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Henneman B, Erkelens AM, Heinsman J, Battjes J, Dame RT. Quantitation of DNA Binding Affinity Using Tethered Particle Motion. Methods Mol Biol 2024; 2819:497-518. [PMID: 39028521 DOI: 10.1007/978-1-0716-3930-6_23] [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] [Indexed: 07/20/2024]
Abstract
The binding constant is an important characteristic of a DNA-binding protein. A large number of methods exist to measure the binding constant, but many of those methods have intrinsic flaws that influence the outcome of the characterization. Tethered particle motion (TPM) is a simple, cheap, and high-throughput single-molecule method that can be used to measure binding constants of proteins binding to DNA reliably, provided that they distort DNA. In TPM, the motion of a bead tethered to a surface by DNA is tracked using light microscopy. A protein binding to the DNA will alter bead motion. This change in bead motion makes it possible to measure the DNA-binding properties of proteins. We use the bacterial protein integration host factor (IHF) and the archaeal histone HMfA as examples to show how specific binding to DNA can be measured. Moreover, we show how the end-to-end distance can provide structural insights into protein-DNA binding.
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Affiliation(s)
- Bram Henneman
- Leiden Institute of Chemistry, Leiden University, Leiden, The Netherlands
| | - Amanda M Erkelens
- Leiden Institute of Chemistry, Leiden University, Leiden, The Netherlands
- Human Genetics, Leiden University Medical Center (LUMC), Leiden, The Netherlands
| | - Joost Heinsman
- Leiden Institute of Physics, Leiden University, Leiden, The Netherlands
| | - Julius Battjes
- Leiden Institute of Chemistry, Leiden University, Leiden, The Netherlands
| | - Remus T Dame
- Leiden Institute of Chemistry, Leiden University, Leiden, The Netherlands.
- Centre for Microbial Cell Biology, Leiden University, Leiden, The Netherlands.
- Centre for Interdisciplinary Genome Research, Leiden University, Leiden, The Netherlands.
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2
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Chen YW, Su BY, Van Duyne GD, Fogg P, Fan HF. The influence of coiled-coil motif of serine recombinase toward the directionality regulation. Biophys J 2023; 122:4656-4669. [PMID: 37974397 PMCID: PMC10754689 DOI: 10.1016/j.bpj.2023.11.009] [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: 05/12/2023] [Revised: 08/25/2023] [Accepted: 11/14/2023] [Indexed: 11/19/2023] Open
Abstract
Serine integrases promote the recombination of two complementary DNA sequences, attP and attB, to create hybrid sequences, attL and attR. The reaction is unidirectional in the absence of an accessory protein called recombination directionality factor. We utilized tethered particle motion (TPM) experiments to investigate the reaction behaviors of two model serine integrases from Listeria innocua phage LI and Streptomyces coelicolor phage C31. Detailed kinetic analyses of wild-type and mutant proteins were carried out to verify the mechanisms of recombination directionality. In particular, we assessed the influence of a coiled-coil motif (CC) that is conserved in the C-terminal domain of serine integrases and is an important prerequisite for efficient recombination. Compared to wild type, we found that CC deletions in both serine integrases reduced the overall abundance of integrase (Int) att-site complexes and favored the formation of nonproductive complexes over recombination-competent complexes. Furthermore, the rate at which CC mutants formed productive synaptic complexes and disassembled aberrant nonproductive complexes was significantly reduced. It is notable that while the φC31 Int CC is essential for recombination, the LI Int CC plays an auxiliary role for recombination to stabilize protein-protein interactions and to control the directionality of the reaction.
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Affiliation(s)
- Yei-Wei Chen
- Institute of Medical Science and Technology, National Sun Yat-sen University, Kaohsiung, Taiwan; Department of Chemistry, National Sun Yat-sen University, Kaohsiung, Taiwan; Aerosol Science Research Center, National Sun Yat-sen University, Kaohsiung, Taiwan
| | - Bo-Yu Su
- Department of Life Sciences and Institute of Genome Sciences, National Yang-Ming University, Taipei, Taiwan
| | - Gregory D Van Duyne
- Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania
| | - Paul Fogg
- Biology Department and York Biomedical Research Institute (YBRI), University of York, York, United Kingdom.
| | - Hsiu-Fang Fan
- Institute of Medical Science and Technology, National Sun Yat-sen University, Kaohsiung, Taiwan; Department of Chemistry, National Sun Yat-sen University, Kaohsiung, Taiwan; Aerosol Science Research Center, National Sun Yat-sen University, Kaohsiung, Taiwan.
