1
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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] [What about the content of this article? (0)] [Affiliation(s)] [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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2
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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. ArXiv 2023:arXiv:2302.12455v2. [PMID: 36866225 PMCID: PMC9980184] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 03/04/2023]
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 of cis/trans photoisomerisation. It is clear now that this mechanism is generally applicable to interactions with any biomolecule and, 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 turn 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, UK, Single Molecule Imaging Group, MRC-London Institute of Medical Sciences, London, W12 0HS, UK
| | - 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
- Kavli Institute for Nanoscience Discovery, Department of Biological Physics, The University of Oxford, UK
| | - Harold D. Kim
- School of Physics, Georgia Institute of Technology, 837 State Street, Atlanta, GA 30332, USA
| | - Marcia Levitus
- School of Molecular Sciences, Arizona State University, 551 E. University Drive, Tempe, AZ, 85287, USA
| | - Timothy M. Lohman
- Department of Biochemistry and Molecular Biophysics, Washington University in St. Louis School of Medicine, St. Louis, MO 63110, USA
| | - Abhishek Mazumder
- Kavli Institute for Nanoscience Discovery, Department of Biological Physics, The University of Oxford, UK
| | - David S. Rueda
- Department of Infectious Disease, Faculty of Medicine, Imperial College London, London, W12 0HS, UK, Single Molecule Imaging Group, MRC-London Institute of Medical Sciences, London, W12 0HS, UK
| | - Fabio D. Steffen
- Department of Chemistry, University of Zurich, Zurich, Switzerland
| | - Thorben Cordes
- Physical and Synthetic Biology, Faculty of Biology, Ludwig-Maximilians-Universität München, Großhadernerstr, 2-4, 82152 Planegg-Martinsried, Germany
| | - Steven W. Magennis
- School of Chemistry, University of Glasgow, Joseph Black Building, University Avenue, Glasgow, G12 8QQ, UK
| | - 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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3
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Karsai A, Cassidy GJ, Rajanala AP, Yang L, Kerimoglu D, Gumbart JC, Kim HD, Goldman DI. Toward a 3D physical model of diffusive polymer chains. Front Phys 2023; 11:1142004. [PMID: 37538992 PMCID: PMC10399318 DOI: 10.3389/fphy.2023.1142004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 08/05/2023]
Abstract
Recent studies in polymer physics have created macro-scale analogs to solute microscopic polymer chains like DNA by inducing diffusive motion on a chain of beads. These bead chains have persistence lengths of O(10) links and undergo diffusive motion under random fluctuations like vibration. We present a bead chain model within a new stochastic forcing system: an air fluidizing bed of granular media. A chain of spherical 6 mm resin beads crimped onto silk thread are buffeted randomly by the multiphase flow of grains and low density rising air "bubbles". We "thermalize" bead chains of various lengths at different fluidizing airflow rates, while X-ray imaging captures a projection of the chains' dynamics within the media. With modern 3D printing techniques, we can better represent complex polymers by geometrically varying bead connections and their relative strength, e.g., mimicking the variable stiffness between adjacent nucleotide pairs of DNA. We also develop Discrete Element Method (DEM) simulations to study the 3D motion of the bead chain, where the bead chain is represented by simulated spherical particles connected by linear and angular spring-like bonds. In experiment, we find that the velocity distributions of the beads follow exponential distributions rather than the Gaussian distributions expected from polymers in solution. Through use of the DEM simulation, we find that this difference can likely be attributed to the distributions of the forces imparted onto the chain from the fluidized bed environment. We anticipate expanding this study in the future to explore a wide range of chain composition and confinement geometry, which will provide insights into the physics of large biopolymers.
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Affiliation(s)
- Andras Karsai
- School of Physics, Georgia Institute of Technology, Atlanta, GA, United States
| | - Grace J Cassidy
- School of Chemical and Biomolecular Engineering, Georgia Institute of Technology, Atlanta, GA, United States
| | - Aradhya P Rajanala
- School of Physics, Georgia Institute of Technology, Atlanta, GA, United States
| | - Lixinhao Yang
- School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, GA, United States
| | - Deniz Kerimoglu
- School of Physics, Georgia Institute of Technology, Atlanta, GA, United States
| | - James C Gumbart
- School of Physics, Georgia Institute of Technology, Atlanta, GA, United States
- School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, GA, United States
| | - Harold D Kim
- School of Physics, Georgia Institute of Technology, Atlanta, GA, United States
| | - Daniel I Goldman
- School of Physics, Georgia Institute of Technology, Atlanta, GA, United States
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Hart DJ, Jeong J, Gumbart JC, Kim HD. Weak tension accelerates hybridization and dehybridization of short oligonucleotides. Nucleic Acids Res 2023; 51:3030-3040. [PMID: 36869666 PMCID: PMC10123125 DOI: 10.1093/nar/gkad118] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2022] [Revised: 02/06/2023] [Accepted: 02/10/2023] [Indexed: 03/05/2023] Open
Abstract
The hybridization and dehybridization of DNA subject to tension is relevant to fundamental genetic processes and to the design of DNA-based mechanobiology assays. While strong tension accelerates DNA melting and decelerates DNA annealing, the effects of tension weaker than 5 pN are less clear. In this study, we developed a DNA bow assay, which uses the bending rigidity of double-stranded DNA (dsDNA) to exert weak tension on a single-stranded DNA (ssDNA) target in the range of 2-6 pN. Combining this assay with single-molecule FRET, we measured the hybridization and dehybridization kinetics between a 15 nt ssDNA under tension and a 8-9 nt oligonucleotide, and found that both the hybridization and dehybridization rates monotonically increase with tension for various nucleotide sequences tested. These findings suggest that the nucleated duplex in its transition state is more extended than the pure dsDNA or ssDNA counterpart. Based on coarse-grained oxDNA simulations, we propose that this increased extension of the transition state is due to steric repulsion between the unpaired ssDNA segments in close proximity to one another. Using linear force-extension relations verified by simulations of short DNA segments, we derived analytical equations for force-to-rate conversion that are in good agreement with our measurements.
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Affiliation(s)
- Derek J Hart
- School of Physics, Georgia Institute of Technology, 837 State Street, Atlanta, GA 30332-0430, USA
| | - Jiyoun Jeong
- School of Physics, Georgia Institute of Technology, 837 State Street, Atlanta, GA 30332-0430, USA
| | - James C Gumbart
- School of Physics, Georgia Institute of Technology, 837 State Street, Atlanta, GA 30332-0430, USA
| | - Harold D Kim
- School of Physics, Georgia Institute of Technology, 837 State Street, Atlanta, GA 30332-0430, USA
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Abstract
Annealing between sticky ends of DNA is an intermediate step in ligation. It can also be utilized to program specific binding sites for DNA tile and origami assembly. This reaction is generally understood as a bimolecular reaction dictated by the local concentration of the sticky ends. Its dependence on the relative orientation between the sticky ends, however, is less understood. Here we report on the interactions between DNA sticky ends using the coarse-grained oxDNA model; specifically, we consider how the orientational alignment of the double-stranded DNA (dsDNA) segments affects the time required for the sticky ends to bind, τb. We specify the orientation of the dsDNA segments with three parameters: θ, which measures the angle between the helical axes, and ϕ1 and ϕ2, which measure rotations of each strand around the helical axis. We find that the binding time depends strongly on both θ and ϕ2: ∼20-fold change with θ and 10-fold change with ϕ2. The binding time is the fastest when the helical axes of duplexes are pointing toward each other and the sticky ends protrude from the farthest two points. Our result is relevant for predicting hybridization efficiency of sticky ends that are rotationally restricted.
