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Schaich MA, Schnable BL, Kumar N, Roginskaya V, Jakielski R, Urban R, Zhong Z, Kad NM, Van Houten B. Single-molecule analysis of DNA-binding proteins from nuclear extracts (SMADNE). Nucleic Acids Res 2023; 51:e39. [PMID: 36861323 PMCID: PMC10123111 DOI: 10.1093/nar/gkad095] [Citation(s) in RCA: 12] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2022] [Revised: 01/19/2023] [Accepted: 02/08/2023] [Indexed: 03/03/2023] Open
Abstract
Single-molecule characterization of protein-DNA dynamics provides unprecedented mechanistic details about numerous nuclear processes. Here, we describe a new method that rapidly generates single-molecule information with fluorescently tagged proteins isolated from nuclear extracts of human cells. We demonstrated the wide applicability of this novel technique on undamaged DNA and three forms of DNA damage using seven native DNA repair proteins and two structural variants, including: poly(ADP-ribose) polymerase (PARP1), heterodimeric ultraviolet-damaged DNA-binding protein (UV-DDB), and 8-oxoguanine glycosylase 1 (OGG1). We found that PARP1 binding to DNA nicks is altered by tension, and that UV-DDB did not act as an obligate heterodimer of DDB1 and DDB2 on UV-irradiated DNA. UV-DDB bound to UV photoproducts with an average lifetime of 39 seconds (corrected for photobleaching, τc), whereas binding lifetimes to 8-oxoG adducts were < 1 second. Catalytically inactive OGG1 variant K249Q bound oxidative damage 23-fold longer than WT OGG1, at 47 and 2.0 s, respectively. By measuring three fluorescent colors simultaneously, we also characterized the assembly and disassembly kinetics of UV-DDB and OGG1 complexes on DNA. Hence, the SMADNE technique represents a novel, scalable, and universal method to obtain single-molecule mechanistic insights into key protein-DNA interactions in an environment containing physiologically-relevant nuclear proteins.
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Affiliation(s)
- Matthew A Schaich
- Department of Pharmacology and Chemical Biology, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
- UPMC-Hillman Cancer Center, Pittsburgh, PA, 15232, USA
| | - Brittani L Schnable
- UPMC-Hillman Cancer Center, Pittsburgh, PA, 15232, USA
- Molecular Biophysics and Structural Biology Program, University of Pittsburgh, Pittsburgh, PA, USA
| | - Namrata Kumar
- UPMC-Hillman Cancer Center, Pittsburgh, PA, 15232, USA
- Molecular Genetics and Developmental Biology Graduate Program, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| | | | - Rachel C Jakielski
- Department of Pharmacology and Chemical Biology, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
- UPMC-Hillman Cancer Center, Pittsburgh, PA, 15232, USA
| | - Roman Urban
- School of Biosciences, University of Kent, Kent, UK
| | - Zhou Zhong
- Department of Pharmacology and Chemical Biology, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
- UPMC-Hillman Cancer Center, Pittsburgh, PA, 15232, USA
- LUMICKS, Waltham, MA, USA
| | - Neil M Kad
- School of Biosciences, University of Kent, Kent, UK
| | - Bennett Van Houten
- Department of Pharmacology and Chemical Biology, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
- UPMC-Hillman Cancer Center, Pittsburgh, PA, 15232, USA
- Molecular Genetics and Developmental Biology Graduate Program, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
- Molecular Biophysics and Structural Biology Program, University of Pittsburgh, Pittsburgh, PA, USA
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2
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Erbaş A, Marko JF. How do DNA-bound proteins leave their binding sites? The role of facilitated dissociation. Curr Opin Chem Biol 2019; 53:118-124. [PMID: 31586479 PMCID: PMC6926143 DOI: 10.1016/j.cbpa.2019.08.007] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2019] [Revised: 07/11/2019] [Accepted: 08/24/2019] [Indexed: 10/25/2022]
Abstract
Dissociation of a protein from DNA is often assumed to be described by an off rate that is independent of other molecules in solution. Recent experiments and computational analyses have challenged this view by showing that unbinding rates (residence times) of DNA-bound proteins can depend on concentrations of nearby molecules that are competing for binding. This 'facilitated dissociation' (FD) process can occur at the single-binding site level via formation of a ternary complex, and can dominate over 'spontaneous dissociation' at low (submicromolar) concentrations. In the crowded intracellular environment FD introduces new regulatory possibilities at the level of individual biomolecule interactions.
