51
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Zhang H, Li T. Effects of spermidine and ATP on stabilities of chromatosomes and histone H1-depleted chromatosomes. Bioorg Med Chem Lett 2017; 27:1149-1153. [PMID: 28169161 DOI: 10.1016/j.bmcl.2017.01.072] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2016] [Revised: 01/17/2017] [Accepted: 01/24/2017] [Indexed: 11/15/2022]
Abstract
It is shown in our FRET studies that both chromatosomes and histone H1-depleted chromatosomes exist in their arm-closed forms in the absence of spermidine. In the presence of spermidine, however, these two types of structural assemblies are converted into their arm-open forms. In addition, ATP as polyanion is capable of suppressing the polycationic effect of spermidine, thus facilitating re-formation of arm-closed forms of these two types of structural assemblies. Our studies therefore illustrate that conversion between arm-closed and arm-open forms of chromatosomes and histone H1-depleted chromatosomes can be manipulated by varying concentrations of polycationic spermidine and polyanionic ATP.
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Affiliation(s)
- Hao Zhang
- Division of Chemistry and Biological Chemistry, School of Physical and Mathematical Sciences, Nanyang Technological University, 21 Nanyang Link, Singapore 637371, Singapore
| | - Tianhu Li
- Division of Chemistry and Biological Chemistry, School of Physical and Mathematical Sciences, Nanyang Technological University, 21 Nanyang Link, Singapore 637371, Singapore.
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52
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Design of photofunctional oligonucleotides by copolymerization of natural nucleobases with base surrogates prepared from acyclic scaffolds. Polym J 2016. [DOI: 10.1038/pj.2016.120] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
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53
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Dimura M, Peulen TO, Hanke CA, Prakash A, Gohlke H, Seidel CA. Quantitative FRET studies and integrative modeling unravel the structure and dynamics of biomolecular systems. Curr Opin Struct Biol 2016; 40:163-185. [PMID: 27939973 DOI: 10.1016/j.sbi.2016.11.012] [Citation(s) in RCA: 113] [Impact Index Per Article: 14.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2016] [Revised: 11/11/2016] [Accepted: 11/11/2016] [Indexed: 01/11/2023]
Abstract
Förster Resonance Energy Transfer (FRET) combined with single-molecule spectroscopy probes macromolecular structure and dynamics and identifies coexisting conformational states. We review recent methodological developments in integrative structural modeling by satisfying spatial restraints on networks of FRET pairs (hybrid-FRET). We discuss procedures to incorporate prior structural knowledge and to obtain optimal distance networks. Finally, a workflow for hybrid-FRET is presented that automates integrative structural modeling and experiment planning to put hybrid-FRET on rails. To test this workflow, we simulate realistic single-molecule experiments and resolve three protein conformers, exchanging at 30μs and 10ms, with accuracies of 1-3Å RMSD versus the target structure. Incorporation of data from other spectroscopies and imaging is also discussed.
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Affiliation(s)
- Mykola Dimura
- Chair for Molecular Physical Chemistry, Heinrich Heine University Düsseldorf, 40225 Düsseldorf, Germany; Institute for Pharmaceutical and Medicinal Chemistry, Heinrich Heine University Düsseldorf, 40225 Düsseldorf, Germany
| | - Thomas O Peulen
- Chair for Molecular Physical Chemistry, Heinrich Heine University Düsseldorf, 40225 Düsseldorf, Germany
| | - Christian A Hanke
- Chair for Molecular Physical Chemistry, Heinrich Heine University Düsseldorf, 40225 Düsseldorf, Germany
| | - Aiswaria Prakash
- Chair for Molecular Physical Chemistry, Heinrich Heine University Düsseldorf, 40225 Düsseldorf, Germany
| | - Holger Gohlke
- Institute for Pharmaceutical and Medicinal Chemistry, Heinrich Heine University Düsseldorf, 40225 Düsseldorf, Germany
| | - Claus Am Seidel
- Chair for Molecular Physical Chemistry, Heinrich Heine University Düsseldorf, 40225 Düsseldorf, Germany.
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54
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Merkel M, Dehmel L, Ernsting NP, Wagenknecht HA. An Isosteric and Fluorescent DNA Base Pair Consisting of 4-aminophthalimide and 2,4-diaminopyrimidine as C-Nucleosides. Angew Chem Int Ed Engl 2016; 56:384-388. [DOI: 10.1002/anie.201608712] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2016] [Revised: 10/05/2016] [Indexed: 12/28/2022]
Affiliation(s)
- Marcus Merkel
- Institut für Organische Chemie; Karlsruher Institut für Technologie (KIT); Fritz-Haber-Weg 6 76131 Karlsruhe Germany
| | - Lars Dehmel
- Humboldt Universität zu Berlin; Department Chemie; Brook-Taylor-Str. 2 12489 Berlin Germany
| | - Nikolaus P. Ernsting
- Humboldt Universität zu Berlin; Department Chemie; Brook-Taylor-Str. 2 12489 Berlin Germany
| | - Hans-Achim Wagenknecht
- Institut für Organische Chemie; Karlsruher Institut für Technologie (KIT); Fritz-Haber-Weg 6 76131 Karlsruhe Germany
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55
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Merkel M, Dehmel L, Ernsting NP, Wagenknecht H. Ein isosteres und fluoreszierendes DNA‐Basenpaar aus 4‐Aminophthalimid und 2,4‐Diaminopyrimidin als C‐Nucleoside. Angew Chem Int Ed Engl 2016. [DOI: 10.1002/ange.201608712] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Affiliation(s)
- Marcus Merkel
- Institut für Organische Chemie Karlsruher Institut für Technologie (KIT) Fritz-Haber-Weg 6 76131 Karlsruhe Deutschland
| | - Lars Dehmel
- Humboldt-Universität zu Berlin Department Chemie Brook-Taylor-Straße 2 12489 Berlin Deutschland
| | - Nikolaus P. Ernsting
- Humboldt-Universität zu Berlin Department Chemie Brook-Taylor-Straße 2 12489 Berlin Deutschland
| | - Hans‐Achim Wagenknecht
- Institut für Organische Chemie Karlsruher Institut für Technologie (KIT) Fritz-Haber-Weg 6 76131 Karlsruhe Deutschland
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56
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Boonlua C, Charoenpakdee C, Vilaivan T, Praneenararat T. Preparation and Performance Evaluation of a Pyrrolidinyl Peptide Nucleic-Acid-Based Displacement Probe as a DNA Sensor. ChemistrySelect 2016. [DOI: 10.1002/slct.201601075] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Affiliation(s)
- Chalothorn Boonlua
- Organic Synthesis Research Unit, Department of Chemistry; Faculty of Science, Chulalongkorn University; Phayathai Rd., Pathumwan Bangkok 10330 Thailand
| | - Chayan Charoenpakdee
- Organic Synthesis Research Unit, Department of Chemistry; Faculty of Science, Chulalongkorn University; Phayathai Rd., Pathumwan Bangkok 10330 Thailand
| | - Tirayut Vilaivan
- Organic Synthesis Research Unit, Department of Chemistry; Faculty of Science, Chulalongkorn University; Phayathai Rd., Pathumwan Bangkok 10330 Thailand
| | - Thanit Praneenararat
- Organic Synthesis Research Unit, Department of Chemistry; Faculty of Science, Chulalongkorn University; Phayathai Rd., Pathumwan Bangkok 10330 Thailand
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57
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Börner R, Kowerko D, Miserachs HG, Schaffer MF, Sigel RK. Metal ion induced heterogeneity in RNA folding studied by smFRET. Coord Chem Rev 2016. [DOI: 10.1016/j.ccr.2016.06.002] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
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58
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Hohlbein J, Kapanidis AN. Probing the Conformational Landscape of DNA Polymerases Using Diffusion-Based Single-Molecule FRET. Methods Enzymol 2016; 581:353-378. [PMID: 27793286 DOI: 10.1016/bs.mie.2016.08.023] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
Monitoring conformational changes in DNA polymerases using single-molecule Förster resonance energy transfer (smFRET) has provided new tools for studying fidelity-related mechanisms that promote the rejection of incorrect nucleotides before DNA synthesis. In addition to the previously known open and closed conformations of DNA polymerases, our smFRET assays utilizing doubly labeled variants of Escherichia coli DNA polymerase I were pivotal in identifying and characterizing a partially closed conformation as a primary checkpoint for nucleotide selection. Here, we provide a comprehensive overview of the methods we used for the conformational analysis of wild-type DNA polymerase and some of its low-fidelity derivatives; these methods include strategies for protein labeling and our procedures for solution-based single-molecule fluorescence data acquisition and data analysis. We also discuss alternative single-molecule fluorescence strategies for analyzing the conformations of DNA polymerases in vitro and in vivo.
