1
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Steffen FD, Cunha RA, Sigel RKO, Börner R. FRET-guided modeling of nucleic acids. Nucleic Acids Res 2024; 52:e59. [PMID: 38869063 PMCID: PMC11260485 DOI: 10.1093/nar/gkae496] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2023] [Accepted: 05/29/2024] [Indexed: 06/14/2024] Open
Abstract
The functional diversity of RNAs is encoded in their innate conformational heterogeneity. The combination of single-molecule spectroscopy and computational modeling offers new attractive opportunities to map structural transitions within nucleic acid ensembles. Here, we describe a framework to harmonize single-molecule Förster resonance energy transfer (FRET) measurements with molecular dynamics simulations and de novo structure prediction. Using either all-atom or implicit fluorophore modeling, we recreate FRET experiments in silico, visualize the underlying structural dynamics and quantify the reaction coordinates. Using multiple accessible-contact volumes as a post hoc scoring method for fragment assembly in Rosetta, we demonstrate that FRET can be used to filter a de novo RNA structure prediction ensemble by refuting models that are not compatible with in vitro FRET measurement. We benchmark our FRET-assisted modeling approach on double-labeled DNA strands and validate it against an intrinsically dynamic manganese(II)-binding riboswitch. We show that a FRET coordinate describing the assembly of a four-way junction allows our pipeline to recapitulate the global fold of the riboswitch displayed by the crystal structure. We conclude that computational fluorescence spectroscopy facilitates the interpretability of dynamic structural ensembles and improves the mechanistic understanding of nucleic acid interactions.
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Affiliation(s)
- Fabio D Steffen
- Department of Chemistry, University of Zurich, Winterthurerstrasse 190, 8057 Zurich, Switzerland
| | - Richard A Cunha
- Department of Chemistry, University of Zurich, Winterthurerstrasse 190, 8057 Zurich, Switzerland
| | - Roland K O Sigel
- Department of Chemistry, University of Zurich, Winterthurerstrasse 190, 8057 Zurich, Switzerland
| | - Richard Börner
- Department of Chemistry, University of Zurich, Winterthurerstrasse 190, 8057 Zurich, Switzerland
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2
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Murdoch TJ, Quienne B, Pinaud J, Caillol S, Martín-Fabiani I. Understanding associative polymer self-assembly with shrinking gate fluorescence correlation spectroscopy. NANOSCALE 2024; 16:12660-12669. [PMID: 38888295 DOI: 10.1039/d4nr00737a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/20/2024]
Abstract
The self-assembly of polymers is integral to their role in liquid formulations. In this study, we combine a dye whose lifetime is sensitive to the nanoviscosity of its local environment with shrinking gate fluorescence correlation spectroscopy (sgFCS) to study the self-assembly of a model telechelic polymer, hydrophobically modified ethoxylated urethane (HEUR). Fluorescence lifetime measurements show a monotonic increase in average lifetime with increasing HEUR concentration driven by a small fraction of dye (<1%) with long lifetimes strongly bound to HEUR. Despite this small fraction, sgFCS isolates the diffusional dynamics of the bound fraction with no a priori assumptions as to the distribution of lifetimes. Sensitivity is greatly enhanced compared to standard FCS, revealing micellar aggregates forming between 0.2 and 1 wt% followed by formation of a percolated network. This sgFCS approach, which we apply for the first time to polymers in this work, is readily extendable to any dye that changes lifetime on binding.
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Affiliation(s)
- Timothy J Murdoch
- Department of Materials, Loughborough University, LE11 1RJ Loughborough, UK.
| | | | - Julien Pinaud
- ICGM, Univ Montpellier, CNRS, ENSCM, Montpellier, France
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3
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Chu J, Ejaz A, Lin KM, Joseph MR, Coraor AE, Drummond DA, Squires AH. Single-molecule fluorescence multiplexing by multi-parameter spectroscopic detection of nanostructured FRET labels. NATURE NANOTECHNOLOGY 2024:10.1038/s41565-024-01672-8. [PMID: 38750166 DOI: 10.1038/s41565-024-01672-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/03/2023] [Accepted: 04/05/2024] [Indexed: 05/28/2024]
Abstract
Multiplexed, real-time fluorescence detection at the single-molecule level can reveal the stoichiometry, dynamics and interactions of multiple molecular species in mixtures and other complex samples. However, fluorescence-based sensing is typically limited to the detection of just 3-4 colours at a time due to low signal-to-noise ratio, high spectral overlap and the need to maintain the chemical compatibility of dyes. Here we engineered a palette of several dozen composite fluorescent labels, called FRETfluors, for multiplexed spectroscopic measurements at the single-molecule level. FRETfluors are compact nanostructures constructed from three chemical components (DNA, Cy3 and Cy5) with tunable spectroscopic properties due to variations in geometry, fluorophore attachment chemistry and DNA sequence. We demonstrate FRETfluor labelling and detection for low-concentration (<100 fM) mixtures of mRNA, dsDNA and proteins using an anti-Brownian electrokinetic trap. In addition to identifying the unique spectroscopic signature of each FRETfluor, this trap differentiates FRETfluors attached to a target from unbound FRETfluors, enabling wash-free sensing. Although usually considered an undesirable complication of fluorescence, here the inherent sensitivity of fluorophores to the local physicochemical environment provides a new design axis complementary to changing the FRET efficiency. As a result, the number of distinguishable FRETfluor labels can be combinatorically increased while chemical compatibility is maintained, expanding prospects for spectroscopic multiplexing at the single-molecule level using a minimal set of chemical building blocks.
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Affiliation(s)
- Jiachong Chu
- Pritzker School of Molecular Engineering, University of Chicago, Chicago, IL, USA
| | - Ayesha Ejaz
- Department of Chemistry, University of Chicago, Chicago, IL, USA
| | - Kyle M Lin
- Graduate Program in Biophysical Sciences, University of Chicago, Chicago, IL, USA
- Interdisicplinary Scientist Training Program, Pritzker School of Medicine, University of Chicago, Chicago, IL, USA
| | - Madeline R Joseph
- Pritzker School of Molecular Engineering, University of Chicago, Chicago, IL, USA
| | - Aria E Coraor
- Pritzker School of Molecular Engineering, University of Chicago, Chicago, IL, USA
| | - D Allan Drummond
- Department of Biochemistry and Molecular Biophysics, University of Chicago, Chicago, IL, USA
- Department of Medicine, Section of Genetic Medicine, University of Chicago, Chicago, IL, USA
- Institute for Biophysical Dynamics, University of Chicago, Chicago, IL, USA
| | - Allison H Squires
- Pritzker School of Molecular Engineering, University of Chicago, Chicago, IL, USA.
- Institute for Biophysical Dynamics, University of Chicago, Chicago, IL, USA.
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4
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Tor Y. Isomorphic Fluorescent Nucleosides. Acc Chem Res 2024; 57:1325-1335. [PMID: 38613490 PMCID: PMC11079976 DOI: 10.1021/acs.accounts.4c00042] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2024] [Revised: 04/01/2024] [Accepted: 04/02/2024] [Indexed: 04/15/2024]
Abstract
In 1960, Weber prophesied that "There are many ways in which the properties of the excited state can be utilized to study points of ignorance of the structure and function of proteins". This has been realized, illustrating that an intrinsic and highly responsive fluorophore such as tryptophan can alter the course of an entire scientific discipline. But what about RNA and DNA? Adapting Weber's protein photophysics prophecy to nucleic acids requires the development of intrinsically emissive nucleoside surrogates as, unlike Trp, the canonical nucleobases display unusually low emission quantum yields, which render nucleosides, nucleotides, and oligonucleotides practically dark for most fluorescence-based applications.Over the past decades, we have developed emissive nucleoside surrogates that facilitate the monitoring of nucleoside-, nucleotide-, and nucleic acid-based transformations at a nucleobase resolution in real time. The premise underlying our approach is the identification of minimal atomic/structural perturbations that endow the synthetic analogs with favorable photophysical features while maintaining native conformations and pairing. As illuminating probes, the photophysical parameters of such isomorphic nucleosides display sensitivity to microenvironmental factors. Responsive isomorphic analogs that function similarly to their native counterparts in biochemical contexts are defined as isofunctional.Early analogs included pyrimidines substituted with five-membered aromatic heterocycles at their 5 position and have been used to assess the polarity of the major groove in duplexes. Polarized quinazolines have proven useful in assembling FRET pairs with established fluorophores and have been used to study RNA-protein and RNA-small-molecule binding. Completing a fluorescent ribonucleoside alphabet, composed of visibly emissive purine (thA, thG) and pyrimidine (thU, thC) analogs, all derived from thieno[3,4-d]pyrimidine as the heterocyclic nucleus, was a major breakthrough. To further augment functionality, a second-generation emissive RNA alphabet based on an isothiazolo[4,3-d]pyrimidine core (thA, tzG, tzU, and tzC) was fabricated. This single-atom "mutagenesis" restored the basic/coordinating nitrogen corresponding to N7 in the purine skeleton and elevated biological recognition.The isomorphic emissive nucleosides and nucleotides, particularly the purine analogs, serve as substrates for diverse enzymes. Beyond polymerases, we have challenged the emissive analogs with metabolic and catabolic enzymes, opening optical windows into the biochemistry of nucleosides and nucleotides as metabolites as well as coenzymes and second messengers. Real-time fluorescence-based assays for adenosine deaminase, guanine deaminase, and cytidine deaminase have been fabricated and used for inhibitor discovery. Emissive cofactors (e.g., SthAM), coenzymes (e.g., NtzAD+), and second messengers (e.g., c-di-tzGMP) have been enzymatically synthesized, using xyNTPs and native enzymes. Both their biosynthesis and their transformations can be fluorescently monitored in real time.Highly isomorphic and isofunctional emissive surrogates can therefore be fabricated and judiciously implemented. Beyond their utility, side-by-side comparison to established analogs, particularly to 2-aminopurine, the workhorse of nucleic acid biophysics over 5 decades, has proven prudent as they refined the scope and limitations of both the new analogs and their predecessors. Challenges, however, remain. Associated with such small heterocycles are relatively short emission wavelengths and limited brightness. Recent advances in multiphoton spectroscopy and further structural modifications have shown promise for overcoming such barriers.
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Affiliation(s)
- 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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5
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Fan F, Povedailo VA, Lysenko IL, Seviarynchyk TP, Sharko OL, Mazunin IO, Shmanai VV. Fluorescent Properties of Cyanine Dyes As a Matter of the Environment. J Fluoresc 2024; 34:925-933. [PMID: 37421567 DOI: 10.1007/s10895-023-03321-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2023] [Accepted: 06/16/2023] [Indexed: 07/10/2023]
Abstract
In non-viscous aqueous solutions, the cyanine fluorescent dyes Cy3 and Cy5 have rather low fluorescence efficiency (the fluorescence quantum yields of Cy3 and Cy5 are 0.04 and 0.3, respectively [1, 2]) and short excited state lifetimes due to their structural features. In this work, we investigated the effect of solubility and rotational degrees of freedom on the fluorescence efficiency of Cy3 and Cy5 in several ways. We compared the fluorescence efficiencies of two cyanine dyes sCy3 and sCy5 with the introduction of a sulfonyl substituent in the aromatic ring as well as covalently bound to T10 oligonucleotides. The results show that because of the different lengths of the polymethine chains between the aromatic rings of the dyes, cis-trans-isomerization has a much greater effect on the Cy3 molecule than on the Cy5 molecule, while the effect of aggregation is also significant.
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Affiliation(s)
- Fan Fan
- Institute of Physical Organic Chemistry, National Academy of Sciences of Belarus, 13 Surganova str., 220072, Minsk, Belarus
| | - Vladimir A Povedailo
- B.I. Stepanov Institute of Physics, National Academy of Sciences of Belarus, 68 Nezavisimost' Ave., 220072, Minsk, Belarus
| | - Ivan L Lysenko
- Institute of Physical Organic Chemistry, National Academy of Sciences of Belarus, 13 Surganova str., 220072, Minsk, Belarus
| | - Tatsiana P Seviarynchyk
- Institute of Physical Organic Chemistry, National Academy of Sciences of Belarus, 13 Surganova str., 220072, Minsk, Belarus
| | - Olga L Sharko
- Institute of Physical Organic Chemistry, National Academy of Sciences of Belarus, 13 Surganova str., 220072, Minsk, Belarus
| | - Ilya O Mazunin
- Center for Molecular and Cellular Biology, Skolkovo Institute of Science and Technology, Moscow, Russia
| | - Vadim V Shmanai
- Institute of Physical Organic Chemistry, National Academy of Sciences of Belarus, 13 Surganova str., 220072, Minsk, Belarus.
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6
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Green CM, Sementa D, Mathur D, Melinger JS, Deshpande P, Elbaum-Garfinkle S, Medintz IL, Ulijn RV, Díaz SA. Sequestration within peptide coacervates improves the fluorescence intensity, kinetics, and limits of detection of dye-based DNA biosensors. Commun Chem 2024; 7:49. [PMID: 38424154 PMCID: PMC10904739 DOI: 10.1038/s42004-024-01124-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2023] [Accepted: 02/08/2024] [Indexed: 03/02/2024] Open
Abstract
Peptide-based liquid-liquid phase separated domains, or coacervates, are a biomaterial gaining new interest due to their exciting potential in fields ranging from biosensing to drug delivery. In this study, we demonstrate that coacervates provide a simple and biocompatible medium to improve nucleic acid biosensors through the sequestration of both the biosensor and target strands within the coacervate, thereby increasing their local concentration. Using the well-established polyarginine (R9) - ATP coacervate system and an energy transfer-based DNA molecular beacon we observed three key improvements: i) a greater than 20-fold reduction of the limit of detection within coacervates when compared to control buffer solutions; ii) an increase in the kinetics, equilibrium was reached more than 4-times faster in coacervates; and iii) enhancement in the dye fluorescent quantum yields within the coacervates, resulting in greater signal-to-noise. The observed benefits translate into coacervates greatly improving bioassay functionality.
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Affiliation(s)
- Christopher M Green
- Center for Bio/Molecular Science and Engineering Code 6900, U.S. Naval Research Laboratory, Washington, DC, 20375, USA
| | - Deborah Sementa
- Nanoscience Initiative at Advanced Science Research Center, Graduate Center of the City University of New York, New York, NY, 10031, USA
| | - Divita Mathur
- Department of Chemistry, Case Western Reserve University, Cleveland, OH, 44106, USA
| | - Joseph S Melinger
- Electronics Sciences and Technology Division Code 6816, U.S. Naval Research Laboratory, Washington, DC, 20375, USA
| | - Priyasha Deshpande
- Structural Biology Initiative at Advanced Science Research Center, Graduate Center of the City University of New York, New York, NY, 10031, USA
| | - Shana Elbaum-Garfinkle
- Structural Biology Initiative at Advanced Science Research Center, Graduate Center of the City University of New York, New York, NY, 10031, USA
- Ph.D. Programs in Biochemistry and Chemistry, The Graduate Center of the City University of New York, New York, NY, 10016, USA
| | - Igor L Medintz
- Center for Bio/Molecular Science and Engineering Code 6900, U.S. Naval Research Laboratory, Washington, DC, 20375, USA
| | - Rein V Ulijn
- Nanoscience Initiative at Advanced Science Research Center, Graduate Center of the City University of New York, New York, NY, 10031, USA
- Ph.D. Programs in Biochemistry and Chemistry, The Graduate Center of the City University of New York, New York, NY, 10016, USA
- Department of Chemistry Hunter College, City University of New York, New York, NY, 10065, USA
| | - Sebastián A Díaz
- Center for Bio/Molecular Science and Engineering Code 6900, U.S. Naval Research Laboratory, Washington, DC, 20375, USA.