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Affiliation(s)
- Aykut Erbaş
- UNAM-National Nanotechnology Research Center and Institute of Materials Science & Nanotechnology, Bilkent University, Ankara 06800, Turkey
| | - John F Marko
- Department of Molecular Biosciences, Northwestern University, Evanston, IL 60208, USA; Department of Physics & Astronomy, Northwestern University, Evanston, IL 60208, USA
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3
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Dahlke K, Zhao J, Sing CE, Banigan EJ. Force-Dependent Facilitated Dissociation Can Generate Protein-DNA Catch Bonds. Biophys J 2019; 117:1085-1100. [PMID: 31427067 DOI: 10.1016/j.bpj.2019.07.044] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2019] [Revised: 07/08/2019] [Accepted: 07/29/2019] [Indexed: 12/31/2022] Open
Abstract
Cellular structures are continually subjected to forces, which may serve as mechanical signals for cells through their effects on biomolecule interaction kinetics. Typically, molecular complexes interact via "slip bonds," so applied forces accelerate off rates by reducing transition energy barriers. However, biomolecules with multiple dissociation pathways may have considerably more complicated force dependencies. This is the case for DNA-binding proteins that undergo "facilitated dissociation," in which competitor biomolecules from solution enhance molecular dissociation in a concentration-dependent manner. Using simulations and theory, we develop a generic model that shows that proteins undergoing facilitated dissociation can form an alternative type of molecular bond, known as a "catch bond," for which applied forces suppress protein dissociation. This occurs because the binding by protein competitors responsible for the facilitated dissociation pathway can be inhibited by applied forces. Within the model, we explore how the force dependence of dissociation is regulated by intrinsic factors, including molecular sensitivity to force and binding geometry and the extrinsic factor of competitor protein concentration. We find that catch bonds generically emerge when the force dependence of the facilitated unbinding pathway is stronger than that of the spontaneous unbinding pathway. The sharpness of the transition between slip- and catch-bond kinetics depends on the degree to which the protein bends its DNA substrate. This force-dependent kinetics is broadly regulated by the concentration of competitor biomolecules in solution. Thus, the observed catch bond is mechanistically distinct from other known physiological catch bonds because it requires an extrinsic factor-competitor proteins-rather than a specific intrinsic molecular structure. We hypothesize that this mechanism for regulating force-dependent protein dissociation may be used by cells to modulate protein exchange, regulate transcription, and facilitate diffusive search processes.
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Affiliation(s)
- Katelyn Dahlke
- Department of Chemical and Biomolecular Engineering, University of Illinois at Urbana-Champaign, Urbana, Illinois
| | - Jing Zhao
- Department of Chemical and Biomolecular Engineering, University of Illinois at Urbana-Champaign, Urbana, Illinois
| | - Charles E Sing
- Department of Chemical and Biomolecular Engineering, University of Illinois at Urbana-Champaign, Urbana, Illinois.
| | - Edward J Banigan
- Institute for Medical Engineering and Science and Department of Physics, Massachusetts Institute of Technology, Cambridge, Massachusetts.
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4
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Abstract
We review the current understanding of the mechanics of DNA and DNA-protein complexes, from scales of base pairs up to whole chromosomes. Mechanics of the double helix as revealed by single-molecule experiments will be described, with an emphasis on the role of polymer statistical mechanics. We will then discuss how topological constraints- entanglement and supercoiling-impact physical and mechanical responses. Models for protein-DNA interactions, including effects on polymer properties of DNA of DNA-bending proteins will be described, relevant to behavior of protein-DNA complexes in vivo. We also discuss control of DNA entanglement topology by DNA-lengthwise-compaction machinery acting in concert with topoisomerases. Finally, the chapter will conclude with a discussion of relevance of several aspects of physical properties of DNA and chromatin to oncology.
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5
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Zhou R, Yang O, Déclais AC, Jin H, Gwon GH, Freeman ADJ, Cho Y, Lilley DMJ, Ha T. Junction resolving enzymes use multivalency to keep the Holliday junction dynamic. Nat Chem Biol 2019; 15:269-275. [PMID: 30664685 PMCID: PMC6377835 DOI: 10.1038/s41589-018-0209-y] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2017] [Accepted: 11/30/2018] [Indexed: 11/21/2022]
Abstract
Holliday junction (HJ) resolution by resolving enzymes is essential for chromosome segregation and recombination-mediated DNA repair. HJs undergo two types of structural dynamics that determine the outcome of recombination: conformer exchange between two isoforms and branch migration. However, it is unknown how the preferred branch point and conformer are achieved between enzyme binding and HJ resolution given the extensive binding interactions seen in static crystal structures. Single-molecule fluorescence resonance energy transfer analysis of resolving enzymes from bacteriophages (T7 endonuclease I), bacteria (RuvC), fungi (GEN1) and humans (hMus81-Eme1) showed that both types of HJ dynamics still occur after enzyme binding. These dimeric enzymes use their multivalent interactions to achieve this, going through a partially dissociated intermediate in which the HJ undergoes nearly unencumbered dynamics. This evolutionarily conserved property of HJ resolving enzymes provides previously unappreciated insight on how junction resolution, conformer exchange and branch migration may be coordinated.
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Affiliation(s)
- Ruobo Zhou
- Department of Physics and Center for the Physics of Living Cells, University of Illinois at Urbana-Champaign, Champaign, IL, USA.