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3
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Fan H. Single‐molecule tethered particle motion to study
protein‐DNA
interaction. J CHIN CHEM SOC-TAIP 2023. [DOI: 10.1002/jccs.202300051] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/31/2023]
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4
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Fan HF, Su S. The regulation mechanism of the C-terminus of RecA proteins during DNA strand-exchange process. Biophys J 2021; 120:3166-3179. [PMID: 34197804 DOI: 10.1016/j.bpj.2021.06.004] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2020] [Revised: 04/21/2021] [Accepted: 06/03/2021] [Indexed: 12/14/2022] Open
Abstract
The C-terminus of Escherichia coli RecA protein can affect the DNA binding affinity, interact with accessory proteins, and regulate the RecA activity. A substantial upward shift in the pH-reaction profile of RecA-mediated DNA strand-exchange reactions was observed for C-terminal-truncated E. coli ΔC17 RecA, Deinococcus radiodurans RecA, and Deinococcus ficus RecA. Here, the process of RecA-mediated strand exchange from the beginning to the end was investigated with florescence resonance energy transfer and tethered particle motion experiments to determine the detailed regulation mechanism. RecA proteins with a shorter C-terminus possess more stable nuclei, higher DNA binding affinities, and lower protonation requirements for the formation of nucleoprotein filaments. Moreover, more stable synaptic complexes in the homologous sequence searching process were also observed for RecA proteins with a shorter C-terminus. Our results suggest that the C-terminus of RecA proteins regulates not only the formation of RecA nucleoprotein filaments but also the entrance of secondary DNA into RecA nucleoprotein filaments.
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Affiliation(s)
- Hsiu-Fang Fan
- Institute of Medical Science and Technology, Kaohsiung, Taiwan; Department of Chemistry, Kaohsiung, Taiwan; Aerosol Science Research Center, National Sun Yat-sen University, Kaohsiung, Taiwan.
| | - Shu Su
- Department of Life Sciences and Institute of Genome Sciences, National Yang-Ming University, Taipei, Taiwan
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5
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Shoura MJ, Giovan SM, Vetcher AA, Ziraldo R, Hanke A, Levene SD. Loop-closure kinetics reveal a stable, right-handed DNA intermediate in Cre recombination. Nucleic Acids Res 2020; 48:4371-4381. [PMID: 32182357 PMCID: PMC7192630 DOI: 10.1093/nar/gkaa153] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2019] [Revised: 02/24/2020] [Accepted: 02/29/2020] [Indexed: 11/12/2022] Open
Abstract
In Cre site-specific recombination, the synaptic intermediate is a recombinase homotetramer containing a pair of loxP DNA target sites. The enzyme system's strand-exchange mechanism proceeds via a Holliday-junction (HJ) intermediate; however, the geometry of DNA segments in the synapse has remained highly controversial. In particular, all crystallographic structures are consistent with an achiral, planar Holliday-junction (HJ) structure, whereas topological assays based on Cre-mediated knotting of plasmid DNAs are consistent with a right-handed chiral junction. We use the kinetics of loop closure involving closely spaced (131-151 bp) loxP sites to investigate the in-aqueo ensemble of conformations for the longest-lived looped DNA intermediate. Fitting the experimental site-spacing dependence of the loop-closure probability, J, to a statistical-mechanical theory of DNA looping provides evidence for substantial out-of-plane HJ distortion, which unequivocally stands in contrast to the square-planar intermediate geometry from Cre-loxP crystal structures and those of other int-superfamily recombinases. J measurements for an HJ-isomerization-deficient Cre mutant suggest that the apparent geometry of the wild-type complex is consistent with temporal averaging of right-handed and achiral structures. Our approach connects the static pictures provided by crystal structures and the natural dynamics of macromolecules in solution, thus advancing a more comprehensive dynamic analysis of large nucleoprotein structures and their mechanisms.