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7
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Chacko N, Motiei M, Suryakant JS, Firer M, Ankri R. Au nanodyes as enhanced contrast agents in wide field near infrared fluorescence lifetime imaging. DISCOVER NANO 2024; 19:18. [PMID: 38270794 PMCID: PMC10810770 DOI: 10.1186/s11671-024-03958-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/11/2023] [Accepted: 01/14/2024] [Indexed: 01/26/2024]
Abstract
The near-infrared (NIR) range of the electromagnetic (EM) spectrum offers a nearly transparent window for imaging tissue. Despite the significant potential of NIR fluorescence-based imaging, its establishment in basic research and clinical applications remains limited due to the scarcity of fluorescent molecules with absorption and emission properties in the NIR region, especially those suitable for biological applications. In this study, we present a novel approach by combining the widely used IRdye 800NHS fluorophore with gold nanospheres (GNSs) and gold nanorods (GNRs) to create Au nanodyes, with improved quantum yield (QY) and distinct lifetimes. These nanodyes exhibit varying photophysical properties due to the differences in the separation distance between the dye and the gold nanoparticles (GNP). Leveraging a rapid and highly sensitive wide-field fluorescence lifetime imaging (FLI) macroscopic set up, along with phasor based analysis, we introduce multiplexing capabilities for the Au nanodyes. Our approach showcases the ability to differentiate between NIR dyes with very similar, short lifetimes within a single image, using the combination of Au nanodyes and wide-field FLI. Furthermore, we demonstrate the uptake of Au nanodyes by mineral-oil induced plasmacytomas (MOPC315.bm) cells, indicating their potential for in vitro and in vivo applications.
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Affiliation(s)
- Neelima Chacko
- Department of Physics, Faculty of Natural Science, Ariel University, 40700, Ariel, Israel
| | - Menachem Motiei
- Faculty of Engineering, The Institute of Nanotechnology and Advanced Materials, Bar-Ilan University, 5290002, Ramat Gan, Israel
| | - Jadhav Suchita Suryakant
- Department of Chemical Engineering, Faculty of Engineering, Ariel University, 40700, Ariel, Israel
| | - Michael Firer
- Department of Chemical Engineering, Faculty of Engineering, Ariel University, 40700, Ariel, Israel
| | - Rinat Ankri
- Department of Physics, Faculty of Natural Science, Ariel University, 40700, Ariel, Israel.
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8
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Lu H, Wang Y, Hill SK, Jiang H, Ke Y, Huang S, Zheng D, Perrier S, Song Q. Supra-Cyanines: Ultrabright Cyanine-Based Fluorescent Supramolecular Materials in Solution and in the Solid State. Angew Chem Int Ed Engl 2023; 62:e202311224. [PMID: 37840434 DOI: 10.1002/anie.202311224] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2023] [Revised: 09/29/2023] [Accepted: 10/13/2023] [Indexed: 10/17/2023]
Abstract
Fluorescent materials with high brightness play a crucial role in the advancement of various technologies such as bioimaging, photonics, and OLEDs. While significant efforts are dedicated to designing new organic dyes with improved performance, enhancing the brightness of existing dyes holds equal importance. In this study, we present a simple supramolecular strategy to develop ultrabright cyanine-based fluorescent materials by addressing long-standing challenges associated with cyanine dyes, including undesired cis-trans photoisomerization and aggregation-caused quenching. Supra-cyanines are obtained by incorporating cyanine moieties in a cyclic peptide-based supramolecular scaffold, and exhibit high fluorescence quantum yields (up to 50 %) in both solution and in the solid state. These findings offer a versatile approach for constructing highly emissive cyanine-based supramolecular materials.
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Affiliation(s)
- Haicheng Lu
- Shenzhen Grubbs Institute, Southern University of Science and Technology, Shenzhen, 518055, China
| | - Yuqian Wang
- Shenzhen Grubbs Institute, Southern University of Science and Technology, Shenzhen, 518055, China
| | - Sophie K Hill
- Department of Chemistry, University of Warwick, Coventry, CV4 7AL, UK
| | - Hanqiu Jiang
- Institute of High Energy Physics, Chinese Academy of Sciences (CAS), Beijing, 100049, China
- Spallation Neutron Source Science Center, Dongguan, 523803, China
| | - Yubin Ke
- Institute of High Energy Physics, Chinese Academy of Sciences (CAS), Beijing, 100049, China
- Spallation Neutron Source Science Center, Dongguan, 523803, China
| | - Shaohui Huang
- School of Life Sciences, University of Chinese Academy of Sciences, Beijing, 101499, China
| | - Dunjin Zheng
- LightEdge Technologies Limited, Zhongshan, 528451, China
| | - Sébastien Perrier
- Department of Chemistry, University of Warwick, Coventry, CV4 7AL, UK
- Warwick Medical School, University of Warwick, Coventry, CV4 7AL, UK
- Faculty of Pharmacy and Pharmaceutical Sciences, Monash University, Parkville, VIC 3052, Australia
| | - Qiao Song
- Shenzhen Grubbs Institute, Southern University of Science and Technology, Shenzhen, 518055, China
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9
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Ploetz E, Ambrose B, Barth A, Börner R, Erichson F, Kapanidis AN, Kim HD, Levitus M, Lohman TM, Mazumder A, Rueda DS, Steffen FD, Cordes T, Magennis SW, Lerner E. A new twist on PIFE: photoisomerisation-related fluorescence enhancement. Methods Appl Fluoresc 2023; 12:012001. [PMID: 37726007 PMCID: PMC10570931 DOI: 10.1088/2050-6120/acfb58] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2023] [Revised: 07/24/2023] [Accepted: 09/19/2023] [Indexed: 09/21/2023]
Abstract
PIFE was first used as an acronym for protein-induced fluorescence enhancement, which refers to the increase in fluorescence observed upon the interaction of a fluorophore, such as a cyanine, with a protein. This fluorescence enhancement is due to changes in the rate ofcis/transphotoisomerisation. It is clear now that this mechanism is generally applicable to interactions with any biomolecule. In this review, we propose that PIFE is thereby renamed according to its fundamental working principle as photoisomerisation-related fluorescence enhancement, keeping the PIFE acronym intact. We discuss the photochemistry of cyanine fluorophores, the mechanism of PIFE, its advantages and limitations, and recent approaches to turning PIFE into a quantitative assay. We provide an overview of its current applications to different biomolecules and discuss potential future uses, including the study of protein-protein interactions, protein-ligand interactions and conformational changes in biomolecules.
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Affiliation(s)
- Evelyn Ploetz
- Department of Chemistry and Center for NanoScience (CeNS), Ludwig-Maximilians-Universität München, Butenandtstr. 5-13, 81377 München, Germany
| | - Benjamin Ambrose
- Department of Infectious Disease, Faculty of Medicine, Imperial College London, London, W12 0HS, United Kingdom
- Single Molecule Imaging Group, MRC-London Institute of Medical Sciences, London, W12 0HS, United Kingdom
| | - Anders Barth
- Department of Bionanoscience, Kavli Institute of Nanoscience, Delft University of Technology, Delft 2629 HZ, The Netherlands
| | - Richard Börner
- Laserinstitut Hochschule Mittweida, Mittweida University of Applied Sciences, Mittweida, Germany
| | - Felix Erichson
- Laserinstitut Hochschule Mittweida, Mittweida University of Applied Sciences, Mittweida, Germany
| | - Achillefs N Kapanidis
- Biological Physics Research Group, Department of Physics, University of Oxford, Oxford, United Kingdom
- Kavli Institute for Nanoscience Discovery, Dorothy Crowfoot Hodgkin Building, University of Oxford, Oxford, United Kingdom
| | - Harold D Kim
- School of Physics, Georgia Institute of Technology, 837 State Street, Atlanta, GA 30332, United States of America
| | - Marcia Levitus
- School of Molecular Sciences, Arizona State University, 551 E. University Drive, Tempe, AZ,85287, United States of America
| | - Timothy M Lohman
- Department of Biochemistry and Molecular Biophysics, Washington University in St. Louis School of Medicine, St. Louis, MO 63110, United States of America
| | - Abhishek Mazumder
- CSIR-Institute of Chemical Biology, 4, Raja S.C. Mullick Road, Jadavpur, Kolkata-700032, West Bengal, India
| | - David S Rueda
- Department of Infectious Disease, Faculty of Medicine, Imperial College London, London, W12 0HS, United Kingdom
- Single Molecule Imaging Group, MRC-London Institute of Medical Sciences, London, W12 0HS, United Kingdom
| | - Fabio D Steffen
- Department of Chemistry, University of Zurich, Zurich, Switzerland
| | - Thorben Cordes
- Physical and Synthetic Biology, Faculty of Biology, Großhadernerstr. 2-4, Ludwig-Maximilians-Universität München, 82152 Planegg-Martinsried, Germany
| | - Steven W Magennis
- School of Chemistry, University of Glasgow, Joseph Black Building, University Avenue, Glasgow, G12 8QQ, United Kingdom
| | - Eitan Lerner
- Department of Biological Chemistry, Alexander Silberman Institute of Life Sciences, Faculty of Mathematics & Science, Edmond J. Safra Campus, Hebrew University of Jerusalem; Jerusalem 9190401, Israel
- Center for Nanoscience and Nanotechnology, Hebrew University of Jerusalem; Jerusalem 9190401, Israel
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10
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Rocchetti S, Ohmann A, Chikkaraddy R, Kang G, Keyser UF, Baumberg JJ. Amplified Plasmonic Forces from DNA Origami-Scaffolded Single Dyes in Nanogaps. NANO LETTERS 2023. [PMID: 37364270 DOI: 10.1021/acs.nanolett.3c01016] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/28/2023]
Abstract
Developing highly enhanced plasmonic nanocavities allows direct observation of light-matter interactions at the nanoscale. With DNA origami, the ability to precisely nanoposition single-quantum emitters in ultranarrow plasmonic gaps enables detailed study of their modified light emission. By developing protocols for creating nanoparticle-on-mirror constructs in which DNA nanostructures act as reliable and customizable spacers for nanoparticle binding, we reveal that the simple picture of Purcell-enhanced molecular dye emission is misleading. Instead, we show that the enhanced dipolar dye polarizability greatly amplifies optical forces acting on the facet Au atoms, leading to their rapid destabilization. Using different dyes, we find that emission spectra are dominated by inelastic (Raman) scattering from molecules and metals, instead of fluorescence, with molecular bleaching also not evident despite the large structural rearrangements. This implies that the competition between recombination pathways demands a rethink of routes to quantum optics using plasmonics.
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Affiliation(s)
- Sara Rocchetti
- Nanophotonics Centre, Department of Physics, Cavendish Laboratory, University of Cambridge, Cambridge CB3 0HE, England, U.K
| | - Alexander Ohmann
- Nanophotonics Centre, Department of Physics, Cavendish Laboratory, University of Cambridge, Cambridge CB3 0HE, England, U.K
| | - Rohit Chikkaraddy
- Nanophotonics Centre, Department of Physics, Cavendish Laboratory, University of Cambridge, Cambridge CB3 0HE, England, U.K
- School of Physics and Astronomy, University of Birmingham, Edgbaston, Birmingham B15 2TT, England, U.K
| | - Gyeongwon Kang
- Nanophotonics Centre, Department of Physics, Cavendish Laboratory, University of Cambridge, Cambridge CB3 0HE, England, U.K
| | - Ulrich F Keyser
- Nanophotonics Centre, Department of Physics, Cavendish Laboratory, University of Cambridge, Cambridge CB3 0HE, England, U.K
| | - Jeremy J Baumberg
- Nanophotonics Centre, Department of Physics, Cavendish Laboratory, University of Cambridge, Cambridge CB3 0HE, England, U.K
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11
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Wang C, Jiang W, Tan D, Huang L, Li J, Qiao Q, Yadav P, Liu X, Xu Z. Monitoring amyloid aggregation via a twisted intramolecular charge transfer (TICT)-based fluorescent sensor array. Chem Sci 2023; 14:4786-4795. [PMID: 37181777 PMCID: PMC10171079 DOI: 10.1039/d2sc06710b] [Citation(s) in RCA: 16] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2022] [Accepted: 04/05/2023] [Indexed: 05/16/2023] Open
Abstract
Imaging amyloid-beta (Aβ) aggregation is critical for understanding the pathology and aiding the pre-symptomatic intervention of Alzheimer's disease (AD). Amyloid aggregation consists of multiple phases with increasing viscosities and demands probes with broad dynamic ranges and gradient sensitivities for continuous monitoring. Yet, existing probes designed based on the twisted intramolecular charge transfer (TICT) mechanism mainly focused on donor engineering, limiting the sensitivities and/or dynamic ranges of these fluorophores to a narrow window. Herein, using quantum chemical calculations, we investigated multiple factors affecting the TICT process of fluorophores. It includes the conjugation length, the net charge of the fluorophore scaffold, the donor strength, and the geometric pre-twisting. We have established an integrative framework for tuning TICT tendencies. Based on this framework, a platter of hemicyanines with varied sensitivities and dynamic ranges is synthesized, forming a sensor array and enabling the observation of various stages of Aβ aggregations. This approach will significantly facilitate the development of TICT-based fluorescent probes with tailored environmental sensitivities for numerous applications.