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA, USA.
| | - Olivia Yang
- Department of Biophysics and Biophysical Chemistry, Johns Hopkins University, Baltimore, MD, USA
| | - Anne-Cécile Déclais
- Cancer Research UK Nucleic Acid Structure Research Group, School of Life Sciences, The University of Dundee, Dundee, UK
| | - Hyeonseok Jin
- Department of Life Science, Pohang University of Science and Technology, Pohang, South Korea
| | - Gwang Hyeon Gwon
- Department of Life Science, Pohang University of Science and Technology, Pohang, South Korea
| | - Alasdair D J Freeman
- Cancer Research UK Nucleic Acid Structure Research Group, School of Life Sciences, The University of Dundee, Dundee, UK
| | - Yunje Cho
- Department of Life Science, Pohang University of Science and Technology, Pohang, South Korea
| | - David M J Lilley
- Cancer Research UK Nucleic Acid Structure Research Group, School of Life Sciences, The University of Dundee, Dundee, UK
| | - Taekjip Ha
- Department of Physics and Center for the Physics of Living Cells, University of Illinois at Urbana-Champaign, Champaign, IL, USA.
- Department of Biophysics and Biophysical Chemistry, Johns Hopkins University, Baltimore, MD, USA.
- Howard Hughes Medical Institute, Baltimore, MD, USA.
- Department of Biophysics, Johns Hopkins University, Baltimore, MD, USA.
- Department of Biomedical Engineering, Johns Hopkins University, Baltimore, MD, USA.
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6
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Abstract
Genetic recombination occurs in all organisms and is vital for genome stability. Indeed, in humans, aberrant recombination can lead to diseases such as cancer. Our understanding of homologous recombination is built upon more than a century of scientific inquiry, but achieving a more complete picture using ensemble biochemical and genetic approaches is hampered by population heterogeneity and transient recombination intermediates. Recent advances in single-molecule and super-resolution microscopy methods help to overcome these limitations and have led to new and refined insights into recombination mechanisms, including a detailed understanding of DNA helicase function and synaptonemal complex structure. The ability to view cellular processes at single-molecule resolution promises to transform our understanding of recombination and related processes.
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7
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Abstract
The complex genetic programs of eukaryotic cells are often regulated by key transcription factors occupying or clearing out of a large number of genomic locations. Orchestrating the residence times of these factors is therefore important for the well organized functioning of a large network. The classic models of genetic switches sidestep this timing issue by assuming the binding of transcription factors to be governed entirely by thermodynamic protein-DNA affinities. Here we show that relying on passive thermodynamics and random release times can lead to a "time-scale crisis" for master genes that broadcast their signals to a large number of binding sites. We demonstrate that this time-scale crisis for clearance in a large broadcasting network can be resolved by actively regulating residence times through molecular stripping. We illustrate these ideas by studying a model of the stochastic dynamics of the genetic network of the central eukaryotic master regulator NFκB which broadcasts its signals to many downstream genes that regulate immune response, apoptosis, etc.
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Affiliation(s)
- Davit A Potoyan
- Department of Chemistry and Center for Theoretical Biological Physics, Rice University, Houston, Texas 77005, USA
| | - Peter G Wolynes
- Department of Chemistry and Center for Theoretical Biological Physics, Rice University, Houston, Texas 77005, USA
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8
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Ma CJ, Gibb B, Kwon Y, Sung P, Greene EC. Protein dynamics of human RPA and RAD51 on ssDNA during assembly and disassembly of the RAD51 filament. Nucleic Acids Res 2016; 45:749-761. [PMID: 27903895 PMCID: PMC5314761 DOI: 10.1093/nar/gkw1125] [Citation(s) in RCA: 109] [Impact Index Per Article: 13.6] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2016] [Revised: 10/21/2016] [Accepted: 10/27/2016] [Indexed: 12/31/2022] Open
Abstract
Homologous recombination (HR) is a crucial pathway for double-stranded DNA break (DSB) repair. During the early stages of HR, the newly generated DSB ends are processed to yield long single-stranded DNA (ssDNA) overhangs, which are quickly bound by replication protein A (RPA). RPA is then replaced by the DNA recombinase Rad51, which forms extended helical filaments on the ssDNA. The resulting nucleoprotein filament, known as the presynaptic complex, is responsible for pairing the ssDNA with homologous double-stranded DNA (dsDNA), which serves as the template to guide DSB repair. Here, we use single-molecule imaging to visualize the interplay between human RPA (hRPA) and human RAD51 during presynaptic complex assembly and disassembly. We demonstrate that ssDNA-bound hRPA can undergo facilitated exchange, enabling hRPA to undergo rapid exchange between free and ssDNA-bound states only when free hRPA is present in solution. Our results also indicate that the presence of free hRPA inhibits RAD51 filament nucleation, but has a lesser impact upon filament elongation. This finding suggests that hRPA exerts important regulatory influence over RAD51 and may in turn affect the properties of the assembled RAD51 filament. These experiments provide an important basis for further investigations into the regulation of human presynaptic complex assembly.
