1
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A Novel Fluorescent FRET Hairpin Probe Switch for aflD Gene Detection in Real Fermented Soybean Paste. FOOD ANAL METHOD 2021. [DOI: 10.1007/s12161-021-02080-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
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2
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Doll L, Lackner J, Rönicke F, Nienhaus GU, Wagenknecht HA. Fluorescence Lifetime Imaging Microscopy (FLIM) of Intracellular Transport by Means of Doubly Labelled siRNA Architectures. Chembiochem 2021; 22:2561-2567. [PMID: 34125482 PMCID: PMC8453559 DOI: 10.1002/cbic.202100150] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2021] [Revised: 06/02/2021] [Indexed: 12/01/2022]
Abstract
For monitoring the intracellular pathway of small interfering RNA (siRNA), both strands were labelled at internal positions by two ATTO dyes as an interstrand Förster resonance energy transfer pair. siRNA double strands show red emission and a short donor lifetime as readout, whereas siRNA antisense single strands show green emission and a long donor lifetime. This readout signals if GFP silencing can be expected (green) or not (red). We attached both dyes to three structurally different alkyne anchors by postsynthetic modifications. There is only a slight preference for the ribofuranoside anchors with the dyes at their 2’‐positions. For the first time, the delivery and fate of siRNA in live HeLa cells was tracked by fluorescence lifetime imaging microscopy (FLIM), which revealed a clear relationship between intracellular transport using different transfection methods and knockdown of GFP expression, which demonstrates the potential of our siRNA architectures as a tool for future development of effective siRNA.
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Affiliation(s)
- Larissa Doll
- Karlsruhe Institute of Technology (KIT), Institute of Organic Chemistry, Fritz-Haber-Weg 6, 76131, Karlsruhe, Germany
| | - Jens Lackner
- Karlsruhe Institute of Technology (KIT), Institute of Applied Physics, Wolfgang-Gaede-Str. 1, 76131, Karlsruhe, Germany
| | - Franziska Rönicke
- Karlsruhe Institute of Technology (KIT), Institute of Organic Chemistry, Fritz-Haber-Weg 6, 76131, Karlsruhe, Germany
| | - Gerd Ulrich Nienhaus
- Karlsruhe Institute of Technology (KIT), Institute of Applied Physics, Wolfgang-Gaede-Str. 1, 76131, Karlsruhe, Germany.,Institute of Nanotechnology (INT), Karlsruhe Institute of Technology (KIT), 76344, Eggenstein-Leopoldshafen, Germany.,Institute of Biological and Chemical Systems (IBCS), Karlsruhe Institute of Technology (KIT), 76344, Eggenstein-Leopoldshafen, Germany.,Department of Physics, University of Illinois at Urbana-Champaign, 1110 West Green Street, Urbana, IL 61801, USA
| | - Hans-Achim Wagenknecht
- Karlsruhe Institute of Technology (KIT), Institute of Organic Chemistry, Fritz-Haber-Weg 6, 76131, Karlsruhe, Germany
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3
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Aparin IO, Sergeeva OV, Mishin AS, Khaydukov EV, Korshun VA, Zatsepin TS. Excimer-FRET Cascade in Dual DNA Probes: Open Access to Large Stokes Shift, Enhanced Acceptor Light up, and Robust RNA Sensing. Anal Chem 2020; 92:7028-7036. [DOI: 10.1021/acs.analchem.0c00270] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Affiliation(s)
- Ilya O. Aparin
- Skolkovo Institute of Science and Technology, 143026 Skolkovo, Russia
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, 117997 Moscow, Russia
| | - Olga V. Sergeeva
- Skolkovo Institute of Science and Technology, 143026 Skolkovo, Russia
| | - Alexander S. Mishin
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, 117997 Moscow, Russia
| | - Evgeny V. Khaydukov
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, 117997 Moscow, Russia
- Federal Scientific Research Centre “Crystallography and Photonics” RAS, 119333 Moscow, Russia
- Sechenov First Moscow State Medical University, 119991 Moscow, Russia
| | - Vladimir A. Korshun
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, 117997 Moscow, Russia
- Gause Institute of New Antibiotics, 119021 Moscow, Russia
- Department of Biology and Biotechnology, National Research University Higher School of Economics, 117312 Moscow, Russia
| | - Timofei S. Zatsepin
- Skolkovo Institute of Science and Technology, 143026 Skolkovo, Russia
- Department of Chemistry, M.V. Lomonosov Moscow State University, 119992 Moscow, Russia
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4
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Wang J, Wang DX, Ma JY, Wang YX, Kong DM. Three-dimensional DNA nanostructures to improve the hyperbranched hybridization chain reaction. Chem Sci 2019; 10:9758-9767. [PMID: 32055345 PMCID: PMC6993746 DOI: 10.1039/c9sc02281c] [Citation(s) in RCA: 99] [Impact Index Per Article: 19.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2019] [Accepted: 08/29/2019] [Indexed: 11/21/2022] Open
Abstract
Nonenzymatic nucleic acid amplification techniques (e.g. the hybridization chain reaction, HCR) have shown promising potential for amplified detection of biomarkers.
Nonenzymatic nucleic acid amplification techniques (e.g. the hybridization chain reaction, HCR) have shown promising potential for amplified detection of biomarkers. However, the traditional HCR occurs through random diffusion of DNA hairpins, making the kinetics and efficiency quite low. By assembling DNA hairpins at the vertexes of tetrahedral DNA nanostructures (TDNs), the reaction kinetics of the HCR is greatly accelerated due to the synergetic contributions of multiple reaction orientations, increased collision probability and enhanced local concentrations. The proposed quadrivalent TDN (qTDN)-mediated hyperbranched HCR has a ∼70-fold faster reaction rate than the traditional HCR. The approximately 76% fluorescence resonance energy transfer (FRET) efficiency obtained is the highest in the reported DNA-based FRET sensing systems as far as we know. Moreover, qTDNs modified by hairpins can easily load drugs, freely traverse plasma membranes and be rapidly cross-linked via the target-triggered HCR in live cells. The reduced freedom of movement as a result of the large crosslinked structure might constrain the hyperbranched HCR in a confined environment, thus making it a promising candidate for in situ imaging and photodynamic therapy. Hence, we present a paradigm of perfect integration of DNA nanotechnology with nucleic acid amplification, thus paving a promising way to the improved performance of nucleic acid amplification techniques and their wider application.