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Affiliation(s)
- Chao Wang
- CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences 457 Zhongshan Road Dalian 116023 China
- Fluorescence Research Group, Singapore University of Technology and Design 8 Somapah Road Singapore 487372 Singapore
| | - Wenchao Jiang
- CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences 457 Zhongshan Road Dalian 116023 China
- University of Chinese Academy of Sciences Beijing 100049 China
| | - Davin Tan
- Fluorescence Research Group, Singapore University of Technology and Design 8 Somapah Road Singapore 487372 Singapore
| | - Lu Huang
- Fluorescence Research Group, Singapore University of Technology and Design 8 Somapah Road Singapore 487372 Singapore
- Ocean College, Minjiang University Fuzhou 350108 China
| | - Jin Li
- CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences 457 Zhongshan Road Dalian 116023 China
- University of Chinese Academy of Sciences Beijing 100049 China
| | - Qinglong Qiao
- CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences 457 Zhongshan Road Dalian 116023 China
| | - Priya Yadav
- Fluorescence Research Group, Singapore University of Technology and Design 8 Somapah Road Singapore 487372 Singapore
| | - Xiaogang Liu
- Fluorescence Research Group, Singapore University of Technology and Design 8 Somapah Road Singapore 487372 Singapore
| | - Zhaochao Xu
- CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences 457 Zhongshan Road Dalian 116023 China
- University of Chinese Academy of Sciences Beijing 100049 China
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12
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Zhang Y, Yang C, Peng S, Ling J, Chen P, Ma Y, Wang W, Chen Z, Chen C. General Strategy To Improve the Photon Budget of Thiol-Conjugated Cyanine Dyes. J Am Chem Soc 2023; 145:4187-4198. [PMID: 36756850 DOI: 10.1021/jacs.2c12635] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/10/2023]
Abstract
Maleimide-cysteine chemistry has been a routine practice for the site-specific labeling of fluorophores to proteins since the 1950s. This approach, however, cannot bring out the best photon budget of fluorophores. Here, we systematically measured the Cyanine3/5 dye conjugates via maleimide-thiol and amide linkages by counting the total emitted photons at the single-molecule level. While brightness and signal-to-noise ratios do not change significantly, dyes with thioether linkages exhibit more severe photobleaching than amide linkers. We then screened modern arylation-type bioconjugation strategies to alleviate this damage. Labeling thiols with phenyloxadiazole (POD) methyl sulfone, p-chloronitrobenzene, and fluorobenzene probes gave rise to electron-deficient aryl thioethers, effectively increasing the total emitted photons by 1.5-3 fold. Among the linkers, POD maintains labeling efficiency and specificity that are comparable to maleimide. Such an increase has proved to be universal among bulk and single-molecule assays, with or without triplet-state quenchers and oxygen scavengers, and on conformationally unrestricted or restricted cyanines. We demonstrated that cyanine-POD conjugates are general and superior fluorophores for thiol labeling in single-molecule FRET measurements of biomolecular conformational dynamics and in two-color STED nanoscopy using site-selectively labeled nanobodies. This work sheds light on the photobleaching mechanism of cyanines under single-molecule imaging while highlighting the interplay between the protein microenvironment, bioconjugation chemistry, and fluorophore photochemistry.
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Affiliation(s)
- Yuan Zhang
- Institute of Molecular Medicine, National Biomedical Imaging Center, Beijing Key Laboratory of Cardiometabolic Molecular Medicine, College of Future Technology, Peking University, Beijing 100871, China
| | - Chen Yang
- School of Life Sciences, Beijing Advanced Innovation Center for Structural Biology, Beijing Frontier Research Center for Biological Structure, Tsinghua University, Beijing 100084, China
| | - Sijia Peng
- School of Life Sciences, Beijing Advanced Innovation Center for Structural Biology, Beijing Frontier Research Center for Biological Structure, Tsinghua University, Beijing 100084, China
| | - Jing Ling
- Institute of Molecular Medicine, National Biomedical Imaging Center, Beijing Key Laboratory of Cardiometabolic Molecular Medicine, College of Future Technology, Peking University, Beijing 100871, China
- Peking-Tsinghua Center for Life Science, Academy for Advanced Interdisciplinary Studies, Peking University, Beijing 100871, China
| | - Peng Chen
- PKU-Nanjing Institute of Translational Medicine, Nanjing 211800, China
| | - Yumiao Ma
- BSJ Institute, Beijing 100084, China
- Hangzhou Yanqu Information Technology Co., Ltd., Xihu District, Hangzhou City, Zhejiang Province 310003, China
| | - Wenjuan Wang
- School of Life Sciences, Technology Center for Protein Sciences, Tsinghua University, Beijing 100084, China
| | - Zhixing Chen
- Institute of Molecular Medicine, National Biomedical Imaging Center, Beijing Key Laboratory of Cardiometabolic Molecular Medicine, College of Future Technology, Peking University, Beijing 100871, China
- Peking-Tsinghua Center for Life Science, Academy for Advanced Interdisciplinary Studies, Peking University, Beijing 100871, China
- PKU-Nanjing Institute of Translational Medicine, Nanjing 211800, China
| | - Chunlai Chen
- School of Life Sciences, Beijing Advanced Innovation Center for Structural Biology, Beijing Frontier Research Center for Biological Structure, Tsinghua University, Beijing 100084, China
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13
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Saurabh A, Fazel M, Safar M, Sgouralis I, Pressé S. Single-photon smFRET. I: Theory and conceptual basis. BIOPHYSICAL REPORTS 2022; 3:100089. [PMID: 36582655 PMCID: PMC9793182 DOI: 10.1016/j.bpr.2022.100089] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/21/2022] [Accepted: 11/28/2022] [Indexed: 12/03/2022]
Abstract
We present a unified conceptual framework and the associated software package for single-molecule Förster resonance energy transfer (smFRET) analysis from single-photon arrivals leveraging Bayesian nonparametrics, BNP-FRET. This unified framework addresses the following key physical complexities of a single-photon smFRET experiment, including: 1) fluorophore photophysics; 2) continuous time kinetics of the labeled system with large timescale separations between photophysical phenomena such as excited photophysical state lifetimes and events such as transition between system states; 3) unavoidable detector artefacts; 4) background emissions; 5) unknown number of system states; and 6) both continuous and pulsed illumination. These physical features necessarily demand a novel framework that extends beyond existing tools. In particular, the theory naturally brings us to a hidden Markov model with a second-order structure and Bayesian nonparametrics on account of items 1, 2, and 5 on the list. In the second and third companion articles, we discuss the direct effects of these key complexities on the inference of parameters for continuous and pulsed illumination, respectively.
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Affiliation(s)
- Ayush Saurabh
- Center for Biological Physics, Arizona State University, Tempe, Arizona,Department of Physics, Arizona State University, Tempe, Arizona
| | - Mohamadreza Fazel
- Center for Biological Physics, Arizona State University, Tempe, Arizona,Department of Physics, Arizona State University, Tempe, Arizona
| | - Matthew Safar
- Center for Biological Physics, Arizona State University, Tempe, Arizona,Department of Mathematics and Statistical Science, Arizona State University, Tempe, Arizona
| | - Ioannis Sgouralis
- Department of Mathematics, University of Tennessee Knoxville, Knoxville, Tennesse
| | - Steve Pressé
- Center for Biological Physics, Arizona State University, Tempe, Arizona,Department of Physics, Arizona State University, Tempe, Arizona,School of Molecular Sciences, Arizona State University, Tempe, Arizona,Corresponding author
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14
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Patterson K, Romero-Reyes MA, Heemstra JM. Fluorescence Quenching of Xanthene Dyes during Amide Bond Formation Using DMTMM. ACS OMEGA 2022; 7:33046-33053. [PMID: 36157719 PMCID: PMC9494652 DOI: 10.1021/acsomega.2c03085] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/17/2022] [Accepted: 08/16/2022] [Indexed: 06/16/2023]
Abstract
Fluorophore bioconjugation to proteins, nucleic acids, and other important molecules can provide a powerful approach to sensing, imaging, and quantifying chemical and biological processes. One of the most prevalent methods for fluorophore attachment is through the formation of amide bonds, which are often facilitated by coupling agents to activate carboxylic acid moieties for subsequent nucleophilic attack by amines. 4-(4,6-Dimethoxy-1,3,5-triazin-2-yl)-4-methyl-morpholinium chloride (DMTMM) is among the most popular of these coupling agents for bioconjugation due to its ability to facilitate amide bond formation in water. After observing quenching of 5-fluoresceinamine (5-FAM)-conjugated oligonucleotides in the presence of DMTMM, we sought to evaluate the magnitude and scope of this challenge by surveying the effect of DMTMM on a range of fluorescent dyes. A higher quenching effect was consistently observed for xanthene dyes compared to that for cyanine dyes. Further analysis of the impact of DMTMM on FAM shows that quenching occurs independently of whether the dye is free in solution or attached to an oligonucleotide or antibody. Furthermore, we found that FAM-conjugated DNA was unable to recover its fluorescence after the removal of DMTMM, and UV-vis and NMR analyses suggest the formation of new products, such as an adduct formed between FAM and the dimethoxytriazine of DMTMM. As such, DMTMM at high concentrations is not recommended for coupling reactions where targets are fluorescently labeled. This research serves as a word of caution to those utilizing xanthene-containing fluorophores in bioconjugation reactions involving DMTMM.
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Affiliation(s)
- Kristen
N. Patterson
- Department
of Chemistry, Emory University, Atlanta, Georgia 30322, United States
| | - Misael A. Romero-Reyes
- Department
of Chemistry, Emory University, Atlanta, Georgia 30322, United States
- Department
of Chemistry, Hanover College, Hanover, Indiana 47243, United States
| | - Jennifer M. Heemstra
- Department
of Chemistry, Emory University, Atlanta, Georgia 30322, United States
- Department
of Chemistry, Washington University in St.
Louis, St. Louis, Missouri 63130, United States
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15
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Harris PD, Lerner E. Identification and quantification of within-burst dynamics in singly labeled single-molecule fluorescence lifetime experiments. BIOPHYSICAL REPORTS 2022; 2. [PMID: 36204594 PMCID: PMC9534301 DOI: 10.1016/j.bpr.2022.100071] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Abstract
Single-molecule spectroscopy has revolutionized molecular biophysics and provided means to probe how structural moieties within biomolecules spatially reorganize at different timescales. There are several single-molecule methodologies that probe local structural dynamics in the vicinity of a single dye-labeled residue, which rely on fluorescence lifetimes as readout. Nevertheless, an analytical framework to quantify dynamics in such single-molecule single dye fluorescence bursts, at timescales of microseconds to milliseconds, has not yet been demonstrated. Here, we suggest an analytical framework for identifying and quantifying within-burst lifetime-based dynamics, such as conformational dynamics recorded in single-molecule photo-isomerization-related fluorescence enhancement. After testing the capabilities of the analysis on simulations, we proceed to exhibit within-burst millisecond local structural dynamics in the unbound α-synuclein monomer. The analytical framework provided in this work paves the way for extracting a full picture of the energy landscape for the coordinate probed by fluorescence lifetime-based single-molecule measurements.
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Affiliation(s)
- Paul David Harris
- Department of Biological Chemistry, The Alexander Silberman Institute of Life Sciences, Faculty of Mathematics & Science, The Edmond J. Safra Campus, The Hebrew University of Jerusalem, Jerusalem 9190401, Israel
| | - Eitan Lerner
- Department of Biological Chemistry, The Alexander Silberman Institute of Life Sciences, Faculty of Mathematics & Science, The Edmond J. Safra Campus, The Hebrew University of Jerusalem, Jerusalem 9190401, Israel.,The Center for Nanoscience and Nanotechnology, The Hebrew University of Jerusalem, Jerusalem 9190401, Israel
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16
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Sequence-dependence of Cy3 and Cy5 dyes in 3' terminally-labeled single-stranded DNA. Sci Rep 2022; 12:14803. [PMID: 36045146 PMCID: PMC9428881 DOI: 10.1038/s41598-022-19069-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2022] [Accepted: 08/24/2022] [Indexed: 11/16/2022] Open
Abstract
Fluorescence is an ideal tool to see and manipulate nucleic acids, and engage in their rich and complex biophysical properties. Labeling is the preferred approach to track and quantify fluorescence with nucleic acids and cyanine dyes are emblematic in this context. The fluorescent properties of cyanine dyes are known to be sequence-dependent, with purines in the immediate vicinity increasing the fluorescence intensity of Cy3 and Cy5 dyes, and the ability of nucleobases to modulate the photophysical properties of common fluorophores may influence fluorescence measurements in critical assays such as FISH, qPCR or high-throughput sequencing. In this paper, we comprehensively map the sequence-dependence of Cy3 and Cy5 dyes in 3ʹ-fluorescently labeled single-stranded DNA by preparing the complete permutation library of the 5 consecutive nucleotides immediately adjacent to the dye, or 1024 sequences. G-rich motifs dominate the high fluorescence range, while C-rich motifs lead to significant quenching, an observation consistent with 5ʹ-labeled systems. We also uncover GCGC patterns in the extreme top range of fluorescence, a feature specific to 3ʹ-Cy3 and Cy5 oligonucleotides. This study represents the final piece in linking nucleotide identity to fluorescence changes for Cy3, Cy5 and fluorescein in all 3ʹ, 5ʹ, single-stranded and double-stranded DNA formats.
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17
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Cappellari MV, Marcano-García LF, Simoncelli S, Aramendía PF. Determination of association equilibrium constant from single molecule fluorescence localization microscopy. Photochem Photobiol Sci 2022; 21:1751-1760. [PMID: 35749053 DOI: 10.1007/s43630-022-00254-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2022] [Accepted: 05/31/2022] [Indexed: 11/26/2022]
Abstract
Single molecule fluorescence localization microscopy provides molecular localization with a precision in the tens of nanometer range in the plane perpendicular to the light propagation. This opens the possibility to count molecules and correlate their locations, starting from a map of the actual positions in a single molecule super resolution image. Considering molecular pair correlation as an indication of interaction, and a way to discern them from free molecules, we describe a method to calculate thermodynamic equilibrium constants. In this work, we use as a test system two complementary homo-oligonucleotides, one strand marked with Cyanine 3.5 and the other with Alexa Fluor 647. Hybridization is controlled by the amount of each strand, temperature, and the ionic force, and measured in steady state emission. The same samples are examined in Stochastic Optical Reconstruction Microscopy (STORM) experiments with split-field simultaneous two-colour detection. The effect of multiblinking, labelling-detection efficiency, and determination of the critical distance for association are discussed. We consistently determine values in STORM coincident with those of the bulk experiment.
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Affiliation(s)
- M Victoria Cappellari
- Centro de Investigaciones en Bionanociencias -''Elizabeth Jares-Erijman'' (CIBION), CONICET, Godoy Cruz 2390, 1425, Ciudad de Buenos Aires, Argentina
| | - Luis F Marcano-García
- Centro de Investigaciones en Bionanociencias -''Elizabeth Jares-Erijman'' (CIBION), CONICET, Godoy Cruz 2390, 1425, Ciudad de Buenos Aires, Argentina
| | - Sabrina Simoncelli
- London Centre for Nanotechnology and Department of Chemistry, University College London, London, WC1H 0AH, UK
| | - Pedro F Aramendía
- Centro de Investigaciones en Bionanociencias -''Elizabeth Jares-Erijman'' (CIBION), CONICET, Godoy Cruz 2390, 1425, Ciudad de Buenos Aires, Argentina.
- Departamento de Química Inorgánica, Analítica y Química Física. Facultad de Ciencias Exactas Y Naturales, Universidad de Buenos Aires, 1428, Ciudad de Buenos Aires, Argentina.
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18
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Thienoguanosine, a unique non-perturbing reporter for investigating rotational dynamics of DNA duplexes and their complexes with proteins. Int J Biol Macromol 2022; 213:210-225. [DOI: 10.1016/j.ijbiomac.2022.05.162] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2022] [Revised: 05/02/2022] [Accepted: 05/23/2022] [Indexed: 11/05/2022]
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19
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Pramanik S, Mahato P, Pramanik U, Nandy A, Khamari L, Shrivastava S, Rai S, Mukherjee S. DNA-Templated Modulation in the Photophysical Properties of a Fluorescent Molecular Rotor Auramine O by Varying the DNA Composition. J Phys Chem B 2022; 126:2658-2668. [PMID: 35357836 DOI: 10.1021/acs.jpcb.2c00172] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
This work delineates an integrative approach combining spectroscopic and computational studies to decipher the association-induced fluorescence properties of a fluorescent molecular rotor, viz., auramine O (AuO), after interacting with 20-mer duplex DNA having diverse well-matched base pairs. While exploring the scarcely explored sequence-dependent interaction mechanism of AuO and DNA, we observed that DNA could act as a conducive scaffold to the formation of AuO dimer through noncovalent interactions at lower molecular density. The photophysical properties of AuO depend on the nucleotide compositions as described from sequence-dependent shifting in the emission and absorption maxima. Furthermore, we explored such DNA base pair-dependent fluorescence spectral characteristics of AuO toward discriminating the thermodynamically most stable single nucleotide mismatch in a 20-mer sequence. Our results are interesting and could be useful in developing analogues with further enhanced emission properties toward mismatched DNA sequences.