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Affiliation(s)
- J Hohlbein
- Laboratory of Biophysics, Wageningen University and Research, Wageningen, The Netherlands; Microspectroscopy Centre, Wageningen University and Research, Wageningen, The Netherlands.
| | - A N Kapanidis
- Clarendon Laboratory, University of Oxford, Oxford, United Kingdom.
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59
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DNA-Dye-Conjugates: Conformations and Spectra of Fluorescence Probes. PLoS One 2016; 11:e0160229. [PMID: 27467071 PMCID: PMC4965132 DOI: 10.1371/journal.pone.0160229] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2016] [Accepted: 07/16/2016] [Indexed: 02/04/2023] Open
Abstract
Extensive molecular-dynamics (MD) simulations have been used to investigate DNA-dye and DNA-photosensitizer conjugates, which act as reactants in templated reactions leading to the generation of fluorescent products in the presence of specific desoxyribonucleic acid sequences (targets). Such reactions are potentially suitable for detecting target nucleic acids in live cells by fluorescence microscopy or flow cytometry. The simulations show how the attached dyes/photosensitizers influence DNA structure and reveal the relative orientations of the chromophores with respect to each other. Our results will help to optimize the reactants for the templated reactions, especially length and structure of the spacers used to link reporter dyes or photosensitizers to the oligonucleotides responsible for target recognition. Furthermore, we demonstrate that the structural ensembles obtained from the simulations can be used to calculate steady-state UV-vis absorption and emission spectra. We also show how important quantities describing the quenching of the reporter dye via fluorescence resonance energy transfer (FRET) can be calculated from the simulation data, and we compare these for different relative chromophore geometries.
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60
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Farooq S, Hohlbein J. Camera-based single-molecule FRET detection with improved time resolution. Phys Chem Chem Phys 2016; 17:27862-72. [PMID: 26439729 DOI: 10.1039/c5cp04137f] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The achievable time resolution of camera-based single-molecule detection is often limited by the frame rate of the camera. Especially in experiments utilizing single-molecule Förster resonance energy transfer (smFRET) to probe conformational dynamics of biomolecules, increasing the frame rate by either pixel-binning or cropping the field of view decreases the number of molecules that can be monitored simultaneously. Here, we present a generalised excitation scheme termed stroboscopic alternating-laser excitation (sALEX) that significantly improves the time resolution without sacrificing highly parallelised detection in total internal reflection fluorescence (TIRF) microscopy. In addition, we adapt a technique known from diffusion-based confocal microscopy to analyse the complex shape of FRET efficiency histograms. We apply both sALEX and dynamic probability distribution analysis (dPDA) to resolve conformational dynamics of interconverting DNA hairpins in the millisecond time range.
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Affiliation(s)
- Shazia Farooq
- Laboratory of Biophysics, Wageningen UR, Dreijenlaan 3, 6703 HA Wageningen, The Netherlands.
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61
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Hildebrandt N, Spillmann CM, Algar WR, Pons T, Stewart MH, Oh E, Susumu K, Díaz SA, Delehanty JB, Medintz IL. Energy Transfer with Semiconductor Quantum Dot Bioconjugates: A Versatile Platform for Biosensing, Energy Harvesting, and Other Developing Applications. Chem Rev 2016; 117:536-711. [DOI: 10.1021/acs.chemrev.6b00030] [Citation(s) in RCA: 457] [Impact Index Per Article: 57.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Affiliation(s)
- Niko Hildebrandt
- NanoBioPhotonics
Institut d’Electronique Fondamentale (I2BC), Université Paris-Saclay, Université Paris-Sud, CNRS, 91400 Orsay, France
| | | | - W. Russ Algar
- Department
of Chemistry, University of British Columbia, Vancouver, BC V6T 1Z1, Canada
| | - Thomas Pons
- LPEM;
ESPCI Paris, PSL Research University; CNRS; Sorbonne Universités, UPMC, F-75005 Paris, France
| | | | - Eunkeu Oh
- Sotera Defense Solutions, Inc., Columbia, Maryland 21046, United States
| | - Kimihiro Susumu
- Sotera Defense Solutions, Inc., Columbia, Maryland 21046, United States
| | - Sebastian A. Díaz
- American Society for Engineering Education, Washington, DC 20036, United States
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62
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Bouchaala R, Mercier L, Andreiuk B, Mély Y, Vandamme T, Anton N, Goetz JG, Klymchenko AS. Integrity of lipid nanocarriers in bloodstream and tumor quantified by near-infrared ratiometric FRET imaging in living mice. J Control Release 2016; 236:57-67. [PMID: 27327767 PMCID: PMC4968657 DOI: 10.1016/j.jconrel.2016.06.027] [Citation(s) in RCA: 76] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2016] [Revised: 06/10/2016] [Accepted: 06/16/2016] [Indexed: 11/29/2022]
Abstract
Lipid nanocarriers are considered as promising candidates for drug delivery and cancer targeting because of their low toxicity, biodegradability and capacity to encapsulate drugs and/or contrasting agents. However, their biomedical applications are currently limited because of a poor understanding of their integrity in vivo. To address this problem, we report on fluorescent nano-emulsion droplets of 100 nm size encapsulating lipophilic near-infrared cyanine 5.5 and 7.5 dyes with a help of bulky hydrophobic counterion tetraphenylborate. Excellent brightness and efficient Förster Resonance Energy Transfer (FRET) inside lipid NCs enabled for the first time quantitative fluorescence ratiometric imaging of NCs integrity directly in the blood circulation, liver and tumor xenografts of living mice using a whole-animal imaging set-up. This unique methodology revealed that the integrity of our FRET NCs in the blood circulation of healthy mice is preserved at 93% at 6 h of post-administration, while it drops to 66% in the liver (half-life is 8.2 h). Moreover, these NCs show fast and efficient accumulation in tumors, where they enter in nearly intact form (77% integrity at 2 h) before losing their integrity to 40% at 6 h (half-life is 4.4 h). Thus, we propose a simple and robust methodology based on ratiometric FRET imaging in vivo to evaluate quantitatively nanocarrier integrity in small animals. We also demonstrate that nano-emulsion droplets are remarkably stable nano-objects that remain nearly intact in the blood circulation and release their content mainly after entering tumors.