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Affiliation(s)
- Jing Wang
- State Key Laboratory of Medicinal Chemical Biology , Tianjin Key Laboratory of Biosensing and Molecular Recognition , Research Centre for Analytical Sciences , College of Chemistry , Nankai University , Tianjin 300071 , P. R. China .
| | - Dong-Xia Wang
- State Key Laboratory of Medicinal Chemical Biology , Tianjin Key Laboratory of Biosensing and Molecular Recognition , Research Centre for Analytical Sciences , College of Chemistry , Nankai University , Tianjin 300071 , P. R. China .
| | - Jia-Yi Ma
- State Key Laboratory of Medicinal Chemical Biology , Tianjin Key Laboratory of Biosensing and Molecular Recognition , Research Centre for Analytical Sciences , College of Chemistry , Nankai University , Tianjin 300071 , P. R. China .
| | - Ya-Xin Wang
- State Key Laboratory of Medicinal Chemical Biology , Tianjin Key Laboratory of Biosensing and Molecular Recognition , Research Centre for Analytical Sciences , College of Chemistry , Nankai University , Tianjin 300071 , P. R. China .
| | - De-Ming Kong
- State Key Laboratory of Medicinal Chemical Biology , Tianjin Key Laboratory of Biosensing and Molecular Recognition , Research Centre for Analytical Sciences , College of Chemistry , Nankai University , Tianjin 300071 , P. R. China . .,Collaborative Innovation Center of Chemical Science and Engineering (Tianjin) , Tianjin , 300071 , P. R. China
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5
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Abstract
Fluorogenic oligonucleotide probes that can produce a change in fluorescence signal upon binding to specific biomolecular targets, including nucleic acids as well as non-nucleic acid targets, such as proteins and small molecules, have applications in various important areas. These include diagnostics, drug development and as tools for studying biomolecular interactions in situ and in real time. The probes usually consist of a labeled oligonucleotide strand as a recognition element together with a mechanism for signal transduction that can translate the binding event into a measurable signal. While a number of strategies have been developed for the signal transduction, relatively little attention has been paid to the recognition element. Peptide nucleic acids (PNA) are DNA mimics with several favorable properties making them a potential alternative to natural nucleic acids for the development of fluorogenic probes, including their very strong and specific recognition and excellent chemical and biological stabilities in addition to their ability to bind to structured nucleic acid targets. In addition, the uncharged backbone of PNA allows for other unique designs that cannot be performed with oligonucleotides or analogues with negatively-charged backbones. This review aims to introduce the principle, showcase state-of-the-art technologies and update recent developments in the areas of fluorogenic PNA probes during the past 20 years.
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Affiliation(s)
- Tirayut Vilaivan
- Organic Synthesis Research Unit, Department of Chemistry, Faculty of Science, Chulalongkorn University, Phayathai Road, Patumwan, Bangkok 10330, Thailand
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6
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Barthes NPF, Gavvala K, Bonhomme D, Dabert-Gay AS, Debayle D, Mély Y, Michel BY, Burger A. Design and Development of a Two-Color Emissive FRET Pair Based on a Photostable Fluorescent Deoxyuridine Donor Presenting a Mega-Stokes Shift. J Org Chem 2016; 81:10733-10741. [DOI: 10.1021/acs.joc.6b01807] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Affiliation(s)
- Nicolas P. F. Barthes
- Institut
de Chimie de Nice, UMR 7272, Université Côte d'Azur, CNRS, Parc Valrose, 06108 Nice Cedex 2, France
| | - Krishna Gavvala
- Laboratoire
de Biophotonique et Pharmacologie, UMR 7213, Faculté de Pharmacie, Université de Strasbourg, CNRS, 74 Route du Rhin, 67401 Illkirch, France
| | - Dominique Bonhomme
- Institut
de Chimie de Nice, UMR 7272, Université Côte d'Azur, CNRS, Parc Valrose, 06108 Nice Cedex 2, France
| | - Anne Sophie Dabert-Gay
- Institut
de Pharmacologie Moléculaire et Cellulaire, UMR 6097, Université Côte d'Azur, CNRS, 660 Route des Lucioles, 06560 Valbonne, France
| | - Delphine Debayle
- Institut
de Pharmacologie Moléculaire et Cellulaire, UMR 6097, Université Côte d'Azur, CNRS, 660 Route des Lucioles, 06560 Valbonne, France
| | - Yves Mély
- Laboratoire
de Biophotonique et Pharmacologie, UMR 7213, Faculté de Pharmacie, Université de Strasbourg, CNRS, 74 Route du Rhin, 67401 Illkirch, France
| | - Benoît Y. Michel
- Institut
de Chimie de Nice, UMR 7272, Université Côte d'Azur, CNRS, Parc Valrose, 06108 Nice Cedex 2, France
| | - Alain Burger
- Institut
de Chimie de Nice, UMR 7272, Université Côte d'Azur, CNRS, Parc Valrose, 06108 Nice Cedex 2, France
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7
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Lim EK, Guk K, Kim H, Chung BH, Jung J. Simple, rapid detection of influenza A (H1N1) viruses using a highly sensitive peptide-based molecular beacon. Chem Commun (Camb) 2016; 52:175-8. [PMID: 26509476 DOI: 10.1039/c5cc05684e] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
A peptide-based molecular beacon (PEP-MB) was prepared for the simple, rapid, and specific detection of H1N1 viruses using a fluorescence resonance energy transfer (FRET) system. The PEP-MB exhibited minimal fluorescence in its "closed" hairpin structure. However, in the presence of H1N1 viruses, the specific recognition of the hemagglutinin (HA) protein of H1 strains by the PEP-MB causes the beacon to assume an "open" structure that emits strong fluorescence. The PEP-MB could detect H1N1 viruses within 15 min or even 5 min and can exhibit strong fluorescence even at low viral concentrations, with a detection limit of 4 copies.