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Affiliation(s)
- Srikrishna Pramanik
- Department of Chemistry, Indian Institute of Science Education and Research Bhopal, Bhopal Bypass Road, Bhopal 462 066, Madhya Pradesh, India
| | - Paritosh Mahato
- Department of Chemistry, Indian Institute of Science Education and Research Bhopal, Bhopal Bypass Road, Bhopal 462 066, Madhya Pradesh, India
| | - Ushasi Pramanik
- Department of Chemistry, Indian Institute of Science Education and Research Bhopal, Bhopal Bypass Road, Bhopal 462 066, Madhya Pradesh, India
| | - Atanu Nandy
- Department of Chemistry, Indian Institute of Science Education and Research Bhopal, Bhopal Bypass Road, Bhopal 462 066, Madhya Pradesh, India
| | - Laxmikanta Khamari
- Department of Chemistry, Indian Institute of Science Education and Research Bhopal, Bhopal Bypass Road, Bhopal 462 066, Madhya Pradesh, India
| | - Shivam Shrivastava
- Department of Chemistry, Indian Institute of Science Education and Research Bhopal, Bhopal Bypass Road, Bhopal 462 066, Madhya Pradesh, India
| | - Saurabh Rai
- Department of Chemistry, Indian Institute of Science Education and Research Bhopal, Bhopal Bypass Road, Bhopal 462 066, Madhya Pradesh, India
| | - Saptarshi Mukherjee
- Department of Chemistry, Indian Institute of Science Education and Research Bhopal, Bhopal Bypass Road, Bhopal 462 066, Madhya Pradesh, India
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20
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Bos I, Brink E, Michels L, Sprakel J. DNA dynamics in complex coacervate droplets and micelles. SOFT MATTER 2022; 18:2012-2027. [PMID: 35191449 PMCID: PMC8905490 DOI: 10.1039/d1sm01787j] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/20/2021] [Accepted: 02/16/2022] [Indexed: 06/14/2023]
Abstract
Single stranded DNA (ssDNA), or another polyanion, can be mixed with polycations to form liquid-like complex coacervates. When the polycations are replaced by cationic-neutral diblock copolymers, complex coacervate core micelles (C3Ms) can be formed instead. In both complex coacervates and C3Ms, dynamics plays an important role. Yet, to date, the effect of chain length on the dynamics effect is still not fully understood. The DNA complexes provide a versatile platform to further elucidate these chain length effects because the DNA is monodisperse and its length can be easily adapted. Therefore, we study in this paper the dynamics of fluorescently labelled ssDNA in both complex coacervate droplets and micelles. The DNA dynamics in the complex coacervate droplets is probed by fluorescence recovery after photobleaching (FRAP). We observe that the DNA diffusion coefficient depends more strongly on the DNA length than predicted by the sticky Rouse model and we show that this can be partly explained by changes in complex coacervate density, but that also other factors might play a role. We measure the molecular exchange of C3Ms by making use of Förster resonance energy transfer (FRET) and complement these measurements with Langevin dynamics simulations. We conclude that chain length polydispersity is the main cause of a broad distribution of exchange rates. We hypothesise that the different exchange rates that we observe for the monodisperse DNA are mainly caused by differences in dye interactions and show that the dye can indeed have a large effect on the C3M exchange. In addition, we show that a new description of the C3M molecular exchange is required that accounts among others for the effect of the length of the oppositely charged core species. Together our findings can help to better understand the dynamics in both specific DNA systems and in complex coacervate droplets and micelles in general.
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Affiliation(s)
- Inge Bos
- Physical Chemistry and Soft Matter, Wageningen University & Research, Stippeneng 4, 6708 WE, Wageningen, The Netherlands.
| | - Eline Brink
- Physical Chemistry and Soft Matter, Wageningen University & Research, Stippeneng 4, 6708 WE, Wageningen, The Netherlands.
| | - Lucile Michels
- Physical Chemistry and Soft Matter, Wageningen University & Research, Stippeneng 4, 6708 WE, Wageningen, The Netherlands.
| | - Joris Sprakel
- Physical Chemistry and Soft Matter, Wageningen University & Research, Stippeneng 4, 6708 WE, Wageningen, The Netherlands.
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21
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Hart SM, Wang X, Guo J, Bathe M, Schlau-Cohen GS. Tuning Optical Absorption and Emission Using Strongly Coupled Dimers in Programmable DNA Scaffolds. J Phys Chem Lett 2022; 13:1863-1871. [PMID: 35175058 DOI: 10.1021/acs.jpclett.1c03848] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Molecular materials for light harvesting, computing, and fluorescence imaging require nanoscale integration of electronically active subunits. Variation in the optical absorption and emission properties of the subunits has primarily been achieved through modifications to the chemical structure, which is often synthetically challenging. Here, we introduce a facile method for varying optical absorption and emission properties by changing the geometry of a strongly coupled Cy3 dimer on a double-crossover (DX) DNA tile. Leveraging the versatility and programmability of DNA, we tune the length of the complementary strand so that it "pushes" or "pulls" the dimer, inducing dramatic changes in the photophysics including lifetime differences observable at the ensemble and single-molecule level. The separable lifetimes, along with environmental sensitivity also observed in the photophysics, suggest that the Cy3-DX tile constructs could serve as fluorescence probes for multiplexed imaging. More generally, these constructs establish a framework for easily controllable photophysics via geometric changes to coupled chromophores, which could be applied in light-harvesting devices and molecular electronics.
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Affiliation(s)
- Stephanie M Hart
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - Xiao Wang
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - Jiajia Guo
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - Mark Bathe
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - Gabriela S Schlau-Cohen
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
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22
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Ji S, Kim S, Kim H, Koh HR. Investigation on photobleaching of fluorophores: Effect of excitation power and buffer system. B KOREAN CHEM SOC 2021. [DOI: 10.1002/bkcs.12455] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Affiliation(s)
- Sangmin Ji
- Department of Chemistry Chung‐Ang University Seoul South Korea
| | - Seohyun Kim
- Department of Chemistry Chung‐Ang University Seoul South Korea
| | - Hyunggi Kim
- Department of Chemistry Chung‐Ang University Seoul South Korea
| | - Hye Ran Koh
- Department of Chemistry Chung‐Ang University Seoul South Korea
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23
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Friedman HC, Cosco ED, Atallah TL, Jia S, Sletten EM, Caram JR. Establishing design principles for emissive organic SWIR chromophores from energy gap laws. Chem 2021; 7:3359-3376. [PMID: 34901520 PMCID: PMC8664240 DOI: 10.1016/j.chempr.2021.09.001] [Citation(s) in RCA: 40] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Rational design of bright near and shortwave infrared (NIR: 700-1000 SWIR: 1000- 2000 nm) emitters remains an open question with applications spanning imaging and photonics. Combining experiment and theory, we derive an energy gap quantum yield master equation (EQME), describing the fundamental limits in SWIR quantum yields (ϕ F ) for organic chromophores. Evaluating the photophysics of 21 polymethine NIR/SWIR chromophores to parameterize the EQME, we explain the precipitous decline of ϕ F past 900 nm through decreasing radiative rates and increasing nonradiative losses via high frequency vibrations relating to the energy gap. Using the EQME we develop an energy gap independent ϕ F NIR/SWIR chromophore comparison metric. We show electron donating character on polymethine heterocycles results in relative increases in radiative efficiency obscured by a simultaneous redshift. Finally, the EQME yields rational chromophore design insights shown by how deuteration (backed by our experimental results) or molecular aggregation increases SWIR ϕ F .
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Affiliation(s)
- Hannah C Friedman
- Department of Chemistry and Biochemistry, University of California, Los Angeles, 607 Charles E. Young Drive, Los Angeles, California 90095-1569, United States
| | - Emily D Cosco
- Department of Chemistry and Biochemistry, University of California, Los Angeles, 607 Charles E. Young Drive, Los Angeles, California 90095-1569, United States
- Department of Pathology, Stanford University School of Medicine, 300 Pasteur Drive, Stanford, California 94305 USA
| | - Timothy L Atallah
- Department of Chemistry and Biochemistry, University of California, Los Angeles, 607 Charles E. Young Drive, Los Angeles, California 90095-1569, United States
- Department of Chemistry and Biochemistry, Denison University, 500 West Loop, Granville, Ohio 43023
| | - Shang Jia
- Department of Chemistry and Biochemistry, University of California, Los Angeles, 607 Charles E. Young Drive, Los Angeles, California 90095-1569, United States
| | - Ellen M Sletten
- Department of Chemistry and Biochemistry, University of California, Los Angeles, 607 Charles E. Young Drive, Los Angeles, California 90095-1569, United States
| | - Justin R Caram
- Department of Chemistry and Biochemistry, University of California, Los Angeles, 607 Charles E. Young Drive, Los Angeles, California 90095-1569, United States
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24
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Jonely M, Singh RK, Donelick HM, Bass BL, Noriega R. Loquacious-PD regulates the terminus-dependent molecular recognition of Dicer-2 toward double-stranded RNA. Chem Commun (Camb) 2021; 57:10879-10882. [PMID: 34590626 DOI: 10.1039/d1cc03843e] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Dicer-2 cleaves double-stranded RNA into siRNAs in a terminus-dependent manner as part of D. melanogaster's RNA interference pathway. Using ultrafast fluorescence, we probe the local environment of chromophores at the dsRNA terminus upon binding by Dicer-2 and interrogate the effects of Loquacious-PD, an accessory protein. We find substrate-selective modes of molecular recognition that distinguish between blunt and 3'overhang termini, but whose differences are greatly reduced by Loquacious-PD. These results connect the molecular recognition properties of Dicer-2 to its selective processing of dsRNAs with different termini and to its need for Loquacious-PD to efficiently produce endogenous siRNAs.
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Affiliation(s)
- McKenzie Jonely
- University of Utah, Department of Chemistry, Salt Lake City, UT 84112, USA.
| | - Raushan K Singh
- University of Utah, Department of Biochemistry, Salt Lake City, UT 84112, USA
| | - Helen M Donelick
- University of Utah, Department of Biochemistry, Salt Lake City, UT 84112, USA
| | - Brenda L Bass
- University of Utah, Department of Biochemistry, Salt Lake City, UT 84112, USA
| | - Rodrigo Noriega
- University of Utah, Department of Chemistry, Salt Lake City, UT 84112, USA.
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25
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Pace NA, Hennelly SP, Goodwin PM. Immobilization of Cyanines in DNA Produces Systematic Increases in Fluorescence Intensity. J Phys Chem Lett 2021; 12:8963-8971. [PMID: 34506152 DOI: 10.1021/acs.jpclett.1c02022] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
Cyanines are useful fluorophores for a myriad of biological labeling applications, but their interactions with biomolecules are unpredictable. Cyanine fluorescence intensity can be highly variable due to complex photoisomerization kinetics, which are exceedingly sensitive to the surrounding environment. This introduces large errors in Förster resonance energy transfer (FRET)-based experiments where fluorescence intensity is the output parameter. However, this environmental sensitivity is a strength from a biological sensing point of view if specific relationships between biomolecular structure and cyanine photophysics can be identified. We describe a set of DNA structures that modulate cyanine fluorescence intensity through the insertion of adenine or thymine bases. These structures simultaneously provide photophysical predictability and tunability. We characterize these structures using steady-state fluorescence measurements, fluorescence correlation spectroscopy (FCS), and time-resolved photoluminescence (TRPL). We find that the photoisomerization rate decreases over an order of magnitude across the adenine series, which is consistent with increasing immobilization of the cyanine moiety by the surrounding DNA structure.
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Affiliation(s)
- Natalie A Pace
- Center for Integrated Nanotechnologies, Los Alamos National Laboratory, Los Alamos, New Mexico 87545, United States
| | - Scott P Hennelly
- Bioenergy and Biome Sciences Group, Los Alamos National Laboratory, Los Alamos, New Mexico 87545, United States
| | - Peter M Goodwin
- Center for Integrated Nanotechnologies, Los Alamos National Laboratory, Los Alamos, New Mexico 87545, United States
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26
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Israels B, Albrecht CS, Dang A, Barney M, von Hippel PH, Marcus AH. Submillisecond Conformational Transitions of Short Single-Stranded DNA Lattices by Photon Correlation Single-Molecule Förster Resonance Energy Transfer. J Phys Chem B 2021; 125:9426-9440. [PMID: 34379430 DOI: 10.1021/acs.jpcb.1c04119] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
Thermally driven conformational fluctuations (or "breathing") of DNA play important roles in the function and regulation of the "macromolecular machinery of genome expression." Fluctuations in double-stranded (ds) DNA are involved in the transient exposure of pathways to protein binding sites within the DNA framework, leading to the binding of regulatory proteins to single-stranded (ss) DNA templates. These interactions often require that the ssDNA sequences, as well as the proteins involved, assume transient conformations critical for successful binding. Here, we use microsecond-resolved single-molecule Förster resonance energy transfer (smFRET) experiments to investigate the backbone fluctuations of short [oligo(dT)n] templates within DNA constructs that also serve as models for ss-dsDNA junctions. Such junctions, together with the attached ssDNA sequences, are involved in interactions with the ssDNA binding (ssb) proteins that control and integrate the functions of DNA replication complexes. We analyze these data using a chemical network model based on multiorder time-correlation functions and probability distribution functions that characterize the kinetic and thermodynamic behavior of the system. We find that the oligo(dT)n tails of ss-dsDNA constructs interconvert, on submillisecond time scales, between three macrostates with distinctly different end-to-end distances. These are (i) a "compact" macrostate that represents the dominant species at equilibrium; (ii) a "partially extended" macrostate that exists as minority species; and (iii) a "highly extended" macrostate that is present in trace amounts. We propose a model for ssDNA secondary structure that advances our understanding of how spontaneously formed nucleic acid conformations may facilitate the activities of ssDNA-associating proteins.