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Affiliation(s)
- Chu Jian Ma
- Department of Biochemistry & Molecular Biophysics, Columbia University, New York, NY 10032, USA
| | - Bryan Gibb
- Department of Biochemistry & Molecular Biophysics, Columbia University, New York, NY 10032, USA
| | - YoungHo Kwon
- Department of Molecular Biophysics and Biochemistry, Yale University School of Medicine, New Haven, CT 06520, USA
| | - Patrick Sung
- Department of Molecular Biophysics and Biochemistry, Yale University School of Medicine, New Haven, CT 06520, USA
| | - Eric C Greene
- Department of Biochemistry & Molecular Biophysics, Columbia University, New York, NY 10032, USA
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9
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Abstract
Homologous recombination is an important pathway involved in the repair of double-stranded DNA breaks. Genetic studies form the foundation of our knowledge on homologous recombination. Significant progress has also been made toward understanding the biochemical and biophysical properties of the proteins, complexes, and reaction intermediates involved in this essential DNA repair pathway. However, heterogeneous or transient recombination intermediates remain extremely difficult to assess through traditional ensemble methods, leaving an incomplete mechanistic picture of many steps that take place during homologous recombination. To help overcome some of these limitations, we have established DNA curtain methodologies as an experimental platform for studying homologous DNA recombination in real-time at the single-molecule level. Here, we present a detailed overview describing the preparation and use of single-stranded DNA curtains in applications related to the study of homologous DNA recombination with emphasis on recent work related to the study of the eukaryotic recombinase Rad51.
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10
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Abstract
Chromatin regulatory processes, like all biological reactions, are dynamic and stochastic in nature but can give rise to stable and inheritable changes in gene expression patterns. A molecular understanding of those processes is key for fundamental biological insight into gene regulation, epigenetic inheritance, lineage determination, and therapeutic intervention in the case of disease. In recent years, great progress has been made in identifying important molecular players involved in key chromatin regulatory pathways. Conversely, we are only beginning to understand the dynamic interplay between protein effectors, transcription factors, and the chromatin substrate itself. Single-molecule approaches employing both highly defined chromatin substrates in vitro, as well as direct observation of complex regulatory processes in vivo, open new avenues for a molecular view of chromatin regulation. This review highlights recent applications of single-molecule methods and related techniques to investigate fundamental chromatin regulatory processes.
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Affiliation(s)
- Beat Fierz
- Laboratory
of Biophysical
Chemistry of Macromolecules, Institute of Chemical Sciences and Engineering, Ecole Polytechnique Fédérale de Lausanne (EPFL), 1015 Lausanne, Switzerland
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11
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Kath JE, Chang S, Scotland MK, Wilbertz JH, Jergic S, Dixon NE, Sutton MD, Loparo JJ. Exchange between Escherichia coli polymerases II and III on a processivity clamp. Nucleic Acids Res 2015; 44:1681-90. [PMID: 26657641 PMCID: PMC4770218 DOI: 10.1093/nar/gkv1375] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2015] [Accepted: 11/25/2015] [Indexed: 12/21/2022] Open
Abstract
Escherichia coli has three DNA polymerases implicated in the bypass of DNA damage, a process called translesion synthesis (TLS) that alleviates replication stalling. Although these polymerases are specialized for different DNA lesions, it is unclear if they interact differently with the replication machinery. Of the three, DNA polymerase (Pol) II remains the most enigmatic. Here we report a stable ternary complex of Pol II, the replicative polymerase Pol III core complex and the dimeric processivity clamp, β. Single-molecule experiments reveal that the interactions of Pol II and Pol III with β allow for rapid exchange during DNA synthesis. As with another TLS polymerase, Pol IV, increasing concentrations of Pol II displace the Pol III core during DNA synthesis in a minimal reconstitution of primer extension. However, in contrast to Pol IV, Pol II is inefficient at disrupting rolling-circle synthesis by the fully reconstituted Pol III replisome. Together, these data suggest a β-mediated mechanism of exchange between Pol II and Pol III that occurs outside the replication fork.