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Affiliation(s)
- Eun-Kyung Lim
- BioNanotechnology Research Center, Korea Research Institute of Bioscience and Biotechnology, 305-806, Daejeon, Republic of Korea. and BioNano Health Guard Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), 305-806, Daejeon, Republic of Korea
| | - Kyeonghye Guk
- BioNanotechnology Research Center, Korea Research Institute of Bioscience and Biotechnology, 305-806, Daejeon, Republic of Korea. and Nanobiotechnology Major, School of Engineering, University of Science and Technology (UST), 125 Gwahak-ro, Yuseong-gu, Daejeon, 305-806, Republic of Korea
| | - Hyeran Kim
- BioNano Health Guard Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), 305-806, Daejeon, Republic of Korea
| | - Bong-Hyun Chung
- BioNanotechnology Research Center, Korea Research Institute of Bioscience and Biotechnology, 305-806, Daejeon, Republic of Korea. and BioNano Health Guard Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), 305-806, Daejeon, Republic of Korea
| | - Juyeon Jung
- BioNanotechnology Research Center, Korea Research Institute of Bioscience and Biotechnology, 305-806, Daejeon, Republic of Korea. and BioNano Health Guard Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), 305-806, Daejeon, Republic of Korea
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8
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Talukder P, Chen S, Roy B, Yakovchuk P, Spiering MM, Alam MP, Madathil MM, Bhattacharya C, Benkovic SJ, Hecht SM. Cyanotryptophans as Novel Fluorescent Probes for Studying Protein Conformational Changes and DNA–Protein Interaction. Biochemistry 2015; 54:7457-69. [DOI: 10.1021/acs.biochem.5b01085] [Citation(s) in RCA: 49] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Poulami Talukder
- Center
for BioEnergetics, Biodesign Institute, and School of Molecular Sciences, Arizona State University, Tempe, Arizona 85287, United States
| | - Shengxi Chen
- Center
for BioEnergetics, Biodesign Institute, and School of Molecular Sciences, Arizona State University, Tempe, Arizona 85287, United States
| | - Basab Roy
- Center
for BioEnergetics, Biodesign Institute, and School of Molecular Sciences, Arizona State University, Tempe, Arizona 85287, United States
| | - Petro Yakovchuk
- Center
for BioEnergetics, Biodesign Institute, and School of Molecular Sciences, Arizona State University, Tempe, Arizona 85287, United States
| | - Michelle M. Spiering
- Department
of Chemistry, The Pennsylvania State University, University Park, Pennsylvania 16802, United States
| | - Mohammad P. Alam
- Center
for BioEnergetics, Biodesign Institute, and School of Molecular Sciences, Arizona State University, Tempe, Arizona 85287, United States
| | - Manikandadas M. Madathil
- Center
for BioEnergetics, Biodesign Institute, and School of Molecular Sciences, Arizona State University, Tempe, Arizona 85287, United States
| | - Chandrabali Bhattacharya
- Center
for BioEnergetics, Biodesign Institute, and School of Molecular Sciences, Arizona State University, Tempe, Arizona 85287, United States
| | - Stephen J. Benkovic
- Department
of Chemistry, The Pennsylvania State University, University Park, Pennsylvania 16802, United States
| | - Sidney M. Hecht
- Center
for BioEnergetics, Biodesign Institute, and School of Molecular Sciences, Arizona State University, Tempe, Arizona 85287, United States
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9
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Li ZY, Wu YT, Tseng WL. UV-Light-Induced Improvement of Fluorescence Quantum Yield of DNA-Templated Gold Nanoclusters: Application to Ratiometric Fluorescent Sensing of Nucleic Acids. ACS APPLIED MATERIALS & INTERFACES 2015; 7:23708-16. [PMID: 26443919 DOI: 10.1021/acsami.5b07766] [Citation(s) in RCA: 49] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/08/2023]
Abstract
The use of DNA as a template has been demonstrated as an effective method for synthesizing different-sized silver nanoclusters. Although DNA-templated silver nanoclusters show outstanding performance as fluorescent probes for chemical sensing and cellular imaging, the synthesis of DNA-stabilized gold nanoclusters (AuNCs) with high fluorescence intensity remains a challenge. Here a facile, reproducible, scalable, NaBH4-free, UV-light-assisted method was developed to prepare AuNCs using repeats of 30 adenosine nucleotides (A30). The maximal fluorescence of A30-stabilized AuNCs appeared at 475 nm with moderate quantum yield, two fluorescence lifetimes, and a small amount of Au(+) on the surface of the Au core. Results of size-exclusion chromatography revealed that A30-stabilized AuNCs were more compact than A30. A series of control experiments showed that UV light played a dual role in the reduction of gold-ion precursors and the decomposition of citrate ions. A30 also acted as a stabilizer to prevent the aggregation of AuNCs. In addition, single-stranded DNA (ssDNA) consisting of an AuNC-nucleation sequence and a hybridization sequence was utilized to develop a AuNC-based ratiometric fluorescent probe in the presence of the double-strand-chelating dye SYBR Green I (SG). Under conditions of single-wavelength excitation, the combination of AuNC/SG-bearing ssDNA and perfectly matched DNA emitted fluorescence at 475 and 525 nm, respectively. The formed AuNC/SG-bearing ssDNA enabled the sensitive, selective, and ratiometric detection of specific nucleic acid targets. Finally, the AuNC-based ratiometric probes were successfully applied to determine specific nucleic acid targets in human serum.
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Affiliation(s)
- Zong-Yu Li
- Department of Chemistry, National Sun Yat-sen University , 70 Lien-hai Road, Kaohsiung 804, Taiwan
| | - Yun-Tse Wu
- Department of Chemistry, National Sun Yat-sen University , 70 Lien-hai Road, Kaohsiung 804, Taiwan
| | - Wei-Lung Tseng
- Department of Chemistry, National Sun Yat-sen University , 70 Lien-hai Road, Kaohsiung 804, Taiwan
- School of Pharmacy, College of Pharmacy, Kaohsiung Medical University , Kaohsiung 807, Taiwan
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10
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Martí AA. Metal complexes and time-resolved photoluminescence spectroscopy for sensing applications. J Photochem Photobiol A Chem 2015. [DOI: 10.1016/j.jphotochem.2015.03.020] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
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11
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Walter HK, Bohländer PR, Wagenknecht HA. Development of a wavelength-shifting fluorescent module for the adenosine aptamer using photostable cyanine dyes. ChemistryOpen 2015; 4:92-6. [PMID: 25969803 PMCID: PMC4420577 DOI: 10.1002/open.201402137] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2014] [Indexed: 12/20/2022] Open
Abstract
DNA-based aptamers are commonly used recognition elements in biosensors for a range of target molecules. Here, the development of a wavelength-shifting optical module for a DNA-based adenosine-binding aptamer is described. It applies the combination of two photostable cyanine-styryl dyes as covalent modifications. This energy-transfer pair is postsynthetically attached to oligonucleotides via a copper(I)-catalyzed azide-alkyne cycloaddition by two structurally different approaches: 1) as nucleotide modifications at the 2'-position of uridines and 2) as nucleotide substitutions using (S)-amino-1,2-propanediol as acyclic linker between the phosphodiester bridges. Both dyes exhibit a remarkable photostability. A library of DNA aptamers consisting of different combinations of the two dyes in diagonal orientations were evaluated by their emission color contrast as readout. Further optimization led to aptasensors with improved fluorescent readout as compared with previously reported aptasensors. This approach described is synthetically facile using simple propargylated phosphoramidites as DNA building blocks. As such, this approach could be applied for other dyes and other chemical/biological applications.