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Affiliation(s)
- Brett Israels
- Department of Chemistry and Biochemistry, Institute of Molecular Biology, University of Oregon, Eugene, Oregon 97403, United States.,Department of Chemistry and Biochemistry, Center for Optical, Molecular and Quantum Science, University of Oregon, Eugene, Oregon 97403, United States
| | - Claire S Albrecht
- Department of Physics, Center for Optical, Molecular and Quantum Science, Institute of Molecular Biology, University of Oregon, Eugene, Oregon 97403, United States
| | - Anson Dang
- Department of Chemistry and Biochemistry, Institute of Molecular Biology, University of Oregon, Eugene, Oregon 97403, United States
| | - Megan Barney
- Department of Chemistry and Biochemistry, Institute of Molecular Biology, University of Oregon, Eugene, Oregon 97403, United States
| | - Peter H von Hippel
- Department of Chemistry and Biochemistry, Institute of Molecular Biology, University of Oregon, Eugene, Oregon 97403, United States
| | - Andrew H Marcus
- Department of Chemistry and Biochemistry, Institute of Molecular Biology, University of Oregon, Eugene, Oregon 97403, United States.,Department of Chemistry and Biochemistry, Center for Optical, Molecular and Quantum Science, University of Oregon, Eugene, Oregon 97403, United States.,Department of Physics, Center for Optical, Molecular and Quantum Science, Institute of Molecular Biology, University of Oregon, Eugene, Oregon 97403, United States
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27
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Gebhardt C, Lehmann M, Reif MM, Zacharias M, Gemmecker G, Cordes T. Molecular and Spectroscopic Characterization of Green and Red Cyanine Fluorophores from the Alexa Fluor and AF Series*. Chemphyschem 2021; 22:1566-1583. [PMID: 34185946 PMCID: PMC8457111 DOI: 10.1002/cphc.202000935] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2020] [Revised: 06/01/2021] [Indexed: 12/23/2022]
Abstract
The use of fluorescence techniques has an enormous impact on various research fields including imaging, biochemical assays, DNA-sequencing and medical technologies. This has been facilitated by the development of numerous commercial dyes with optimized photophysical and chemical properties. Often, however, information about the chemical structures of dyes and the attached linkers used for bioconjugation remain a well-kept secret. This can lead to problems for research applications where knowledge of the dye structure is necessary to predict or understand (unwanted) dye-target interactions, or to establish structural models of the dye-target complex. Using a combination of optical spectroscopy, mass spectrometry, NMR spectroscopy and molecular dynamics simulations, we here investigate the molecular structures and spectroscopic properties of dyes from the Alexa Fluor (Alexa Fluor 555 and 647) and AF series (AF555, AF647, AFD647). Based on available data and published structures of the AF and Cy dyes, we propose a structure for Alexa Fluor 555 and refine that of AF555. We also resolve conflicting reports on the linker composition of Alexa Fluor 647 maleimide. We also conducted a comprehensive comparison between Alexa Fluor and AF dyes by continuous-wave absorption and emission spectroscopy, quantum yield determination, fluorescence lifetime and anisotropy spectroscopy of free and protein-attached dyes. All these data support the idea that Alexa Fluor and AF dyes have a cyanine core and are a derivative of Cy3 and Cy5. In addition, we compared Alexa Fluor 555 and Alexa Fluor 647 to their structural homologs AF555 and AF(D)647 in single-molecule FRET applications. Both pairs showed excellent performance in solution-based smFRET experiments using alternating laser excitation. Minor differences in apparent dye-protein interactions were investigated by molecular dynamics simulations. Our findings clearly demonstrate that the AF-fluorophores are an attractive alternative to Alexa- and Cy-dyes in smFRET studies or other fluorescence applications.
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Affiliation(s)
- Christian Gebhardt
- Physical and Synthetic Biology, Faculty of BiologyLudwig-Maximilians-Universität MünchenGroßhadernerstr. 2–482152Planegg-MartinsriedGermany
| | - Martin Lehmann
- Plant Molecular Biology, Faculty of BiologyLudwig-Maximilians-Universität MünchenGroßhadernerstr. 2–482152Planegg-MartinsriedGermany
| | - Maria M. Reif
- Theoretical Biophysics (T38), Physics DepartmentTechnical University of MunichCenter for Functional Protein Assemblies (CPA), Ernst-Otto-Fischer-Str. 885748GarchingGermany
| | - Martin Zacharias
- Theoretical Biophysics (T38), Physics DepartmentTechnical University of MunichCenter for Functional Protein Assemblies (CPA), Ernst-Otto-Fischer-Str. 885748GarchingGermany
| | - Gerd Gemmecker
- Bavarian NMR Center (B NMRZ), Department of ChemistryTechnical University of MunichLichtenbergstr. 485748GarchingGermany
| | - Thorben Cordes
- Physical and Synthetic Biology, Faculty of BiologyLudwig-Maximilians-Universität MünchenGroßhadernerstr. 2–482152Planegg-MartinsriedGermany
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28
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Wilson H, Wang Q. ABEL-FRET: tether-free single-molecule FRET with hydrodynamic profiling. Nat Methods 2021; 18:816-820. [PMID: 34127856 DOI: 10.1038/s41592-021-01173-9] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2019] [Accepted: 05/04/2021] [Indexed: 02/03/2023]
Abstract
Single-molecule Förster resonance energy transfer (smFRET) has become a versatile and widespread method to probe nanoscale conformation and dynamics. However, current experimental modalities often resort to molecule immobilization for long observation times and do not always approach the resolution limit of FRET-based nanoscale metrology. Here we present ABEL-FRET, an immobilization-free platform for smFRET measurements with ultrahigh resolving power in FRET efficiency. Importantly, single-molecule diffusivity is used to provide additional size and shape information for hydrodynamic profiling of individual molecules, which, together with the concurrently measured intramolecular conformation through FRET, enables a holistic and dynamic view of biomolecules and their complexes.
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Affiliation(s)
- Hugh Wilson
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ, USA
| | - Quan Wang
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ, USA.
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29
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Emerson NT, Yang H. Reproducibly Measuring Plasmon-Enhanced Fluorescence in Bulk Solution Across a 20-Fold Range of Optical Densities. Anal Chem 2021; 93:8045-8053. [PMID: 34038099 DOI: 10.1021/acs.analchem.1c01210] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
It is well-known that plasmonic nanoparticles can modify the spectroscopic properties of nearby optical probes, for example, enhanced emission of a fluorescent dye. Yet, the detection and quantification of this effect in bulk solution remain challenging even while size- and shape-controlled nanoparticles have become readily available. We investigated this problem and identified two main difficulties which we were able to overcome through systematic studies. For the detection of fluorescence emanating from optically dense nanoparticle solutions, we describe an analytical model that provides guidelines for experimentalists to maximize the fluorescence intensity by optimizing the concentration, light paths, and excitation-detection volume of the sample. For the quantification of enhancement, which critically hinges upon the comparison to an accurate reference sample, we exploit the tools of DNA nanotechnology to remove the fluorophore from plasmonic coupling on-demand, forming an in situ reference. Using a model system of fluorophore Cy3 and 80 nm gold nanoparticles, we show that these strategies enable the quantitative measurement of plasmonic enhancement across a 20-fold range of optical densities. We anticipate that the presented experimental framework will allow for routine, quantitative measurements for the research and development of plasmon-enhanced phenomena.
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Affiliation(s)
- Nyssa T Emerson
- Department of Chemistry, Princeton University 225A Frick Laboratory, Princeton, New Jersey 08544-1023, United States
| | - Haw Yang
- Department of Chemistry, Princeton University 225A Frick Laboratory, Princeton, New Jersey 08544-1023, United States
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30
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31
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Nilsson JR, Baladi T, Gallud A, Baždarević D, Lemurell M, Esbjörner EK, Wilhelmsson LM, Dahlén A. Fluorescent base analogues in gapmers enable stealth labeling of antisense oligonucleotide therapeutics. Sci Rep 2021; 11:11365. [PMID: 34059711 PMCID: PMC8166847 DOI: 10.1038/s41598-021-90629-1] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2021] [Accepted: 05/13/2021] [Indexed: 01/28/2023] Open
Abstract
To expand the antisense oligonucleotide (ASO) fluorescence labeling toolbox beyond covalent conjugation of external dyes (e.g. ATTO-, Alexa Fluor-, or cyanine dyes), we herein explore fluorescent base analogues (FBAs) as a novel approach to endow fluorescent properties to ASOs. Both cytosine and adenine analogues (tC, tCO, 2CNqA, and pA) were incorporated into a 16mer ASO sequence with a 3-10-3 cEt-DNA-cEt (cEt = constrained ethyl) gapmer design. In addition to a comprehensive photophysical characterization, we assess the label-induced effects on the gapmers' RNA affinities, RNA-hybridized secondary structures, and knockdown efficiencies. Importantly, we find practically no perturbing effects for gapmers with single FBA incorporations in the biologically critical gap region and, except for pA, the FBAs do not affect the knockdown efficiencies. Incorporating two cytosine FBAs in the gap is equally well tolerated, while two adenine analogues give rise to slightly reduced knockdown efficiencies and what could be perturbed secondary structures. We furthermore show that the FBAs can be used to visualize gapmers inside live cells using fluorescence microscopy and flow cytometry, enabling comparative assessment of their uptake. This altogether shows that FBAs are functional ASO probes that provide a minimally perturbing in-sequence labeling option for this highly relevant drug modality.
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Affiliation(s)
- Jesper R Nilsson
- Department of Chemistry and Chemical Engineering, Chalmers University of Technology, 412 96, Gothenburg, Sweden
| | - Tom Baladi
- Department of Chemistry and Chemical Engineering, Chalmers University of Technology, 412 96, Gothenburg, Sweden.,Medicinal Chemistry, Research and Early Development, Cardiovascular, Renal and Metabolism (CVRM), BioPharmaceuticals R&D, AstraZeneca, Gothenburg, Sweden.,Oligonucleotide Discovery, Discovery Sciences, BioPharmaceuticals R&D, AstraZeneca, Gothenburg, Sweden
| | - Audrey Gallud
- Department of Biology and Biological Engineering, Chalmers University of Technology, 41296, Gothenburg, Sweden.,Advanced Drug Delivery, Pharmaceutical Sciences, R&D, AstraZeneca, Gothenburg, Sweden
| | - Dženita Baždarević
- Bioscience, Research and Early Development, Cardiovascular, Renal and Metabolism (CVRM), BioPharmaceuticals R&D, AstraZeneca, Gothenburg, Sweden
| | - Malin Lemurell
- Medicinal Chemistry, Research and Early Development, Cardiovascular, Renal and Metabolism (CVRM), BioPharmaceuticals R&D, AstraZeneca, Gothenburg, Sweden
| | - Elin K Esbjörner
- Department of Biology and Biological Engineering, Chalmers University of Technology, 41296, Gothenburg, Sweden
| | - L Marcus Wilhelmsson
- Department of Chemistry and Chemical Engineering, Chalmers University of Technology, 412 96, Gothenburg, Sweden
| | - Anders Dahlén
- Oligonucleotide Discovery, Discovery Sciences, BioPharmaceuticals R&D, AstraZeneca, Gothenburg, Sweden.
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32
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Mahzabeen F, Vermesh O, Levi J, Tan M, Alam IS, Chan CT, Gambhir SS, Harris JS. Real-time point-of-care total protein measurement with a miniaturized optoelectronic biosensor and fast fluorescence-based assay. Biosens Bioelectron 2021; 180:112823. [PMID: 33715946 DOI: 10.1016/j.bios.2020.112823] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2019] [Revised: 11/10/2020] [Accepted: 11/12/2020] [Indexed: 01/01/2023]
Abstract
Measurement of total protein in urine is key to monitoring kidney health in diabetes. However, most total protein assays are performed using large, expensive laboratory chemistry analyzers that are not amenable to point-of-care analysis or home monitoring and cannot provide real-time readouts. We developed a miniaturized optoelectronic biosensor using a vertical cavity surface-emitting laser (VCSEL), coupled with a fast protein assay based on protein-induced fluorescence enhancement (PIFE), that can dynamically measure protein concentrations in protein-spiked buffer, serum, and urine in seconds with excellent sensitivity (urine LOD = 0.023 g/L, LOQ = 0.075 g/L) and over a broad range of physiologically relevant concentrations. Comparison with gold standard clinical assays and standard fluorimetry tools showed that the sensor can accurately and reliably quantitate total protein in clinical urine samples from patients with diabetes. Our VCSEL biosensor is amenable to integration with miniaturized electronics, which could afford a portable, low-cost, easy-to-use device for sensitive, accurate, and real-time total protein measurements from small biofluid volumes.
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Affiliation(s)
- Fariah Mahzabeen
- Department of Electrical Engineering, Stanford University, Stanford, CA, 94305, USA
| | - Ophir Vermesh
- Department of Radiology, Stanford University, Stanford, CA, 94305, USA; Molecular Imaging Program at Stanford, Stanford University, Stanford, CA, 94305, USA.
| | - Jelena Levi
- Department of Radiology, Stanford University, Stanford, CA, 94305, USA; Molecular Imaging Program at Stanford, Stanford University, Stanford, CA, 94305, USA
| | - Marilyn Tan
- Department of Medicine, Stanford University, Stanford, CA, 94305, USA
| | - Israt S Alam
- Department of Radiology, Stanford University, Stanford, CA, 94305, USA; Molecular Imaging Program at Stanford, Stanford University, Stanford, CA, 94305, USA
| | - Carmel T Chan
- Department of Radiology, Stanford University, Stanford, CA, 94305, USA; Molecular Imaging Program at Stanford, Stanford University, Stanford, CA, 94305, USA
| | - Sanjiv S Gambhir
- Department of Radiology, Stanford University, Stanford, CA, 94305, USA; Molecular Imaging Program at Stanford, Stanford University, Stanford, CA, 94305, USA; Department of Bioengineering, Stanford University, Stanford, CA, 94305, USA; Stanford Bio-X, Stanford University, Stanford, CA, 94305, USA
| | - James S Harris
- Department of Electrical Engineering, Stanford University, Stanford, CA, 94305, USA.
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33
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Jeng SCY, Trachman RJ, Weissenboeck F, Truong L, Link KA, Jepsen MDE, Knutson JR, Andersen ES, Ferré-D'Amaré AR, Unrau PJ. Fluorogenic aptamers resolve the flexibility of RNA junctions using orientation-dependent FRET. RNA (NEW YORK, N.Y.) 2021; 27:433-444. [PMID: 33376189 PMCID: PMC7962493 DOI: 10.1261/rna.078220.120] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/28/2020] [Accepted: 12/20/2020] [Indexed: 05/26/2023]
Abstract
To further understand the transcriptome, new tools capable of measuring folding, interactions, and localization of RNA are needed. Although Förster resonance energy transfer (FRET) is an angle- and distance-dependent phenomenon, the majority of FRET measurements have been used to report distances, by assuming rotationally averaged donor-acceptor pairs. Angle-dependent FRET measurements have proven challenging for nucleic acids due to the difficulties in incorporating fluorophores rigidly into local substructures in a biocompatible manner. Fluorescence turn-on RNA aptamers are genetically encodable tags that appear to rigidly confine their cognate fluorophores, and thus have the potential to report angular-resolved FRET. Here, we use the fluorescent aptamers Broccoli and Mango-III as donor and acceptor, respectively, to measure the angular dependence of FRET. Joining the two fluorescent aptamers by a helix of variable length allowed systematic rotation of the acceptor fluorophore relative to the donor. FRET oscillated in a sinusoidal manner as a function of helix length, consistent with simulated data generated from models of oriented fluorophores separated by an inflexible helix. Analysis of the orientation dependence of FRET allowed us to demonstrate structural rigidification of the NiCo riboswitch upon transition metal-ion binding. This application of fluorescence turn-on aptamers opens the way to improved structural interpretation of ensemble and single-molecule FRET measurements of RNA.
