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Noh C, Kang Y, Heo S, Kim T, Kim H, Chang J, Sundharbaabu PR, Shim S, Lim KI, Lee JH, Jo K. Scanning Electron Microscopy Imaging of Large DNA Molecules Using a Metal-Free Electro-Stain Composed of DNA-Binding Proteins and Synthetic Polymers. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2024:e2309702. [PMID: 38704672 DOI: 10.1002/advs.202309702] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/11/2023] [Revised: 04/19/2024] [Indexed: 05/06/2024]
Abstract
This paper presents the first scanning electron microscopy (SEM)-based DNA imaging in biological samples. This novel approach incorporates a metal-free electro-stain reagent, formulated by combining DNA-binding proteins and synthetic polymers to enhance the visibility of 2-nm-thick DNA under SEM. Notably, DNA molecules stain with proteins and polymers appear as dark lines under SEM. The resulting DNA images exhibit a thickness of 15.0±4.0 nm. As SEM is the primary platform, it integrates seamlessly with various chemically functionalized large surfaces with the aid of microfluidic devices. The approach allows high-resolution imaging of various DNA structures including linear, circular, single-stranded DNA and RNA, originating from nuclear and mitochondrial genomes. Furthermore, quantum dots are successfully visualized as bright labels that are sequence-specifically incorporated into DNA molecules, which highlights the potential for SEM-based optical DNA mapping. In conclusion, DNA imaging using SEM with the novel electro-stain offers electron microscopic resolution with the ease of optical microscopy.
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Affiliation(s)
- Chanyoung Noh
- Department of Chemistry, Sogang University, Seoul, 04107, South Korea
| | - Yoonjung Kang
- Department of Chemistry, Sogang University, Seoul, 04107, South Korea
| | - Sujung Heo
- Department of Chemistry, Sogang University, Seoul, 04107, South Korea
| | - Taesoo Kim
- Department of Chemistry, Sogang University, Seoul, 04107, South Korea
| | - Hayeon Kim
- Department of Chemistry, Sogang University, Seoul, 04107, South Korea
| | - Junhyuck Chang
- School of Advanced Materials Science and Engineering, Department of MetaBioHealth Sungkyunkwan University (SKKU), Suwon, 16419, South Korea
| | - Priyannth Ramasami Sundharbaabu
- School of Advanced Materials Science and Engineering, Department of MetaBioHealth Sungkyunkwan University (SKKU), Suwon, 16419, South Korea
| | - Sanghee Shim
- Department of Chemistry, Korea University, Seoul, 02841, South Korea
| | - Kwang-Il Lim
- Department of Chemical and Biological Engineering, Sookmyung Women's University, Seoul, 04312, South Korea
| | - Jung Heon Lee
- School of Advanced Materials Science and Engineering, Department of MetaBioHealth Sungkyunkwan University (SKKU), Suwon, 16419, South Korea
| | - Kyubong Jo
- Department of Chemistry, Sogang University, Seoul, 04107, South Korea
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2
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Liu Y, Lo JHY, Nunes JK, Stone HA, Shum HC. High-throughput measurement of elastic moduli of microfibers by rope coiling. Proc Natl Acad Sci U S A 2024; 121:e2303679121. [PMID: 38478687 PMCID: PMC10962939 DOI: 10.1073/pnas.2303679121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2023] [Accepted: 02/05/2024] [Indexed: 03/27/2024] Open
Abstract
There are many fields where it is of interest to measure the elastic moduli of tiny fragile fibers, such as filamentous bacteria, actin filaments, DNA, carbon nanotubes, and functional microfibers. The elastic modulus is typically deduced from a sophisticated tensile test under a microscope, but the throughput is low and limited by the time-consuming and skill-intensive sample loading/unloading. Here, we demonstrate a simple microfluidic method enabling the high-throughput measurement of the elastic moduli of microfibers by rope coiling using a localized compression, where sample loading/unloading are not needed between consecutive measurements. The rope coiling phenomenon occurs spontaneously when a microfiber flows from a small channel into a wide channel. The elastic modulus is determined by measuring either the buckling length or the coiling radius. The throughput of this method, currently 3,300 fibers per hour, is a thousand times higher than that of a tensile tester. We demonstrate the feasibility of the method by testing a nonuniform fiber with axially varying elastic modulus. We also demonstrate its capability for in situ inline measurement in a microfluidic production line. We envisage that high-throughput measurements may facilitate potential applications such as screening or sorting by mechanical properties and real-time control during production of microfibers.
