol as a crowding agent. Thermodynamic analysis of the results revealed the addition of counterions to the oligonucleotide backbones, DeltaPsi, to be dependent on the strand GC content and the molecular crowding. A decrease in DeltaPsi was observed, with both increasing GC% and solution PEG content. In contrast, the number of bound water molecules depended on the activity of Na(+), where two regimes were observed. At a(Na(+)) < 0.05 and increasing molecular crowding, water molecules were released into the DNA solutions, and oligonucleotide pairing was favored with both increasing hydrophobic forces, whereas at a(Na(+)) >or= 0.05, water molecules were bound to the strands, and the extent of double strand formation decreased with increasing PEG wt %.
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Affiliation(s)
- Marie Z Markarian
- Department of Chemistry and Biochemistry, The Florida State University, Tallahassee, Florida 32306, USA
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36
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Kang J, Loew M, Arbuzova A, Andreou I, Dähne L. Nucleic acid diagnostic FRET particles based on layer-by-layer technology. ADVANCED MATERIALS (DEERFIELD BEACH, FLA.) 2010; 22:3548-3552. [PMID: 20665568 DOI: 10.1002/adma.201000794] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/29/2023]
Affiliation(s)
- Jing Kang
- Surflay Nanotec GmbH, Berlin, Schwarzschildstr. 8, 12489 Berlin, Germany
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37
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Kobayashi H, Ogawa M, Alford R, Choyke PL, Urano Y. New strategies for fluorescent probe design in medical diagnostic imaging. Chem Rev 2010; 110:2620-40. [PMID: 20000749 PMCID: PMC3241938 DOI: 10.1021/cr900263j] [Citation(s) in RCA: 1514] [Impact Index Per Article: 108.1] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Hisataka Kobayashi
- Molecular Imaging Program, Center for Cancer Research, National Cancer Institute, National Institutes of Health, 10 Center Drive, Bethesda, Maryland 20892-1088, USA.
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38
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Ogawa M, Kosaka N, Longmire MR, Urano Y, Choyke PL, Kobayashi H. Fluorophore-quencher based activatable targeted optical probes for detecting in vivo cancer metastases. Mol Pharm 2009; 6:386-95. [PMID: 19718793 DOI: 10.1021/mp800115t] [Citation(s) in RCA: 79] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
In vivo molecularly targeted fluorescence imaging of tumors has been proposed as a strategy for improving cancer detection and management. Activatable fluorophores, which increased their fluorescence by 10-fold after binding tumor cells, result in much higher target to background ratios than conventional fluorophores. We developed an in vivo targeted activatable optical imaging probe based on a fluorophore-quencher pair, bound to a targeting moiety. With this system, fluorescence is quenched by the fluorophore-quencher interaction outside cancer cells, but is activated within the target cells by dissociation of the fluorophore-quencher pair. We selected the TAMRA (fluorophore)-QSY7 (quencher) pair and conjugated it to either avidin (targeting the D-galactose receptor) or trastuzumab (a monoclonal antibody against the human epithelial growth factor receptor type2 (HER2/neu)) and evaluated their performance in mouse models of cancer. Two probes, TAMRA-QSY7 conjugated avidin (Av-TM-Q7) and trastuzumab (Traz-TM-Q7) were synthesized. Both demonstrated better than similar self-quenching probes. In vitro fluorescence microscopic studies of SHIN3 and NIH/3T3/HER2+ cells demonstrated that Av-TM-Q7 and Traz-TM-Q7 produced high intracellular fluorescent signal. In vivo imaging with Av-TM-Q7 and Traz-TM-Q7 in mice enabled the detection of small tumors. This molecular imaging probe, based on a fluorophore-quencher pair conjugated to a targeting ligand, successfully detected tumors in vivo due to its high activation ratio and low background signal. Thus, these activatable probes, based on the fluorophore-quencher system, hold promise clinically for "see and treat" strategies of cancer management.