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Affiliation(s)
- Heidi-Kristin Walter
- Institute of Organic Chemistry, Karlsruhe Institute of Technology (KITFritz-Haber-Weg 6, 76131, Karlsruhe, Germany
| | - Peggy R Bohländer
- Institute of Organic Chemistry, Karlsruhe Institute of Technology (KITFritz-Haber-Weg 6, 76131, Karlsruhe, Germany
| | - Hans-Achim Wagenknecht
- Institute of Organic Chemistry, Karlsruhe Institute of Technology (KITFritz-Haber-Weg 6, 76131, Karlsruhe, Germany
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12
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Talukder P, Chen S, Liu CT, Baldwin EA, Benkovic SJ, Hecht SM. Tryptophan-based fluorophores for studying protein conformational changes. Bioorg Med Chem 2014; 22:5924-34. [PMID: 25284250 PMCID: PMC4254292 DOI: 10.1016/j.bmc.2014.09.015] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2014] [Revised: 09/03/2014] [Accepted: 09/08/2014] [Indexed: 11/19/2022]
Abstract
With the continuing interest in deciphering the interplay between protein function and conformational changes, small fluorescence probes will be especially useful for tracking changes in the crowded protein interior space. Presently, we describe the potential utility of six unnatural amino acid fluorescence donors structurally related to tryptophan and show how they can be efficiently incorporated into a protein as fluorescence probes. We also examine the various photophysical properties of the new Trp analogues, which are significantly redshifted in their fluorescence spectra relative to tryptophan. In general, the Trp analogues were well tolerated when inserted into Escherichia coli DHFR, and did not perturb enzyme activity, although substitution for Trp22 did result in a diminution in DHFR activity. Further, it was demonstrated that D and E at position 37 formed efficient FRET pairs with acridon-2-ylalanine (Acd) at position 17. The same was also true for a DHFR construct containing E at position 79 and Acd at position 17. Together, these findings demonstrate that these tryptophan analogues can be introduced into DHFR with minimal disruption of function, and that they can be employed for the selective study of targeted conformational changes in proteins, even in the presence of unmodified tryptophans.
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Affiliation(s)
- Poulami Talukder
- Center for BioEnergetics, Biodesign Institute, and Department of Chemistry and Biochemistry, Arizona State University, Tempe, AZ 85287, USA
| | - Shengxi Chen
- Center for BioEnergetics, Biodesign Institute, and Department of Chemistry and Biochemistry, Arizona State University, Tempe, AZ 85287, USA
| | - C Tony Liu
- Department of Chemistry, The Pennsylvania State University, University Park, PA 16802, USA
| | - Edwin A Baldwin
- Center for BioEnergetics, Biodesign Institute, and Department of Chemistry and Biochemistry, Arizona State University, Tempe, AZ 85287, USA
| | - Stephen J Benkovic
- Department of Chemistry, The Pennsylvania State University, University Park, PA 16802, USA.
| | - Sidney M Hecht
- Center for BioEnergetics, Biodesign Institute, and Department of Chemistry and Biochemistry, Arizona State University, Tempe, AZ 85287, USA.
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13
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Huang J, Yang X, He X, Wang K, Liu J, Shi H, Wang Q, Guo Q, He D. Design and bioanalytical applications of DNA hairpin-based fluorescent probes. Trends Analyt Chem 2014. [DOI: 10.1016/j.trac.2013.08.007] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
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14
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Wang Q, Wang W, Lei J, Xu N, Gao F, Ju H. Fluorescence quenching of carbon nitride nanosheet through its interaction with DNA for versatile fluorescence sensing. Anal Chem 2013; 85:12182-8. [PMID: 24274810 DOI: 10.1021/ac403646n] [Citation(s) in RCA: 187] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
This work investigates the interaction of carbon nitride nanosheet (CNNS), a recently developed two-dimensional nanomaterial, with DNA and its fluorescence quenching mechanism on fluorophore labeled single-stranded DNA probes. The static quenching through the photoinduced electron transfer (PET) from the excited fluorophore to the conductive band of CNNS is identified. Utilizing the affinity change of CNNS to DNA probes upon their recognition to targets and the PET-based fluorescence quenching effect, a universal sensing strategy is proposed for design of several homogeneous fluorescence detection methods with short assay time and high sensitivity. This strategy is versatile and can be combined with different amplification tools for quick fluorescence sensing of DNA and extensive DNA related analytes such as metal cations, small molecules, and proteins. As examples, two simple fluorescence detection methods for DNA and Hg(2+), one facile detection method coupled with Exo III-mediated target recycling for sensitive DNA analysis, and a ratiometric fluorescence protocol for DNA detection are proposed. This work provides an avenue for understanding the interaction between two-dimensional nanomaterials and biomolecules and designing novel sensing strategies for extending the applications of nanomaterials in bioanalysis.
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Affiliation(s)
- Quanbo Wang
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University , Nanjing, Jiangsu 210093, P.R. China
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15
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Chen S, Fahmi NE, Bhattacharya C, Wang L, Jin Y, Benkovic SJ, Hecht SM. Fluorescent biphenyl derivatives of phenylalanine suitable for protein modification. Biochemistry 2013; 52:8580-9. [PMID: 24152169 PMCID: PMC3875372 DOI: 10.1021/bi401275v] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
In a recent study, we demonstrated that structurally compact fluorophores incorporated into the side chains of amino acids could be introduced into dihydrofolate reductase from Escherichia coli (ecDHFR) with minimal disruption of protein structure or function, even when the site of incorporation was within a folded region of the protein. The modified proteins could be employed for FRET measurements, providing sensitive monitors of changes in protein conformation. The very favorable results achieved in that study encouraged us to prepare additional fluorescent amino acids of potential utility for studying protein dynamics. Presently, we describe the synthesis and photophysical characterization of four positional isomers of biphenyl-phenylalanine, all of which were found to exhibit potentially useful fluorescent properties. All four phenylalanine derivatives were used to activate suppressor tRNA transcripts and incorporated into multiple positions of ecDHFR. All phenylalanine derivatives were incorporated with good efficiency into position 16 of ecDHFR and afforded modified proteins that consumed NADPH at rates up to about twice the rate measured for wild type. This phenomenon has been noted on a number of occasions previously and shown to be due to an increase in the off-rate of tetrahydrofolate from the enzyme, altering a step that is normally rate limiting. When introduced into sterically accessible position 49, the four phenylalanine derivatives afforded DHFRs having catalytic function comparable to wild type. The four phenylalanine derivatives were also introduced into position 115 of ecDHFR, which is known to be a folded region of the protein less tolerant of structural alteration. As anticipated, significant differences were noted in the catalytic efficiencies of the derived proteins. The ability of two of the sizable biphenyl-phenylalanine derivatives to be accommodated at position 115 with minimal perturbation of DHFR function is attributed to rotational flexibility about the biphenyl bonds.