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Affiliation(s)
- Nicholas M Gravina
- School of Physics, Georgia Institute of Technology, Atlanta, Georgia 30332, United States
| | - James C Gumbart
- School of Physics, Georgia Institute of Technology, Atlanta, Georgia 30332, United States
| | - Harold D Kim
- School of Physics, Georgia Institute of Technology, Atlanta, Georgia 30332, United States
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6
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Broadwater DWB, Cook AW, Kim HD. First passage time study of DNA strand displacement. Biophys J 2021; 120:2400-2412. [PMID: 33894217 DOI: 10.1016/j.bpj.2021.01.043] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2020] [Revised: 12/18/2020] [Accepted: 01/12/2021] [Indexed: 12/15/2022] Open
Abstract
DNA strand displacement, in which a single-stranded nucleic acid invades a DNA duplex, is pervasive in genomic processes and DNA engineering applications. The kinetics of strand displacement have been studied in bulk; however, the kinetics of the underlying strand exchange were obfuscated by a slow bimolecular association step. Here, we use a novel single-molecule fluorescence resonance energy transfer approach termed the "fission" assay to obtain the full distribution of first passage times of unimolecular strand displacement. At a frame time of 4.4 ms, the first passage time distribution for a 14-nucleotide displacement domain exhibited a nearly monotonic decay with little delay. Among the eight different sequences we tested, the mean displacement time was on average 35 ms and varied by up to a factor of 13. The measured displacement kinetics also varied between complementary invaders and between RNA and DNA invaders of the same base sequence, except for T → U substitution. However, displacement times were largely insensitive to the monovalent salt concentration in the range of 0.25-1 M. Using a one-dimensional random walk model, we infer that the single-step displacement time is in the range of ∼30-300 μs, depending on the base identity. The framework presented here is broadly applicable to the kinetic analysis of multistep processes investigated at the single-molecule level.
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Affiliation(s)
- D W Bo Broadwater
- School of Physics, Georgia Institute of Technology, Atlanta, Georgia
| | - Alexander W Cook
- School of Physics, Georgia Institute of Technology, Atlanta, Georgia
| | - Harold D Kim
- School of Physics, Georgia Institute of Technology, Atlanta, Georgia.
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7
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Park YJ, Kim SH, Kim TS, Lee SM, Cho BS, Seo CI, Kim HD, Kim J. Ribosomal protein S3 associates with the TFIIH complex and positively regulates nucleotide excision repair. Cell Mol Life Sci 2021; 78:3591-3606. [PMID: 33464383 PMCID: PMC11072392 DOI: 10.1007/s00018-020-03754-x] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2020] [Revised: 12/14/2020] [Accepted: 12/29/2020] [Indexed: 10/22/2022]
Abstract
In mammalian cells, the bulky DNA adducts caused by ultraviolet radiation are mainly repaired via the nucleotide excision repair (NER) pathway; some defects in this pathway lead to a genetic disorder known as xeroderma pigmentosum (XP). Ribosomal protein S3 (rpS3), a constituent of the 40S ribosomal subunit, is a multi-functional protein with various extra-ribosomal functions, including a role in the cellular stress response and DNA repair-related activities. We report that rpS3 associates with transcription factor IIH (TFIIH) via an interaction with the xeroderma pigmentosum complementation group D (XPD) protein and complements its function in the NER pathway. For optimal repair of UV-induced duplex DNA lesions, the strong helicase activity of the TFIIH complex is required for unwinding damaged DNA around the lesion. Here, we show that XP-D cells overexpressing rpS3 showed markedly increased resistance to UV radiation through XPD and rpS3 interaction. Additionally, the knockdown of rpS3 caused reduced NER efficiency in HeLa cells and the overexpression of rpS3 partially restored helicase activity of the TFIIH complex of XP-D cells in vitro. We also present data suggesting that rpS3 is involved in post-excision processing in NER, assisting TFIIH in expediting the repair process by increasing its turnover rate when DNA is damaged. We propose that rpS3 is an accessory protein of the NER pathway and its recruitment to the repair machinery augments repair efficiency upon UV damage by enhancing XPD helicase function and increasing its turnover rate.
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Affiliation(s)
- Y J Park
- Lab of Biochemistry, Division of Life Sciences, Korea University, Seoul, 02841, Korea
| | - S H Kim
- Lab of Biochemistry, Division of Life Sciences, Korea University, Seoul, 02841, Korea
| | - T S Kim
- Lab of Biochemistry, Division of Life Sciences, Korea University, Seoul, 02841, Korea
| | - S M Lee
- Lab of Biochemistry, Division of Life Sciences, Korea University, Seoul, 02841, Korea
| | - B S Cho
- Lab of Biochemistry, Division of Life Sciences, Korea University, Seoul, 02841, Korea
| | - C I Seo
- Lab of Biochemistry, Division of Life Sciences, Korea University, Seoul, 02841, Korea
| | - H D Kim
- TechnoComplex Building, HAEL Lab, Korea University, Seoul, 02841, Korea
| | - J Kim
- Lab of Biochemistry, Division of Life Sciences, Korea University, Seoul, 02841, Korea.
- TechnoComplex Building, HAEL Lab, Korea University, Seoul, 02841, Korea.
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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: 117] [Impact Index Per Article: 39.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [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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9
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Cook AW, Broadwater B, Kim HD. First Passage Time Study of DNA Strand Displacement. Biophys J 2021. [DOI: 10.1016/j.bpj.2020.11.1479] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022] Open
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10
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Ryan ML, Jeong J, Lemos T, Kim HD. Anharmonic Bending of DNA Base-Pair Mismatch. Biophys J 2021. [DOI: 10.1016/j.bpj.2020.11.1472] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022] Open
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11
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Cho HJ, Shin MS, Song Y, Park SK, Park SM, Kim HD. Severe Periodontal Disease Increases Acute Myocardial Infarction and Stroke: A 10-Year Retrospective Follow-up Study. J Dent Res 2021; 100:706-713. [PMID: 33478309 DOI: 10.1177/0022034520986097] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
This study aimed to evaluate the causal association of periodontal disease with acute myocardial infarction (AMI) and stroke, after controlling for various confounders among the Korean population. A retrospective cohort study using the National Health Insurance Service-National Health Screening Cohort (NHIS-HEALS) was performed during 2002 to 2015 (baseline: 2002 to 2005; follow-up: 2006 to 2015) in the Republic of Korea. A total of 298,128 participants with no history of AMI or stroke were followed up for 10 y. AMI and stroke were defined by a diagnosis using the International Classification of Diseases, 10th Revision (ICD-10) guideline. Periodontal condition was classified into 3 groups (healthy, moderate periodontal disease, severe periodontal disease [SPD]) using the combination of ICD codes, treatment codes in the NHIS, and recommendation of periodontal treatment by the dentists in HEALS. Various confounders, such as sociodemographic, behavioral, systemic, and oral health factors, including hypercholesterolemia, were considered. Multivariable Cox regression analysis was applied to estimate adjusted incidence rate ratio (adjusted hazard ratio [aHR]) based on person-year of periodontal condition for AMI, stroke, and nonfatal major adverse cardiovascular events (MACEs) encompassing AMI or stroke controlling for various confounders. Stratified analyses according to age group, sex, and toothbrushing frequency were also performed. After controlling for various confounders, participants with SPD compared with non-SPD participants had a higher incidence by 11% for AMI (aHR, 1.11; 95% confidence interval [CI], 1.02-1.20), by 3.5% for stroke (aHR, 1.035; 95% CI, 1.01-1.07), and by 4.1% for MACEs (aHR, 1.04; 95% CI, 1.01-1.07). The association of SPD with AMI and MACE was highly modified in females and adults aged 40 to 59 y. In the total Korean population, SPD increased total AMI events by 4.3%, total stroke events by 1.4%, and the total MACEs by 1.6%. Our data confirmed that SPD was causally associated with the new events of AMI and stroke.