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Affiliation(s)
- Mikako Ogawa
- Molecular Imaging Program, Center for Cancer Research, National Cancer Institute, National Institutes of Health, 10 Center Drive, Bethesda, Maryland 20892-1088, USA
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39
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Fung JJ, Deupi X, Pardo L, Yao XJ, Velez-Ruiz GA, Devree BT, Sunahara RK, Kobilka BK. Ligand-regulated oligomerization of beta(2)-adrenoceptors in a model lipid bilayer. EMBO J 2009; 28:3315-28. [PMID: 19763081 PMCID: PMC2748299 DOI: 10.1038/emboj.2009.267] [Citation(s) in RCA: 154] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2009] [Accepted: 08/18/2009] [Indexed: 01/14/2023] Open
Abstract
The β2-adrenoceptor (β2AR) was one of the first Family A G protein-coupled receptors (GPCRs) shown to form oligomers in cellular membranes, yet we still know little about the number and arrangement of protomers in oligomers, the influence of ligands on the organization or stability of oligomers, or the requirement for other proteins to promote oligomerization. We used fluorescence resonance energy transfer (FRET) to characterize the oligomerization of purified β2AR site-specifically labelled at three different positions with fluorophores and reconstituted into a model lipid bilayer. Our results suggest that the β2AR is predominantly tetrameric following reconstitution into phospholipid vesicles. Agonists and antagonists have little effect on the relative orientation of protomers in oligomeric complexes. In contrast, binding of inverse agonists leads to significant increases in FRET efficiencies for most labelling pairs, suggesting that this class of ligand promotes tighter packing of protomers and/or the formation of more complex oligomers by reducing conformational fluctuations in individual protomers. The results provide new structural insights into β2AR oligomerization and suggest a possible mechanism for the functional effects of inverse agonists.
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Affiliation(s)
- Juan José Fung
- Department of Molecular and Cellular Physiology, Stanford University School of Medicine, Stanford, CA 94305, USA
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40
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Synthesis of PEG derivatives bearing aminophenyl and their application for liquid-phase synthesis of water-soluble unsymmetrical cyanine dyes. Tetrahedron 2009. [DOI: 10.1016/j.tet.2009.04.086] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
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41
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Al Attar HA, Monkman AP. FRET and Competing Processes between Conjugated Polymer and Dye Substituted DNA Strands: A Comparative Study of Probe Selection in DNA Detection. Biomacromolecules 2009; 10:1077-83. [DOI: 10.1021/bm801194n] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Hameed A. Al Attar
- Organic Electroactive Materials Research Group, Department of Physics, University of Durham, South Road, Durham DH1 3LE, United Kingdom
| | - Andy P. Monkman
- Organic Electroactive Materials Research Group, Department of Physics, University of Durham, South Road, Durham DH1 3LE, United Kingdom
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42
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Singh MP, Jennings TL, Strouse GF. Tracking spatial disorder in an optical ruler by time-resolved NSET. J Phys Chem B 2009; 113:552-8. [PMID: 19099435 DOI: 10.1021/jp808997h] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
For biomolecular applications, potential interactions between newly developed dye molecules and the biomolecule of interest can dramatically influence the accuracy of optical ruler techniques. By utilizing nanometal surface energy transfer (NSET), an optical technique is developed that allows the nature of interactions between dyes and a biomolecule, namely DNA, to be directly assessed. To demonstrate the method, interactions between well-known molecular dyes based on carboxyfluorescein (FAM, noninteracting) and Cy5 (known intercalator) with DNA is probed. The results demonstrate that FAM exhibits no interactions with the DNA backbone and is adequately represented as a solvent exposed dye, while the commonly used near-IR dye Cy5 exhibits two discrete interactions that depend on the site of appendage and the length of the linker arm. The exact population and nature of Cy5 interaction with the DNA indicates a 37% ratio of intercalation for the internal C(6), a 42% ratio for an internal C(3) spacer length, and no evidence of interaction for terminal labeling. The results allow quantitative assignment of the site occupation of donors to be analyzed providing a powerful set of information for use of dyes in FRET based optical ruler technologies without the need of single molecule methods or the assumption of an averaged site occupation for the donor.