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Affiliation(s)
- Redouane Bouchaala
- Laboratoire de Biophotonique et Pharmacologie, UMR CNRS 7213, University of Strasbourg, 74 route du Rhin, 67401 Illkirch Cedex, France; Laboratory of Photonic Systems and Nonlinear Optics, Institute of Optics and Fine Mechanics, University of Setif 1, 19000, Algeria
| | - Luc Mercier
- MN3T, Inserm U1109, LabEx Medalis, Fédération de Médecine Translationnelle de Strasbourg (FMTS), University of Strasbourg, F-67200, France
| | - Bohdan Andreiuk
- Laboratoire de Biophotonique et Pharmacologie, UMR CNRS 7213, University of Strasbourg, 74 route du Rhin, 67401 Illkirch Cedex, France; Organic Chemistry Department, Chemistry Faculty, Taras Shevchenko National University of Kyiv, 01601 Kyiv, Ukraine
| | - Yves Mély
- Laboratoire de Biophotonique et Pharmacologie, UMR CNRS 7213, University of Strasbourg, 74 route du Rhin, 67401 Illkirch Cedex, France
| | - Thierry Vandamme
- CNRS UMR 7199, Laboratoire de Conception et Application de Molécules Bioactives, University of Strasbourg, 74 route du Rhin, 67401 Illkirch Cedex, France
| | - Nicolas Anton
- CNRS UMR 7199, Laboratoire de Conception et Application de Molécules Bioactives, University of Strasbourg, 74 route du Rhin, 67401 Illkirch Cedex, France.
| | - Jacky G Goetz
- MN3T, Inserm U1109, LabEx Medalis, Fédération de Médecine Translationnelle de Strasbourg (FMTS), University of Strasbourg, F-67200, France.
| | - Andrey S Klymchenko
- Laboratoire de Biophotonique et Pharmacologie, UMR CNRS 7213, University of Strasbourg, 74 route du Rhin, 67401 Illkirch Cedex, France.
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63
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Freeman NS, Moore CE, Wilhelmsson LM, Tor Y. Chromophoric Nucleoside Analogues: Synthesis and Characterization of 6-Aminouracil-Based Nucleodyes. J Org Chem 2016; 81:4530-9. [PMID: 27128151 PMCID: PMC5493935 DOI: 10.1021/acs.joc.6b00310] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
Nucleodyes, visibly colored chromophoric nucleoside analogues, are reported. Design criteria are outlined and the syntheses of cytidine and uridine azo dye analogues derived from 6-aminouracil are described. Structural analysis shows that the nucleodyes are sound structural analogues of their native nucleoside counterparts, and photophysical studies demonstrate that the nucleodyes are sensitive to microenvironmental changes. Quantum chemical calculations are presented as a valuable complementary tool for the design of strongly absorbing nucleodyes, which overlap with the emission of known fluorophores. Förster critical distance (R0) calculations determine that the nucleodyes make good FRET pairs with both 2-aminopurine (2AP) and pyrrolocytosine (PyC). Additionally, unique tautomerization features exhibited by 5-(4-nitrophenylazo)-6-oxocytidine (8) are visualized by an extraordinary crystal structure.
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Affiliation(s)
- Noam S. Freeman
- Department of Chemistry and Biochemistry, University of
California, San Diego, 9500 Gilman Drive, La Jolla, California 92093, United
States
| | - Curtis E. Moore
- Department of Chemistry and Biochemistry, University of
California, San Diego, 9500 Gilman Drive, La Jolla, California 92093, United
States
| | - L. Marcus Wilhelmsson
- Department of Chemistry and Chemical Engineering/Chemistry
and Biochemistry, Chalmers University of Technology, Gothenburg 41296, Sweden
| | - Yitzhak Tor
- Department of Chemistry and Biochemistry, University of
California, San Diego, 9500 Gilman Drive, La Jolla, California 92093, United
States
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64
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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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65
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Pradère U, Hall J. Site-Specific Difunctionalization of Structured RNAs Yields Probes for microRNA Maturation. Bioconjug Chem 2016; 27:681-7. [PMID: 26806029 DOI: 10.1021/acs.bioconjchem.5b00661] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Modified oligonucleotides bearing multiple functional labels are valuable tools in RNA biology. Efficient synthetic access to singly modified short DNAs and RNAs has been developed in the past years and paved the way to a first generation of oligonucleotide tools. Here, we describe an efficient procedure for the site-specific hetero bis-labeling of long RNAs. We exemplified the method with the preparation of Cy3/Cy5 pre-microRNAs labeled at selected internal sites as probes for microRNA maturation.
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Affiliation(s)
- Ugo Pradère
- Institute of Pharmaceutical Sciences, Department of Chemistry and Applied Biosciences, ETH Zurich , 8093 Zurich, Switzerland
| | - Jonathan Hall
- Institute of Pharmaceutical Sciences, Department of Chemistry and Applied Biosciences, ETH Zurich , 8093 Zurich, Switzerland
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66
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Saad ST, Metherell AJ, Baggaley E, Ward MD. Synthesis and photophysical properties of Ir(iii)/Re(i) dyads: control of Ir→Re photoinduced energy transfer. Dalton Trans 2016; 45:11568-79. [DOI: 10.1039/c6dt01614f] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The extent of Ir→Re photoinduced energy transfer in Ir(iii)/Re(i) dyads can be controlled using a solvent-sensitive conformationally flexible bridging ligand.
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Affiliation(s)
- Suad T. Saad
- Department of Chemistry
- University of Sheffield
- Sheffield S3 7HF
- UK
- College of Sciences WSCI
| | | | | | - Michael D. Ward
- Department of Chemistry
- University of Sheffield
- Sheffield S3 7HF
- UK
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67
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68
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Kundu R. G-Tetraplex-Induced FRET within Telomeric Repeat Sequences Using (Py) A-(Per) A as Energy Donor-Acceptor Pair. Chem Asian J 2015; 11:198-201. [PMID: 26490798 DOI: 10.1002/asia.201500996] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2015] [Indexed: 01/08/2023]
Abstract
G-tetraplex induced fluorescence resonance energy transfer (FRET) within telomeric repeat sequences has been studied using a nucleoside-tethered FRET pair embedded in the human telomeric G-quadruplex forming sequence (5'-A GGG TT(Py) A GGG TT(Per) A GGG TTA GGG-3', Py=pyrene, Per=perylene). Conformational change from a single strand to an anti-parallel G-quadruplex leads to FRET from energy donor ((Py) A) to acceptor ((Per) A). The distance between the FRET donor/acceptor partners was controlled by changing the number of G-quartet spacer units. The FRET efficiency decreases with increase in G-quartet units. Overall findings indicate that this could be further used for the development of FRET-based sensing and measurement techniques.
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Affiliation(s)
- Rajen Kundu
- Department of Chemistry, Pohang University of Science and Technology, Pohang, 790784, South Korea. .,Department of Chemistry and Biochemistry, University of Colorado, Boulder, 80303, USA.