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Affiliation(s)
- Shengxi Chen
- Center for BioEnergetics, Biodesign Institute, and Department of Chemistry and Biochemistry, Arizona State University, Tempe, AZ 85287, USA
| | - Nour Eddine Fahmi
- Center for BioEnergetics, Biodesign Institute, and Department of Chemistry and Biochemistry, Arizona State University, Tempe, AZ 85287, USA
| | - Chandrabali Bhattacharya
- Center for BioEnergetics, Biodesign Institute, and Department of Chemistry and Biochemistry, Arizona State University, Tempe, AZ 85287, USA
| | - Lin Wang
- Department of Chemistry, the Pennsylvania State University, University Park, PA 106802, USA
| | - Yuguang Jin
- Center for BioEnergetics, Biodesign Institute, and Department of Chemistry and Biochemistry, Arizona State University, Tempe, AZ 85287, USA
| | - Stephen J. Benkovic
- Department of Chemistry, the Pennsylvania State University, University Park, PA 106802, USA
| | - Sidney M. Hecht
- Center for BioEnergetics, Biodesign Institute, and Department of Chemistry and Biochemistry, Arizona State University, Tempe, AZ 85287, USA
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16
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Chen S, Fahmi NE, Wang L, Bhattacharya C, Benkovic SJ, Hecht SM. Detection of dihydrofolate reductase conformational change by FRET using two fluorescent amino acids. J Am Chem Soc 2013; 135:12924-7. [PMID: 23941571 PMCID: PMC3785542 DOI: 10.1021/ja403007r] [Citation(s) in RCA: 52] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Abstract
Two fluorescent amino acids, including the novel fluorescent species 4-biphenyl-l-phenylalanine (1), have been incorporated at positions 17 and 115 of dihydrofolate reductase (DHFR) to enable a study of conformational changes associated with inhibitor binding. Unlike most studies involving fluorescently labeled proteins, the fluorophores were incorporated into the amino acid side chains, and both probes [1 and L-(7-hydroxycoumarin-4-yl)ethylglycine (2)] were smaller than fluorophores typically used for such studies. The DHFR positions were chosen as potentially useful for Förster resonance energy transfer (FRET) measurements on the basis of their estimated separation (17-18 Å) and the expected change in distance along the reaction coordinate. Also of interest was the steric accessibility of the two sites: Glu17 is on the surface of DHFR, while Ile115 is within a folded region of the protein. Modified DHFR I (1 at position 17; 2 at position 115) and DHFR II (2 at position 17; 1 at position 115) were both catalytically competent. However, DHFR II containing the potentially rotatable biphenylphenylalanine moiety at sterically encumbered position 115 was significantly more active than DHFR I. Irradiation of the modified DHFRs at 280 nm effected excitation of 1, energy transfer to 2, and emission by 2 at 450 nm. However, the energy transfer was substantially more efficient in DHFR II. The effect of inhibitor binding was also measured. Trimethoprim mediated concentration-dependent diminution of the emission observed at 450 nm for DHFR II but not for DHFR I. These findings demonstrate that amino acids containing small fluorophores can be introduced into DHFR with minimal disruption of function and in a fashion that enables sensitive monitoring of changes in DHFR conformation.
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Affiliation(s)
- Shengxi Chen
- Center for BioEnergetics, Biodesign Institute, and Department of Chemistry and Biochemistry, Arizona State University, Tempe, AZ 85287, USA
| | - Nour Eddine Fahmi
- Center for BioEnergetics, Biodesign Institute, and Department of Chemistry and Biochemistry, Arizona State University, Tempe, AZ 85287, USA
| | - Lin Wang
- Department of Chemistry, the Pennsylvania State University, University Park, PA 16802, USA
| | - Chandrabali Bhattacharya
- Center for BioEnergetics, Biodesign Institute, and Department of Chemistry and Biochemistry, Arizona State University, Tempe, AZ 85287, USA
| | - Stephen J. Benkovic
- Department of Chemistry, the Pennsylvania State University, University Park, PA 16802, USA
| | - Sidney M. Hecht
- Center for BioEnergetics, Biodesign Institute, and Department of Chemistry and Biochemistry, Arizona State University, Tempe, AZ 85287, USA
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17
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Holzhauser C, Wagenknecht HA. DNA and RNA “Traffic Lights”: Synthetic Wavelength-Shifting Fluorescent Probes Based on Nucleic Acid Base Substitutes for Molecular Imaging. J Org Chem 2013; 78:7373-9. [DOI: 10.1021/jo4010102] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Affiliation(s)
- Carolin Holzhauser
- Institute of Organic Chemistry, Karlsruhe Institute of Technology (KIT), D-76131 Karlsruhe,
Germany
| | - Hans-Achim Wagenknecht
- Institute of Organic Chemistry, Karlsruhe Institute of Technology (KIT), D-76131 Karlsruhe,
Germany
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18
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Jacroux T, Rieck DC, Cui R, Ouyang Y, Dong WJ. Enzymatic amplification of DNA/RNA hybrid molecular beacon signaling in nucleic acid detection. Anal Biochem 2013; 432:106-14. [PMID: 23000602 PMCID: PMC3522425 DOI: 10.1016/j.ab.2012.09.015] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2012] [Revised: 09/10/2012] [Accepted: 09/12/2012] [Indexed: 11/22/2022]
Abstract
A rapid assay operable under isothermal or nonisothermal conditions is described, where the sensitivity of a typical molecular beacon (MB) system is improved by using thermostable RNase H to enzymatically cleave an MB composed of a DNA stem and an RNA loop (R/D-MB). On hybridization of the R/D-MB to target DNA, there was a modest increase in fluorescence intensity (~5.7× above background) due to an opening of the probe and a concomitant reduction in the Förster resonance energy transfer efficiency. The addition of thermostable RNase H resulted in the cleavage of the RNA loop, which eliminated energy transfer. The cleavage step also released bound target DNA, enabling it to bind to another R/D-MB probe and rendering the approach a cyclic amplification scheme. Full processing of R/D-MBs maximized the fluorescence signal to the fullest extent possible (12.9× above background), resulting in an approximately 2- to 2.8-fold increase in the signal-to-noise ratio observed isothermally at 50 °C following the addition of RNase H. The probe was also used to monitor real-time polymerase chain reactions by measuring enhancement of donor fluorescence on R/D-MB binding to amplified pUC19 template dilutions. Hence, the R/D-MB-RNase H scheme can be applied to a broad range of nucleic acid amplification methods.