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Affiliation(s)
- Sunny C Y Jeng
- Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, British Columbia, Canada V5A 1S6
| | - Robert J Trachman
- Biochemistry and Biophysics Center, National Heart, Lung, and Blood Institute, Bethesda, Maryland 20892-8012, USA
| | - Florian Weissenboeck
- Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, British Columbia, Canada V5A 1S6
| | - Lynda Truong
- Biochemistry and Biophysics Center, National Heart, Lung, and Blood Institute, Bethesda, Maryland 20892-8012, USA
| | - Katie A Link
- Biochemistry and Biophysics Center, National Heart, Lung, and Blood Institute, Bethesda, Maryland 20892-8012, USA
| | - Mette D E Jepsen
- Interdisciplinary Nanoscience Center, Aarhus University, 8000 Aarhus C, Denmark
| | - Jay R Knutson
- Biochemistry and Biophysics Center, National Heart, Lung, and Blood Institute, Bethesda, Maryland 20892-8012, USA
| | - Ebbe S Andersen
- Interdisciplinary Nanoscience Center, Aarhus University, 8000 Aarhus C, Denmark
| | - Adrian R Ferré-D'Amaré
- Biochemistry and Biophysics Center, National Heart, Lung, and Blood Institute, Bethesda, Maryland 20892-8012, USA
| | - Peter J Unrau
- Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, British Columbia, Canada V5A 1S6
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34
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Singh RK, Jonely M, Leslie E, Rejali NA, Noriega R, Bass BL. Transient kinetic studies of the antiviral Drosophila Dicer-2 reveal roles of ATP in self-nonself discrimination. eLife 2021; 10:65810. [PMID: 33787495 PMCID: PMC8079148 DOI: 10.7554/elife.65810] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2020] [Accepted: 03/31/2021] [Indexed: 11/25/2022] Open
Abstract
Some RIG-I-like receptors (RLRs) discriminate viral and cellular dsRNA by their termini, and Drosophila melanogaster Dicer-2 (dmDcr-2) differentially processes dsRNA with blunt or 2 nucleotide 3’-overhanging termini. We investigated the transient kinetic mechanism of the dmDcr-2 reaction using a rapid reaction stopped-flow technique and time-resolved fluorescence spectroscopy. Indeed, we found that ATP binding to dmDcr-2’s helicase domain impacts association and dissociation kinetics of dsRNA in a termini-dependent manner, revealing termini-dependent discrimination of dsRNA on a biologically relevant time scale (seconds). ATP hydrolysis promotes transient unwinding of dsRNA termini followed by slow rewinding, and directional translocation of the enzyme to the cleavage site. Time-resolved fluorescence anisotropy reveals a nucleotide-dependent modulation in conformational fluctuations (nanoseconds) of the helicase and Platform–PAZ domains that is correlated with termini-dependent dsRNA cleavage. Our study offers a kinetic framework for comparison to other Dicers, as well as all members of the RLRs involved in innate immunity.
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Affiliation(s)
- Raushan K Singh
- Department of Biochemistry, University of Utah, Salt Lake City, United States
| | - McKenzie Jonely
- Department of Chemistry, University of Utah, Salt Lake City, United States
| | - Evan Leslie
- Department of Biochemistry, University of Utah, Salt Lake City, United States
| | - Nick A Rejali
- Department of Pathology, University of Utah, Salt Lake City, United States
| | - Rodrigo Noriega
- Department of Chemistry, University of Utah, Salt Lake City, United States
| | - Brenda L Bass
- Department of Biochemistry, University of Utah, Salt Lake City, United States
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35
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Lerner E, Barth A, Hendrix J, Ambrose B, Birkedal V, Blanchard SC, Börner R, Sung Chung H, Cordes T, Craggs TD, Deniz AA, Diao J, Fei J, Gonzalez RL, Gopich IV, Ha T, Hanke CA, Haran G, Hatzakis NS, Hohng S, Hong SC, Hugel T, Ingargiola A, Joo C, Kapanidis AN, Kim HD, Laurence T, Lee NK, Lee TH, Lemke EA, Margeat E, Michaelis J, Michalet X, Myong S, Nettels D, Peulen TO, Ploetz E, Razvag Y, Robb NC, Schuler B, Soleimaninejad H, Tang C, Vafabakhsh R, Lamb DC, Seidel CAM, Weiss S. FRET-based dynamic structural biology: Challenges, perspectives and an appeal for open-science practices. eLife 2021; 10:e60416. [PMID: 33779550 PMCID: PMC8007216 DOI: 10.7554/elife.60416] [Citation(s) in RCA: 125] [Impact Index Per Article: 41.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2020] [Accepted: 02/09/2021] [Indexed: 12/18/2022] Open
Abstract
Single-molecule FRET (smFRET) has become a mainstream technique for studying biomolecular structural dynamics. The rapid and wide adoption of smFRET experiments by an ever-increasing number of groups has generated significant progress in sample preparation, measurement procedures, data analysis, algorithms and documentation. Several labs that employ smFRET approaches have joined forces to inform the smFRET community about streamlining how to perform experiments and analyze results for obtaining quantitative information on biomolecular structure and dynamics. The recent efforts include blind tests to assess the accuracy and the precision of smFRET experiments among different labs using various procedures. These multi-lab studies have led to the development of smFRET procedures and documentation, which are important when submitting entries into the archiving system for integrative structure models, PDB-Dev. This position paper describes the current 'state of the art' from different perspectives, points to unresolved methodological issues for quantitative structural studies, provides a set of 'soft recommendations' about which an emerging consensus exists, and lists openly available resources for newcomers and seasoned practitioners. To make further progress, we strongly encourage 'open science' practices.
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Affiliation(s)
- Eitan Lerner
- Department of Biological Chemistry, The Alexander Silberman Institute of Life Sciences, and The Center for Nanoscience and Nanotechnology, Faculty of Mathematics & Science, The Edmond J. Safra Campus, The Hebrew University of JerusalemJerusalemIsrael
| | - Anders Barth
- Lehrstuhl für Molekulare Physikalische Chemie, Heinrich-Heine-UniversitätDüsseldorfGermany
| | - Jelle Hendrix
- Dynamic Bioimaging Lab, Advanced Optical Microscopy Centre and Biomedical Research Institute (BIOMED), Hasselt UniversityDiepenbeekBelgium
| | - Benjamin Ambrose
- Department of Chemistry, University of SheffieldSheffieldUnited Kingdom
| | - Victoria Birkedal
- Department of Chemistry and iNANO center, Aarhus UniversityAarhusDenmark
| | - Scott C Blanchard
- Department of Structural Biology, St. Jude Children's Research HospitalMemphisUnited States
| | - Richard Börner
- Laserinstitut HS Mittweida, University of Applied Science MittweidaMittweidaGermany
| | - Hoi Sung Chung
- Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of HealthBethesdaUnited States
| | - Thorben Cordes
- Physical and Synthetic Biology, Faculty of Biology, Ludwig-Maximilians-Universität MünchenPlanegg-MartinsriedGermany
| | - Timothy D Craggs
- Department of Chemistry, University of SheffieldSheffieldUnited Kingdom
| | - Ashok A Deniz
- Department of Integrative Structural and Computational Biology, The Scripps Research InstituteLa JollaUnited States
| | - Jiajie Diao
- Department of Cancer Biology, University of Cincinnati School of MedicineCincinnatiUnited States
| | - Jingyi Fei
- Department of Biochemistry and Molecular Biology and The Institute for Biophysical Dynamics, University of ChicagoChicagoUnited States
| | - Ruben L Gonzalez
- Department of Chemistry, Columbia UniversityNew YorkUnited States
| | - Irina V Gopich
- Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of HealthBethesdaUnited States
| | - Taekjip Ha
- Department of Biophysics and Biophysical Chemistry, Department of Biomedical Engineering, Johns Hopkins University School of Medicine, Howard Hughes Medical InstituteBaltimoreUnited States
| | - Christian A Hanke
- Lehrstuhl für Molekulare Physikalische Chemie, Heinrich-Heine-UniversitätDüsseldorfGermany
| | - Gilad Haran
- Department of Chemical and Biological Physics, Weizmann Institute of ScienceRehovotIsrael
| | - Nikos S Hatzakis
- Department of Chemistry & Nanoscience Centre, University of CopenhagenCopenhagenDenmark
- Denmark Novo Nordisk Foundation Centre for Protein Research, Faculty of Health and Medical Sciences, University of CopenhagenCopenhagenDenmark
| | - Sungchul Hohng
- Department of Physics and Astronomy, and Institute of Applied Physics, Seoul National UniversitySeoulRepublic of Korea
| | - Seok-Cheol Hong
- Center for Molecular Spectroscopy and Dynamics, Institute for Basic Science and Department of Physics, Korea UniversitySeoulRepublic of Korea
| | - Thorsten Hugel
- Institute of Physical Chemistry and Signalling Research Centres BIOSS and CIBSS, University of FreiburgFreiburgGermany
| | - Antonino Ingargiola
- Department of Chemistry and Biochemistry, and Department of Physiology, University of California, Los AngelesLos AngelesUnited States
| | - Chirlmin Joo
- Department of BioNanoScience, Kavli Institute of Nanoscience, Delft University of TechnologyDelftNetherlands
| | - Achillefs N Kapanidis
- Biological Physics Research Group, Clarendon Laboratory, Department of Physics, University of OxfordOxfordUnited Kingdom
| | - Harold D Kim
- School of Physics, Georgia Institute of TechnologyAtlantaUnited States
| | - Ted Laurence
- Physical and Life Sciences Directorate, Lawrence Livermore National LaboratoryLivermoreUnited States
| | - Nam Ki Lee
- School of Chemistry, Seoul National UniversitySeoulRepublic of Korea
| | - Tae-Hee Lee
- Department of Chemistry, Pennsylvania State UniversityUniversity ParkUnited States
| | - Edward A Lemke
- Departments of Biology and Chemistry, Johannes Gutenberg UniversityMainzGermany
- Institute of Molecular Biology (IMB)MainzGermany
| | - Emmanuel Margeat
- Centre de Biologie Structurale (CBS), CNRS, INSERM, Universitié de MontpellierMontpellierFrance
| | | | - Xavier Michalet
- Department of Chemistry and Biochemistry, and Department of Physiology, University of California, Los AngelesLos AngelesUnited States
| | - Sua Myong
- Department of Biophysics, Johns Hopkins UniversityBaltimoreUnited States
| | - Daniel Nettels
- Department of Biochemistry and Department of Physics, University of ZurichZurichSwitzerland
| | - Thomas-Otavio Peulen
- Department of Bioengineering and Therapeutic Sciences, University of California, San FranciscoSan FranciscoUnited States
| | - Evelyn Ploetz
- Physical Chemistry, Department of Chemistry, Center for Nanoscience (CeNS), Center for Integrated Protein Science Munich (CIPSM) and Nanosystems Initiative Munich (NIM), Ludwig-Maximilians-UniversitätMünchenGermany
| | - Yair Razvag
- Department of Biological Chemistry, The Alexander Silberman Institute of Life Sciences, and The Center for Nanoscience and Nanotechnology, Faculty of Mathematics & Science, The Edmond J. Safra Campus, The Hebrew University of JerusalemJerusalemIsrael
| | - Nicole C Robb
- Warwick Medical School, University of WarwickCoventryUnited Kingdom
| | - Benjamin Schuler
- Department of Biochemistry and Department of Physics, University of ZurichZurichSwitzerland
| | - Hamid Soleimaninejad
- Biological Optical Microscopy Platform (BOMP), University of MelbourneParkvilleAustralia
| | - Chun Tang
- College of Chemistry and Molecular Engineering, PKU-Tsinghua Center for Life Sciences, Beijing National Laboratory for Molecular Sciences, Peking UniversityBeijingChina
| | - Reza Vafabakhsh
- Department of Molecular Biosciences, Northwestern UniversityEvanstonUnited States
| | - Don C Lamb
- Physical Chemistry, Department of Chemistry, Center for Nanoscience (CeNS), Center for Integrated Protein Science Munich (CIPSM) and Nanosystems Initiative Munich (NIM), Ludwig-Maximilians-UniversitätMünchenGermany
| | - Claus AM Seidel
- Lehrstuhl für Molekulare Physikalische Chemie, Heinrich-Heine-UniversitätDüsseldorfGermany
| | - Shimon Weiss
- Department of Chemistry and Biochemistry, and Department of Physiology, University of California, Los AngelesLos AngelesUnited States
- Department of Physiology, CaliforniaNanoSystems Institute, University of California, Los AngelesLos AngelesUnited States
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36
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Makela M, Lin PT. Detection of SARS-CoV-2 DNA Targets Using Femtoliter Optofluidic Waveguides. Anal Chem 2021; 93:4154-4159. [PMID: 33645217 PMCID: PMC7944394 DOI: 10.1021/acs.analchem.0c02971] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2020] [Accepted: 02/19/2021] [Indexed: 12/30/2022]
Abstract
Chip-scale SARS-CoV-2 testing was demonstrated using silicon nitride (Si3N4) nanoslot fluidic waveguides to detect a tagged oligonucleotide with a coronavirus DNA sequence. The slot waveguides were fabricated using complementary metal-oxide-semiconductor (CMOS) fabrication processes, including multiscale lithography and selective reactive ion etching (RIE), forming femtoliter fluidic channels. Finite difference method (FDM) simulation was used to calculate the optical field distribution of the waveguide mode when the waveguide sensor was excited by transverse electric (TE) and transverse magnetic (TM) polarized light. For the TE polarization, a strong optical field was created in the slot region and its field intensity was 14× stronger than the evanescent sensing field from the TM polarization. The nanoscale confinement of the optical sensing field significantly enhanced the light-analyte interaction and improved the optical sensitivity. The sensitivity enhancement was experimentally demonstrated by measuring the polarization-dependent fluorescence emission from the tagged oligonucleotide. The photonic chips consisting of femtoliter Si3N4 waveguides provide a low-cost and high throughput platform for real-time virus identification, which is critical for point-of-care (PoC) diagnostic applications.
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Affiliation(s)
- Megan Makela
- Department of Electrical
and Computer Engineering, Texas A&M
University, College Station 77843, Texas, United States
- Department of Materials Science and Engineering, Texas A&M University, College Station 77843, Texas, United States
- The Center for Remote
Health Technologies and Systems, Texas A&M
University, College Station 77843, Texas, United States
| | - Pao Tai Lin
- Department of Electrical
and Computer Engineering, Texas A&M
University, College Station 77843, Texas, United States
- Department of Materials Science and Engineering, Texas A&M University, College Station 77843, Texas, United States
- The Center for Remote
Health Technologies and Systems, Texas A&M
University, College Station 77843, Texas, United States
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37
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Hart SM, Chen WJ, Banal JL, Bricker WP, Dodin A, Markova L, Vyborna Y, Willard AP, Häner R, Bathe M, Schlau-Cohen GS. Engineering couplings for exciton transport using synthetic DNA scaffolds. Chem 2021. [DOI: 10.1016/j.chempr.2020.12.020] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
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38
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Helmerich DA, Beliu G, Matikonda SS, Schnermann MJ, Sauer M. Photoblueing of organic dyes can cause artifacts in super-resolution microscopy. Nat Methods 2021; 18:253-257. [PMID: 33633409 PMCID: PMC10802917 DOI: 10.1038/s41592-021-01061-2] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2020] [Accepted: 01/08/2021] [Indexed: 11/08/2022]
Abstract
Illumination of fluorophores can induce a loss of the ability to fluoresce, known as photobleaching. Interestingly, some fluorophores photoconvert to a blue-shifted fluorescent molecule as an intermediate on the photobleaching pathway, which can complicate multicolor fluorescence imaging, especially under the intense laser irradiation used in super-resolution fluorescence imaging. Here, we discuss the mechanisms of photoblueing of fluorophores and its impact on fluorescence imaging, and show how it can be prevented.