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69
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Ensslen P, Wagenknecht HA. One-Dimensional Multichromophor Arrays Based on DNA: From Self-Assembly to Light-Harvesting. Acc Chem Res 2015; 48:2724-33. [PMID: 26411920 DOI: 10.1021/acs.accounts.5b00314] [Citation(s) in RCA: 104] [Impact Index Per Article: 11.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
Light-harvesting complexes collect light energy and deliver it by a cascade of energy and electron transfer processes to the reaction center where charge separation leads to storage as chemical energy. The design of artificial light-harvesting assemblies faces enormous challenges because several antenna chromophores need to be kept in close proximity but self-quenching needs to be avoided. Double stranded DNA as a supramolecular scaffold plays a promising role due to its characteristic structural properties. Automated DNA synthesis allows incorporation of artificial chromophore-modified building blocks, and sequence design allows precise control of the distances and orientations between the chromophores. The helical twist between the chromophores, which is induced by the DNA framework, controls energy and electron transfer and thereby reduces the self-quenching that is typically observed in chromophore aggregates. This Account summarizes covalently multichromophore-modified DNA and describes how such multichromophore arrays were achieved by Watson-Crick-specific and DNA-templated self-assembly. The covalent DNA systems were prepared by incorporation of chromophores as DNA base substitutions (either as C-nucleosides or with acyclic linkers as substitutes for the 2'-deoxyribofuranoside) and as DNA base modifications. Studies with DNA base substitutions revealed that distances but more importantly relative orientations of the chromophores govern the energy transfer efficiencies and thereby the light-harvesting properties. With DNA base substitutions, duplex stabilization was faced and could be overcome, for instance, by zipper-like placement of the chromophores in both strands. For both principal structural approaches, DNA-based light-harvesting antenna could be realized. The major disadvantages, however, for covalent multichromophore DNA conjugates are the poor yields of synthesis and the solubility issues for oligonucleotides with more than 5-10 chromophore modifications in a row. A logical alternative approach is to leave out the phosphodiester bridges between the chromophores and let chromophore-nucleoside conjugates self-assemble specifically along single stranded DNA as template. The self-organization of chromophores along the DNA template based on canonical base pairing would be advantageous because sequence selective base pairing could provide a structural basis for programmed complexity within the chromophore assembly. The self-assembly is governed by two interactions. The chromophore-nucleoside conjugates as guest molecules are recognized via hydrogen bonds to the corresponding counter bases in the single stranded DNA template. Moreover, the π-π interactions between the stacked chromophores stabilize these self-assembled constructs with increasing length. Longer DNA templates are more attractive for self-assembled antenna. The helicity in the stack of porphyrins as guest molecules assembled on the DNA template can be switched by environmental changes, such as pH variations. DNA-templated stacks of ethynyl pyrene and nile red exhibit left-handed chirality, which stands in contrast to similar covalent multichromophore-DNA conjugates with enforced right-handed helicity. With ethynyl nile red, it is possible to occupy every available binding site on the templates. Mixed assemblies of ethynyl pyrene and nile red show energy transfer and thereby provide a proof-of-principle that simple light-harvesting antennae can be obtained in a noncovalent and self-assembled fashion. With respect to the next important step, chemical storage of the absorbed light energy, future research has to focus on the coupling of sophisticated DNA-based light-harvesting antenna to reaction centers.
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Affiliation(s)
- Philipp Ensslen
- Karlsruhe Institute of Technology (KIT), Institute of Organic Chemistry, Fritz-Haber-Weg 6, 76131 Karlsruhe, Germany
| | - Hans-Achim Wagenknecht
- Karlsruhe Institute of Technology (KIT), Institute of Organic Chemistry, Fritz-Haber-Weg 6, 76131 Karlsruhe, Germany
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70
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Kwon HS, Yoo JS, Lee HY, Choi JH. Synthesis of Innovative Colorants Based on Cyanine Dye and Their FRET Efficiency to Reduce the Emission of Fluorescence for LCD Color Filter. B KOREAN CHEM SOC 2015. [DOI: 10.1002/bkcs.10471] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
- Hye-Sun Kwon
- Department of Textile System Engineering; Kyungpook National University; Daegu 702-701 Korea
| | - Jae-Sung Yoo
- Department of Textile System Engineering; Kyungpook National University; Daegu 702-701 Korea
| | - Hyun-Young Lee
- Department of Textile System Engineering; Kyungpook National University; Daegu 702-701 Korea
| | - Jae-Hong Choi
- Department of Textile System Engineering; Kyungpook National University; Daegu 702-701 Korea
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71
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Hildebrandt LL, Preus S, Birkedal V. Quantitative single molecule FRET efficiencies using TIRF microscopy. Faraday Discuss 2015; 184:131-42. [PMID: 26416760 DOI: 10.1039/c5fd00100e] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Förster resonance energy transfer (FRET) microscopy at the single molecule level has the potential to yield information on intra and intermolecular distances within the 2-10 nm range of molecules or molecular complexes that undergo frequent conformation changes. A pre-requirement for obtaining accurate distance information is to determine quantitative instrument independent FRET efficiency values. Here, we applied and evaluated a procedure to determine quantitative FRET efficiencies directly from individual fluorescence time traces of surface immobilized DNA molecules without the need for external calibrants. To probe the robustness of the approach over a wide range of FRET efficiencies we used a set of doubly labelled double stranded DNA samples, where the acceptor position was varied systematically. Interestingly, we found that fluorescence contributions arising from direct acceptor excitation following donor excitation are intrinsically taken into account in these conditions as other correction factors can compensate for inaccurate values of these parameters. We give here guidelines, that can be used through tools within the iSMS software (), for determining quantitative FRET and assess uncertainties linked with the procedure. Our results provide insights into the experimental parameters governing quantitative FRET determination, which is essential for obtaining accurate structural information from a wide range of biomolecules.
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Affiliation(s)
- Lasse L Hildebrandt
- Interdisciplinary Nanoscience Center (iNANO), Aarhus University, Aarhus, Denmark.
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72
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Qiu J, Liu J, Chen S, Ou TM, Tan JH, Gu LQ, Huang ZS, Li D. Role of Hairpin-Quadruplex DNA Secondary Structural Conversion in the Promoter of hnRNP K in Gene Transcriptional Regulation. Org Lett 2015; 17:4584-7. [DOI: 10.1021/acs.orglett.5b02310] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Affiliation(s)
- Jun Qiu
- School of Pharmaceutical
Sciences, Sun Yat-sen University, Guangzhou University City, 132 Waihuan
East Road, Guangzhou, Guangdong 510006, P. R. China
| | - Jinggong Liu
- School of Pharmaceutical
Sciences, Sun Yat-sen University, Guangzhou University City, 132 Waihuan
East Road, Guangzhou, Guangdong 510006, P. R. China
| | - Shuobin Chen
- School of Pharmaceutical
Sciences, Sun Yat-sen University, Guangzhou University City, 132 Waihuan
East Road, Guangzhou, Guangdong 510006, P. R. China
| | - Tian-Miao Ou
- School of Pharmaceutical
Sciences, Sun Yat-sen University, Guangzhou University City, 132 Waihuan
East Road, Guangzhou, Guangdong 510006, P. R. China
| | - Jia-Heng Tan
- School of Pharmaceutical
Sciences, Sun Yat-sen University, Guangzhou University City, 132 Waihuan
East Road, Guangzhou, Guangdong 510006, P. R. China
| | - Lian-Quan Gu
- School of Pharmaceutical
Sciences, Sun Yat-sen University, Guangzhou University City, 132 Waihuan
East Road, Guangzhou, Guangdong 510006, P. R. China
| | - Zhi-Shu Huang
- School of Pharmaceutical
Sciences, Sun Yat-sen University, Guangzhou University City, 132 Waihuan
East Road, Guangzhou, Guangdong 510006, P. R. China
| | - Ding Li
- School of Pharmaceutical
Sciences, Sun Yat-sen University, Guangzhou University City, 132 Waihuan
East Road, Guangzhou, Guangdong 510006, P. R. China
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73
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Takahashi K, Ito S, Nakamoto K, Ito Y, Ueno Y. Photoinduced Electron-Transfer-Based Hybridization Probes for Detection of DNA and RNA. J Org Chem 2015; 80:8561-70. [PMID: 26258850 DOI: 10.1021/acs.joc.5b01132] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Here, we report the synthesis of a hybridization probe for detection of RNA and DNA based on photoinduced electron transfer (PeT). We designed and synthesized an oligonucleotide containing an adenosine analogue with a 9-(N,N-dimethylaminomethyl)anthracenyl moiety at its 6-position via an ethynylene linker as the hybridization probe. When the probe was hybridized with a complementary RNA or DNA, the fluorescence intensity increased 3-fold or 4.5-fold, respectively, compared to the single-stranded state.