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Affiliation(s)
- Massa J Shoura
- Department of Bioengineering, University of Texas at Dallas, Richardson, TX 75080, USA
- Department of Biological Sciences, University of Texas at Dallas, Richardson, TX 75080, USA
| | - Stefan M Giovan
- Department of Biological Sciences, University of Texas at Dallas, Richardson, TX 75080, USA
| | - Alexandre A Vetcher
- Department of Biological Sciences, University of Texas at Dallas, Richardson, TX 75080, USA
| | - Riccardo Ziraldo
- Department of Bioengineering, University of Texas at Dallas, Richardson, TX 75080, USA
| | - Andreas Hanke
- Department of Physics, University of Texas Rio Grande Valley, Brownsville, TX 78520, USA
| | - Stephen D Levene
- Department of Bioengineering, University of Texas at Dallas, Richardson, TX 75080, USA
- Department of Biological Sciences, University of Texas at Dallas, Richardson, TX 75080, USA
- Physics, University of Texas at Dallas, Richardson, TX 75080, USA
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Henneman B, Heinsman J, Battjes J, Dame RT. Quantitation of DNA-Binding Affinity Using Tethered Particle Motion. Methods Mol Biol 2019; 1837:257-275. [PMID: 30109615 DOI: 10.1007/978-1-4939-8675-0_14] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
The binding constant is an important characteristic of a DNA-binding protein. A large number of methods exist to measure the binding constant, but many of those methods have intrinsic flaws that influence the outcome of the characterization. Tethered Particle Motion (TPM) is a simple, cheap, and high-throughput single-molecule method that can be used to reliably measure binding constants of proteins binding to DNA, provided that they distort DNA. In TPM, the motion of a bead tethered to a surface by DNA is tracked using light microscopy. A protein binding to the DNA will alter bead motion. This makes it possible to measure binding properties. We use the bacterial protein Integration Host Factor (IHF) as an example to show how specific binding to DNA can be measured. Moreover, we show a new intuitive quantitative approach to displaying data obtained via TPM.
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Affiliation(s)
- Bram Henneman
- Leiden Institute of Chemistry, Leiden University, Leiden, The Netherlands
| | - Joost Heinsman
- Leiden Institute of Physics, Leiden University, Leiden, The Netherlands
| | - Julius Battjes
- Leiden Institute of Chemistry, Leiden University, Leiden, The Netherlands
| | - Remus T Dame
- Leiden Institute of Chemistry and Centre for Microbial Cell Biology, Leiden University, Leiden, The Netherlands.
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Hsu KW, Chow SY, Su BY, Lu YH, Chen CJ, Chen WL, Cheng MY, Fan HF. The synergy between RSC, Nap1 and adjacent nucleosome in nucleosome remodeling. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2018; 1862:129-140. [PMID: 30593928 DOI: 10.1016/j.bbagrm.2018.11.008] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Received: 09/04/2018] [Revised: 11/23/2018] [Accepted: 11/30/2018] [Indexed: 12/29/2022]
Abstract
Eukaryotes have evolved a specific strategy to package DNA. The nucleosome is a 147-base-pair DNA segment wrapped around histone core proteins that plays important roles regulating DNA-dependent biosynthesis and gene expression. Chromatin remodeling complexes (RSC, Remodel the Structure of Chromatin) hydrolyze ATP to perturb DNA-histone contacts, leading to nucleosome sliding and ejection. Here, we utilized tethered particle motion (TPM) experiments to investigate the mechanism of RSC-mediated nucleosome remodeling in detail. We observed ATP-dependent RSC-mediated DNA looping and nucleosome ejection along individual mononucleosomes and dinucleosomes. We found that nucleosome assembly protein 1 (Nap1) enhanced RSC-mediated nucleosome ejection in a two-step disassembly manner from dinucleosomes but not from mononucleosomes. Based on this work, we provide an entire reaction scheme for the RSC-mediated nucleosome remodeling process that includes DNA looping, nucleosome ejection, the influence of adjacent nucleosomes, and the coordinated action between Nap1 and RSC.
