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Serag MF, Aikeremu A, Tsukamoto R, Piwoński H, Abadi M, Kaji N, Dwyer JR, Baba Y, Habuchi S. Geometry-Based Self-Assembly of Histone-DNA Nanostructures at Single-Nucleotide Resolution. ACS NANO 2019; 13:8155-8168. [PMID: 31244030 DOI: 10.1021/acsnano.9b03259] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Histones are basic protein monomers capable of interacting with DNA, providing the mechanism of DNA compaction inside the cell nucleus. The well-ordered assembly process of histone and DNA is a potential candidate as the approach for building DNA-protein nanostructures. Here, utilizing the sequence-independent histone-DNA interaction, we present an approach to self-assemble histones and single-stranded DNA (ssDNA) to form well-defined histone-DNA (sHD) nanoparticles and their multidimensional cross-linked complexes (cHD). By using various molecular biology and microscopy techniques, we elucidate the structure of these complexes, and we show that they are formed at carefully controlled conditions of temperature, ionic strength, concentration, and incubation time. We also demonstrate using a set of ssDNA molecular rulers and a geometric accommodation model that the assembly of sHD and cHD particles proceeds with precise geometry so that the number of ssDNA in these particles can be programmed by the length of ssDNA. We further show that the formation of cHD amplifies the effect of the length of ssDNA on the self-assembly, allowing for distinguishing ssDNA of different lengths at single nucleotide resolution. We envision that our geometry-directed approach of self-assembling histone-DNA nanostructures and the fundamental insights can serve as a structural platform to advance building precisely ordered DNA-protein nanostructures.
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Affiliation(s)
- Maged F Serag
- Biological and Environmental Science and Engineering Division , King Abdullah University of Science and Technology (KAUST) , Thuwal 23955-6900 , Saudi Arabia
- Department of Biomolecular Engineering, Graduate School of Engineering , Nagoya University , Furo-cho, Chikusa-ku, Nagoya 464-8603 , Japan
- ImPACT Research Center for Advanced Nanobiodevices , Nagoya University , Furo-cho, Chikusa-ku, Nagoya 464-8603 , Japan
| | - Aimaiti Aikeremu
- Biological and Environmental Science and Engineering Division , King Abdullah University of Science and Technology (KAUST) , Thuwal 23955-6900 , Saudi Arabia
| | - Ryoko Tsukamoto
- Department of Biomolecular Engineering, Graduate School of Engineering , Nagoya University , Furo-cho, Chikusa-ku, Nagoya 464-8603 , Japan
- ImPACT Research Center for Advanced Nanobiodevices , Nagoya University , Furo-cho, Chikusa-ku, Nagoya 464-8603 , Japan
| | - Hubert Piwoński
- Biological and Environmental Science and Engineering Division , King Abdullah University of Science and Technology (KAUST) , Thuwal 23955-6900 , Saudi Arabia
| | - Maram Abadi
- Biological and Environmental Science and Engineering Division , King Abdullah University of Science and Technology (KAUST) , Thuwal 23955-6900 , Saudi Arabia
| | - Noritada Kaji
- Department of Applied Chemistry, Graduate School of Engineering , Kyushu University , 744 Motooka , Nishi-ku, Fukuoka 819-0395 , Japan
- JST, PRESTO , 4-1-8 Honcho , Kawaguchi , Saitama 332-0012 , Japan
| | - Jason R Dwyer
- Department of Chemistry , University of Rhode Island , 140 Flagg Road , Kingston , Rhode Island 02881 , United States
| | - Yoshinobu Baba
- Department of Biomolecular Engineering, Graduate School of Engineering , Nagoya University , Furo-cho, Chikusa-ku, Nagoya 464-8603 , Japan
- ImPACT Research Center for Advanced Nanobiodevices , Nagoya University , Furo-cho, Chikusa-ku, Nagoya 464-8603 , Japan
- National Institute of Advanced Industrial Science and Technology (AIST) , Takamatsu 761-0395 , Japan
- School of Pharmacy , Kaohsiung Medical University , Kaohsiung 807 , Taiwan , R.O.C
| | - Satoshi Habuchi
- Biological and Environmental Science and Engineering Division , King Abdullah University of Science and Technology (KAUST) , Thuwal 23955-6900 , Saudi Arabia
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Zeid AM, Kaji N, Nasr JJM, Belal FF, Baba Y, Walash MI. Stacking-cyclodextrin-microchip electrokinetic chromatographic determination of gabapentinoid drugs in pharmaceutical and biological matrices. J Chromatogr A 2017; 1503:65-75. [DOI: 10.1016/j.chroma.2017.04.049] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2017] [Revised: 04/20/2017] [Accepted: 04/24/2017] [Indexed: 12/25/2022]
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Hendrickx S, de Malsche W, Cabooter D. An overview of the use of microchips in electrophoretic separation techniques: fabrication, separation modes, sample preparation opportunities, and on-chip detection. Methods Mol Biol 2015; 1274:3-17. [PMID: 25673478 DOI: 10.1007/978-1-4939-2353-3_1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
This chapter is intended as a basic introduction to microchip-based capillary electrophoresis to set the scene for newcomers and give pointers to reference material. An outline of some commonly used setups and key concepts is given, many of which are explored in greater depth in later chapters.
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Affiliation(s)
- Stijn Hendrickx
- Department of Pharmaceutical and Pharmacological Sciences, Pharmaceutical Analysis, KU Leuven, O&N2 923, Herestraat 49, 3000, Leuven, Belgium
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Neethirajan S, Kobayashi I, Nakajima M, Wu D, Nandagopal S, Lin F. Microfluidics for food, agriculture and biosystems industries. LAB ON A CHIP 2011; 11:1574-86. [PMID: 21431239 DOI: 10.1039/c0lc00230e] [Citation(s) in RCA: 115] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/07/2023]
Abstract
Microfluidics, a rapidly emerging enabling technology has the potential to revolutionize food, agriculture and biosystems industries. Examples of potential applications of microfluidics in food industry include nano-particle encapsulation of fish oil, monitoring pathogens and toxins in food and water supplies, micro-nano-filtration for improving food quality, detection of antibiotics in dairy food products, and generation of novel food structures. In addition, microfluidics enables applications in agriculture and animal sciences such as nutrients monitoring and plant cells sorting for improving crop quality and production, effective delivery of biopesticides, simplified in vitro fertilization for animal breeding, animal health monitoring, vaccination and therapeutics. Lastly, microfluidics provides new approaches for bioenergy research. This paper synthesizes information of selected microfluidics-based applications for food, agriculture and biosystems industries.
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Affiliation(s)
- Suresh Neethirajan
- Biological and Nanoscale Systems Group, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA.
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Ramautar R, Mayboroda OA, Somsen GW, de Jong GJ. CE-MS for metabolomics: Developments and applications in the period 2008-2010. Electrophoresis 2010; 32:52-65. [DOI: 10.1002/elps.201000378] [Citation(s) in RCA: 103] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2010] [Revised: 09/28/2010] [Accepted: 09/28/2010] [Indexed: 12/20/2022]
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Felhofer JL, Blanes L, Garcia CD. Recent developments in instrumentation for capillary electrophoresis and microchip-capillary electrophoresis. Electrophoresis 2010; 31:2469-86. [PMID: 20665910 PMCID: PMC2928674 DOI: 10.1002/elps.201000203] [Citation(s) in RCA: 67] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Abstract
Over the last years, there has been an explosion in the number of developments and applications of CE and microchip-CE. In part, this growth has been the direct consequence of recent developments in instrumentation associated with CE. This review, which is focused on the contributions published in the last 5 years, is intended to complement the articles presented in this special issue dedicated to instrumentation and to provide an overview of the general trends and some of the most remarkable developments published in the areas of high-voltage power supplies, detectors, auxiliary components, and compact systems. It also includes a few examples of alternative uses of and modifications to traditional CE instruments.