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Affiliation(s)
| | | | | | - Yasutomo Ito
- Division for Medical Research Engineering, Nagoya University Graduate School of Medicine , Nagoya 466-8550, Japan
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74
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Foller Larsen A, Dumat B, Wranne MS, Lawson CP, Preus S, Bood M, Gradén H, Marcus Wilhelmsson L, Grøtli M. Development of bright fluorescent quadracyclic adenine analogues: TDDFT-calculation supported rational design. Sci Rep 2015; 5:12653. [PMID: 26227585 PMCID: PMC4530663 DOI: 10.1038/srep12653] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2015] [Accepted: 07/06/2015] [Indexed: 02/01/2023] Open
Abstract
Fluorescent base analogues (FBAs) comprise a family of increasingly important molecules for the investigation of nucleic acid structure and dynamics. We recently reported the quantum chemical calculation supported development of four microenvironment sensitive analogues of the quadracyclic adenine (qA) scaffold, the qANs, with highly promising absorptive and fluorescence properties that were very well predicted by TDDFT calculations. Herein, we report on the efficient synthesis, experimental and theoretical characterization of nine novel quadracyclic adenine derivatives. The brightest derivative, 2-CNqA, displays a 13-fold increased brightness (εΦF = 4500) compared with the parent compound qA and has the additional benefit of being a virtually microenvironment-insensitive fluorophore, making it a suitable candidate for nucleic acid incorporation and use in quantitative FRET and anisotropy experiments. TDDFT calculations, conducted on the nine novel qAs a posteriori, successfully describe the relative fluorescence quantum yield and brightness of all qA derivatives. This observation suggests that the TDDFT-based rational design strategy may be employed for the development of bright fluorophores built up from a common scaffold to reduce the otherwise costly and time-consuming screening process usually required to obtain useful and bright FBAs.
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Affiliation(s)
- Anders Foller Larsen
- Department of Chemistry and Chemical Engineering/Chemistry and Biochemistry, Chalmers University of Technology, S-41296 Gothenburg, Sweden
| | - Blaise Dumat
- Department of Chemistry and Chemical Engineering/Chemistry and Biochemistry, Chalmers University of Technology, S-41296 Gothenburg, Sweden
| | - Moa S. Wranne
- Department of Chemistry and Chemical Engineering/Chemistry and Biochemistry, Chalmers University of Technology, S-41296 Gothenburg, Sweden
| | - Christopher P. Lawson
- Department of Chemistry and Molecular Biology, University of Gothenburg, S-41296 Gothenburg, Sweden
| | - Søren Preus
- Interdisciplinary Nanoscience Center (iNANO), Aarhus University, Aarhus C, DK-8000, Denmark
| | - Mattias Bood
- Department of Chemistry and Molecular Biology, University of Gothenburg, S-41296 Gothenburg, Sweden
| | | | - L. Marcus Wilhelmsson
- Department of Chemistry and Chemical Engineering/Chemistry and Biochemistry, Chalmers University of Technology, S-41296 Gothenburg, Sweden
| | - Morten Grøtli
- Department of Chemistry and Molecular Biology, University of Gothenburg, S-41296 Gothenburg, Sweden
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75
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Warminski M, Warminska Z, Kowalska J, Jemielity J. mRNA Cap Modification through Carbamate Chemistry: Synthesis of Amino- and Carboxy-Functionalised Cap Analogues Suitable for Labelling and Bioconjugation. European J Org Chem 2015. [DOI: 10.1002/ejoc.201500672] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
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76
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77
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Lawson CP, Dierckx A, Miannay FA, Wellner E, Wilhelmsson LM, Grøtli M. Synthesis and photophysical characterisation of new fluorescent triazole adenine analogues. Org Biomol Chem 2015; 12:5158-67. [PMID: 24912077 DOI: 10.1039/c4ob00904e] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Fluorescent nucleic acid base analogues are powerful probes of DNA structure. Here we describe the synthesis and photo-physical characterisation of a series of 2-(4-amino-5-(1H-1,2,3-triazol-4-yl)-7H-pyrrolo[2,3-d]pyrimidin-7-yl) and 2-(4-amino-3-(1H-1,2,3-triazol-4-yl)-1H-pyrazolo[3,4-d]pyrimidin-1-yl) analogues via Sonogashira cross-coupling and [3 + 2]-cycloaddition reactions as the key steps in the synthesis. Compounds with a nitrogen atom in position 8 showed an approximately ten-fold increase in quantum yield and decreased Stokes shift compared to analogues with a carbon atom in position 8. Furthermore, the analogues containing nitrogen in the 8-position showed a more red-shifted and structured absorption as opposed to those which have a carbon incorporated in the same position. Compared to the previously characterised C8-triazole modified adenine, the emissive potential was significantly lower (tenfold or more) for this new family of triazoles-adenine compounds. However, three of the compounds have photophysical properties which will make them interesting to monitor inside DNA.
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Affiliation(s)
- Christopher P Lawson
- Department of Chemistry, Medicinal Chemistry, University of Gothenburg, S-41296 Gothenburg, Sweden.
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78
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Dumat B, Bood M, Wranne MS, Lawson CP, Larsen AF, Preus S, Streling J, Gradén H, Wellner E, Grøtli M, Wilhelmsson LM. Second-generation fluorescent quadracyclic adenine analogues: environment-responsive probes with enhanced brightness. Chemistry 2015; 21:4039-48. [PMID: 25641628 DOI: 10.1002/chem.201405759] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2014] [Indexed: 01/10/2023]
Abstract
Fluorescent base analogues comprise a group of increasingly important molecules for the investigation of nucleic acid structure, dynamics, and interactions with other molecules. Herein, we report on the quantum chemical calculation aided design, synthesis, and characterization of four new putative quadracyclic adenine analogues. The compounds were efficiently synthesized from a common intermediate through a two-step pathway with the Suzuki-Miyaura coupling as the key step. Two of the compounds, qAN1 and qAN4, display brightnesses (εΦF) of 1700 and 2300, respectively, in water and behave as wavelength-ratiometric pH probes under acidic conditions. The other two, qAN2 and qAN3, display lower brightnesses but exhibit polarity-sensitive dual-band emissions that could prove useful to investigate DNA structural changes induced by DNA-protein or -drug interactions. The four qANs are very promising microenvironment-sensitive fluorescent adenine analogues that display considerable brightness for such compounds.
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Affiliation(s)
- Blaise Dumat
- Department of Chemical and Chemical Engineering/, Chemistry and Biochemistry, Chalmers University of Technology, 41296 Gothenburg (Sweden)
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79
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Das S, Samanta PK, Pati SK. Watson–Crick base pairing, electronic and photophysical properties of triazole modified adenine analogues: a computational study. NEW J CHEM 2015. [DOI: 10.1039/c5nj01566a] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Abstract
Triazole adenine nucleobase analogues show fluorescence in the UV-Vis region and form Watson–Crick base pairing with thymine nucleobases.