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Affiliation(s)
- H J Cho
- Department of Preventive and Social Dentistry, School of Dentistry, Seoul National University, Seoul, Republic of Korea.,Dental Research Institute, Seoul National University, Seoul, Korea
| | - M S Shin
- Department of Preventive and Social Dentistry, School of Dentistry, Seoul National University, Seoul, Republic of Korea
| | - Y Song
- Australian Research Centre for Population Oral Health, Adelaide Dental School, The University of Adelaide, South Australia, Australia
| | - S K Park
- Department of Preventive Medicine, College of Medicine, Seoul National University, Seoul, Republic of Korea
| | - S M Park
- Department of Biomedical Sciences, Seoul National University Graduate School, Seoul, Republic of Korea.,Department of Family Medicine, College of Medicine, Seoul National University, Seoul, Republic of Korea
| | - H D Kim
- Department of Preventive and Social Dentistry, School of Dentistry, Seoul National University, Seoul, Republic of Korea.,Dental Research Institute, Seoul National University, Seoul, Korea
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12
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Jeong J, Kim HD. Determinants of cyclization-decyclization kinetics of short DNA with sticky ends. Nucleic Acids Res 2020; 48:5147-5156. [PMID: 32282905 PMCID: PMC7229855 DOI: 10.1093/nar/gkaa207] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2020] [Revised: 03/17/2020] [Accepted: 03/25/2020] [Indexed: 12/16/2022] Open
Abstract
Cyclization of DNA with sticky ends is commonly used to measure DNA bendability as a function of length and sequence, but how its kinetics depend on the rotational positioning of the sticky ends around the helical axis is less clear. Here, we measured cyclization (looping) and decyclization (unlooping) rates (kloop and kunloop) of DNA with sticky ends over three helical periods (100-130 bp) using single-molecule fluorescence resonance energy transfer (FRET). kloop showed a nontrivial undulation as a function of DNA length whereas kunloop showed a clear oscillation with a period close to the helical turn of DNA (∼10.5 bp). The oscillation of kunloop was almost completely suppressed in the presence of gaps around the sticky ends. We explain these findings by modeling double-helical DNA as a twisted wormlike chain with a finite width, intrinsic curvature, and stacking interaction between the end base pairs. We also discuss technical issues for converting the FRET-based cyclization/decyclization rates to an equilibrium quantity known as the J factor that is widely used to characterize DNA bending mechanics.
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Affiliation(s)
- Jiyoun Jeong
- School of Physics, Georgia Institute of Technology, 837 State Street, Atlanta, GA 30332-0430, USA
| | - Harold D Kim
- School of Physics, Georgia Institute of Technology, 837 State Street, Atlanta, GA 30332-0430, USA
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13
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Garcia PD, Leach RW, Wadsworth GM, Choudhary K, Li H, Aviran S, Kim HD, Zakian VA. Stability and nuclear localization of yeast telomerase depend on protein components of RNase P/MRP. Nat Commun 2020; 11:2173. [PMID: 32358529 PMCID: PMC7195438 DOI: 10.1038/s41467-020-15875-9] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2019] [Accepted: 03/27/2020] [Indexed: 01/17/2023] Open
Abstract
RNase P and MRP are highly conserved, multi-protein/RNA complexes with essential roles in processing ribosomal and tRNAs. Three proteins found in both complexes, Pop1, Pop6, and Pop7 are also telomerase-associated. Here, we determine how temperature sensitive POP1 and POP6 alleles affect yeast telomerase. At permissive temperatures, mutant Pop1/6 have little or no effect on cell growth, global protein levels, the abundance of Est1 and Est2 (telomerase proteins), and the processing of TLC1 (telomerase RNA). However, in pop mutants, TLC1 is more abundant, telomeres are short, and TLC1 accumulates in the cytoplasm. Although Est1/2 binding to TLC1 occurs at normal levels, Est1 (and hence Est3) binding is highly unstable. We propose that Pop-mediated stabilization of Est1 binding to TLC1 is a pre-requisite for formation and nuclear localization of the telomerase holoenzyme. Furthermore, Pop proteins affect TLC1 and the RNA subunits of RNase P/MRP in very different ways.
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Affiliation(s)
- P Daniela Garcia
- Department of Molecular Biology, Princeton University, Princeton, NJ, 08544, USA
| | - Robert W Leach
- Bioinformatics Group, Genomics Core Facility, Carl Icahn Laboratory, Princeton University, Princeton, New Jersey, 08544, USA
| | - Gable M Wadsworth
- School of Physics, Georgia Institute of Technology, Atlanta, Georgia, 30332, USA
| | - Krishna Choudhary
- Department of Biomedical Engineering and Genome Center, University of California, Davis, California, 95616, USA
- Gladstone Institute of Data Science and Biotechnology, San Francisco, CA, 94158, USA
| | - Hua Li
- Department of Biomedical Engineering and Genome Center, University of California, Davis, California, 95616, USA
| | - Sharon Aviran
- Department of Biomedical Engineering and Genome Center, University of California, Davis, California, 95616, USA
| | - Harold D Kim
- School of Physics, Georgia Institute of Technology, Atlanta, Georgia, 30332, USA
| | - Virginia A Zakian
- Department of Molecular Biology, Princeton University, Princeton, NJ, 08544, USA.
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14
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Broadwater DWB, Altman RB, Blanchard SC, Kim HD. ERASE: a novel surface reconditioning strategy for single-molecule experiments. Nucleic Acids Res 2019; 47:e14. [PMID: 30462308 PMCID: PMC6379648 DOI: 10.1093/nar/gky1168] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2018] [Revised: 10/02/2018] [Accepted: 11/01/2018] [Indexed: 11/13/2022] Open
Abstract
While surface-based single-molecule experiments have revolutionized our understanding of biology and biomolecules, the workflow in preparing for such experiments, especially surface cleaning and functionalization, remains labor-intensive and time-consuming. Even worse, meticulously assembled flow channels can be used only once for most experiments. A reusable surface would thus dramatically increase productivity and efficiency of single-molecule experiments. In this paper, we report a novel surface reconditioning strategy termed ERASE (Epitaxial Removal Aided by Strand Exchange) that allows a single flow cell to be used for vast repetition of single-molecule experiments. In this method, biomolecules immobilized to the surface through a nucleic acid duplex are liberated when a competing DNA strand disrupts the duplex via toehold-mediated strand displacement. We demonstrate the wide-range applicability of this method with various common surface preparation techniques, fluorescent dyes, and biomolecules including the bacterial ribosome. Beyond time and cost savings, we also show ERASE can assort molecules based on a nucleic acid barcode sequence, thus allowing experiments on different molecules in parallel. Our method increases the utility of prepared surfaces and is a significant improvement to the current single-use paradigm.
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Affiliation(s)
- D W Bo Broadwater
- School of Physics, Georgia Institute of Technology, 770 State Street NW, Atlanta, GA 30318, USA
| | - Roger B Altman
- Department of Physiology and Biophysics, Weill Cornell Medicine, New York, NY, USA
| | - Scott C Blanchard
- Department of Physiology and Biophysics, Weill Cornell Medicine, New York, NY, USA
| | - Harold D Kim
- School of Physics, Georgia Institute of Technology, 770 State Street NW, Atlanta, GA 30318, USA
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15
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Abstract
Base-pair mismatch can relieve mechanical stress in highly strained DNA molecules, but how it affects their kinetic stability is not known. Using single-molecule fluorescence resonance energy transfer, we measured the lifetimes of tightly bent DNA loops with and without base-pair mismatch. Surprisingly, for loops captured by stackable sticky ends which leave single-stranded DNA breaks (or nicks) upon annealing, the mismatch decreased the loop lifetime despite reducing the overall bending stress, and the decrease was largest when the mismatch was placed at the DNA midpoint. These findings suggest that base-pair mismatch increases bending stress at the opposite side of the loop through an allosteric mechanism known as cooperative kinking. Based on this mechanism, we present a three-state model that explains the apparent dichotomy between thermodynamic and kinetic stability.