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Affiliation(s)
- Mani Prabha Singh
- Department of Chemistry and Biochemistry, Molecular Biophysics Program, Florida State University, Tallahassee, Florida 32306-4390, USA
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43
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Jagannath A, Wood MJA. Localization of double-stranded small interfering RNA to cytoplasmic processing bodies is Ago2 dependent and results in up-regulation of GW182 and Argonaute-2. Mol Biol Cell 2008; 20:521-9. [PMID: 18946079 DOI: 10.1091/mbc.e08-08-0796] [Citation(s) in RCA: 58] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022] Open
Abstract
Processing bodies (P-bodies) are cytoplasmic foci implicated in the regulation of mRNA translation, storage, and degradation. Key effectors of microRNA (miRNA)-mediated RNA interference (RNAi), such as Argonaute-2 (Ago2), miRNAs, and their cognate mRNAs, are localized to these structures; however, the precise role that P-bodies and their component proteins play in small interfering RNA (siRNA)-mediated RNAi remains unclear. Here, we investigate the relationship between siRNA-mediated RNAi, RNAi machinery proteins, and P-bodies. We show that upon transfection into cells, siRNAs rapidly localize to P-bodies in their native double-stranded conformation, as indicated by fluorescence resonance energy transfer imaging and that Ago2 is at least in part responsible for this siRNA localization pattern, indicating RISC involvement. Furthermore, siRNA transfection induces up-regulated expression of both GW182, a key P-body component, and Ago2, indicating that P-body localization and interaction with GW182 and Ago2 are important in siRNA-mediated RNAi. By virtue of being centers where these proteins and siRNAs aggregate, we propose that the P-body microenvironment, whether as microscopically visible foci or submicroscopic protein complexes, facilitates siRNA processing and siRNA-mediated silencing through the action of its component proteins.
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Affiliation(s)
- Aarti Jagannath
- Department of Physiology, Anatomy, and Genetics, University of Oxford, United Kingdom
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44
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Astakhova IV, Korshun VA, Jahn K, Kjems J, Wengel J. Perylene attached to 2'-amino-LNA: synthesis, incorporation into oligonucleotides, and remarkable fluorescence properties in vitro and in cell culture. Bioconjug Chem 2008; 19:1995-2007. [PMID: 18771303 DOI: 10.1021/bc800202v] [Citation(s) in RCA: 44] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
During recent years, fluorescently labeled oligonucleotides have been extensively investigated within diagnostic approaches. Among a large variety of available fluorochromes, the polyaromatic hydrocarbon perylene is an object of increasing interest due to its high fluorescence quantum yield, long-wave emission compared to widely used pyrene, and photostability. These properties make perylene an attractive label for fluorescence-based detection in vitro and in vivo. Herein, the synthesis of 2'- N-(perylen-3-yl)carbonyl-2'-amino-LNA monomer X and its incorporation into oligonucleotides is described. Modification X induces high thermal stability of DNA:DNA and DNA:RNA duplexes, high Watson-Crick mismatch selectivity, red-shifted fluorescence emission compared to pyrene, and high fluorescence quantum yields. The thermal denaturation temperatures of duplexes involving two modified strands are remarkably higher than those for double-stranded DNAs containing modification X in only one strand, suggesting interstrand communication between perylene moieties in the studied 'zipper' motifs. Fluorescence of single-stranded oligonucleotides having three monomers X is quenched compared to modified monomer (quantum yields Phi F = 0.03-0.04 and 0.67, respectively). However, hybridization to DNA/RNA complements leads to Phi F increase of up to 0.20-0.25. We explain it by orientation of the fluorochrome attached to the 2'-position of 2'-amino-LNA in the minor groove of the nucleic acid duplexes, thus protecting perylene fluorescence from quenching with nucleobases or from the environment. At the same time, the presence of a single mismatch in DNA or RNA targets results in up to 8-fold decreased fluorescence intensity of the duplex. Thus, distortion of the duplex geometry caused by even one mismatched nucleotide induces remarkable quenching of fluorescence. Additionally, a perylene-LNA probe is successfully applied for detection of mRNA in vivo providing excitation wavelength, which completely eliminates cell autofluorescence.