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Affiliation(s)
- Jessica L. Felhofer
- Department of Chemistry, The University of Texas at San Antonio, One UTSA Circle, San Antonio, TX 78249, United States of America
| | - Lucas Blanes
- Centre for Forensic Science, University of Technology, Sydney, PO Box 123, Broadway, NSW 2007, Australia
| | - Carlos D. Garcia
- Department of Chemistry, The University of Texas at San Antonio, One UTSA Circle, San Antonio, TX 78249, United States of America
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Arora A, Simone G, Salieb-Beugelaar GB, Kim JT, Manz A. Latest Developments in Micro Total Analysis Systems. Anal Chem 2010; 82:4830-47. [PMID: 20462185 DOI: 10.1021/ac100969k] [Citation(s) in RCA: 372] [Impact Index Per Article: 26.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Affiliation(s)
- Arun Arora
- KIST Europe, Korea Institute of Science and Technology, Campus E71, 66123 Saarbrücken, Germany, FRIAS, Freiburg Institute for Advanced Studies, Albert-Ludwigs-Universität Freiburg, Albertstrasse 19, 79104 Freiburg, Germany, IMTEK, Institute for Microsystem Technology, University of Freiburg, Georges-Köhler-Allee 103, 79110 Freiburg, Germany, and MESA+ Institute for Nanotechnology/Lab-on-a-Chip Group, Twente University, Building Carré, 7500 AE, Enschede, The Netherlands
| | - Giuseppina Simone
- KIST Europe, Korea Institute of Science and Technology, Campus E71, 66123 Saarbrücken, Germany, FRIAS, Freiburg Institute for Advanced Studies, Albert-Ludwigs-Universität Freiburg, Albertstrasse 19, 79104 Freiburg, Germany, IMTEK, Institute for Microsystem Technology, University of Freiburg, Georges-Köhler-Allee 103, 79110 Freiburg, Germany, and MESA+ Institute for Nanotechnology/Lab-on-a-Chip Group, Twente University, Building Carré, 7500 AE, Enschede, The Netherlands
| | - Georgette B. Salieb-Beugelaar
- KIST Europe, Korea Institute of Science and Technology, Campus E71, 66123 Saarbrücken, Germany, FRIAS, Freiburg Institute for Advanced Studies, Albert-Ludwigs-Universität Freiburg, Albertstrasse 19, 79104 Freiburg, Germany, IMTEK, Institute for Microsystem Technology, University of Freiburg, Georges-Köhler-Allee 103, 79110 Freiburg, Germany, and MESA+ Institute for Nanotechnology/Lab-on-a-Chip Group, Twente University, Building Carré, 7500 AE, Enschede, The Netherlands
| | - Jung Tae Kim
- KIST Europe, Korea Institute of Science and Technology, Campus E71, 66123 Saarbrücken, Germany, FRIAS, Freiburg Institute for Advanced Studies, Albert-Ludwigs-Universität Freiburg, Albertstrasse 19, 79104 Freiburg, Germany, IMTEK, Institute for Microsystem Technology, University of Freiburg, Georges-Köhler-Allee 103, 79110 Freiburg, Germany, and MESA+ Institute for Nanotechnology/Lab-on-a-Chip Group, Twente University, Building Carré, 7500 AE, Enschede, The Netherlands
| | - Andreas Manz
- KIST Europe, Korea Institute of Science and Technology, Campus E71, 66123 Saarbrücken, Germany, FRIAS, Freiburg Institute for Advanced Studies, Albert-Ludwigs-Universität Freiburg, Albertstrasse 19, 79104 Freiburg, Germany, IMTEK, Institute for Microsystem Technology, University of Freiburg, Georges-Köhler-Allee 103, 79110 Freiburg, Germany, and MESA+ Institute for Nanotechnology/Lab-on-a-Chip Group, Twente University, Building Carré, 7500 AE, Enschede, The Netherlands
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Quantitative determination of glucoraphanin in Brassica vegetables by micellar electrokinetic capillary chromatography. Anal Chim Acta 2010; 663:105-8. [DOI: 10.1016/j.aca.2010.01.043] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2009] [Revised: 01/22/2010] [Accepted: 01/22/2010] [Indexed: 12/17/2022]
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Kraly JR, Holcomb RE, Guan Q, Henry CS. Review: Microfluidic applications in metabolomics and metabolic profiling. Anal Chim Acta 2009; 653:23-35. [PMID: 19800473 DOI: 10.1016/j.aca.2009.08.037] [Citation(s) in RCA: 75] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2009] [Revised: 08/28/2009] [Accepted: 08/28/2009] [Indexed: 01/19/2023]
Abstract
Metabolomics is an emerging area of research focused on measuring small molecules in biological samples. There are a number of different types of metabolomics, ranging from global profiling of all metabolites in a single sample to measurement of a selected group of analytes. Microfluidics and related technologies have been used in this research area with good success. The aim of this review article is to summarize the use of microfluidics in metabolomics. Direct application of microfluidics to the determination of small molecules is covered first. Next, important sample preparation methods developed for microfluidics and applicable to metabolomics are covered. Finally, a summary of metabolomic work as it relates to analysis of cellular events using microfluidics is covered.
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Affiliation(s)
- James R Kraly
- Department of Chemistry, Colorado State University, Fort Collins, Colorado, CO 80523, United States
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