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16
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Wadsworth GM, Kim HD. RNA Isoform Identification via Sequential Hybridization and Strand Displacement Based Amplication in the Caenorhabditis Elegans Germline. Biophys J 2019. [DOI: 10.1016/j.bpj.2018.11.1153] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022] Open
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17
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Wadsworth GM, Parikh RY, Kim HD. Dual-probe RNA FRET-FISH in Yeast. Bio Protoc 2018; 8:e2867. [PMID: 34285981 PMCID: PMC8275227 DOI: 10.21769/bioprotoc.2867] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2018] [Revised: 05/09/2018] [Accepted: 05/12/2018] [Indexed: 11/02/2022] Open
Abstract
mRNA Fluorescence In Situ Hybridization (FISH) is a technique commonly used to profile the distribution of transcripts in cells. When combined with the common single molecule technique Fluorescence Resonance Energy Transfer (FRET), FISH can also be used to profile the co-expression of nearby sequences in the transcript to measure processes such as alternate initiation or splicing variation of the transcript. Unlike in a conventional FISH method using multiple probes to target a single transcript, FRET is limited to the use of two probes labeled with matched dyes and requires the use of sensitized emission. Any widefield microscope capable of sensitive single molecule detection of Cy3 and Cy5 should be able to measure FRET in yeast cells. Alternatively, a FRET-FISH method can be used to unambiguously ascertain identity of the transcript without the use of a guide probe set used in other FISH techniques.
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Affiliation(s)
| | - Rasesh Y. Parikh
- School of Physics, Georgia Institute of Technology, Atlanta, GA, USA
| | - Harold D. Kim
- School of Physics, Georgia Institute of Technology, Atlanta, GA, USA
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18
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Wadsworth GM, Parikh RY, Kim HD. Single-probe RNA FISH in Yeast. Bio Protoc 2018; 8:e2868. [PMID: 34285982 PMCID: PMC8275289 DOI: 10.21769/bioprotoc.2868] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2018] [Revised: 05/09/2018] [Accepted: 05/14/2018] [Indexed: 11/02/2022] Open
Abstract
Quantitative profiling of mRNA expression is an important part of understanding the state of a cell. The technique of RNA Fluorescence In Situ Hybridization (FISH) involves targeting an RNA transcript with a set of 40 complementary fluorescently labeled DNA oligonucleotide probes. However, there are many circumstances such as transcripts shorter than 200 nt, splicing variations, or alternate initiation sites that create transcripts that would be indistinguishable to a set of multiple probes. To this end we adapted the standard FISH protocol to allow the use of a single probe with a single fluorophore to quantify the amount of transcripts inside budding yeast cells. In addition to allowing the quantification of short transcripts or short features of transcripts, this technique reduces the cost of performing FISH.
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Affiliation(s)
| | - Rasesh Y. Parikh
- School of Physics, Georgia Institute of Technology, Atlanta, GA, USA
| | - Harold D. Kim
- School of Physics, Georgia Institute of Technology, Atlanta, GA, USA
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19
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Bo Broadwater D, Kim HD. The Sequence-Dependent Effects of Branch Migration. Biophys J 2018. [DOI: 10.1016/j.bpj.2017.11.3259] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022] Open
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20
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Wadsworth GM, Kim HD. Highly Specific Circular RNA Quantification in Single Yeast Cells. Biophys J 2018. [DOI: 10.1016/j.bpj.2017.11.1378] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022] Open
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21
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Wadsworth GM, Parikh RY, Choy JS, Kim HD. mRNA detection in budding yeast with single fluorophores. Nucleic Acids Res 2017; 45:e141. [PMID: 28666354 PMCID: PMC5587780 DOI: 10.1093/nar/gkx568] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2017] [Accepted: 06/21/2017] [Indexed: 12/29/2022] Open
Abstract
Quantitative measurement of mRNA levels in single cells is necessary to understand phenotypic variability within an otherwise isogenic population of cells. Single-molecule mRNA Fluorescence In Situ Hybridization (FISH) has been established as the standard method for this purpose, but current protocols require a long region of mRNA to be targeted by multiple DNA probes. Here, we introduce a new single-probe FISH protocol termed sFISH for budding yeast, Saccharomyces cerevisiae using a single DNA probe labeled with a single fluorophore. In sFISH, we markedly improved probe specificity and signal-to-background ratio by using methanol fixation and inclined laser illumination. We show that sFISH reports mRNA changes that correspond to protein levels and gene copy number. Using this new FISH protocol, we can detect >50% of the total target mRNA. We also demonstrate the versatility of sFISH using FRET detection and mRNA isoform profiling as examples. Our FISH protocol with single-fluorophore sensitivity significantly reduces cost and time compared to the conventional FISH protocols and opens up new opportunities to investigate small changes in RNA at the single cell level.
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Affiliation(s)
- Gable M Wadsworth
- School of Physics, Georgia Institute of Technology, 837 State Street, Atlanta, GA 30332-0430, USA
| | - Rasesh Y Parikh
- School of Physics, Georgia Institute of Technology, 837 State Street, Atlanta, GA 30332-0430, USA
| | - John S Choy
- Department of Biology, The Catholic University of America, 620 Michigan Avenue NE, Washington, DC 20064, USA
| | - Harold D Kim
- School of Physics, Georgia Institute of Technology, 837 State Street, Atlanta, GA 30332-0430, USA
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22
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Seo Kyung H, Park JY, Kim HD, Lee Dea Y, Choi Doo J, Lee Jea W, Lee YS, Lee SE, Kim Geum S. Antioxidant and anti-inflammatory Studies of mushrooms. Am J Transl Res 2017. [DOI: 10.1055/s-0037-1608556] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Affiliation(s)
- H Seo Kyung
- Rual Development Adiministration, Eumseing, Korea, Republic of (South)
| | - JY Park
- Rual Development Adiministration, Eumseing, Korea, Republic of (South)
| | - HD Kim
- Rual Development Adiministration, Eumseing, Korea, Republic of (South)
| | - Y Lee Dea
- Rual Development Adiministration, Eumseing, Korea, Republic of (South)
| | - J Choi Doo
- Rual Development Adiministration, Eumseing, Korea, Republic of (South)
| | - W Lee Jea
- Rual Development Adiministration, Eumseing, Korea, Republic of (South)
| | - YS Lee
- Rual Development Adiministration, Eumseing, Korea, Republic of (South)
| | - SE Lee
- Rual Development Adiministration, Eumseing, Korea, Republic of (South)
| | - S Kim Geum
- Rual Development Adiministration, Eumseing, Korea, Republic of (South)
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23
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Abstract
BACKGROUND Chronic facial paralysis induces degenerative facial muscle changes on the involved side, thus, making the individual seem as older than their actual age. Furthermore, contralateral facial hypertrophy aggravates facial asymmetry. A thread-lifting procedure has been used widely for correction of a drooping or wrinkled face due to the aging process. In addition, botulinum toxin injection can be used to reduce facial hypertrophy. The aim of study was to evaluate the effectiveness of thread lifting with botulinum toxin injection for chronic facial paralysis. METHODS A total 34 of patients with chronic facial paralysis were enrolled from March to October 2014. Thread lifting for elevating loose facial muscles on the ipsilateral side and botulinum toxin A for controlling the facial muscle hypertrophy on the contralateral side were conducted. Facial function was evaluated using the Sunnybrook grading system and dynamic facial asymmetry ratios 1 year after treatment. RESULTS All 34 patients displayed improved facial symmetry and showed improvement in Sunnybrook scores (37.4 vs. 83.3) and dynamic facial asymmetry ratios (0.58 vs 0.92). Of the 34 patients, 28 (82.4%) reported being satisfied with treatment. CONCLUSION The application of subdermal suspension with a reabsorbable thread in conjunction with botulinum toxin A to optimize facial rejuvenation of the contralateral side constitutes an effective and safe procedure for face lifting and rejuvenation of a drooping face as a result of long-lasting facial paralysis.