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Affiliation(s)
- Kuan-Wei Hsu
- Department of Life Sciences and Institute of Genome Sciences, National Yang-Ming University, Taiwan
| | - Sih-Yao Chow
- Department of Life Sciences and Institute of Genome Sciences, National Yang-Ming University, Taiwan
| | - Bo-Yu Su
- Department of Life Sciences and Institute of Genome Sciences, National Yang-Ming University, Taiwan
| | - Yi-Han Lu
- Department of Life Sciences and Institute of Genome Sciences, National Yang-Ming University, Taiwan
| | - Cyuan-Ji Chen
- Department of Life Sciences and Institute of Genome Sciences, National Yang-Ming University, Taiwan
| | - Wen-Ling Chen
- Department of Life Sciences and Institute of Genome Sciences, National Yang-Ming University, Taiwan
| | - Ming-Yuan Cheng
- Department of Life Sciences and Institute of Genome Sciences, National Yang-Ming University, Taiwan
| | - Hsiu-Fang Fan
- Department of Life Sciences and Institute of Genome Sciences, National Yang-Ming University, Taiwan.
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Fan HF, Ma CH, Jayaram M. Single-Molecule Tethered Particle Motion: Stepwise Analyses of Site-Specific DNA Recombination. MICROMACHINES 2018; 9:E216. [PMID: 30424148 PMCID: PMC6187709 DOI: 10.3390/mi9050216] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/15/2018] [Revised: 04/25/2018] [Accepted: 04/28/2018] [Indexed: 12/17/2022]
Abstract
Tethered particle motion/microscopy (TPM) is a biophysical tool used to analyze changes in the effective length of a polymer, tethered at one end, under changing conditions. The tether length is measured indirectly by recording the Brownian motion amplitude of a bead attached to the other end. In the biological realm, DNA, whose interactions with proteins are often accompanied by apparent or real changes in length, has almost exclusively been the subject of TPM studies. TPM has been employed to study DNA bending, looping and wrapping, DNA compaction, high-order DNA⁻protein assembly, and protein translocation along DNA. Our TPM analyses have focused on tyrosine and serine site-specific recombinases. Their pre-chemical interactions with DNA cause reversible changes in DNA length, detectable by TPM. The chemical steps of recombination, depending on the substrate and the type of recombinase, may result in a permanent length change. Single molecule TPM time traces provide thermodynamic and kinetic information on each step of the recombination pathway. They reveal how mechanistically related recombinases may differ in their early commitment to recombination, reversibility of individual steps, and in the rate-limiting step of the reaction. They shed light on the pre-chemical roles of catalytic residues, and on the mechanisms by which accessory proteins regulate recombination directionality.
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Affiliation(s)
- Hsiu-Fang Fan
- Biophotonics and Molecular Imaging Center, Department of Life Sciences and Institute of Genome Sciences, National Yang-Ming University, Taipei 112, Taiwan.
- Institute of Cellular and Organismic Biology, Academia Sinica, Taipei 115, Taiwan.
| | - Chien-Hui Ma
- Department of Molecular Biosciences, University of Texas at Austin, Austin, TX 78712, USA.
| | - Makkuni Jayaram
- Department of Molecular Biosciences, University of Texas at Austin, Austin, TX 78712, USA.
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Shi HB, Lou JL, Shi HL, Ren F, Chen Y, Duan ZP. Construction of Gpm6a/Reelin GFPCreERT2 by BAC recombination using a specific gene in hepatic mesothelial or stellate cells. World J Gastroenterol 2017; 23:224-231. [PMID: 28127196 PMCID: PMC5236502 DOI: 10.3748/wjg.v23.i2.224] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/02/2016] [Revised: 10/05/2016] [Accepted: 11/02/2016] [Indexed: 02/06/2023] Open
Abstract
AIM To prepare a Gpm6a/ReelinGFPCreERT2 construct with a rapid and reliable strategy using a bacterial artificial chromosome (BAC). METHODS Gpm6a and Reelin BACs were purified and transformed into SW102 E. coli by electroporation. The GFPCreERT2 fragment was prepared from a shuttle vector and transformed into SW102 E. coli carrying a BAC. Homologous recombination was induced in SW102 E. coli. Recombinant clones were screened and confirmed by PCR and restriction enzyme digestion. Recombinant clones were transformed into SW102 E. coli to remove the kanamycin unit. RESULTS A complete BAC was successfully transformed into SW102 E. coli by electroporation because BAC purified from SW102 E. coli showed the same pattern as the original BAC with BamHI digestion. The GFPCreERT2 fragment was deemed to have been prepared successfully because we obtained the same size fragment as expected. Homologous recombination was induced, and GFPCreERT2 was deemed to have been inserted into the correct site of the BAC because we found the band change was the same as the expected pattern after restriction enzyme digestion. The kanamycin unit was deemed to have been removed successfully because we obtained different sizes of bands that were consistent with the results expected by PCR with different primers. CONCLUSION The construct of Gpm6aGFPCreERT2 or ReelinGFPCreERT2 was prepared successfully, which will establish a foundation for tracing the hepatic stellate cell lineage and studying its function.