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Affiliation(s)
- Irina V Astakhova
- Nucleic Acid Center, Department of Physics and Chemistry, University of Southern Denmark, DK-5230 Odense M, Denmark
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45
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Shanker N, Bane SL. Basic Aspects of Absorption and Fluorescence Spectroscopy and Resonance Energy Transfer Methods. Methods Cell Biol 2008; 84:213-42. [DOI: 10.1016/s0091-679x(07)84008-8] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/21/2023]
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46
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Algar WR, Krull UJ. Quantum dots as donors in fluorescence resonance energy transfer for the bioanalysis of nucleic acids, proteins, and other biological molecules. Anal Bioanal Chem 2007; 391:1609-18. [PMID: 17987281 DOI: 10.1007/s00216-007-1703-3] [Citation(s) in RCA: 128] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2007] [Revised: 10/10/2007] [Accepted: 10/11/2007] [Indexed: 10/22/2022]
Abstract
Quantum dots (QDs) have a number of unique optical properties that are advantageous in the development of bioanalyses based on fluorescence resonance energy transfer (FRET). Researchers have used QDs as energy donors in FRET schemes for the analysis of nucleic acids, proteins, proteases, haptens, and other small molecules. This paper reviews these applications of QDs. Existing FRET technologies can potentially be improved by using QDs as energy donors instead of conventional fluorophores. Superior brightness, resistance to photobleaching, greater optimization of FRET efficiency, and/or simplified multiplexing are possible with QD donors. The applicability of the Förster formalism to QDs and the feasibility of using QDs as energy acceptors are also reviewed.
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Affiliation(s)
- W Russ Algar
- Chemical Sensors Group, Department of Chemical and Physical Sciences, University of Toronto Mississauga, 3359 Mississauga Rd. North, Mississauga, ON, L5L 1C6, Canada
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Algar WR, Massey M, Krull UJ. Fluorescence resonance energy transfer and complex formation between thiazole orange and various dye-DNA conjugates: implications in signaling nucleic acid hybridization. J Fluoresc 2006; 16:555-67. [PMID: 16794869 DOI: 10.1007/s10895-006-0091-y] [Citation(s) in RCA: 34] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2006] [Accepted: 03/22/2006] [Indexed: 11/25/2022]
Abstract
Fluorescence resonance energy transfer (FRET) was investigated between the intercalating dye thiazole orange (TO), and the dyes Cyanine 3 (Cy3), Cyanine 5 (Cy5), Carboxytetramethyl Rhodamine (TAMRA), Iowa Black FQ (IabFQ), and Iowa Black RQ (IabRQ), which were covalently immobilized at the end of dsDNA oligonucleotides. In addition to determining that TO was an effective energy donor, FRET efficiency data obtained from fluorescence lifetime measurements indicated that TO intercalated near the middle of the 19mer oligonucleotide sequence that was used in this study. Discrepancies in FRET efficiencies obtained from intensity and lifetime measurements led to the investigation of non-fluorescent complex formation between TAMRA and modified TO. The hydrophobicity of TO was modified by the addition of either an alkyl or polyethylene glycol (PEG) side-chain to study effects of dimer and aggregate formation. It was found that at stoichiometric excesses of modified TO, fluorescence quenching of TAMRA was observed, and that this could be correlated to the hydrophobicity of a TO-chain species. The TAMRA:TO-chain association constant for the TO-alkyl system was 0.043+/-0.002 M(-1), while that obtained for the TO-PEG was 0.037+/-0.002 M(-1). From the perspective of method development for the transduction of hybridization events, we present and evaluate a variety of schemes based on energy transfer between TO and an acceptor dye, and discuss the implications of complex formation in such schemes.
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Affiliation(s)
- W Russ Algar
- Department of Chemical and Physical Sciences, University of Toronto at Mississauga, South Building, Room 2035, 3359 Mississauga Road North, Mississauga, Ontario L5L 1C6, Canada
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