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Affiliation(s)
- Dominic A Helmerich
- Department of Biotechnology and Biophysics, Biocenter, Julius Maximilian University of Würzburg, Würzburg, Germany
| | - Gerti Beliu
- Department of Biotechnology and Biophysics, Biocenter, Julius Maximilian University of Würzburg, Würzburg, Germany
| | - Siddharth S Matikonda
- Chemical Biology Laboratory, Center for Cancer Research, National Cancer Institute, Frederick, MD, USA
| | - Martin J Schnermann
- Chemical Biology Laboratory, Center for Cancer Research, National Cancer Institute, Frederick, MD, USA
| | - Markus Sauer
- Department of Biotechnology and Biophysics, Biocenter, Julius Maximilian University of Würzburg, Würzburg, Germany.
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39
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Francés-Soriano L, Leino M, Dos Santos MC, Kovacs D, Borbas KE, Söderberg O, Hildebrandt N. In Situ Rolling Circle Amplification Förster Resonance Energy Transfer (RCA-FRET) for Washing-Free Real-Time Single-Protein Imaging. Anal Chem 2021; 93:1842-1850. [PMID: 33356162 DOI: 10.1021/acs.analchem.0c04828] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Fluorescence signal enhancement via isothermal nucleic acid amplification is an important approach for sensitive imaging of intra- or extracellular nucleic acid or protein biomarkers. Rolling circle amplification (RCA) is frequently applied for fluorescence in situ imaging but faces limitations concerning multiplexing, dynamic range, and the required multiple washing steps before imaging. Here, we show that Förster resonance energy transfer (FRET) between fluorescent dyes and between lanthanide (Ln) complexes and dyes that hybridize to β-actin-specific RCA products in HaCaT cells can afford washing-free imaging of single β-actin proteins. Proximity-dependent FRET could be monitored directly after or during (real-time monitoring) dye or Ln DNA probe incubation and could efficiently distinguish between photoluminescence from β-actin-specific RCA and DNA probes freely diffusing in solution or nonspecifically attached to cells. Moreover, time-gated FRET imaging with the Ln-dye FRET pairs efficiently suppressed sample autofluorescence and improved the signal-to-background ratio. Our results present an important proof of concept of RCA-FRET imaging with a strong potential to advance in situ RCA toward easier sample preparation, higher-order multiplexing, autofluorescence-free detection, and increased dynamic range by real-time monitoring of in situ RCA.
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Affiliation(s)
- Laura Francés-Soriano
- nanoFRET.com, Laboratoire COBRA (Chimie Organique, Bioorganique, Réactivité et Analyse), Université de Rouen Normandie, CNRS, INSA, 76821 Mont-Saint-Aignan, France.,Institute for Integrative Biology of the Cell (I2BC), Université Paris-Saclay, CNRS, CEA, 91405 Orsay Cedex, France
| | - Mattias Leino
- Department of Pharmaceutical Biosciences, Uppsala University, Biomedical Center, 75124 Uppsala, Sweden
| | - Marcelina Cardoso Dos Santos
- Institute for Integrative Biology of the Cell (I2BC), Université Paris-Saclay, CNRS, CEA, 91405 Orsay Cedex, France
| | - Daniel Kovacs
- Department of Chemistry, Ångström Laboratory, Uppsala University, 75120 Uppsala, Sweden
| | - K Eszter Borbas
- Department of Chemistry, Ångström Laboratory, Uppsala University, 75120 Uppsala, Sweden
| | - Ola Söderberg
- Department of Pharmaceutical Biosciences, Uppsala University, Biomedical Center, 75124 Uppsala, Sweden
| | - Niko Hildebrandt
- nanoFRET.com, Laboratoire COBRA (Chimie Organique, Bioorganique, Réactivité et Analyse), Université de Rouen Normandie, CNRS, INSA, 76821 Mont-Saint-Aignan, France.,Institute for Integrative Biology of the Cell (I2BC), Université Paris-Saclay, CNRS, CEA, 91405 Orsay Cedex, France
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40
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Cho J, Oh S, Lee D, Han JW, Yoo J, Park D, Lee G. Spectroscopic sensing and quantification of AP-endonucleases using fluorescence-enhancement by cis– trans isomerization of cyanine dyes. RSC Adv 2021; 11:11380-11386. [PMID: 35423644 PMCID: PMC8695990 DOI: 10.1039/d0ra08051a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2020] [Accepted: 03/08/2021] [Indexed: 11/21/2022] Open
Abstract
Apurinic/apyrimidinic (AP) endonucleases are vital DNA repair enzymes, and proposed to be a prognostic biomarker for various types of cancer in humans. Numerous DNA sensors have been developed to evaluate the extent of nuclease activity but their DNA termini are not protected against other nucleases, hampering accurate quantification. Here we developed a new fluorescence enhancement (FE)-based method as an enzyme-specific DNA biosensor with nuclease-protection by three functional units (an AP-site, Cy3 and termini that are protected from exonucleolytic cleavage). A robust FE signal arises from the fluorescent cis–trans isomerization of a cyanine dye (e.g., Cy3) upon the enzyme-triggered structural change from double-stranded (ds)DNA to single-stranded (ss)DNA that carries Cy3. The FE-based assay reveals a linear dependency on sub-nanomolar concentrations as low as 10−11 M for the target enzyme and can be also utilized as a sensitive readout of other nuclease activities. Apurinic/apyrimidinic (AP) endonucleases are vital DNA repair enzymes, and proposed to be a prognostic biomarker for various types of cancer in humans.![]()
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Affiliation(s)
- JunHo Cho
- School of Life Sciences
- Gwangju Institute of Science and Technology
- Gwangju
- Korea
| | - Sanghoon Oh
- Department of Biomedical Science and Engineering
- Gwangju Institute of Science and Technology
- Gwangju
- Korea
| | - DongHun Lee
- School of Life Sciences
- Gwangju Institute of Science and Technology
- Gwangju
- Korea
| | - Jae Won Han
- School of Life Sciences
- Gwangju Institute of Science and Technology
- Gwangju
- Korea
| | - Jungmin Yoo
- School of Life Sciences
- Gwangju Institute of Science and Technology
- Gwangju
- Korea
| | - Daeho Park
- School of Life Sciences
- Gwangju Institute of Science and Technology
- Gwangju
- Korea
- Cell Mechanobiology Research Center
| | - Gwangrog Lee
- School of Life Sciences
- Gwangju Institute of Science and Technology
- Gwangju
- Korea
- Department of Biomedical Science and Engineering
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41
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Shaw RA, Johnston-Wood T, Ambrose B, Craggs TD, Hill JG. CHARMM-DYES: Parameterization of Fluorescent Dyes for Use with the CHARMM Force Field. J Chem Theory Comput 2020; 16:7817-7824. [DOI: 10.1021/acs.jctc.0c00721] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Affiliation(s)
- Robert A. Shaw
- Department of Chemistry, University of Sheffield, Sheffield S3 7HF, U.K
- Present address: ARC Centre of Excellence in Exciton Science, School of Science, RMIT University, Melbourne, VIC 3000, Australia
| | - Tristan Johnston-Wood
- Department of Chemistry, University of Sheffield, Sheffield S3 7HF, U.K
- Present address: Department of Chemistry, Physical and Theoretical Chemistry Laboratory, University of Oxford, Oxford OX1 3QZ, U.K
| | - Benjamin Ambrose
- Department of Chemistry, University of Sheffield, Sheffield S3 7HF, U.K
| | - Timothy D. Craggs
- Department of Chemistry, University of Sheffield, Sheffield S3 7HF, U.K
| | - J. Grant Hill
- Department of Chemistry, University of Sheffield, Sheffield S3 7HF, U.K
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42
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Schreier VN, Loehr MO, Deng T, Lattmann E, Hajnal A, Neuhauss SC, Luedtke NW. Fluorescent dATP for DNA Synthesis In Vivo. ACS Chem Biol 2020; 15:2996-3003. [PMID: 33108866 DOI: 10.1021/acschembio.0c00654] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
Fluorescent nucleoside triphosphates are powerful probes of DNA synthesis, but their potential use in living animals has been previously underexplored. Here, we report the synthesis and characterization of 7-deaza-(1,2,3-triazole)-2'-deoxyadenosine-5'-triphosphate (dATP) derivatives of tetramethyl rhodamine ("TAMRA-dATP"), cyanine ("Cy3-dATP"), and boron-dipyrromethene ("BODIPY-dATP"). Upon microinjection into live zebrafish embryos, all three compounds were incorporated into the DNA of dividing cells; however, their impact on embryonic toxicity was highly variable, depending on the exact structure of the dye. TAMRA-EdATP exhibited superior characteristics in terms of its high brightness, low toxicity, and rapid incorporation and depletion kinetics in both a vertebrate (zebrafish) and a nematode (Caenorhabditis elegans). TAMRA-EdATP allows for unprecedented, real-time visualization of DNA replication and chromosome segregation in vivo.
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Affiliation(s)
- Verena N. Schreier
- Department of Chemistry, University of Zurich, Zurich CH-8006, Switzerland
| | - Morten O. Loehr
- Department of Chemistry, University of Zurich, Zurich CH-8006, Switzerland
- Department of Chemistry, McGill University, Montreal, Quebec H3A 0G4, Canada
| | - Ting Deng
- Department of Molecular Life Sciences, University of Zurich, Zurich CH-8006, Switzerland
| | - Evelyn Lattmann
- Department of Molecular Life Sciences, University of Zurich, Zurich CH-8006, Switzerland
| | - Alex Hajnal
- Department of Molecular Life Sciences, University of Zurich, Zurich CH-8006, Switzerland
| | - Stephan C.F. Neuhauss
- Department of Molecular Life Sciences, University of Zurich, Zurich CH-8006, Switzerland
| | - Nathan W. Luedtke
- Department of Chemistry, University of Zurich, Zurich CH-8006, Switzerland
- Department of Chemistry, McGill University, Montreal, Quebec H3A 0G4, Canada
- Department of Pharmacology and Therapeutics, McGill University, Montreal, Quebec H3A 0G4, Canada
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43
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Sobek J, Schlapbach R. Dependence of Fluorescence Quenching of CY3 Oligonucleotide Conjugates on the Oxidation Potential of the Stacking Base Pair. Molecules 2020; 25:molecules25225369. [PMID: 33212871 PMCID: PMC7698394 DOI: 10.3390/molecules25225369] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2020] [Revised: 11/15/2020] [Accepted: 11/16/2020] [Indexed: 01/02/2023] Open
Abstract
To understand the complex fluorescence properties of astraphloxin (CY3)-labelled oligonucleotides, it is necessary to take into account the redox properties of the nucleobases. In oligonucleotide hybrids, we observed a dependence of the fluorescence intensity on the oxidation potential of the neighbouring base pair. For the series I < A < G < 8-oxoG, the extent of fluorescence quenching follows the trend of decreasing oxidation potentials. In a series of 7 nt hybrids, stacking interactions of CY3 with perfect match and mismatch base pairs were found to stabilise the hybrid by 7–8 kJ/mol. The fluorescence measurements can be explained by complex formation resulting in fluorescence quenching that prevails over the steric effect of a reduced excited state trans-cis isomerisation, which was expected to increase the fluorescence efficiency of the dye when stacking to a base pair. This can be explained by the fact that, in a double strand, base pairing and stacking cause a dramatic change in the oxidation potential of the nucleobases. In single-molecule fluorescence measurements, the oxidation of G to 8-oxoG was observed as a result of photoinduced electron transfer and subsequent chemical reactions. Our results demonstrate that covalently linked CY3 is a potent oxidant towards dsDNA. Sulfonated derivatives should be used instead.
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44
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Vallmitjana A, Torrado B, Dvornikov A, Ranjit S, Gratton E. Blind Resolution of Lifetime Components in Individual Pixels of Fluorescence Lifetime Images Using the Phasor Approach. J Phys Chem B 2020; 124:10126-10137. [PMID: 33140960 DOI: 10.1021/acs.jpcb.0c06946] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
The phasor approach is used in fluorescence lifetime imaging microscopy for several purposes, notably to calculate the metabolic index of single cells and tissues. An important feature of the phasor approach is that it is a fit-free method allowing immediate and easy to interpret analysis of images. In a recent paper, we showed that three or four intensity fractions of exponential components can be resolved in each pixel of an image by the phasor approach using simple algebra, provided the component phasors are known. This method only makes use of the rule of linear combination of phasors rather than fits. Without prior knowledge of the components and their single exponential decay times, resolution of components and fractions is much more challenging. Blind decomposition has been carried out only for cuvette experiments wherein the statistics in terms of the number of photons collected is very good. In this paper, we show that using the phasor approach and measurements of the decay at phasor harmonics 2 and 3, available using modern electronics, we could resolve the decay in each pixel of an image in live cells or mice liver tissues with two or more exponential components without prior knowledge of the values of the components. In this paper, blind decomposition is achieved using a graphical method for two components and a minimization method for three components. This specific use of the phasor approach to resolve multicomponents in a pixel enables applications where multiplexing species with different lifetimes and potentially different spectra can provide a different type of super-resolved image content.
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Affiliation(s)
- Alexander Vallmitjana
- Laboratory for Fluorescence Dynamics, Department of Biomedical Engineering, University of California, Irvine, California, United States
| | - Belén Torrado
- Laboratory for Fluorescence Dynamics, Department of Biomedical Engineering, University of California, Irvine, California, United States
| | - Alexander Dvornikov
- Laboratory for Fluorescence Dynamics, Department of Biomedical Engineering, University of California, Irvine, California, United States
| | - Suman Ranjit
- Department of Biochemistry and Molecular & Cellular Biology, Georgetown University, Washington, D.C., United States
| | - Enrico Gratton
- Laboratory for Fluorescence Dynamics, Department of Biomedical Engineering, University of California, Irvine, California, United States
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45
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Liu WH, Zheng J, Feldman JL, Klein MA, Kuznetsov VI, Peterson CL, Griffin PR, Denu JM. Multivalent interactions drive nucleosome binding and efficient chromatin deacetylation by SIRT6. Nat Commun 2020; 11:5244. [PMID: 33067423 PMCID: PMC7568541 DOI: 10.1038/s41467-020-19018-y] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2020] [Accepted: 09/18/2020] [Indexed: 11/30/2022] Open
Abstract
The protein deacetylase SIRT6 maintains cellular homeostasis through multiple pathways that include the deacetylation of histone H3 and repression of transcription. Prior work suggests that SIRT6 is associated with chromatin and can substantially reduce global levels of H3 acetylation, but how SIRT6 is able to accomplish this feat is unknown. Here, we describe an exquisitely tight interaction between SIRT6 and nucleosome core particles, in which a 2:1 enzyme:nucleosome complex assembles via asymmetric binding with distinct affinities. While both SIRT6 molecules associate with the acidic patch on the nucleosome, we find that the intrinsically disordered SIRT6 C-terminus promotes binding at the higher affinity site through recognition of nucleosomal DNA. Together, multivalent interactions couple productive binding to efficient deacetylation of histones on endogenous chromatin. Unique among histone deacetylases, SIRT6 possesses the intrinsic capacity to tightly interact with nucleosomes for efficient activity.