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Affiliation(s)
- W J Choe
- Department of Anaesthesiology and Pain Medicine, Ilsan Paik Hospital, Inje University College of Medicine, Gyeonggi-do, Korea (Republic of)
| | - H D Kim
- Department of Otorhinolaryngology, Head & Neck Surgery, Ilsan Paik Hospital, Inje University College of Medicine, Gyeonggi-do, Korea (Republic of)
| | - B H Han
- Department of Otorhinolaryngology, Head & Neck Surgery, Ilsan Paik Hospital, Inje University College of Medicine, Gyeonggi-do, Korea (Republic of)
| | - J Kim
- Department of Otorhinolaryngology, Head & Neck Surgery, Ilsan Paik Hospital, Inje University College of Medicine, Gyeonggi-do, Korea (Republic of).
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24
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Broadwater DB, Kim HD. Is DNA Branch Migration a One-Dimensional Random Walk? Biophys J 2017. [DOI: 10.1016/j.bpj.2016.11.1187] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
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25
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Abstract
The motors that drive double-stranded DNA (dsDNA) genomes into viral capsids are among the strongest of all biological motors for which forces have been measured, but it is not known how they generate force. We previously proposed that the DNA is not a passive substrate but that it plays an active role in force generation. This "scrunchworm hypothesis" holds that the motor proteins repeatedly dehydrate and rehydrate the DNA, which then undergoes cyclic shortening and lengthening motions. These are captured by a coupled protein-DNA grip-and-release cycle to rectify the motion and translocate the DNA into the capsid. In this study, we examined the interactions of dsDNA with the dodecameric connector protein of bacteriophage ϕ29, using molecular dynamics simulations on four different DNA sequences, starting from two different conformations (A-DNA and B-DNA). In all four simulations starting with the protein equilibrated with A-DNA in the channel, we observed transitions to a common, metastable, highly scrunched conformation, designated A*. This conformation is very similar to one recently reported by Kumar and Grubmüller in much longer MD simulations on B-DNA docked into the ϕ29 connector. These results are significant for four reasons. First, the scrunched conformations occur spontaneously, without requiring lever-like protein motions often believed to be necessary for DNA translocation. Second, the transition takes place within the connector, providing the location of the putative "dehydrator". Third, the protein has more contacts with one strand of the DNA than with the other; the former was identified in single-molecule laser tweezer experiments as the "load-bearing strand". Finally, the spontaneity of the DNA-protein interaction suggests that it may play a role in the initial docking of DNA in motors like that of T4 that can load and package any sequence.
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Affiliation(s)
- James T Waters
- School of Physics, Georgia Institute of Technology , Atlanta, Georgia 30332, United States
| | - Harold D Kim
- School of Physics, Georgia Institute of Technology , Atlanta, Georgia 30332, United States
| | - James C Gumbart
- School of Physics, Georgia Institute of Technology , Atlanta, Georgia 30332, United States
| | - Xiang-Jun Lu
- Department of Biological Sciences, Columbia University , New York, New York 10027, United States
| | - Stephen C Harvey
- Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania , Philadelphia, Pennsylvania 19104, United States
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26
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Abstract
Loops undergoing thermal fluctuations are prevalent in nature. Ringlike or cross-linked polymers, cyclic macromolecules, and protein-mediated DNA loops all belong to this category. Stability of these molecules are generally described in terms of free energy, an average quantity, but it may also be impacted by local fluctuating forces acting within these systems. The full distribution of these forces can thus give us insights into mechanochemistry beyond the predictive capability of thermodynamics. In this paper, we study the force exerted by an inextensible semiflexible polymer constrained in a looped state. By using a simulation method termed "phase-space sampling," we generate the equilibrium distribution of chain conformations in both position and momentum space. We compute the constraint forces between the two ends of the loop in this chain ensemble using Lagrangian mechanics, and show that the mean of these forces is equal to the thermodynamic force. By analyzing kinetic and potential contributions to the forces, we find that the mean force acts in the direction of increasing extension not because of bending stress, but in spite of it. Furthermore, we obtain a distribution of constraint forces as a function of chain length, extension, and stiffness. Notably, increasing contour length decreases the average force, but the additional freedom allows fluctuations in the constraint force to increase. The force distribution is asymmetric and falls off less sharply than a Gaussian distribution. Our work exemplifies a system where large-amplitude fluctuations occur in a way unforeseen by a purely thermodynamic framework, and offers computational tools useful for efficient, unbiased simulation of a constrained system.
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Affiliation(s)
- James T Waters
- School of Physics, Georgia Institute of Technology, 837 State Street, Atlanta, Georgia 30332-0430, USA
| | - Harold D Kim
- School of Physics, Georgia Institute of Technology, 837 State Street, Atlanta, Georgia 30332-0430, USA
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27
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Waters JT, Lu XJ, Galindo-Murillo R, Gumbart JC, Kim HD, Cheatham TE, Harvey SC. Transitions of Double-Stranded DNA Between the A- and B-Forms. J Phys Chem B 2016; 120:8449-56. [PMID: 27135262 DOI: 10.1021/acs.jpcb.6b02155] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The structure of double-stranded DNA (dsDNA) is sensitive to solvent conditions. In solution, B-DNA is the favored conformation under physiological conditions, while A-DNA is the form found under low water activity. The A-form is induced locally in some protein-DNA complexes, and repeated transitions between the B- and A-forms have been proposed to generate the forces used to drive dsDNA into viral capsids during genome packaging. Here, we report analyses on previous molecular dynamics (MD) simulations on B-DNA, along with new MD simulations on the transition from A-DNA to B-DNA in solution. We introduce the A-B Index (ABI), a new metric along the A-B continuum, to quantify our results. When A-DNA is placed in an equilibrated solution at physiological ionic strength, there is no energy barrier to the transition to the B-form, which begins within about 1 ns. The transition is essentially complete within 5 ns, although occasionally a stretch of a few base pairs will remain A-like for up to ∼10 ns. A comparison of four sequences with a range of predicted A-phobicities shows that more A-phobic sequences make the transition more rapidly than less A-phobic sequences. Simulations on dsDNA with a region of roughly one turn locked in the A-form allow us to characterize the A/B junction, which has an average bend angle of 20-30°. Fluctuations in this angle occur with characteristic times of about 10 ns.