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Affiliation(s)
- Yuan Liu
- Department of Mechanical Engineering, University of Hong Kong, Hong Kong SAR, China
| | - Jack H. Y. Lo
- Center for Integrative Petroleum Research, College of Petroleum Engineering and Geosciences, King Fahd University of Petroleum and Minerals, Dhahran31261, Saudi Arabia
| | - Janine K. Nunes
- Department of Mechanical and Aerospace Engineering, Princeton University, Princeton, NJ08544
| | - Howard A. Stone
- Department of Mechanical and Aerospace Engineering, Princeton University, Princeton, NJ08544
| | - Ho Cheung Shum
- Department of Mechanical Engineering, University of Hong Kong, Hong Kong SAR, China
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3
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Morrison G, Thirumalai D. Scaling regimes for wormlike chains confined to cylindrical surfaces under tension. THE EUROPEAN PHYSICAL JOURNAL. E, SOFT MATTER 2024; 47:6. [PMID: 38252375 DOI: 10.1140/epje/s10189-023-00384-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/26/2023] [Accepted: 11/20/2023] [Indexed: 01/23/2024]
Abstract
We compute the free energy of confinement [Formula: see text] for a wormlike chain (WLC), with persistence length [Formula: see text], that is confined to the surface of a cylinder of radius R under an external tension f using a mean field variational approach. For long chains, we analytically determine the behavior of the chain in a variety of regimes, which are demarcated by the interplay of [Formula: see text], the Odijk deflection length ([Formula: see text]), and the Pincus length ([Formula: see text], with [Formula: see text] being the thermal energy). The theory accurately reproduces the Odijk scaling for strongly confined chains at [Formula: see text], with [Formula: see text]. For moderate values of f, the Odijk scaling is discernible only when [Formula: see text] for strongly confined chains. Confinement does not significantly alter the scaling of the mean extension for sufficiently high tension. The theory is used to estimate unwrapping forces for DNA from nucleosomes.
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Affiliation(s)
- Greg Morrison
- Department of Physics, University of Houston, Houston, TX, 77204, USA
- Center for Theoretical Biological Physics, Rice University, Houston, TX, 77005, USA
| | - D Thirumalai
- Departments of Chemistry, The University of Texas at Austin, Austin, TX, 78712, USA.
- Department of Physics, The University of Texas at Austin, Austin, TX, 78712, USA.
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4
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Kk S, Persson F, Fritzsche J, Beech JP, Tegenfeldt JO, Westerlund F. Fluorescence Microscopy of Nanochannel-Confined DNA. Methods Mol Biol 2024; 2694:175-202. [PMID: 37824005 DOI: 10.1007/978-1-0716-3377-9_9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/13/2023]
Abstract
Stretching of DNA in nanoscale confinement allows for several important studies. The genetic contents of the DNA can be visualized on the single DNA molecule level, and the polymer physics of confined DNA and also DNA/protein and other DNA/DNA-binding molecule interactions can be explored. This chapter describes the basic steps to fabricate the nanostructures, perform the experiments, and analyze the data.
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Affiliation(s)
- Sriram Kk
- Department of Life Sciences, Chalmers University of Technology, Gothenburg, Sweden
| | | | - Joachim Fritzsche
- Department of Physics, Chalmers University of Technology, Gothenburg, Sweden
| | - Jason P Beech
- NanoLund and Department of Physics, Lund University, Lund, Sweden
| | | | - Fredrik Westerlund
- Department of Life Sciences, Chalmers University of Technology, Gothenburg, Sweden.
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5
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Sasanian N, