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Melters DP, Dalal Y. Nano-Surveillance: Tracking Individual Molecules in a Sea of Chromatin. J Mol Biol 2020; 433:166720. [PMID: 33221335 PMCID: PMC8770095 DOI: 10.1016/j.jmb.2020.11.019] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2020] [Revised: 11/06/2020] [Accepted: 11/16/2020] [Indexed: 01/12/2023]
Abstract
Chromatin is the epigenomic platform for diverse nuclear processes such as DNA repair, replication, transcription, telomere, and centromere function. In cancer cells, mutations in key processes result in DNA amplification, chromosome translocations, and chromothripsis, severely distorting the natural chromatin state. In normal and diseased states, dozens of chromatin effectors alter the physical integrity and dynamics of chromatin at the level of both single nucleosomes and arrays of nucleosomes folded into 3-dimensional shapes. Integrating these length scales, from the 10 nm sized nucleosome to mitotic chromosomes, whilst jostling within the crowded environment of the cell, cannot yet be achieved by a single technology. In this review, we discuss tools that have proven powerful in the investigation of nucleosome and chromatin fiber dynamics. We also provide a deeper focus into atomic force microscopy (AFM) applications that can bridge diverse length and time scales. Using time course AFM, we observe that chromatin condensation by H1.5 is dynamic, whereas using nano-indentation force spectroscopy we observe that both histone variants and nucleosome binding partners alter material properties of individual nucleosomes. Finally, we demonstrate how high-speed AFM can visualize plasmid DNA dynamics, intermittent nucleosome-nucleosome contacts, and changes in nucleosome phasing along a contiguous chromatin fiber. Altogether, the development of innovative technologies holds the promise of revealing the secret lives of nucleosomes, potentially bridging the gaps in our understanding of how chromatin works within living cells and tissues.
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Affiliation(s)
- Daniël P Melters
- National Cancer Institute, Center for Cancer Research, Laboratory of Receptor Biology and Gene Expression, Bethesda, MD, United States.
| | - Yamini Dalal
- National Cancer Institute, Center for Cancer Research, Laboratory of Receptor Biology and Gene Expression, Bethesda, MD, United States.
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2
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Zhang M, De Bo G. Impact of a Mechanical Bond on the Activation of a Mechanophore. J Am Chem Soc 2018; 140:12724-12727. [DOI: 10.1021/jacs.8b08590] [Citation(s) in RCA: 33] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Affiliation(s)
- Min Zhang
- School of Chemistry, University of Manchester, Oxford Road, Manchester M13 9PL, United Kingdom
| | - Guillaume De Bo
- School of Chemistry, University of Manchester, Oxford Road, Manchester M13 9PL, United Kingdom
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3
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Abstract
Strong and stable under tension?
Strong and stable under tension? In this review we present the recent efforts investigating the mechanochemical properties of interlocked structures by atomic force microscopy and polymer mechanochemistry.
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Affiliation(s)
- Guillaume De Bo
- School of Chemistry , University of Manchester , Oxford Road , Manchester , M13 9PL , UK .
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4
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Liu W, Wu C. Rheological Study of Soft Matters: A Review of Microrheology and Microrheometers. MACROMOL CHEM PHYS 2017. [DOI: 10.1002/macp.201700307] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Affiliation(s)
- Wei Liu
- Department of Physics; The Chinese University of Hong Kong; Shatin N.T. Hong Kong 999077
| | - Chi Wu
- Department of Chemistry; The Chinese University of Hong Kong; Shatin N.T. Hong Kong 999077
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5
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Dunlop A, Bowman K, Aarstad O, Skjåk-Bræk G, Stokke BT, Round AN. Polymer sequencing by molecular machines: a framework for predicting the resolving power of a sliding contact force spectroscopy sequencing method. NANOSCALE 2017; 9:15089-15097. [PMID: 28967943 DOI: 10.1039/c7nr03358c] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
We evaluate an AFM-based single molecule force spectroscopy method for mapping sequences in otherwise difficult to sequence heteropolymers, including glycosylated proteins and glycans. The sliding contact force spectroscopy (SCFS) method exploits a sliding contact made between a nanopore threaded over a polymer axle and an AFM probe. We find that for sliding α- and β-cyclodextrin nanopores over a wide range of hydrophilic monomers, the free energy of sliding is proportional to the sum of two dimensionless, easily calculable parameters representing the relative partitioning of the monomer inside the nanopore or in the aqueous phase, and the friction arising from sliding the nanopore over the monomer. Using this relationship we calculate sliding energies for nucleic acids, amino acids, glycan and synthetic monomers and predict on the basis of these calculations that SCFS will detect N- and O-glycosylation of proteins and patterns of sidechains in glycans. For these applications, SCFS offers an alternative to sequence mapping by mass spectrometry or newly-emerging nanopore technologies that may be easily implemented using a standard AFM.
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Affiliation(s)
- Alex Dunlop
- HH Wills Physics Laboratory, University of Bristol, Tyndall Avenue, Bristol BS8 1TL, UK
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6
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van den Boomen OI, Coumans RG, Akeroyd N, Peters TP, Schlebos PP, Smits J, de Gelder R, Elemans JA, Nolte RJ, Rowan AE. Carbenoid transfer reactions catalyzed by a ruthenium porphyrin macrocycle. Tetrahedron 2017. [DOI: 10.1016/j.tet.2017.05.035] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
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7
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Kimura M, Mizuno T, Ueda M, Miyagawa S, Kawasaki T, Tokunaga Y. Four-State Molecular Shuttling of [2]Rotaxanes in Response to Acid/Base and Alkali-Metal Cation Stimuli. Chem Asian J 2017; 12:1381-1390. [DOI: 10.1002/asia.201700493] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2017] [Revised: 04/10/2017] [Indexed: 11/10/2022]
Affiliation(s)
- Masaki Kimura
- Department of Materials Science and Engineering; Faculty of Engineering; University of Fukui; Bunkyo Fukui 910-8507 Japan
| | - Takuma Mizuno
- Department of Materials Science and Engineering; Faculty of Engineering; University of Fukui; Bunkyo Fukui 910-8507 Japan
| | - Masahiro Ueda
- Department of Materials Science and Engineering; Faculty of Engineering; University of Fukui; Bunkyo Fukui 910-8507 Japan
| | - Shinobu Miyagawa
- Department of Materials Science and Engineering; Faculty of Engineering; University of Fukui; Bunkyo Fukui 910-8507 Japan
| | - Tsuneomi Kawasaki
- Department of Materials Science and Engineering; Faculty of Engineering; University of Fukui; Bunkyo Fukui 910-8507 Japan
| | - Yuji Tokunaga
- Department of Materials Science and Engineering; Faculty of Engineering; University of Fukui; Bunkyo Fukui 910-8507 Japan
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8
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Bowman KA, Aarstad OA, Stokke BT, Skjåk-Bræk G, Round AN. Sliding Contact Dynamic Force Spectroscopy Method for Interrogating Slowly Forming Polymer Cross-Links. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2016; 32:12814-12822. [PMID: 27813412 DOI: 10.1021/acs.langmuir.6b03414] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
Dynamic single-molecule force spectroscopy (SMFS), conducted most commonly using AFM, has become a widespread and valuable tool for understanding the kinetics and thermodynamics of fundamental molecular processes such as ligand-receptor interactions and protein unfolding. Where slowly forming bonds are responsible for the primary characteristics of a material, as is the case in cross-links in some polymer gels, care must be taken to ensure that a fully equilibrated bond has first formed before its rupture can be interpreted. Here we introduce a method, sliding contact force spectroscopy (SCFS), that effectively eliminates the kinetics of bond formation from the measurement of bond rupture. In addition, it permits bond rupture measurements in systems where one of the binding partners may be introduced into solution prior to binding without tethering to a surface. Taking as an example of a slowly forming bond, the "eggbox" junction cross-links between oligoguluronic acid chains (oligoGs) in the commercially important polysaccharide alginate, we show that SCFS accurately measures the equilibrated bond strength of the cross-link when one chain is introduced into the sample solution without tethering to a surface. The results validate the SCFS technique for performing single-molecule force spectroscopy experiments and show that it has advantages in cases where the bond to be studied forms slowly and where tethering of one of the binding partners is impractical.
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Affiliation(s)
- Kate A Bowman
- School of Pharmacy, University of East Anglia , Norwich, United Kingdom
| | | | | | | | - Andrew N Round
- School of Pharmacy, University of East Anglia , Norwich, United Kingdom
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Ueda M, Terazawa S, Deguchi Y, Kimura M, Matsubara N, Miyagawa S, Kawasaki T, Tokunaga Y. Five-State Molecular Shuttling of a Pair of [2]Rotaxanes: Distinct Outputs in Response to Acid and Base Stimuli. Chem Asian J 2016; 11:2291-300. [DOI: 10.1002/asia.201600743] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2016] [Indexed: 11/09/2022]
Affiliation(s)
- Masahiro Ueda
- University of Fukui; Department of Materials Science and Engineering; Bunkyo Fukui 910-8507 Japan
| | - Shoya Terazawa
- University of Fukui; Department of Materials Science and Engineering; Bunkyo Fukui 910-8507 Japan
| | - Yasuaki Deguchi
- University of Fukui; Department of Materials Science and Engineering; Bunkyo Fukui 910-8507 Japan
| | - Masaki Kimura
- University of Fukui; Department of Materials Science and Engineering; Bunkyo Fukui 910-8507 Japan
| | - Naoki Matsubara
- University of Fukui; Department of Materials Science and Engineering; Bunkyo Fukui 910-8507 Japan
| | - Shinobu Miyagawa
- University of Fukui; Department of Materials Science and Engineering; Bunkyo Fukui 910-8507 Japan
| | - Tsuneomi Kawasaki
- University of Fukui; Department of Materials Science and Engineering; Bunkyo Fukui 910-8507 Japan
| | - Yuji Tokunaga
- University of Fukui; Department of Materials Science and Engineering; Bunkyo Fukui 910-8507 Japan
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Bergues-Pupo AE, Bergues JM, Falo F, Fiasconaro A. Thermal and inertial resonances in DNA unzipping. THE EUROPEAN PHYSICAL JOURNAL. E, SOFT MATTER 2015; 38:126. [PMID: 25990632 DOI: 10.1140/epje/i2015-15041-4] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/09/2015] [Revised: 03/18/2015] [Accepted: 03/23/2015] [Indexed: 06/04/2023]
Abstract
Single-molecule experiments combined with alternate forces are able to provide useful information not present in standard constant-force and -velocity pulling protocols. Here, we study the effects of such forces in the DNA mechanical unzipping by using an extension of the Peyrard-Bishop-Dauxois model. By changing the damping regime in the dynamical equations, we obtained two resonant mechanisms in both the mean time and the mean force of unzipping. One is thermally assisted and it is characterized by a matching between the period of the external force and the mean unzipping time of the DNA chain, while the other depends on the inertial properties of the system. Both mechanisms are studied systematically under different opening protocols and different parameters of the system. The main results here presented contribute in characterizing and finding optimized conditions in DNA unzipping experiments.
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Affiliation(s)
- A E Bergues-Pupo
- Departamento de Física de la Materia Condensada, Facultad de Ciencias, Universidad de Zaragoza, 50009, Zaragoza, Spain,
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Long F, Cao B, Khanal A, Fang S, Shahbazian-Yassar R. Modification of a single-molecule AFM probe with highly defined surface functionality. BEILSTEIN JOURNAL OF NANOTECHNOLOGY 2014; 5:2122-2128. [PMID: 25551040 PMCID: PMC4273215 DOI: 10.3762/bjnano.5.221] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/16/2014] [Accepted: 10/31/2014] [Indexed: 06/04/2023]
Abstract
Single-molecule force spectroscopy with an atomic force microscope has been widely used to study inter- and intramolecular interactions. To obtain data consistent with single molecular events, a well-defined method is critical to limit the number of molecules at the apex of an AFM probe to one or to a few. In this paper, we demonstrate an easy method for single-molecule probe modification by using the Cu-catalyzed alkyne-azide cycloaddition reaction. Excess terminal alkynes were covalently attached to the probe, and a bi-functional molecule containing an azide at one end and a carboxylic acid at the other was dissolved in the reaction solution. By simply contacting the probe and the Cu substrate, controlled carboxylation on the probe apex could be achieved, since the 'click' reaction requires the co-exist of alkyne, azide and Cu(I). The finite contact area would result in a highly defined surface functionality of the probe down to single molecule level with high reproducibility.
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Affiliation(s)
- Fei Long
- Department of Mechanical Engineering-Engineering Mechanics, Michigan Technological University, 1400 Townsend Drive, Houghton, Michigan, USA
| | - Bin Cao
- Department of Chemistry, Michigan Technological University, 1400 Townsend Drive, Houghton, Michigan, USA
| | - Ashok Khanal
- Department of Chemistry, Michigan Technological University, 1400 Townsend Drive, Houghton, Michigan, USA
| | - Shiyue Fang
- Department of Chemistry, Michigan Technological University, 1400 Townsend Drive, Houghton, Michigan, USA
| | - Reza Shahbazian-Yassar
- Department of Mechanical Engineering-Engineering Mechanics, Michigan Technological University, 1400 Townsend Drive, Houghton, Michigan, USA
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12
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van Dongen SFM, Cantekin S, Elemans JAAW, Rowan AE, Nolte RJM. Functional interlocked systems. Chem Soc Rev 2014; 43:99-122. [DOI: 10.1039/c3cs60178a] [Citation(s) in RCA: 245] [Impact Index Per Article: 24.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
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13
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Lin JY, Liao JH, Chou SW. Cathodic electrodeposition of highly porous cobalt sulfide counter electrodes for dye-sensitized solar cells. Electrochim Acta 2011. [DOI: 10.1016/j.electacta.2011.07.080] [Citation(s) in RCA: 139] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/17/2022]
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14
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Kuzuya A, Ohnishi T, Yamazaki T, Komiyama M. Dethreading of deoxyribonucleotides through α-cyclodextrin. Chem Asian J 2011; 5:2177-80. [PMID: 20715189 DOI: 10.1002/asia.201000289] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Akinori Kuzuya
- Research Center for Advanced Science and Technology, The University of Tokyo, 4-6-1 Komaba, Meguro-ku, Tokyo 153-8904, Japan.
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15
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Li WW, Claridge TDW, Li Q, Wormald MR, Davis BG, Bayley H. Tuning the cavity of cyclodextrins: altered sugar adaptors in protein pores. J Am Chem Soc 2011; 133:1987-2001. [PMID: 21244029 DOI: 10.1021/ja1100867] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Cyclodextrins (CDs) have been widely used in host-guest molecular recognition because of their chiral and hydrophobic cavities. For example, β-cyclodextrin (βCD) lodged as a molecular adaptor in protein pores such as α-hemolysin (αHL) is used for stochastic sensing. Here, we have tuned the cavity and overall size of βCD by replacing a single oxygen atom in its ring skeleton by a disulfide unit in two different configurations to both expand our ability to detect analytes and understand the interactions of βCD with protein pores. The three-dimensional structures of the two stereoisomeric CDs have been determined by the combined application of NMR spectroscopy and molecular simulation and show distorted conformations as compared to natural βCD. The interactions of these synthetic βCD analogues with mutant αHL protein pores and guest molecules were studied by single-channel electrical recording. The dissociation rate constants for both disulfide CDs from the mutant pores show ∼1000-fold increase as compared to those of unaltered βCD, but are ∼10-fold lower than the dissociation rate constants for βCD from wild-type αHL. Both of the skeleton-modified CDs show altered selectivity toward guest molecules. Our approach expands the breadth in sensitivity and diversity of sensing with protein pores and suggests structural parameters useful for CD design, particularly in the creation of asymmetric cavities.
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Affiliation(s)
- Wen-Wu Li
- Department of Chemistry, University of Oxford, Chemical Research Laboratory, Mansfield Road, Oxford OX1 3TA, United Kingdom
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Huang S, He J, Chang S, Zhang P, Liang F, Li S, Tuchband M, Fuhrmann A, Ros R, Lindsay S. Identifying single bases in a DNA oligomer with electron tunnelling. NATURE NANOTECHNOLOGY 2010; 5:868-73. [PMID: 21076404 PMCID: PMC4121130 DOI: 10.1038/nnano.2010.213] [Citation(s) in RCA: 191] [Impact Index Per Article: 13.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/28/2010] [Accepted: 10/04/2010] [Indexed: 05/21/2023]
Abstract
It has been proposed that single molecules of DNA could be sequenced by measuring the physical properties of the bases as they pass through a nanopore. Theoretical calculations suggest that electron tunnelling can identify bases in single-stranded DNA without enzymatic processing, and it was recently experimentally shown that tunnelling can sense individual nucleotides and nucleosides. Here, we report that tunnelling electrodes functionalized with recognition reagents can identify a single base flanked by other bases in short DNA oligomers. The residence time of a single base in a recognition junction is on the order of a second, but pulling the DNA through the junction with a force of tens of piconewtons would yield reading speeds of tens of bases per second.
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Affiliation(s)
- Shuo Huang
- Biodesign Institute, Arizona State University, Tempe, Arizona 85287, USA
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