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Affiliation(s)
- James E Kath
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115, USA
| | - Seungwoo Chang
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115, USA
| | - Michelle K Scotland
- Department of Biochemistry, University at Buffalo, State University of New York, Buffalo, NY 14214, USA Witebsky Center for Microbial Pathogenesis and Immunology, University at Buffalo, State University of New York, Buffalo, NY 14214, USA
| | - Johannes H Wilbertz
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115, USA
| | - Slobodan Jergic
- Centre for Medical & Molecular Bioscience, Illawarra Health & Medical Research Institute and University of Wollongong, New South Wales 2522, Australia
| | - Nicholas E Dixon
- Centre for Medical & Molecular Bioscience, Illawarra Health & Medical Research Institute and University of Wollongong, New South Wales 2522, Australia
| | - Mark D Sutton
- Department of Biochemistry, University at Buffalo, State University of New York, Buffalo, NY 14214, USA Witebsky Center for Microbial Pathogenesis and Immunology, University at Buffalo, State University of New York, Buffalo, NY 14214, USA Genetics, Genomics and Bioinformatics Program, University at Buffalo, State University of New York, Buffalo, NY 14214, USA
| | - Joseph J Loparo
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115, USA
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12
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Zhang J, Fei J, Leslie BJ, Han KY, Kuhlman TE, Ha T. Tandem Spinach Array for mRNA Imaging in Living Bacterial Cells. Sci Rep 2015; 5:17295. [PMID: 26612428 PMCID: PMC4661537 DOI: 10.1038/srep17295] [Citation(s) in RCA: 71] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2015] [Accepted: 10/15/2015] [Indexed: 12/24/2022] Open
Abstract
Live cell RNA imaging using genetically encoded fluorescent labels is an important tool for monitoring RNA activities. A recently reported RNA aptamer-fluorogen system, the Spinach, in which an RNA aptamer binds and induces the fluorescence of a GFP-like 3,5-difluoro-4-hydroxybenzylidene imidazolinone (DFHBI) ligand, can be readily tagged to the RNA of interest. Although the aptamer-fluorogen system is sufficient for imaging highly abundant non-coding RNAs (tRNAs, rRNAs, etc.), it performs poorly for mRNA imaging due to low brightness. In addition, whether the aptamer-fluorogen system may perturb the native RNA characteristics has not been systematically characterized at the levels of RNA transcription, translation and degradation. To increase the brightness of these aptamer-fluorogen systems, we constructed and tested tandem arrays containing multiple Spinach aptamers (8-64 aptamer repeats). Such arrays enhanced the brightness of the tagged mRNA molecules by up to ~17 fold in living cells. Strong laser excitation with pulsed illumination further increased the imaging sensitivity of Spinach array-tagged RNAs. Moreover, transcriptional fusion to the Spinach array did not affect mRNA transcription, translation or degradation, indicating that aptamer arrays might be a generalizable labeling method for high-performance and low-perturbation live cell RNA imaging.
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Affiliation(s)
- Jichuan Zhang
- Department of Physics and Center for the Physics of Living Cells, University of Illinois at Urbana-Champaign, Urbana, IL 61801 USA
- Department of Materials Science and Engineering, University of Illinois at Urbana-Champaign, Urbana, IL 61801 USA
| | - Jingyi Fei
- Department of Physics and Center for the Physics of Living Cells, University of Illinois at Urbana-Champaign, Urbana, IL 61801 USA
| | - Benjamin J. Leslie
- Department of Physics and Center for the Physics of Living Cells, University of Illinois at Urbana-Champaign, Urbana, IL 61801 USA
- Howard Hughes Medical Institute, Baltimore, MD 21205 USA
| | - Kyu Young Han
- Department of Physics and Center for the Physics of Living Cells, University of Illinois at Urbana-Champaign, Urbana, IL 61801 USA
- Howard Hughes Medical Institute, Baltimore, MD 21205 USA
| | - Thomas E. Kuhlman
- Department of Physics and Center for the Physics of Living Cells, University of Illinois at Urbana-Champaign, Urbana, IL 61801 USA
| | - Taekjip Ha
- Department of Physics and Center for the Physics of Living Cells, University of Illinois at Urbana-Champaign, Urbana, IL 61801 USA
- Department of Biophysics and Biophysical Chemistry, Johns Hopkins University School of Medicine, Baltimore, MD 21205 USA
- Department of Biophysics, Johns Hopkins University, Baltimore, MD 21218 USA
- Department of Biomedical Engineering, Johns Hopkins University, Baltimore, MD 21205 USA
- Howard Hughes Medical Institute, Baltimore, MD 21205 USA
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13
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Concentration- and chromosome-organization-dependent regulator unbinding from DNA for transcription regulation in living cells. Nat Commun 2015; 6:7445. [PMID: 26145755 PMCID: PMC4507017 DOI: 10.1038/ncomms8445] [Citation(s) in RCA: 71] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2014] [Accepted: 05/11/2015] [Indexed: 02/04/2023] Open
Abstract
Binding and unbinding of transcription regulators at operator sites constitute a primary mechanism for gene regulation. While many cellular factors are known to regulate their binding, little is known on how cells can modulate their unbinding for regulation. Using nanometer-precision single-molecule tracking, we study the unbinding kinetics from DNA of two metal-sensing transcription regulators in living Escherichia coli cells. We find that they show unusual concentration-dependent unbinding kinetics from chromosomal recognition sites in both their apo and holo forms. Unexpectedly, their unbinding kinetics further varies with the extent of chromosome condensation, and more surprisingly, varies in opposite ways for their apo-repressor versus holo-activator forms. These findings suggest likely broadly relevant mechanisms for facile switching between transcription activation and deactivation in vivo and in coordinating transcription regulation of resistance genes with the cell cycle. Binding and unbinding of transcription regulators at operator sites regulates gene expression. By single-molecule tracking of metal-sensing regulators, here the authors show that the unbinding kinetics depends on regulator concentration and chromosome condensation, and varies with their metal-binding states.