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Affiliation(s)
- James T Waters
- School of Physics, Georgia Institute of Technology , Atlanta, Georgia 30332, United States
| | - Xiang-Jun Lu
- Department of Biological Sciences, Columbia University , New York, New York 10027, United States
| | - Rodrigo Galindo-Murillo
- Department of Medicinal Chemistry, L.S. Skaggs Pharmacy Institute, University of Utah , Salt Lake City, Utah 84112, United States
| | - James C Gumbart
- School of Physics, Georgia Institute of Technology , Atlanta, Georgia 30332, United States
| | - Harold D Kim
- School of Physics, Georgia Institute of Technology , Atlanta, Georgia 30332, United States
| | - Thomas E Cheatham
- Department of Medicinal Chemistry, L.S. Skaggs Pharmacy Institute, University of Utah , Salt Lake City, Utah 84112, United States
| | - Stephen C Harvey
- Department of Biochemistry and Molecular Biophysics, Perelman School of Medicine, University of Pennsylvania , Philadelphia, Pennsylvania 19104, United States
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28
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Broadwater DWB, Kim HD. The Effect of Basepair Mismatch on DNA Strand Displacement. Biophys J 2016; 110:1476-1484. [PMID: 27074674 PMCID: PMC4833772 DOI: 10.1016/j.bpj.2016.02.027] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2015] [Revised: 02/02/2016] [Accepted: 02/09/2016] [Indexed: 01/31/2023] Open
Abstract
DNA strand displacement is a key reaction in DNA homologous recombination and DNA mismatch repair and is also heavily utilized in DNA-based computation and locomotion. Despite its ubiquity in science and engineering, sequence-dependent effects of displacement kinetics have not been extensively characterized. Here, we measured toehold-mediated strand displacement kinetics using single-molecule fluorescence in the presence of a single basepair mismatch. The apparent displacement rate varied significantly when the mismatch was introduced in the invading DNA strand. The rate generally decreased as the mismatch in the invader was encountered earlier in displacement. Our data indicate that a single base pair mismatch in the invader stalls branch migration and displacement occurs via direct dissociation of the destabilized incumbent strand from the substrate strand. We combined both branch migration and direct dissociation into a model, which we term the concurrent displacement model, and used the first passage time approach to quantitatively explain the salient features of the observed relationship. We also introduce the concept of splitting probabilities to justify that the concurrent model can be simplified into a three-step sequential model in the presence of an invader mismatch. We expect our model to become a powerful tool to design DNA-based reaction schemes with broad functionality.
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Affiliation(s)
- D W Bo Broadwater
- School of Physics, Georgia Institute of Technology, Atlanta, Georgia
| | - Harold D Kim
- School of Physics, Georgia Institute of Technology, Atlanta, Georgia.
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29
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Abstract
Structure and dynamics of DNA impact how the genetic code is processed and maintained. In addition to its biological importance, DNA has been utilized as building blocks of various nanomachines and nanostructures. Thus, understanding the physical properties of DNA is of fundamental importance to basic sciences and engineering applications. DNA can undergo various physical changes. Among them, DNA looping is unique in that it can bring two distal sites together, and thus can be used to mediate interactions over long distances. In this paper, we introduce a FRET-based experimental tool to study DNA looping at the single molecule level. We explain the connection between experimental measurables and a theoretical concept known as the J factor with the intent of raising awareness of subtle theoretical details that should be considered when drawing conclusions. We also explore DNA looping-assisted protein diffusion mechanism called intersegmental transfer using protein induced fluorescence enhancement (PIFE). We present some preliminary results and future outlooks.
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Affiliation(s)
- Jiyoun Jeong
- School of Physics, Georgia Institute of Technology, 837 State Street, Atlanta 30332, USA.
| | - Tung T Le
- School of Physics, Georgia Institute of Technology, 837 State Street, Atlanta 30332, USA.
| | - Harold D Kim
- School of Physics, Georgia Institute of Technology, 837 State Street, Atlanta 30332, USA.
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Harvey SC, Waters JT, Gumbart JC, Kim HD. The Scrunchworm Hypothesis: Transitions between A-DNA and B-DNA Provide the Driving Force for Genome Packaging in Double-Stranded DNA Bacteriophages. Biophys J 2016. [DOI: 10.1016/j.bpj.2015.11.2755] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022] Open
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31
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Jeong J, Kim HD. The Effect of Local Melting of DNA on DNA Loop Formation. Biophys J 2016. [DOI: 10.1016/j.bpj.2015.11.3020] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
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32
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Broadwater DB, Kim HD. Measuring and Modeling the Effect of Single Mismatch on DNA Strand Displacement. Biophys J 2016. [DOI: 10.1016/j.bpj.2015.11.3011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
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33
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Ahn YB, Shin MS, Kim HD. The association of hypertension with periodontitis in Korean females; results from the KNHANES IV. Eur J Public Health 2015. [DOI: 10.1093/eurpub/ckv175.110] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
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34
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Waters JT, Kim HD. Calculation of a fluctuating entropic force by phase space sampling. Phys Rev E Stat Nonlin Soft Matter Phys 2015; 92:013308. [PMID: 26274308 DOI: 10.1103/physreve.92.013308] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/20/2015] [Indexed: 06/04/2023]
Abstract
A polymer chain pinned in space exerts a fluctuating force on the pin point in thermal equilibrium. The average of such fluctuating force is well understood from statistical mechanics as an entropic force, but little is known about the underlying force distribution. Here, we introduce two phase space sampling methods that can produce the equilibrium distribution of instantaneous forces exerted by a terminally pinned polymer. In these methods, both the positions and momenta of mass points representing a freely jointed chain are perturbed in accordance with the spatial constraints and the Boltzmann distribution of total energy. The constraint force for each conformation and momentum is calculated using Lagrangian dynamics. Using terminally pinned chains in space and on a surface, we show that the force distribution is highly asymmetric with both tensile and compressive forces. Most importantly, the mean of the distribution, which is equal to the entropic force, is not the most probable force even for long chains. Our work provides insights into the mechanistic origin of entropic forces, and an efficient computational tool for unbiased sampling of the phase space of a constrained system.
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Affiliation(s)
- James T Waters
- School of Physics, Georgia Institute of Technology and 832 State Street, Atlanta, Georgia 30332-0430
| | - Harold D Kim
- School of Physics, Georgia Institute of Technology and 832 State Street, Atlanta, Georgia 30332-0430
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35
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Abstract
Sharp bending of double-stranded DNA (dsDNA) plays an essential role in genome structure and function. However, the elastic limit of dsDNA bending remains controversial. Here, we measured the opening rates of small dsDNA loops with contour lengths ranging between 40 and 200 bp using single-molecule Fluorescence Resonance Energy Transfer. The relationship of loop lifetime to loop size revealed a critical transition in bending stress. Above the critical loop size, the loop lifetime changed with loop size in a manner consistent with elastic bending stress, but below it, became less sensitive to loop size, indicative of softened dsDNA. The critical loop size increased from ∼60 bp to ∼100 bp with the addition of 5 mM magnesium. We show that our result is in quantitative agreement with the kinkable worm-like chain model, and furthermore, can reproduce previously reported looping probabilities of dsDNA over the range between 50 and 200 bp. Our findings shed new light on the energetics of sharply bent dsDNA.
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Affiliation(s)
- Tung T Le
- School of Physics, Georgia Institute of Technology, 837 State Street, Atlanta, GA 30332, USA
| | - Harold D Kim
- School of Physics, Georgia Institute of Technology, 837 State Street, Atlanta, GA 30332, USA
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36
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Abstract
Bending of double-stranded DNA (dsDNA) is associated with many important biological processes such as DNA-protein recognition and DNA packaging into nucleosomes. Thermodynamics of dsDNA bending has been studied by a method called cyclization which relies on DNA ligase to covalently join short sticky ends of a dsDNA. However, ligation efficiency can be affected by many factors that are not related to dsDNA looping such as the DNA structure surrounding the joined sticky ends, and ligase can also affect the apparent looping rate through mechanisms such as nonspecific binding. Here, we show how to measure dsDNA looping kinetics without ligase by detecting transient DNA loop formation by FRET (Fluorescence Resonance Energy Transfer). dsDNA molecules are constructed using a simple PCR-based protocol with a FRET pair and a biotin linker. The looping probability density known as the J factor is extracted from the looping rate and the annealing rate between two disconnected sticky ends. By testing two dsDNAs with different intrinsic curvatures, we show that the J factor is sensitive to the intrinsic shape of the dsDNA.