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Affiliation(s)
- Shubhajit Das
- New Chemistry Unit
- Jawaharlal Nehru Centre for Advanced Scientific Research
- Bangalore 560064
- India
| | - Pralok K Samanta
- Theoretical Sciences Unit
- Jawaharlal Nehru Centre for Advanced Scientific Research
- Bangalore 560064
- India
| | - Swapan K Pati
- New Chemistry Unit
- Jawaharlal Nehru Centre for Advanced Scientific Research
- Bangalore 560064
- India
- Theoretical Sciences Unit
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80
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Graen T, Hoefling M, Grubmüller H. AMBER-DYES: Characterization of Charge Fluctuations and Force Field Parameterization of Fluorescent Dyes for Molecular Dynamics Simulations. J Chem Theory Comput 2014; 10:5505-12. [PMID: 26583233 DOI: 10.1021/ct500869p] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
Recent advances in single molecule fluorescence experiments and theory allow a direct comparison and improved interpretation of experiment and simulation. To this end, force fields for a larger number of dyes are required which are compatible with and can be integrated into existing biomolecular force fields. Here, we developed, characterized, and implemented AMBER-DYES, a modular fluorescent label force field, for a set of 22 fluorescent dyes and their linkers from the Alexa, Atto, and Cy families, which are in common use for single molecule spectroscopy experiments. The force field is compatible with the AMBER protein force fields and the GROMACS molecular dynamics simulation program. The high electronic polarizability of the delocalized π-electron orbitals, as found in many fluorescent dyes, poses a particular challenge to point charge based force fields such as AMBER. To quantify the charge fluctuations due to the electronic polarizability, we simulated the 22 dyes in explicit solvent and sampled the charge fluctuations using QM/MM simulations at the B3LYP/6-31G*//TIP3P level of theory. The analysis of the simulations enabled us to derive ensemble fitted RESP charges from the solvated charge distributions of multiple trajectories. We observed broad, single peaked charge distributions for the conjugated ring atoms with well-defined mean values. The charge fitting procedure was validated against published charges of the dyelike amino acid tryptophan, which showed good agreement with existing tryptophan parameters from the AMBER, CHARMM, and OPLS force field families. A principal component analysis of the charge fluctuations revealed that a small number of collective coordinates suffices to describe most of the in-plane dye polarizability. The AMBER-DYES force field allows the rapid preparation of all atom molecular dynamics simulations of fluorescent systems for state of the art multi microsecond trajectories.
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Affiliation(s)
- Timo Graen
- Max Planck Institute for Biophysical Chemistry , Am Faβberg 11, 37077 Göttingen, Germany
| | - Martin Hoefling
- Max Planck Institute for Biophysical Chemistry , Am Faβberg 11, 37077 Göttingen, Germany
| | - Helmut Grubmüller
- Max Planck Institute for Biophysical Chemistry , Am Faβberg 11, 37077 Göttingen, Germany
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81
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Ma DH, Kim D, Akisawa T, Lee KH, Kim KT, Ahn KH. An FITC-BODIPY FRET Couple: Application to Selective, Ratiometric Detection and Bioimaging of Cysteine. Chem Asian J 2014; 10:894-902. [DOI: 10.1002/asia.201403073] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2014] [Indexed: 01/24/2023]
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82
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Chen J, Poddar NK, Tauzin LJ, Cooper D, Kolomeisky AB, Landes CF. Single-molecule FRET studies of HIV TAR-DNA hairpin unfolding dynamics. J Phys Chem B 2014; 118:12130-9. [PMID: 25254491 PMCID: PMC4207534 DOI: 10.1021/jp507067p] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
We directly measure the dynamics of the HIV trans-activation response (TAR)-DNA hairpin with multiple loops using single-molecule Förster resonance energy transfer (smFRET) methods. Multiple FRET states are identified that correspond to intermediate melting states of the hairpin. The stability of each intermediate state is calculated from the smFRET data. The results indicate that hairpin unfolding obeys a "fraying and peeling" mechanism, and evidence for the collapse of the ends of the hairpin during folding is observed. These results suggest a possible biological function for hairpin loops serving as additional fraying centers to increase unfolding rates in otherwise stable systems. The experimental and analytical approaches developed in this article provide useful tools for studying the mechanism of multistate DNA hairpin dynamics and of other general systems with multiple parallel pathways of chemical reactions.
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Affiliation(s)
- Jixin Chen
- Department of Chemistry and ‡Department of Electrical and Computer Engineering, Rice University , Houston, Texas 77251-1892, United States
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83
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Bohländer PR, Wagenknecht HA. Synthesis of a Photostable Energy-Transfer Pair for “DNA Traffic Lights”. European J Org Chem 2014. [DOI: 10.1002/ejoc.201403119] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
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84
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Hohlbein J, Craggs TD, Cordes T. Alternating-laser excitation: single-molecule FRET and beyond. Chem Soc Rev 2014; 43:1156-71. [PMID: 24037326 DOI: 10.1039/c3cs60233h] [Citation(s) in RCA: 130] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
The alternating-laser excitation (ALEX) scheme continues to expand the possibilities of fluorescence-based assays to study biological entities and interactions. Especially the combination of ALEX and single-molecule Förster Resonance Energy Transfer (smFRET) has been very successful as ALEX enables the sorting of fluorescently labelled species based on the number and type of fluorophores present. ALEX also provides a convenient way of accessing the correction factors necessary for determining accurate molecular distances. Here, we provide a comprehensive overview of the concept and current applications of ALEX and we explicitly discuss how to obtain fully corrected distance information across the entire FRET range. We also present new ideas for applications of ALEX which will push the limits of smFRET-based experiments in terms of temporal and spatial resolution for the study of complex biological systems.
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Affiliation(s)
- Johannes Hohlbein
- Laboratory of Biophysics, Wageningen UR, Wageningen, The Netherlands.
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85
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Tsukanov R, Tomov TE, Liber M, Berger Y, Nir E. Developing DNA nanotechnology using single-molecule fluorescence. Acc Chem Res 2014; 47:1789-98. [PMID: 24828396 DOI: 10.1021/ar500027d] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Abstract
CONSPECTUS: An important effort in the DNA nanotechnology field is focused on the rational design and manufacture of molecular structures and dynamic devices made of DNA. As is the case for other technologies that deal with manipulation of matter, rational development requires high quality and informative feedback on the building blocks and final products. For DNA nanotechnology such feedback is typically provided by gel electrophoresis, atomic force microscopy (AFM), and transmission electron microscopy (TEM). These analytical tools provide excellent structural information; however, usually they do not provide high-resolution dynamic information. For the development of DNA-made dynamic devices such as machines, motors, robots, and computers this constitutes a major problem. Bulk-fluorescence techniques are capable of providing dynamic information, but because only ensemble averaged information is obtained, the technique may not adequately describe the dynamics in the context of complex DNA devices. The single-molecule fluorescence (SMF) technique offers a unique combination of capabilities that make it an excellent tool for guiding the development of DNA-made devices. The technique has been increasingly used in DNA nanotechnology, especially for the analysis of structure, dynamics, integrity, and operation of DNA-made devices; however, its capabilities are not yet sufficiently familiar to the community. The purpose of this Account is to demonstrate how different SMF tools can be utilized for the development of DNA devices and for structural dynamic investigation of biomolecules in general and DNA molecules in particular. Single-molecule diffusion-based Förster resonance energy transfer and alternating laser excitation (sm-FRET/ALEX) and immobilization-based total internal reflection fluorescence (TIRF) techniques are briefly described and demonstrated. To illustrate the many applications of SMF to DNA nanotechnology, examples of SMF studies of DNA hairpins and Holliday junctions and of the interactions of DNA strands with DNA origami and origami-related devices such as a DNA bipedal motor are provided. These examples demonstrate how SMF can be utilized for measurement of distances and conformational distributions and equilibrium and nonequilibrium kinetics, to monitor structural integrity and operation of DNA devices, and for isolation and investigation of minor subpopulations including malfunctioning and nonreactive devices. Utilization of a flow-cell to achieve measurements of dynamics with increased time resolution and for convenient and efficient operation of DNA devices is discussed briefly. We conclude by summarizing the various benefits provided by SMF for the development of DNA nanotechnology and suggest that the method can significantly assist in the design and manufacture and evaluation of operation of DNA devices.