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Affiliation(s)
- Wallace H Liu
- Department of Biomolecular Chemistry, University of Wisconsin-Madison, Madison, WI, 53706, USA
- Wisconsin Institute for Discovery, University of Wisconsin-Madison, Madison, WI, 53715, USA
| | - Jie Zheng
- Department of Molecular Medicine, Scripps Research Florida, Jupiter, FL, 33458, USA
| | - Jessica L Feldman
- Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, MA, 01605, USA
| | - Mark A Klein
- Department of Biomolecular Chemistry, University of Wisconsin-Madison, Madison, WI, 53706, USA
- Wisconsin Institute for Discovery, University of Wisconsin-Madison, Madison, WI, 53715, USA
| | - Vyacheslav I Kuznetsov
- Department of Biomolecular Chemistry, University of Wisconsin-Madison, Madison, WI, 53706, USA
- Wisconsin Institute for Discovery, University of Wisconsin-Madison, Madison, WI, 53715, USA
| | - Craig L Peterson
- Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, MA, 01605, USA
| | - Patrick R Griffin
- Department of Molecular Medicine, Scripps Research Florida, Jupiter, FL, 33458, USA
| | - John M Denu
- Department of Biomolecular Chemistry, University of Wisconsin-Madison, Madison, WI, 53706, USA.
- Wisconsin Institute for Discovery, University of Wisconsin-Madison, Madison, WI, 53715, USA.
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46
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Lim Y, Bak SY, Lee SH, Kim SK. Comparative Single-Molecule Kinetic Study for the Effect of Base Methylation on a Model DNA-Protein Interaction. J Phys Chem Lett 2020; 11:8048-8052. [PMID: 32885977 DOI: 10.1021/acs.jpclett.0c01929] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
We studied how the interaction between HindIII endonuclease and dsDNA is affected by the single-base modification of the latter by a single-molecule kinetic assay. For a comparative study of chemical modifications, we measured the binding and unbinding rates of the HindIII-DNA complex for normal dsDNA, methylated DNA, and hydroxymethylated DNA. We found that methylation of DNA at the recognition site results in a large increase in the unbinding rate due to the steric effect, which is consistent with the standard free energy change in the transition state. On the contrary, methylation minimally affects the binding rate, as simultaneous increases in the activation energy and the pre-exponential factor compensate for each other.
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Affiliation(s)
- Youngbin Lim
- Department of Chemistry, Seoul National University, Seoul 08826, Korea
| | - So Young Bak
- Department of Chemistry, Seoul National University, Seoul 08826, Korea
| | - Sang Hak Lee
- Department of Chemistry, Pusan National University, Pusan 46241, Korea
| | - Seong Keun Kim
- Department of Chemistry, Seoul National University, Seoul 08826, Korea
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47
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Sobek J, Schmidt M, Grossmann J, Rehrauer H, Schmidt L, Schlapbach R. Single-molecule chemistry. Part I: monitoring oxidation of G in oligonucleotides using CY3 fluorescence. Methods Appl Fluoresc 2020; 8:035010. [PMID: 32428873 DOI: 10.1088/2050-6120/ab947d] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
Single-molecule hybridisation of CY3 dye labelled short oligonucleotides to surface immobilised probes was investigated in zero-mode waveguide nanostructures using a modified DNA sequencer. At longer measuring times, we observed changes of the initial hybridisation fluorescence pulse pattern which we attribute to products created by chemical reactions at the nucleobases. The origin is a charge separated state created by a photoinduced electron transfer from nucleobases to the dye followed by secondary reactions with oxygen and water, respectively. The positive charge can migrate through the hybrid resulting in base modifications at distant sites. Static fluorescence spectra were recorded in order to determine the properties of CY3 stacking to different base pairs, and compared to pulse intensities. A characteristic pulse pattern change was assigned to the oxidation of G to 8-oG besides the formation of a number of secondary products that are not yet identified. Further, we present a method to visualise the degree of chemical reactions to gain an overview of ongoing processes. Our study demonstrates that CY3 is able to oxidise nucleobases in ds DNA, and also in ss overhangs. An important finding is the correlation between nucleobase oxidation potential and fluorescence quenching which explains the intensity changes observed in single molecule measurements. The analysis of fluorescence traces provides the opportunity to track complete and coherent reaction sequences enabling to follow the fate of a single molecule over a long period of time, and to observe chemical reactions in real-time. This opens up the opportunity to analyse reaction pathways, to detect new products and short-lived intermediates, and to investigate rare events due to the large number of single molecules observed in parallel.
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Affiliation(s)
- Jens Sobek
- Functional Genomics Center Zurich, Eidgenössische Technische Hochschule (ETH) Zurich and University of Zurich, Winterthurerstrasse 190, 8057 Zurich, Switzerland
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48
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Isselstein M, Zhang L, Glembockyte V, Brix O, Cosa G, Tinnefeld P, Cordes T. Self-Healing Dyes-Keeping the Promise? J Phys Chem Lett 2020; 11:4462-4480. [PMID: 32401520 DOI: 10.1021/acs.jpclett.9b03833] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/20/2023]
Abstract
Self-healing dyes have emerged as a new promising class of fluorescent labels. They consist of two units, a fluorescent dye and a photostabilizer. The latter heals whenever the fluorescent dye is in danger of taking a reaction pathway toward photobleaching. We describe the underlying concepts and summarize the developmental history and state-of-the-art, including latest applications in high-resolution microscopy, live-cell, and single-molecule imaging. We further discuss remaining limitations, which are (i) lower photostabilization of most self-healing dyes when compared to solution additives, (ii) limited mechanistic understanding on the influence of the biochemical environment and molecular oxygen on self-healing, and (iii) the lack of cheap and facile bioconjugation strategies. Finally, we provide ideas on how to further advance self-healing dyes, show new data on redox blinking caused by double-stranded DNA, and highlight forthcoming work on intramolecular photostabilization of fluorescent proteins.
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Affiliation(s)
- Michael Isselstein
- Physical and Synthetic Biology, Faculty of Biology, Ludwig-Maximilians-Universität München, Großhadernerstr. 2-4, 82152 Planegg-Martinsried, Germany
| | - Lei Zhang
- Physical and Synthetic Biology, Faculty of Biology, Ludwig-Maximilians-Universität München, Großhadernerstr. 2-4, 82152 Planegg-Martinsried, Germany
| | - Viktorija Glembockyte
- Department of Chemistry and Center for NanoScience, Ludwig-Maximilians-Universität München, Butenandtstr. 5-13, Haus E 81377 München, Germany
- Department of Chemistry and Quebec Centre for Applied Materials (QCAM), McGill University, 801 Sherbrooke Street W., H3A 0B8 Montreal, Quebec, Canada
| | - Oliver Brix
- Physical and Synthetic Biology, Faculty of Biology, Ludwig-Maximilians-Universität München, Großhadernerstr. 2-4, 82152 Planegg-Martinsried, Germany
| | - Gonzalo Cosa
- Department of Chemistry and Quebec Centre for Applied Materials (QCAM), McGill University, 801 Sherbrooke Street W., H3A 0B8 Montreal, Quebec, Canada
| | - Philip Tinnefeld
- Department of Chemistry and Center for NanoScience, Ludwig-Maximilians-Universität München, Butenandtstr. 5-13, Haus E 81377 München, Germany
| | - Thorben Cordes
- Physical and Synthetic Biology, Faculty of Biology, Ludwig-Maximilians-Universität München, Großhadernerstr. 2-4, 82152 Planegg-Martinsried, Germany
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49
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Clark R, Nawawi MA, Dobre A, Pugh D, Liu Q, Ivanov AP, White AJP, Edel JB, Kuimova MK, McIntosh AJS, Welton T. The effect of structural heterogeneity upon the microviscosity of ionic liquids. Chem Sci 2020; 11:6121-6133. [PMID: 32874514 PMCID: PMC7448533 DOI: 10.1039/d0sc02009e] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2020] [Accepted: 05/26/2020] [Indexed: 01/25/2023] Open
Abstract
The behaviour of two molecular rotors, one charged - 3,3'-diethylthiacarbocyanine iodide (Cy3) and one neutral - 8-[4-decyloxyphenyl]-4,4-difluoro-4-bora-3a,4a-diaza-s-indacene (BODIPY-C10), have been studied in various ionic liquids. The fluorescent decay lifetime has been used to elucidate the structure of the immediate region around the rotor. The neutral BODIPY-C10 was found to prefer the non-polar alkyl chain environment, leading to two trends in the lifetime of the dye: one when it was fully partitioned into the non-polar domain, and one when it also sampled polar moieties. The positively charged Cy3 dye showed a complex relationship between the bulk viscosity of the ionic liquid and lifetime of the molecular rotor. This was attributed to a combination of polarity related spectral changes, changes in anion cages around the dye, and temperature dependent fluorescent lifetimes alongside the dependence of the rotor upon the viscosity.
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Affiliation(s)
- Ryan Clark
- Department of Chemistry , Molecular Science Research Hub , Imperial College London , 80 Wood Lane , London , W12 0BZ , UK .
| | - Mohd A Nawawi
- Department of Chemistry , Molecular Science Research Hub , Imperial College London , 80 Wood Lane , London , W12 0BZ , UK .
| | - Ana Dobre
- Department of Chemistry , Molecular Science Research Hub , Imperial College London , 80 Wood Lane , London , W12 0BZ , UK .
| | - David Pugh
- Department of Chemistry , Molecular Science Research Hub , Imperial College London , 80 Wood Lane , London , W12 0BZ , UK . .,Department of Chemistry , Kings College London , Britannia House, 7 Trinity Street , London , SE1 1DB , UK
| | - Qingshan Liu
- Department of Chemistry , Molecular Science Research Hub , Imperial College London , 80 Wood Lane , London , W12 0BZ , UK . .,School of Science , Shenyang Agricultural University , Shenyang 110866 , P. R. China
| | - Aleksandar P Ivanov
- Department of Chemistry , Molecular Science Research Hub , Imperial College London , 80 Wood Lane , London , W12 0BZ , UK .
| | - Andrew J P White
- Department of Chemistry , Molecular Science Research Hub , Imperial College London , 80 Wood Lane , London , W12 0BZ , UK .
| | - Joshua B Edel
- Department of Chemistry , Molecular Science Research Hub , Imperial College London , 80 Wood Lane , London , W12 0BZ , UK .
| | - Marina K Kuimova
- Department of Chemistry , Molecular Science Research Hub , Imperial College London , 80 Wood Lane , London , W12 0BZ , UK .
| | - Alastair J S McIntosh
- Department of Chemistry , Molecular Science Research Hub , Imperial College London , 80 Wood Lane , London , W12 0BZ , UK .
| | - Tom Welton
- Department of Chemistry , Molecular Science Research Hub , Imperial College London , 80 Wood Lane , London , W12 0BZ , UK .
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50
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Morla-Folch J, Vargas-Nadal G, Zhao T, Sissa C, Ardizzone A, Kurhuzenkau S, Köber M, Uddin M, Painelli A, Veciana J, Belfield KD, Ventosa N. Dye-Loaded Quatsomes Exhibiting FRET as Nanoprobes for Bioimaging. ACS APPLIED MATERIALS & INTERFACES 2020; 12:20253-20262. [PMID: 32268722 DOI: 10.1021/acsami.0c03040] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Fluorescent organic nanoparticles (FONs) are emerging as an attractive alternative to the well-established fluorescent inorganic nanoparticles or small organic dyes. Their proper design allows one to obtain biocompatible probes with superior brightness and high photostability, although usually affected by low colloidal stability. Herein, we present a type of FONs with outstanding photophysical and physicochemical properties in-line with the stringent requirements for biomedical applications. These FONs are based on quatsome (QS) nanovesicles containing a pair of fluorescent carbocyanine molecules that give rise to Förster resonance energy transfer (FRET). Structural homogeneity, high brightness, photostability, and high FRET efficiency make these FONs a promising class of optical bioprobes. Loaded QSs have been used for in vitro bioimaging, demonstrating the nanovesicle membrane integrity after cell internalization, and the possibility to monitor the intracellular vesicle fate. Taken together, the proposed QSs loaded with a FRET pair constitute a promising platform for bioimaging and theranostics.
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Affiliation(s)
- Judit Morla-Folch
- Institut Ciencia dels Materials de Barcelona (ICMAB-CSIC), Campus UAB, 08193 Cerdanyola, Spain
- Department of Chemistry and Environmental Science, College of Science and Liberal Arts, New Jersey Institute of Technology, 323 Martin Luther King, Jr., Blvd., Newark, New Jersey 07102, United States
| | - Guillem Vargas-Nadal
- Institut Ciencia dels Materials de Barcelona (ICMAB-CSIC), Campus UAB, 08193 Cerdanyola, Spain
| | - Tinghan Zhao
- Department of Chemistry and Environmental Science, College of Science and Liberal Arts, New Jersey Institute of Technology, 323 Martin Luther King, Jr., Blvd., Newark, New Jersey 07102, United States
| | - Cristina Sissa
- Dipartimento di Scienze Chimiche, della Vita e della Sostenibilità Ambientale, Università di Parma, Parco Area delle Scienze 17/A, 43124 Parma, Italy
| | - Antonio Ardizzone
- Institut Ciencia dels Materials de Barcelona (ICMAB-CSIC), Campus UAB, 08193 Cerdanyola, Spain
| | - Siarhei Kurhuzenkau
- Dipartimento di Scienze Chimiche, della Vita e della Sostenibilità Ambientale, Università di Parma, Parco Area delle Scienze 17/A, 43124 Parma, Italy
| | - Mariana Köber
- Institut Ciencia dels Materials de Barcelona (ICMAB-CSIC), Campus UAB, 08193 Cerdanyola, Spain
- Centro de Investigación Biomédica en Red CIBER-BBN, Barcelona, Spain
| | - Mehrun Uddin
- Department of Chemistry and Environmental Science, College of Science and Liberal Arts, New Jersey Institute of Technology, 323 Martin Luther King, Jr., Blvd., Newark, New Jersey 07102, United States
| | - Anna Painelli
- Dipartimento di Scienze Chimiche, della Vita e della Sostenibilità Ambientale, Università di Parma, Parco Area delle Scienze 17/A, 43124 Parma, Italy
| | - Jaume Veciana
- Institut Ciencia dels Materials de Barcelona (ICMAB-CSIC), Campus UAB, 08193 Cerdanyola, Spain
- Centro de Investigación Biomédica en Red CIBER-BBN, Barcelona, Spain
| | - Kevin D Belfield
- Department of Chemistry and Environmental Science, College of Science and Liberal Arts, New Jersey Institute of Technology, 323 Martin Luther King, Jr., Blvd., Newark, New Jersey 07102, United States
| | - Nora Ventosa
- Institut Ciencia dels Materials de Barcelona (ICMAB-CSIC), Campus UAB, 08193 Cerdanyola, Spain
- Centro de Investigación Biomédica en Red CIBER-BBN, Barcelona, Spain
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