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Affiliation(s)
- Tung T Le
- School of Physics, Georgia Institute of Technology
| | - Harold D Kim
- School of Physics, Georgia Institute of Technology;
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37
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Le TT, Kim HD. Measuring Energetics of Sharp DNA Bending from Breakage Kinetics of Small DNA Loops. Biophys J 2014. [DOI: 10.1016/j.bpj.2013.11.1619] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
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38
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Le TT, Kim HD. Measuring shape-dependent looping probability of DNA. Biophys J 2013; 104:2068-76. [PMID: 23663850 DOI: 10.1016/j.bpj.2013.03.029] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2013] [Revised: 03/14/2013] [Accepted: 03/18/2013] [Indexed: 01/06/2023] Open
Abstract
Recently, several studies have shown that short doubled-stranded DNA (dsDNA) loops more readily than the wormlike chain model predicts. In most of these experiments, the intrinsic bendedness of dsDNA, which in theory can dramatically influence looping dynamics, was either avoided or unaccounted for. To investigate the effect of the shape of dsDNA on looping dynamics, we characterized the shapes of several synthetic dsDNA molecules of equal length but different sequences using gel electrophoresis. We then measured their looping rates using a FRET (Förster resonance energy transfer)-based assay and extracted the looping probability density known as the J factor (jM). We also used, for comparison, several dinucleotide angular parameter sets derived from the observed electrophoretic mobility to compute the jM predicted by the wormlike chain model. Although we found a strong correlation between curvature and jM, the measured jM was higher than most dinucleotide model predictions. This result suggests that it is difficult to reconcile the looping probability with the observed gel mobility within the wormlike chain model and underscores the importance of determining the intrinsic shape of dsDNA for proper theoretical analysis.
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Affiliation(s)
- Tung T Le
- School of Physics, Georgia Institute of Technology, Atlanta, Georgia, USA
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39
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Affiliation(s)
- James T. Waters
- School of
Physics, Georgia Institute of Technology, Atlanta, Georgia 30332, United States
| | - Harold D. Kim
- School of
Physics, Georgia Institute of Technology, Atlanta, Georgia 30332, United States
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40
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Abstract
Nucleosomes, which are the basic packaging units of chromatin, are stably positioned in promoters upstream of most stress-inducible genes. These promoter nucleosomes are generally thought to repress gene expression due to exclusion; they prevent transcription factors from accessing their target sites on the DNA. However, the role of promoter nucleosomes that do not directly occlude transcription factor binding sites is not obvious. Here, we varied the stability of a non-occluding nucleosome positioned between a transcription factor binding site and the TATA box region in an inducible yeast promoter and measured downstream gene expression level. We found that gene expression level depends on the occupancy of the non-occluding nucleosome in a non-monotonic manner. We postulated that a non-occluding nucleosome can serve both as a vehicle of and a barrier to chromatin remodeling activity and built a quantitative, nonequilibrium model to explain the observed nontrivial effect of the intervening nucleosome. Our work sheds light on the dual role of nucleosome as a repressor and an activator and expands the standard model of gene expression to include irreversible promoter chromatin transitions.
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Affiliation(s)
- Rasesh Y. Parikh
- School of Physics, Georgia Institute of Technology, Atlanta, Georgia, United States of America
| | - Harold D. Kim
- School of Physics, Georgia Institute of Technology, Atlanta, Georgia, United States of America
- * E-mail:
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41
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Le TT, Kim HD. Catch-Slip Transition in DNA Duplex. Biophys J 2013. [DOI: 10.1016/j.bpj.2012.11.2351] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
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42
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Parikh RY, Kim HD. The Non-Monotonic Effect of Nucleosome Occupancy on Gene Expression. Biophys J 2013. [DOI: 10.1016/j.bpj.2012.11.3223] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022] Open
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43
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Abstract
Immunological changes in elite adolescent female athletes during Taekwondo competitions were investigated on-field. 6 female athletes (16.7 ± 0.8 year-old) volunteered and performed 5 bouts of demonstration Taekwondo competitions simulating real tournaments in intensity, duration, and break-time intervals on the same day. Blood samples were taken before, after the competitions and during the recovery, respectively. Immunological changes and oxidative stress in peripheral blood mononuclear cells were evaluated by flow-cytometry. During the competitions, exercise intensity was 92.2 ± 3.8% (86.1~95.7) of the maximal heart rate. Blood lactate increased immediately after the competitions (p=0.0165) and decreased to baseline during recovery. Intracellular reactive oxygen species (ROS) in the peripheral blood increased continuously during recovery (p<0.05, respectively). Natural killer cells increased immediately after the competitions (p=0.0006), and decreased during recovery. B and T cells increased immediately after the competitions and remained elevated throughout recovery (p<0.05, respectively). CD4/CD8 ratio after the competitions was decreased (p=0.0091) and returned to baseline during recovery. These results suggest that the immunological function of the elite female adolescent athletes could be attenuated after Taekwondo competitions. Further large-scaled Taekwondo studies on immunologic and apoptotic changes related to oxidative stress should be performed for improving and protecting the health of adolescent athletes.
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Affiliation(s)
- Y W Lee
- Division of Allergy-Immunology and Rheumatology, Department of Internal Medicine, Kwandong University College of Medicine, Goyang, Republic of Korea
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44
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Abstract
Transcriptional regulatory circuits govern how cis and trans factors transform signals into messenger RNA (mRNA) expression levels. With advances in quantitative and high-throughput technologies that allow measurement of gene expression state in different conditions, data that can be used to build and test models of transcriptional regulation is being generated at a rapid pace. Here, we review experimental and computational methods used to derive detailed quantitative circuit models on a small scale and cruder, genome-wide models on a large scale. We discuss the potential of combining small- and large-scale approaches to understand the working and wiring of transcriptional regulatory circuits.
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Affiliation(s)
- Harold D Kim
- Howard Hughes Medical Institute, Harvard University Faculty of Arts and Sciences Center for Systems Biology, Department of Molecular and Cellular Biology, Cambridge, MA 02138, USA
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You SJ, Jung DE, Kim HD, Lee HS, Kang HC. Efficacy and prognosis of a short course of prednisolone therapy for pediatric epilepsy. Eur J Paediatr Neurol 2008; 12:314-20. [PMID: 17951084 DOI: 10.1016/j.ejpn.2007.09.003] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/19/2007] [Revised: 08/10/2007] [Accepted: 09/03/2007] [Indexed: 11/28/2022]
Abstract
PURPOSE To evaluate the efficacy and safety of adjunctive prednisolone therapy in children with cryptogenic epileptic encephalopathy, other than infantile spasms, and to determine its prognosis. METHODS Prednisolone, 2mg/kg per day for 6 weeks, tapered for a further 2 weeks, was given in combination with previously prescribed antiepileptic drugs. A retrospective assessment of 41 children thus treated included measurements of seizure frequency, electroencephalographic findings, global assessments of cognitive function, and adverse drug events. Long-term patient prognoses over a mean follow-up period of 3 years and 5 months (range, 14-90 months) were also examined. RESULTS Of 41 patients, 32 had Lennox-Gastaut syndrome, 4 had Doose syndrome, 1 had Otahara syndrome, 2 had Landau-Kleffner syndrome, and 2 had other unspecified generalized epilepsies. After prednisolone therapy, 73% (30/41) of patients showed a reduction in seizure frequency of >50%, and 59% (24/41) became seizure free. However, only seven patients (four with Lennox-Gastaut syndrome, two with Doose syndrome, and one with unspecified generalized epilepsy) who became seizure free remained free of seizures at the time of the final follow-up. Electroencephalographic findings and global assessments of cognitive function correlated well with seizure outcomes. No significant demographic factors influenced the efficacy of prednisolone or patient prognoses after prednisolone tapering. Most adverse events were transient, or were tolerated well with conservative management, with maintenance of the medication. CONCLUSION Prednisolone therapy may be a safe and effective adjunct in patients with cryptogenic epileptic encephalopathies, but the high relapse rate is of concern.