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Affiliation(s)
- Hong-Bo Shi
- Hong-Bo Shi, Hong-Lin Shi, Feng Ren, Zhong-Ping Duan, Beijing Institute of Hepatology, Beijing Youan Hospital, Capital Medical University, Beijing 100069, China
| | - Jin-Li Lou
- Hong-Bo Shi, Hong-Lin Shi, Feng Ren, Zhong-Ping Duan, Beijing Institute of Hepatology, Beijing Youan Hospital, Capital Medical University, Beijing 100069, China
| | - Hong-Lin Shi
- Hong-Bo Shi, Hong-Lin Shi, Feng Ren, Zhong-Ping Duan, Beijing Institute of Hepatology, Beijing Youan Hospital, Capital Medical University, Beijing 100069, China
| | - Feng Ren
- Hong-Bo Shi, Hong-Lin Shi, Feng Ren, Zhong-Ping Duan, Beijing Institute of Hepatology, Beijing Youan Hospital, Capital Medical University, Beijing 100069, China
| | - Yu Chen
- Hong-Bo Shi, Hong-Lin Shi, Feng Ren, Zhong-Ping Duan, Beijing Institute of Hepatology, Beijing Youan Hospital, Capital Medical University, Beijing 100069, China
| | - Zhong-Ping Duan
- Hong-Bo Shi, Hong-Lin Shi, Feng Ren, Zhong-Ping Duan, Beijing Institute of Hepatology, Beijing Youan Hospital, Capital Medical University, Beijing 100069, China
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Fan HF, Hsieh TS, Ma CH, Jayaram M. Single-molecule analysis of ϕC31 integrase-mediated site-specific recombination by tethered particle motion. Nucleic Acids Res 2016; 44:10804-10823. [PMID: 27986956 PMCID: PMC5159548 DOI: 10.1093/nar/gkw861] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2016] [Revised: 09/11/2016] [Accepted: 09/22/2016] [Indexed: 11/14/2022] Open
Abstract
Serine and tyrosine site-specific recombinases (SRs and YRs, respectively) provide templates for understanding the chemical mechanisms and conformational dynamics of strand cleavage/exchange between DNA partners. Current evidence suggests a rather intriguing mechanism for serine recombination, in which one half of the cleaved synaptic complex undergoes a 180° rotation relative to the other. The 'small' and 'large' SRs contain a compact amino-terminal catalytic domain, but differ conspicuously in their carboxyl-terminal domains. So far, only one serine recombinase has been analyzed using single substrate molecules. We now utilized single-molecule tethered particle motion (TPM) to follow step-by-step recombination catalyzed by a large SR, phage ϕC31 integrase. The integrase promotes unidirectional DNA exchange between attB and attP sites to integrate the phage genome into the host chromosome. The recombination directionality factor (RDF; ϕC31 gp3) activates the excision reaction (attL × attR). From integrase-induced changes in TPM in the presence or absence of gp3, we delineated the individual steps of recombination and their kinetic features. The gp3 protein appears to regulate recombination directionality by selectively promoting or excluding active conformations of the synapse formed by specific att site partners. Our results support a 'gated rotation' of the synaptic complex between DNA cleavage and joining.
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Affiliation(s)
- Hsiu-Fang Fan
- Department of Life Sciences and Institute of Genome Sciences, National Yang-Ming University, 112, Taiwan
- Biophotonics and Molecular Imaging Research Center, National Yang-Ming University, 112, Taiwan
| | - Tao-Shih Hsieh
- Institute of Cellular and Organismic Biology Academia Sinica, 115, Taiwan
| | - Chien-Hui Ma
- Department of Molecular Biosciences, University of Texas at Austin, Austin, TX 78712, USA
| | - Makkuni Jayaram
- Department of Molecular Biosciences, University of Texas at Austin, Austin, TX 78712, USA
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