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Affiliation(s)
- Thomas Jacroux
- Gene and Linda Voiland School of Chemical Engineering and Bioengineering, Washington State University, Pullman, WA 99164, USA
| | - Daniel C. Rieck
- Gene and Linda Voiland School of Chemical Engineering and Bioengineering, Washington State University, Pullman, WA 99164, USA
| | - Rong Cui
- Department of Veterinary and Comparative Anatomy, Pharmacology and Physiology, Washington State University, Pullman, WA 99164, USA
| | - Yexin Ouyang
- Department of Veterinary and Comparative Anatomy, Pharmacology and Physiology, Washington State University, Pullman, WA 99164, USA
| | - Wen-Ji Dong
- Gene and Linda Voiland School of Chemical Engineering and Bioengineering, Washington State University, Pullman, WA 99164, USA
- Department of Veterinary and Comparative Anatomy, Pharmacology and Physiology, Washington State University, Pullman, WA 99164, USA
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19
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Huang K, Martí AA. Optimizing the Sensitivity of Photoluminescent Probes Using Time-Resolved Spectroscopy: A Molecular Beacon Case Study. Anal Chem 2012; 84:8075-82. [DOI: 10.1021/ac3019894] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Kewei Huang
- Department
of Chemistry, ‡Department of Bioengineering, and §Smalley Institute for Nanoscale Science and
Technology, 6100 South Main Street, Rice University, Houston Texas 77005, United States
| | - Angel A. Martí
- Department
of Chemistry, ‡Department of Bioengineering, and §Smalley Institute for Nanoscale Science and
Technology, 6100 South Main Street, Rice University, Houston Texas 77005, United States
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20
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Kim B, Jung IH, Kang M, Shim HK, Woo HY. Cationic conjugated polyelectrolytes-triggered conformational change of molecular beacon aptamer for highly sensitive and selective potassium ion detection. J Am Chem Soc 2012; 134:3133-8. [PMID: 22280349 DOI: 10.1021/ja210360v] [Citation(s) in RCA: 151] [Impact Index Per Article: 12.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
We demonstrate highly sensitive and selective potassium ion detection against excess sodium ions in water, by modulating the interaction between the G-quadruplex-forming molecular beacon aptamer (MBA) and cationic conjugated polyelectrolyte (CPE). The K(+)-specific aptamer sequence in MBA is used as the molecular recognition element, and the high binding specificity of MBA for potassium ions offers selectivity against a range of metal ions. The hairpin-type MBA labeled with a fluorophore and quencher at both termini undergoes a conformational change (by complexation with CPEs) to either an open-chain form or a G-quadruplex in the absence or presence of K(+) ions. Conformational changes of MBA as well as fluorescence (of the fluorophore in MBA) quenching or amplification via fluorescence resonance energy transfer from CPEs provide clear signal turn-off and -on in the presence or absence of K(+). The detection limit of the K(+) assays is determined to be ~1.5 nM in the presence of 100 mM Na(+) ions, which is ~3 orders of magnitude lower than those reported previously. The successful detection of 5'-adenosine triphosphate (ATP) with the MBA containing an ATP-specific aptamer sequence is also demonstrated using the same sensor scheme. The scheme reported herein is applicable to the detection of other kinds of G-rich aptamer-binding chemicals and biomolecules.
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Affiliation(s)
- Boram Kim
- Department of Nano Fusion Technology, Pusan National University, Miryang 627-706, Republic of Korea
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21
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Guo J, Ju J, Turro NJ. Fluorescent hybridization probes for nucleic acid detection. Anal Bioanal Chem 2011; 402:3115-25. [PMID: 22086400 DOI: 10.1007/s00216-011-5526-x] [Citation(s) in RCA: 83] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2011] [Accepted: 10/19/2011] [Indexed: 01/09/2023]
Abstract
Due to their high sensitivity and selectivity, minimum interference with living biological systems, and ease of design and synthesis, fluorescent hybridization probes have been widely used to detect nucleic acids both in vivo and in vitro. Molecular beacons (MBs) and binary probes (BPs) are two very important hybridization probes that are designed based on well-established photophysical principles. These probes have shown particular applicability in a variety of studies, such as mRNA tracking, single nucleotide polymorphism (SNP) detection, polymerase chain reaction (PCR) monitoring, and microorganism identification. Molecular beacons are hairpin oligonucleotide probes that present distinctive fluorescent signatures in the presence and absence of their target. Binary probes consist of two fluorescently labeled oligonucleotide strands that can hybridize to adjacent regions of their target and generate distinctive fluorescence signals. These probes have been extensively studied and modified for different applications by modulating their structures or using various combinations of fluorophores, excimer-forming molecules, and metal complexes. This review describes the applicability and advantages of various hybridization probes that utilize novel and creative design to enhance their target detection sensitivity and specificity.
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Affiliation(s)
- Jia Guo
- Department of Chemistry, Columbia University, New York, NY 10027, USA
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22
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Holzhauser C, Wagenknecht HA. In-stem-labeled molecular beacons for distinct fluorescent color readout. Angew Chem Int Ed Engl 2011; 50:7268-72. [PMID: 21717540 DOI: 10.1002/anie.201101968] [Citation(s) in RCA: 63] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2011] [Indexed: 01/09/2023]
Affiliation(s)
- Carolin Holzhauser
- Institute for Organic Chemistry, Karlsruhe Institute of Technology (KIT), Karlsruhe, Germany
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23
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Holzhauser C, Wagenknecht HA. Deutliche Fluoreszenzfarbwechsel durch Markierung des Stamminneren von “Molecular Beacons”. Angew Chem Int Ed Engl 2011. [DOI: 10.1002/ange.201101968] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
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24
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Varghese R, Wagenknecht HA. Red-white-blue emission switching molecular beacons: ratiometric multicolour DNA hybridization probes. Org Biomol Chem 2009; 8:526-8. [PMID: 20090965 DOI: 10.1039/b918381g] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Molecular beacons with two fluorophores derived from ethynyl pyrene and ethynyl nile red exhibit red emission in the hairpin that changes to blue through white upon binding to the target sequence with a dramatic shift of approximately 225 nm.