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Affiliation(s)
- S J You
- Department of Pediatrics, Epilepsy Center, Sanggye Paik Hospital, Inje University College of Medicine, 761-1 Sang-gye 7 Dong, No-won Gu, Seoul 139-707, Republic of Korea
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46
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Abstract
The detailed mechanism of how the ribosome decodes protein sequence information with an abnormally high accuracy, after 40 years of study, remains elusive. A critical element in selecting correct transfer RNA (tRNA) transferring correct amino acid is "induced fit" between the ribosome and tRNA. By using single-molecule methods, the induced fit mechanism is shown to position favorably the correct tRNA after initial codon recognition. We provide evidence that this difference in positioning and thermal fluctuations constitutes the primary mechanism for the initial selection of tRNA. This work demonstrates thermal fluctuations playing a critical role in the substrate selection by an enzyme.
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Affiliation(s)
- Tae-Hee Lee
- *Departments of Physics and Applied Physics, Stanford University, Stanford, CA 94305
| | - Scott C. Blanchard
- *Departments of Physics and Applied Physics, Stanford University, Stanford, CA 94305
- Department of Structural Biology, Stanford University School of Medicine, Stanford, CA 94305; and
| | - Harold D. Kim
- *Departments of Physics and Applied Physics, Stanford University, Stanford, CA 94305
| | - Joseph D. Puglisi
- Department of Structural Biology, Stanford University School of Medicine, Stanford, CA 94305; and
| | - Steven Chu
- Department of Structural Biology, Stanford University School of Medicine, Stanford, CA 94305; and
- Lawrence Berkeley National Laboratory, Departments of Physics and Molecular and Cell Biology, University of California, Berkeley, CA 94720
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47
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Abstract
Adjacent transfer RNAs (tRNAs) in the A- and P-sites of the ribosome are in dynamic equilibrium between two different conformations called classical and hybrid states before translocation. Here, we have used single-molecule fluorescence resonance energy transfer to study the effect of Mg(2+) on tRNA dynamics with and without an acetyl group on the A-site tRNA. When the A-site tRNA is not acetylated, tRNA dynamics do not depend on [Mg(2+)], indicating that the relative positions of the substrates for peptide-bond formation are not affected by Mg(2+). In sharp contrast, when the A-site tRNA is acetylated, Mg(2+) lengthens the lifetime of the classical state but does not change the lifetime of the hybrid state. Based on these findings, the classical state resembles a state with direct stabilization of tertiary structure by Mg(2+) ions whereas the hybrid state resembles a state with little Mg(2+)-assisted stabilization. The antibiotic viomycin, a translocation inhibitor, suppresses tRNA dynamics, suggesting that the enhanced fluctuations of tRNAs after peptide-bond formation drive spontaneous attempts at translocation by the ribosome.
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Affiliation(s)
- Harold D Kim
- Department of Physics, Stanford University, Stanford, California 94305, USA
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48
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Abstract
The ion atmosphere of three-armed symmetric Y-shaped and asymmetric y-shaped A-RNA junctions in aqueous solution containing multivalent ions is described within the framework of a polyelectrolyte model. The fraction of "screening counterions" per polyion charge that shield the residual unneutralized charges from interacting with one another and the condensed counterions per polyion charge as a function of sodium and magnesium ion concentrations are determined. The predictions for the slope of log(k(o)/k(f)) as a function of Na+ and Mg2+ concentration, where k(o) and k(f) are the opening and folding rates of the three-helix junction molecule, respectively, are compared with experimental data (Kim et al. Proc. Nat. Acad. Sci. U.S.A. 2002, 96, 9077-9082).
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Affiliation(s)
- Udayan Mohanty
- Department of Chemistry, Boston College, Chestnut Hill, Massachusetts 02467, USA
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Uemura S, Dorywalska M, Lee TH, Kim HD, Puglisi JD, Chu S. Peptide bond formation destabilizes Shine–Dalgarno interaction on the ribosome. Nature 2007; 446:454-7. [PMID: 17377584 DOI: 10.1038/nature05625] [Citation(s) in RCA: 75] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2006] [Accepted: 01/26/2007] [Indexed: 11/09/2022]
Abstract
The ribosome is a molecular machine that translates the genetic code contained in the messenger RNA into an amino acid sequence through repetitive cycles of transfer RNA selection, peptide bond formation and translocation. Here we demonstrate an optical tweezer assay to measure the rupture force between a single ribosome complex and mRNA. The rupture force was compared between ribosome complexes assembled on an mRNA with and without a strong Shine-Dalgarno (SD) sequence-a sequence found just upstream of the coding region of bacterial mRNAs, involved in translation initiation. The removal of the SD sequence significantly reduced the rupture force in complexes carrying an aminoacyl tRNA, Phe-tRNA(Phe), in the A site, indicating that the SD interactions contribute significantly to the stability of the ribosomal complex on the mRNA before peptide bond formation. In contrast, the presence of a peptidyl tRNA analogue, N-acetyl-Phe-tRNA(Phe), in the A site, which mimicked the post-peptidyl transfer state, weakened the rupture force as compared to the complex with Phe-tRNA(Phe), and the resultant force was the same for both the SD-containing and SD-deficient mRNAs. These results suggest that formation of the first peptide bond destabilizes the SD interaction, resulting in the weakening of the force with which the ribosome grips an mRNA. This might be an important requirement to facilitate movement of the ribosome along mRNA during the first translocation step.
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Affiliation(s)
- Sotaro Uemura
- Department of Physics, Stanford University, Stanford, California 94305, USA
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50
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Abstract
OBJECTIVE To present our experience with vagus nerve stimulation (VNS) and to evaluate the long-term efficacy and safety of the procedure in pediatric intractable epilepsy. METHODS This study included sixteen patients, who were implanted with a vagus nerve stimulator and could be followed up for at least more than 12 months in two epilepsy centers. Data including seizure frequency, EEG, quality of life measures and adverse events were prospectively filed over a 5-year period. RESULTS VNS resulted in a > 50% reduction in seizure frequency in 50.0% (8/16) of children with 31.3% (5/16) of patients achieving a > 90% reduction. Additionally, enhancements in quality of life were as follows: memory in 50.0% (8/16), mood in 62.5% (10/16), behavior in 68.8% (11/16), alertness in 68.8% (11/16), achievement in 37.5% (6/16), and verbal skills in 43.8% (7/16) of the patients. Adverse events included hoarseness in two patients, dyspnea during sleep in two patients, and sialorrhea in one patient. However, these events were tolerable or could be controlled by the adjustment of output currents. In one patient, wound revision was required. CONCLUSION Our data supports the role of VNS as an alternative therapy for pediatric intractable epilepsy.
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Affiliation(s)
- H C Kang
- Department of Pediatrics, Epilepsy Center, Inje University College of Medicine, Sanggye Paik Hospital, Korea
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