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14
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Kilic S, Bachmann AL, Bryan LC, Fierz B. Multivalency governs HP1α association dynamics with the silent chromatin state. Nat Commun 2015; 6:7313. [PMID: 26084584 PMCID: PMC4557296 DOI: 10.1038/ncomms8313] [Citation(s) in RCA: 68] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2014] [Accepted: 04/26/2015] [Indexed: 01/14/2023] Open
Abstract
Multivalent interactions between effector proteins and histone post-translational modifications are an elementary mechanism of dynamic chromatin signalling. Here we elucidate the mechanism how heterochromatin protein 1α (HP1α), a multivalent effector, is efficiently recruited to the silent chromatin state (marked by trimethylated H3 at Lys9, H3K9me3) while remaining highly dynamic. Employing chemically defined nucleosome arrays together with single-molecule total internal reflection fluorescence microscopy (smTIRFM), we demonstrate that the HP1α residence time on chromatin depends on the density of H3K9me3, as dissociated factors can rapidly rebind at neighbouring sites. Moreover, by chemically controlling HP1α dimerization we find that effector multivalency prolongs chromatin retention and, importantly, accelerates the association rate. This effect results from increased avidity together with strengthened nonspecific chromatin interactions of dimeric HP1α. We propose that accelerated chromatin binding is a key feature of effector multivalency, allowing for fast and efficient competition for binding sites in the crowded nuclear compartment. Chromatin effector proteins often employ multivalent interactions with histone post-translational modifications. Here by using chemically defined nucleosome array and single-molecule microscopy, the authors show that effector multivalency prolongs chromatin retention and accelerates the association rate.
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Affiliation(s)
- Sinan Kilic
- Laboratory of Biophysical Chemistry of Macromolecules, Institute of Chemical Sciences and Engineering, Ecole Polytechnique Fédérale de Lausanne (EPFL), 1015 Lausanne, Switzerland
| | - Andreas L Bachmann
- Laboratory of Biophysical Chemistry of Macromolecules, Institute of Chemical Sciences and Engineering, Ecole Polytechnique Fédérale de Lausanne (EPFL), 1015 Lausanne, Switzerland
| | - Louise C Bryan
- Laboratory of Biophysical Chemistry of Macromolecules, Institute of Chemical Sciences and Engineering, Ecole Polytechnique Fédérale de Lausanne (EPFL), 1015 Lausanne, Switzerland
| | - Beat Fierz
- Laboratory of Biophysical Chemistry of Macromolecules, Institute of Chemical Sciences and Engineering, Ecole Polytechnique Fédérale de Lausanne (EPFL), 1015 Lausanne, Switzerland
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15
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Abstract
The function of DNA in cells depends on its interactions with protein molecules, which recognize and act on base sequence patterns along the double helix. These notes aim to introduce basic polymer physics of DNA molecules, biophysics of protein-DNA interactions and their study in single-DNA experiments, and some aspects of large-scale chromosome structure. Mechanisms for control of chromosome topology will also be discussed.
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Affiliation(s)
- John F Marko
- Department of Physics & Astronomy and Department of Molecular Biosciences, Northwestern University, Evanston, Illinois USA 60208
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16
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MacDougall DD, Gonzalez RL. Translation initiation factor 3 regulates switching between different modes of ribosomal subunit joining. J Mol Biol 2014; 427:1801-18. [PMID: 25308340 DOI: 10.1016/j.jmb.2014.09.024] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2014] [Revised: 09/22/2014] [Accepted: 09/24/2014] [Indexed: 11/30/2022]
Abstract
Ribosomal subunit joining is a key checkpoint in the bacterial translation initiation pathway during which initiation factors (IFs) regulate association of the 30S initiation complex (IC) with the 50S subunit to control formation of a 70S IC that can enter into the elongation stage of protein synthesis. The GTP-bound form of IF2 accelerates subunit joining, whereas IF3 antagonizes subunit joining and plays a prominent role in maintaining translation initiation fidelity. The molecular mechanisms through which IF2 and IF3 collaborate to regulate the efficiency of 70S IC formation, including how they affect the dynamics of subunit joining, remain poorly defined. Here, we use single-molecule fluorescence resonance energy transfer to monitor the interactions between IF2 and the GTPase-associated center (GAC) of the 50S subunit during real-time subunit joining reactions in the absence and presence of IF3. In the presence of IF3, IF2-mediated subunit joining becomes reversible, and subunit joining events cluster into two distinct classes corresponding to formation of shorter- and longer-lifetime 70S ICs. Inclusion of IF3 within the 30S IC was also found to alter the conformation of IF2 relative to the GAC, suggesting that IF3's regulatory effects may stem in part from allosteric modulation of IF2-GAC interactions. The results are consistent with a model in which IF3 can exert control over the efficiency of subunit joining by modulating the conformation of the 30S IC, which in turn influences the formation of stabilizing intersubunit contacts and thus the reaction's degree of reversibility.
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Affiliation(s)
- Daniel D MacDougall
- Columbia University Department of Chemistry, 3000 Broadway, New York, NY 10027, USA
| | - Ruben L Gonzalez
- Columbia University Department of Chemistry, 3000 Broadway, New York, NY 10027, USA.