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Affiliation(s)
- Reji Varghese
- Univeristy of Regensburg, Institute for Organic Chemistry, Universitätsstr. 31, D-93053 Regensburg, Germany
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25
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Abstract
Commonly used techniques for analyzing gene expression, such as polymerase chain reaction (PCR), microarrays, and in situ hybridization, have proven invaluable in understanding RNA processing and regulation. However, these techniques rely on the use of lysed and/or fixed cells and are therefore limited in their ability to provide important spatial-temporal information. This has led to the development of numerous techniques for imaging RNA in living cells, some of which have already provided important insight into the dynamic role RNA plays in dictating cell behavior. Here we review the fluorescent probes that have allowed for RNA imaging in living cells and discuss their utility and limitations. Common challenges faced by fluorescent probes, such as probe design, delivery, and target accessibility, are also discussed. It is expected that continued advancements in live cell imaging of RNA will open new and exciting opportunities in a wide range of biological and medical applications.
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Affiliation(s)
- Gang Bao
- Department of Biomedical Engineering, Georgia Institute of Technology and Emory University, Atlanta, Georgia 30332;
| | - Won Jong Rhee
- Department of Biomedical Engineering, Georgia Institute of Technology and Emory University, Atlanta, Georgia 30332;
| | - Andrew Tsourkas
- Department of Bioengineering, University of Pennsylvania, Philadelphia, Pennsylvania 19104
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26
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Nardo L, Bondani M, Andreoni A. DNA-ligand binding mode discrimination by characterizing fluorescence resonance energy transfer through lifetime measurements with picosecond resolution. Photochem Photobiol 2008; 84:101-10. [PMID: 18173709 DOI: 10.1111/j.1751-1097.2007.00204.x] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
We describe a method for distinguishing between minor groove binders and base intercalators that is based on measurements of the fluorescence lifetime of a donor (D) in the presence of an acceptor (A). The D-A pair is separated by a short double helix DNA with which the ligands interact. By plotting the D fluorescence lifetime as a function of the ligand-to-base pair concentration ratio we find a clear signature that distinguishes between the two binding mechanisms: minor groove binding induces an asymptotic decrease of the D fluorescence lifetime, while intercalation gives a monotonically increasing lifetime and the appearance of an additional short lifetime. We assayed Quinacrine, Hoechst and 4'-6'diamidine-2-phenyl indole, which in control experiments performed on oligodeoxyribonucleotides (oligos) lacking the A are demonstrated not to interfere with the D fluorescence. The changes in fluorescence lifetimes measured in the case of dual-labeled oligos are thus caused by structural changes in the DNA that modify the D-A distance. The appearance of the short-lived transient in the fluorescence decay of Ds attached to dual-labeled oligos upon binding of an intercalator can be interpreted as denaturation.
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Affiliation(s)
- Luca Nardo
- Dipartimento di Fisica e Matematica, Universita' degli Studi dell'Insubria, Como, Italy.
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27
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Conlon P, Yang CJ, Wu Y, Chen Y, Martinez K, Kim Y, Stevens N, Marti AA, Jockusch S, Turro NJ, Tan W. Pyrene excimer signaling molecular beacons for probing nucleic acids. J Am Chem Soc 2008; 130:336-42. [PMID: 18078339 PMCID: PMC2531189 DOI: 10.1021/ja076411y] [Citation(s) in RCA: 246] [Impact Index Per Article: 15.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Molecular beacon DNA probes, containing 1-4 pyrene monomers on the 5' end and the quencher DABCYL on the 3' end, were engineered and employed for real-time probing of DNA sequences. In the absence of a target sequence, the multiple-pyrene labeled molecular beacons (MBs) assumed a stem-closed conformation resulting in quenching of the pyrene excimer fluorescence. In the presence of target, the beacons switched to a stem-open conformation, which separated the pyrene label from the quencher molecule and generated an excimer emission signal proportional to the target concentration. Steady-state fluorescence assays resulted in a subnanomolar limit of detection in buffer, whereas time-resolved signaling enabled low-nanomolar target detection in cell-growth media. It was found that the excimer emission intensity could be scaled by increasing the number of pyrene monomers conjugated to the 5' terminal. Each additional pyrene monomer resulted in substantial increases in the excimer emission intensities, quantum yields, and excited-state lifetimes of the hybridized MBs. The long fluorescence lifetime ( approximately 40 ns), large Stokes shift (130 nm), and tunable intensity of the excimer make this multiple-pyrene moiety a useful alternative to traditional fluorophore labeling in nucleic acid probes.
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Affiliation(s)
- Patrick Conlon
- Center for Research at Bio/NanoInterface, Department of Chemistry and Shands Cancer Center,University of Florida Genetics Institute, University of Florida, Gainesville, FL 32611-7200. 352-846-2410
| | - Chaoyong James Yang
- Center for Research at Bio/NanoInterface, Department of Chemistry and Shands Cancer Center,University of Florida Genetics Institute, University of Florida, Gainesville, FL 32611-7200. 352-846-2410
| | - Yanrong Wu
- Center for Research at Bio/NanoInterface, Department of Chemistry and Shands Cancer Center,University of Florida Genetics Institute, University of Florida, Gainesville, FL 32611-7200. 352-846-2410
| | - Yan Chen
- Center for Research at Bio/NanoInterface, Department of Chemistry and Shands Cancer Center,University of Florida Genetics Institute, University of Florida, Gainesville, FL 32611-7200. 352-846-2410
| | - Karen Martinez
- Center for Research at Bio/NanoInterface, Department of Chemistry and Shands Cancer Center,University of Florida Genetics Institute, University of Florida, Gainesville, FL 32611-7200. 352-846-2410
| | - Youngmi Kim
- Center for Research at Bio/NanoInterface, Department of Chemistry and Shands Cancer Center,University of Florida Genetics Institute, University of Florida, Gainesville, FL 32611-7200. 352-846-2410
| | - Nathan Stevens
- Department of Chemistry, Columbia University, New York, NY 10027
| | - Angel A. Marti
- Department of Chemistry, Columbia University, New York, NY 10027
| | - Steffen Jockusch
- Department of Chemistry, Columbia University, New York, NY 10027
| | | | - Weihong Tan
- Center for Research at Bio/NanoInterface, Department of Chemistry and Shands Cancer Center,University of Florida Genetics Institute, University of Florida, Gainesville, FL 32611-7200. 352-846-2410
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28
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Martí AA, Jockusch S, Stevens N, Ju J, Turro NJ. Fluorescent hybridization probes for sensitive and selective DNA and RNA detection. Acc Chem Res 2007; 40:402-9. [PMID: 17458926 DOI: 10.1021/ar600013q] [Citation(s) in RCA: 165] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
We outline the different approaches taken by our group in the design of fluorescent hybridization sensors. Molecular beacons (MBs) and binary probes (BPs) using two dyes (2d-MB and 2d-BP, respectively) have been synthesized; these sensors serve as switches in emission upon binding to target biomolecules, such as DNA. These sensors allow for ratiometric fluorescence detection of polynucleotides (PNs) by visualization of the probes when bound to a target PN. Additionally, three-dye MBs (3d-MB) and BPs (3d-BP) have been developed, where an energy-transfer cascade is employed to decrease the overlap between the fluorophore emission spectra, resulting in a low direct excitation of the acceptor fluorophore. Pyrene-based MB (Py-MB) and BP (Py-BP), which possess the advantage of long fluorescence lifetimes, have also been synthesized. Time-resolved fluorescence spectra (TRES) can be used to discriminate between short-lived background fluorescence and long-lived fluorescence of the pyrene probes. This technique was demonstrated by time-resolving the signal of a Py-BP from the background fluorescence in Aplysia californica cell extracts.