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Affiliation(s)
- Roman Tsukanov
- Department of Chemistry and the
Ilse Katz Institute for Nanoscale Science and Technology, Ben-Gurion University of the Negev, Beer Sheva, 84105, Israel
| | - Toma E. Tomov
- Department of Chemistry and the
Ilse Katz Institute for Nanoscale Science and Technology, Ben-Gurion University of the Negev, Beer Sheva, 84105, Israel
| | - Miran Liber
- Department of Chemistry and the
Ilse Katz Institute for Nanoscale Science and Technology, Ben-Gurion University of the Negev, Beer Sheva, 84105, Israel
| | - Yaron Berger
- Department of Chemistry and the
Ilse Katz Institute for Nanoscale Science and Technology, Ben-Gurion University of the Negev, Beer Sheva, 84105, Israel
| | - Eyal Nir
- Department of Chemistry and the
Ilse Katz Institute for Nanoscale Science and Technology, Ben-Gurion University of the Negev, Beer Sheva, 84105, Israel
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86
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Robison AD, Finkelstein IJ. High-throughput single-molecule studies of protein-DNA interactions. FEBS Lett 2014; 588:3539-46. [PMID: 24859086 DOI: 10.1016/j.febslet.2014.05.021] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2014] [Revised: 05/11/2014] [Accepted: 05/12/2014] [Indexed: 10/25/2022]
Abstract
Fluorescence and force-based single-molecule studies of protein-nucleic acid interactions continue to shed critical insights into many aspects of DNA and RNA processing. As single-molecule assays are inherently low-throughput, obtaining statistically relevant datasets remains a major challenge. Additionally, most fluorescence-based single-molecule particle-tracking assays are limited to observing fluorescent proteins that are in the low-nanomolar range, as spurious background signals predominate at higher fluorophore concentrations. These technical limitations have traditionally limited the types of questions that could be addressed via single-molecule methods. In this review, we describe new approaches for high-throughput and high-concentration single-molecule biochemical studies. We conclude with a discussion of outstanding challenges for the single-molecule biologist and how these challenges can be tackled to further approach the biochemical complexity of the cell.
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Affiliation(s)
- Aaron D Robison
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX 78712, United States
| | - Ilya J Finkelstein
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX 78712, United States; Institute for Cellular and Molecular Biology, The University of Texas at Austin, Austin, TX 78712, United States; Center for Systems and Synthetic Biology, The University of Texas at Austin, Austin, TX 78712, United States.
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87
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Savinov A, Perez CF, Block SM. Single-molecule studies of riboswitch folding. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2014; 1839:1030-1045. [PMID: 24727093 DOI: 10.1016/j.bbagrm.2014.04.005] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/20/2013] [Revised: 03/27/2014] [Accepted: 04/03/2014] [Indexed: 10/25/2022]
Abstract
The folding dynamics of riboswitches are central to their ability to modulate gene expression in response to environmental cues. In most cases, a structural competition between the formation of a ligand-binding aptamer and an expression platform (or some other competing off-state) determines the regulatory outcome. Here, we review single-molecule studies of riboswitch folding and function, predominantly carried out using single-molecule FRET or optical trapping approaches. Recent results have supplied new insights into riboswitch folding energy landscapes, the mechanisms of ligand binding, the roles played by divalent ions, the applicability of hierarchical folding models, and kinetic vs. thermodynamic control schemes. We anticipate that future work, based on improved data sets and potentially combining multiple experimental techniques, will enable the development of more complete models for complex RNA folding processes. This article is part of a Special Issue entitled: Riboswitches.
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Affiliation(s)
- Andrew Savinov
- Biophysics Program, Stanford University, Stanford, CA 94305, USA
| | | | - Steven M Block
- Department of Applied Physics, Stanford University, Stanford, CA 94305, USA; Department of Biology, Stanford University, Stanford, CA 94305, USA.
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88
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Farooq S, Fijen C, Hohlbein J. Studying DNA-protein interactions with single-molecule Förster resonance energy transfer. PROTOPLASMA 2014; 251:317-32. [PMID: 24374460 DOI: 10.1007/s00709-013-0596-6] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/06/2013] [Accepted: 12/09/2013] [Indexed: 05/21/2023]
Abstract
Single-molecule Förster resonance energy transfer (smFRET) has emerged as a powerful tool for elucidating biological structure and mechanisms on the molecular level. Here, we focus on applications of smFRET to study interactions between DNA and enzymes such as DNA and RNA polymerases. SmFRET, used as a nanoscopic ruler, allows for the detection and precise characterisation of dynamic and rarely occurring events, which are otherwise averaged out in ensemble-based experiments. In this review, we will highlight some recent developments that provide new means of studying complex biological systems either by combining smFRET with force-based techniques or by using data obtained from smFRET experiments as constrains for computer-aided modelling.
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Affiliation(s)
- Shazia Farooq
- Laboratory of Biophysics, Wageningen UR, Wageningen, The Netherlands
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89
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The Power of Single-Molecule FRET Microscopy Applied to DNA Nanotechnology. NUCLEIC ACIDS AND MOLECULAR BIOLOGY 2014. [DOI: 10.1007/978-3-642-38815-6_3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
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90
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Bag SS, Talukdar S, Kundu R, Saito I, Jana S. Dual door entry to exciplex emission in a chimeric DNA duplex containing non-nucleoside–nucleoside pair. Chem Commun (Camb) 2014; 50:829-32. [DOI: 10.1039/c3cc46967k] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
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91
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Holzhauser C, Rubner MM, Wagenknecht HA. Energy-transfer-based wavelength-shifting DNA probes with "clickable" cyanine dyes. Photochem Photobiol Sci 2013; 12:722-4. [PMID: 23314253 DOI: 10.1039/c2pp25366f] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
The insertion of cyanine dye azides as energy donor dyes via postsynthetic "click"-type cycloaddition chemistry with e.g. a new thiazole orange azide combined with thiazole red yields dual emitting DNA probes with good fluorescence readout properties.
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Affiliation(s)
- Carolin Holzhauser
- Institute of Organic Chemistry, Karlsruhe Institute of Technology, Fritz-Haber-Weg 6, 76131 Karlsruhe, Germany
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92
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Single molecule FRET data analysis procedures for FRET efficiency determination: Probing the conformations of nucleic acid structures. Methods 2013; 64:36-42. [DOI: 10.1016/j.ymeth.2013.04.001] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2013] [Revised: 04/02/2013] [Accepted: 04/03/2013] [Indexed: 11/23/2022] Open
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93
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Preus S, Jønck S, Pittelkow M, Dierckx A, Karpkird T, Albinsson B, Wilhelmsson LM. The photoinduced transformation of fluorescent DNA base analogue tC triggers DNA melting. Photochem Photobiol Sci 2013; 12:1416-22. [PMID: 23689311 DOI: 10.1039/c3pp50057h] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
While fluorescent analogues of the canonical nucleobases have proven to be highly valuable in a large number of applications, up until today, fluorescent DNA base analogues remain virtually inapplicable for single-molecule fluorescence experiments which require extremely bright and photostable dyes. Insight into the photodegradation processes of these fluorophores is thus a key step in the continuous development towards dyes with improved performances. Here, we show that the commercially available fluorescent nucleobase analogue tC under intense long-term illumination and in the presence of O2 is degraded to form a single photoreaction product which we suggest to be the sulfoxide form of tC. The photoproduct is characterized by a blue-shifted absorption and a less intense fluorescence compared to that of tC. Interestingly, when tC is positioned inside double-stranded DNA this photodriven conversion of tC to its photoproduct greatly reduces the duplex stability of the overall double helix in which the probe is positioned. Since tC can be excited selectively at 400 nm, well outside the absorption band of the natural DNA bases, this observation points towards the application of tC as a general light-triggered switch of DNA duplex stability.