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17
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Fiore VF, Ju L, Chen Y, Zhu C, Barker TH. Dynamic catch of a Thy-1–α5β1+syndecan-4 trimolecular complex. Nat Commun 2014; 5:4886. [DOI: 10.1038/ncomms5886] [Citation(s) in RCA: 74] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2014] [Accepted: 08/01/2014] [Indexed: 01/09/2023] Open
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18
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Huber T, Sakmar T. Chemical Biology Methods for Investigating G Protein-Coupled Receptor Signaling. ACTA ACUST UNITED AC 2014; 21:1224-37. [DOI: 10.1016/j.chembiol.2014.08.009] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2014] [Revised: 07/21/2014] [Accepted: 08/20/2014] [Indexed: 11/26/2022]
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19
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Cocco S, Marko JF, Monasson R. Stochastic ratchet mechanisms for replacement of proteins bound to DNA. PHYSICAL REVIEW LETTERS 2014; 112:238101. [PMID: 24972228 PMCID: PMC4131839 DOI: 10.1103/physrevlett.112.238101] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/20/2013] [Indexed: 06/01/2023]
Abstract
Experiments indicate that unbinding rates of proteins from DNA can depend on the concentration of proteins in nearby solution. Here we present a theory of multistep replacement of DNA-bound proteins by solution-phase proteins. For four different kinetic scenarios we calculate the dependence of protein unbinding and replacement rates on solution protein concentration. We find (1) strong effects of progressive "rezipping" of the solution-phase protein onto DNA sites liberated by "unzipping" of the originally bound protein, (2) that a model in which solution-phase proteins bind nonspecifically to DNA can describe experiments on exchanges between the nonspecific DNA-binding proteins Fis-Fis and Fis-HU, and (3) that a binding specific model describes experiments on the exchange of CueR proteins on specific binding sites.
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Affiliation(s)
- S Cocco
- 1Laboratoire de Physique Statistique de l'Ecole Normale Supérieure, CNRS and Université Pierre and Marie Curie, 75005 Paris, France
| | - J F Marko
- 2Department of Molecular Biosciences and Department of Physics and Astronomy, Northwestern University, Evanston, Illinois 60208, USA
| | - R Monasson
- 3Laboratoire de Physique Théorique de l'Ecole Normale Supérieure, CNRS and Université Pierre and Marie Curie, 75005 Paris, France
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20
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Polymerase exchange on single DNA molecules reveals processivity clamp control of translesion synthesis. Proc Natl Acad Sci U S A 2014; 111:7647-52. [PMID: 24825884 DOI: 10.1073/pnas.1321076111] [Citation(s) in RCA: 70] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Translesion synthesis (TLS) by Y-family DNA polymerases alleviates replication stalling at DNA damage. Ring-shaped processivity clamps play a critical but ill-defined role in mediating exchange between Y-family and replicative polymerases during TLS. By reconstituting TLS at the single-molecule level, we show that the Escherichia coli β clamp can simultaneously bind the replicative polymerase (Pol) III and the conserved Y-family Pol IV, enabling exchange of the two polymerases and rapid bypass of a Pol IV cognate lesion. Furthermore, we find that a secondary contact between Pol IV and β limits Pol IV synthesis under normal conditions but facilitates Pol III displacement from the primer terminus following Pol IV induction during the SOS DNA damage response. These results support a role for secondary polymerase clamp interactions in regulating exchange and establishing a polymerase hierarchy.
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21
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Pick H, Kilic S, Fierz B. Engineering chromatin states: chemical and synthetic biology approaches to investigate histone modification function. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2014; 1839:644-56. [PMID: 24768924 DOI: 10.1016/j.bbagrm.2014.04.016] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/17/2014] [Revised: 03/26/2014] [Accepted: 04/16/2014] [Indexed: 01/11/2023]
Abstract
Patterns of histone post-translational modifications (PTMs) and DNA modifications establish a landscape of chromatin states with regulatory impact on gene expression, cell differentiation and development. These diverse modifications are read out by effector protein complexes, which ultimately determine their functional outcome by modulating the activity state of underlying genes. From genome-wide studies employing high-throughput ChIP-Seq methods as well as proteomic mass spectrometry studies, a large number of PTMs are known and their coexistence patterns and associations with genomic regions have been mapped in a large number of different cell types. Conversely, the molecular interplay between chromatin effector proteins and modified chromatin regions as well as their resulting biological output is less well understood on a molecular level. Within the last decade a host of chemical approaches has been developed with the goal to produce synthetic chromatin with a defined arrangement of PTMs. These methods now permit systematic functional studies of individual histone and DNA modifications, and additionally provide a discovery platform to identify further interacting nuclear proteins. Complementary chemical- and synthetic-biology methods have emerged to directly observe and modulate the modification landscape in living cells and to readily probe the effect of altered PTM patterns on biological processes. Herein, we review current methodologies allowing chemical and synthetic biological engineering of distinct chromatin states in vitro and in vivo with the aim of obtaining a molecular understanding of histone and DNA modification function. This article is part of a Special Issue entitled: Molecular mechanisms of histone modification function.