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Affiliation(s)
- Angel A Martí
- Department of Chemistry, Columbia University, New York, NY 10027, USA
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29
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Stevens N, Dyer J, Martí AA, Solomon M, Turro NJ. FRETView: a computer program to simplify the process of obtaining fluorescence resonance energy transfer parameters. Photochem Photobiol Sci 2007; 6:909-11. [PMID: 17668122 DOI: 10.1039/b702631e] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The process of modeling the fluorescence resonance energy transfer (FRET) process for a donor-acceptor pair can be rather challenging, yet few computer programs exist that allow such modeling to be done with relative ease. In order to address this, we have developed a Java-based program, FRETView, which allows numerous FRET parameters to be obtained with just a few mouse clicks. Being a Java-based program, it runs equally well on all the major operating systems such as Windows, Mac OS X, Linux, Solaris. The program allows the user to effortlessly input pertinent information about the donor-acceptor pair, including the absorption and/or emission spectra, and outputs the calculated FRET parameters in table format, as well as graphical plots.
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Affiliation(s)
- Nathan Stevens
- Department of Chemistry, Columbia University, New York, NY 10027, USA
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30
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Martí AA, Li X, Jockusch S, Stevens N, Li Z, Raveendra B, Kalachikov S, Morozova I, Russo JJ, Akins DL, Ju J, Turro NJ. Design and characterization of two-dye and three-dye binary fluorescent probes for mRNA detection. Tetrahedron 2007; 63:3591-3600. [PMID: 19907676 PMCID: PMC2775546 DOI: 10.1016/j.tet.2006.08.109] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
We report the design, synthesis and characterization of binary oligonucleotide probes for mRNA detection. The probes were designed to avoid common problems found in standard binary probes such as direct excitation of the acceptor fluorophore and overlap between the donor and acceptor emission spectra. Two different probes were constructed that contained an array of either two or three dyes and that were characterized using steady-state fluorescence spectroscopy, time-resolved fluorescence spectroscopy and fluorescence depolarization measurements. The three-dye binary probe (BP-3d) consists of a Fam fluorophore which acts as a donor, collecting light and transferring it as energy to Tamra, which subsequently transfers energy to Cy5 when the two probes are hybridized to mRNA. This design allows the use of 488 nm excitation, which avoids the direct excitation of Cy5 and at the same time provides a good fluorescence resonance energy transfer (FRET) efficiency. The two-dye binary probe system (BP-2d) was constructed of Alexa488 and Cy5 fluorophores. Although the overlap between the fluorescence of Alexa488 and the absorption of Cy5 is relatively low, FRET still occurs due to their close physical proximity when the probes are hybridized to mRNA. This framework also decreases the direct excitation of Cy5 and reduces the fluorescence overlap between the donor and the acceptor. Picosecond time-resolved spectroscopy showed a reduction in the fluorescence lifetime of donor fluorophores after the formation of the hybrid between the probes and target mRNA. Interestingly, BP-2d in the presence of mRNA shows a slow rise in the fluorescence decay of Cy5 due to a relatively low FRET rate, which together with the reduction in the Alexa488 lifetime provides a way to improve the signal to background ratio using time-resolved fluorescence spectra (TRES). In addition, fluorescence depolarization measurements showed complete depolarization of the acceptor dyes (Cy5) for both BP-3d (due to sequential FRET steps) and BP-2d (due to the relatively low FRET rate) in the presence of the mRNA target.
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Affiliation(s)
- Angel A Martí
- Department of Chemistry, Columbia University, New York, NY, 10027
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31
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Li X, Li Z, Martí AA, Jockusch S, Stevens N, Akins DL, Turro NJ, Ju J. Combinatorial fluorescence energy transfer molecular beacons for probing nucleic acid sequences. Photochem Photobiol Sci 2006; 5:896-902. [PMID: 17019467 DOI: 10.1039/b605936h] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
We report the design, synthesis, and characterization of molecular beacons (MB) consisting of three distinct fluorophores, 6-carboxyfluorescein (Fam), N,N,N',N'-tetramethyl-6-carboxyrhodamine (Tam), and Cyanine-5 (Cy5). The primary light absorber/energy donor (Fam) is located on one terminus of the MB, whereas the primary energy acceptor/secondary donor (Tam) and secondary acceptor (Cy5) are located at the other terminus of the MB. In the absence of target DNA or RNA, the MB exists in the stem-closed form. Excitation of Fam initiates an energy transfer cascade from Fam to Tam and further to Cy5 generating unique fluorescence signatures defined as the ratio of the emission from each of the three fluorophores. This energy transfer cascade was investigated in detail by steady-state and time-resolved fluorescence spectroscopy, as well as fluorescence depolarization studies. In the presence of the complementary target DNA, the MB opened efficiently and hybridized with the target separating Fam and Tam by a large distance, so that energy transfer from Fam to Tam was blocked in the stem-open form. This opening of the MB generates a "bar code" fluorescence signature, which is different from the signature of the stem-closed MB. The fluorescence signature of this combinatorial fluorescence energy transfer MB can be tuned by variation of the spacer length between the individual fluorophores.
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Affiliation(s)
- Xiaoxu Li
- Columbia Genome Center, Columbia University College of Physicians and Surgeons, New York, NY 10032, USA
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