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Affiliation(s)
- Søren Preus
- Department of Chemistry, University of Copenhagen, Copenhagen, DK-2100, Denmark
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94
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Thillier Y, Stevens SK, Moy C, Taylor J, Vasseur JJ, Beigelman L, Debart F. Solid-phase synthesis of 5'-triphosphate 2'-5'-oligoadenylates analogs with 3'-O-biolabile groups and their evaluation as RNase L activators and antiviral drugs. Bioorg Med Chem 2013; 21:5461-9. [PMID: 23810677 DOI: 10.1016/j.bmc.2013.06.008] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2013] [Revised: 05/30/2013] [Accepted: 06/04/2013] [Indexed: 11/19/2022]
Abstract
5'-Triphosphate 2'-5'-oligoadenylate (2-5A) is the central player in the 2-5A system that is an innate immunity pathway in response to the presence of infectious agents. Intracellular endoribonuclease RNase L activated by 2-5A cleaves viral and cellular RNA resulting in apoptosis. The major limitations of 2-5A for therapeutic applications is the short biological half-life and poor cellular uptake. Modification of 2-5A with biolabile and lipophilic groups that facilitate its uptake, increase its in vivo stability and release the parent 2-5A drug in an intact form offer an alternative approach to therapeutic use of 2-5A. Here we have synthesized the trimeric and tetrameric 2-5A species bearing hydrophobic and enzymolabile pivaloyloxymethyl groups at 3'-positions and a triphosphate at the 5'-end. Both analogs were able to activate RNase L and the production of the trimer 2-5A (the most active) was scaled up to the milligram scale for antiviral evaluation in cells infected by influenza virus or respiratory syncytial virus. The trimer analog demonstrated some significant antiviral activity.
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Affiliation(s)
- Yann Thillier
- IBMM, UMR 5247, CNRS-UM1-UM2, Université Montpellier 2, Place Eugène Bataillon, 34095 Montpellier, France
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95
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Cooper D, Uhm H, Tauzin LJ, Poddar N, Landes CF. Photobleaching lifetimes of cyanine fluorophores used for single-molecule Förster resonance energy transfer in the presence of various photoprotection systems. Chembiochem 2013; 14:1075-80. [PMID: 23733413 DOI: 10.1002/cbic.201300030] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2013] [Indexed: 12/19/2022]
Abstract
Lengthening smFRET lifetimes: We investigated various photoprotection system combinations to find the combination that optimally extended the photobleach lifetime of a Cy3/Cy5 smFRET pair attached to a DNA hairpin in a single-molecule environment. We found that the glucose/glucose oxygen-scavenging solution in combination with redox-based photostabilization solutions yielded the longest average photobleaching lifetimes.
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Affiliation(s)
- David Cooper
- Department of Chemistry, Rice University, 6100 Main St. Houston, TX 77005, USA
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96
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Kumar TS, Myznikova A, Samokhina E, Astakhova IK. Rapid genotyping using pyrene-perylene locked nucleic acid complexes. ARTIFICIAL DNA, PNA & XNA 2013; 4:58-68. [PMID: 24044052 PMCID: PMC3771999 DOI: 10.4161/adna.25903] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/29/2013] [Revised: 07/07/2013] [Accepted: 07/25/2013] [Indexed: 01/27/2023]
Abstract
We have developed an assay for single strand DNA and RNA detection which is based on novel pyrene-perylene FRET pairs attached to short LNA/DNA probes. The assay is based on ratiometric emission upon binding of target DNA/RNA by three combinations of fluorescent LNA/DNA reporter strands. Specific geometry of the pyrene fluorophore attached to the 2'-amino group of 2'-amino-LNA in position 4 allows for the first time to efficiently utilize dipole-dipole orientation parameter for sensing of single-nucleotide polymorphisms (SNPs) in nucleic acid targets by FRET. Using novel probes, SNP detection is achieved with advantages of large Stokes shift (115 nm), high fluorescence quantum yields and low limit of target detection values (< 5 nM). Rapid and accurate genotyping of highly polymorphic HIV Pol cDNA and RNA fragments performed herein proves the possibility for broad application of the novel pyrene-perylene FRET pairs, e.g., in imaging and clinical diagnostics.
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Affiliation(s)
- T. Santhosh Kumar
- Nucleic Acid Center; Department of Physics, Chemistry and Pharmacy; University of Southern Denmark; Odense, Denmark
- National Institute of Diabetes and Digestive and Kidney Diseases; National Institutes of Health; Molecular Recognition Section; Bethesda, MD USA
| | - Anna Myznikova
- Central Research Institute of Epidemiology; Moscow, Russia
| | | | - Irina Kira Astakhova
- Nucleic Acid Center; Department of Physics, Chemistry and Pharmacy; University of Southern Denmark; Odense, Denmark
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97
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Weinberger M, Berndt F, Mahrwald R, Ernsting NP, Wagenknecht HA. Synthesis of 4-Aminophthalimide and 2,4-Diaminopyrimidine C-Nucleosides as Isosteric Fluorescent DNA Base Substitutes. J Org Chem 2013; 78:2589-99. [DOI: 10.1021/jo302768f] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Michael Weinberger
- Department of Chemistry, Karlsruhe Institute of Technology, Fritz-Haber-Weg
6, Campus Süd, Geb. 30.42, 76131 Karlsruhe, Germany
| | - Falko Berndt
- Institute of Chemistry, Humboldt University Berlin, Brook-Taylor-Strasse 2,
12489 Berlin, Germany
| | - Rainer Mahrwald
- Institute of Chemistry, Humboldt University Berlin, Brook-Taylor-Strasse 2,
12489 Berlin, Germany
| | - Nikolaus P. Ernsting
- Institute of Chemistry, Humboldt University Berlin, Brook-Taylor-Strasse 2,
12489 Berlin, Germany
| | - Hans-Achim Wagenknecht
- Department of Chemistry, Karlsruhe Institute of Technology, Fritz-Haber-Weg
6, Campus Süd, Geb. 30.42, 76131 Karlsruhe, Germany
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98
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Kato T, Kashida H, Kishida H, Yada H, Okamoto H, Asanuma H. Development of a Robust Model System of FRET using Base Surrogates Tethering Fluorophores for Strict Control of Their Position and Orientation within DNA Duplex. J Am Chem Soc 2013; 135:741-50. [DOI: 10.1021/ja309279w] [Citation(s) in RCA: 60] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Affiliation(s)
- Tomohiro Kato
- Graduate School of Engineering, Nagoya University, Furo-cho, Chikusa-ku, Nagoya 464-8603,
Japan
| | - Hiromu Kashida
- Graduate School of Engineering, Nagoya University, Furo-cho, Chikusa-ku, Nagoya 464-8603,
Japan
| | - Hideo Kishida
- Graduate School of Engineering, Nagoya University, Furo-cho, Chikusa-ku, Nagoya 464-8603,
Japan
| | - Hiroyuki Yada
- Department of Advanced
Materials
Science, The University of Tokyo, 5-1-5
Kashiwanoha, Kashiwa, Chiba 277-8561, Japan
| | - Hiroshi Okamoto
- Department of Advanced
Materials
Science, The University of Tokyo, 5-1-5
Kashiwanoha, Kashiwa, Chiba 277-8561, Japan
| | - Hiroyuki Asanuma
- Graduate School of Engineering, Nagoya University, Furo-cho, Chikusa-ku, Nagoya 464-8603,
Japan
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