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Affiliation(s)
- Horst Pick
- Fondation Sandoz Chair in Biophysical Chemistry of Macromolecules, École Polytechnique Fédérale de Lausanne, CH-1015 Lausanne, Switzerland
| | - Sinan Kilic
- Fondation Sandoz Chair in Biophysical Chemistry of Macromolecules, École Polytechnique Fédérale de Lausanne, CH-1015 Lausanne, Switzerland
| | - Beat Fierz
- Fondation Sandoz Chair in Biophysical Chemistry of Macromolecules, École Polytechnique Fédérale de Lausanne, CH-1015 Lausanne, Switzerland
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22
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Pfreundschuh M, Martinez-Martin D, Mulvihill E, Wegmann S, Muller DJ. Multiparametric high-resolution imaging of native proteins by force-distance curve–based AFM. Nat Protoc 2014; 9:1113-30. [DOI: 10.1038/nprot.2014.070] [Citation(s) in RCA: 84] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
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23
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Continuous throughput and long-term observation of single-molecule FRET without immobilization. Nat Methods 2014; 11:297-300. [DOI: 10.1038/nmeth.2809] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2013] [Accepted: 12/16/2013] [Indexed: 11/08/2022]
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24
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Sing CE, Olvera de la Cruz M, Marko JF. Multiple-binding-site mechanism explains concentration-dependent unbinding rates of DNA-binding proteins. Nucleic Acids Res 2014; 42:3783-91. [PMID: 24393773 PMCID: PMC3973338 DOI: 10.1093/nar/gkt1327] [Citation(s) in RCA: 49] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Recent work has demonstrated concentration-dependent unbinding rates of proteins from DNA, using fluorescence visualization of the bacterial nucleoid protein Fis [Graham et al. (2011) (Concentration-dependent exchange accelerates turnover of proteins bound to double-stranded DNA. Nucleic Acids Res., 39:2249)]. The physical origin of this concentration-dependence is unexplained. We use a combination of coarse-grained simulation and theory to demonstrate that this behavior can be explained by taking into account the dimeric nature of the protein, which permits partial dissociation and exchange with other proteins in solution. Concentration-dependent unbinding is generated by this simple model, quantitatively explaining experimental data. This effect is likely to play a major role in determining binding lifetimes of proteins in vivo where there are very high concentrations of solvated molecules.
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Affiliation(s)
- Charles E Sing
- Department of Materials Science, Northwestern University, 2220 Cook Dr. Evanston, IL 60208, USA, Department of Molecular Biosciences, Northwestern University, Evanston, IL 60208, USA and Department of Physics and Astronomy, Northwestern University, Evanston, IL 60208, USA
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25
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Zhao Y, Chen D, Yue H, Spiering M, Zhao C, Benkovic SJ, Huang TJ. Dark-field illumination on zero-mode waveguide/microfluidic hybrid chip reveals T4 replisomal protein interactions. NANO LETTERS 2014; 14:1952-60. [PMID: 24628474 PMCID: PMC4183369 DOI: 10.1021/nl404802f] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/17/2023]
Abstract
The ability of zero-mode waveguides (ZMWs) to guide light energy into subwavelength-diameter cylindrical nanoapertures has been exploited for single-molecule fluorescence studies of biomolecules at micromolar concentrations, the typical dissociation constants for biomolecular interactions. Although epi-fluorescence microscopy is now adopted for ZMW-based imaging as an alternative to the commercialized ZMW imaging platform, its suitability and performance awaits rigorous examination. Here, we present conical lens-based dark-field fluorescence microscopy in combination with a ZMW/microfluidic chip for single-molecule fluorescence imaging. We demonstrate that compared to epi-illumination, the dark-field configuration displayed diminished background and noise and enhanced signal-to-noise ratios. This signal-to-noise ratio for imaging using the dark-field setup remains essentially unperturbed by the presence of background fluorescent molecules at micromolar concentration. Our design allowed single-molecule FRET studies that revealed weak DNA-protein and protein-protein interactions found with T4 replisomal proteins.
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Affiliation(s)
- Yanhui Zhao
- Department of Engineering Science and Mechanics and Department of Chemistry, The Pennsylvania State University, University Park, Pennsylvania 16802, United States
| | - Danqi Chen
- Department of Engineering Science and Mechanics and Department of Chemistry, The Pennsylvania State University, University Park, Pennsylvania 16802, United States
| | - Hongjun Yue
- Department of Engineering Science and Mechanics and Department of Chemistry, The Pennsylvania State University, University Park, Pennsylvania 16802, United States
| | - Michelle
M. Spiering
- Department of Engineering Science and Mechanics and Department of Chemistry, The Pennsylvania State University, University Park, Pennsylvania 16802, United States
| | - Chenglong Zhao
- Department of Engineering Science and Mechanics and Department of Chemistry, The Pennsylvania State University, University Park, Pennsylvania 16802, United States
| | - Stephen J. Benkovic
- Department of Engineering Science and Mechanics and Department of Chemistry, The Pennsylvania State University, University Park, Pennsylvania 16802, United States
- E-mail: (S.L.B.)
| | - Tony Jun Huang
- Department of Engineering Science and Mechanics and Department of Chemistry, The Pennsylvania State University, University Park, Pennsylvania 16802, United States
- E-mail: (T.J.H.)
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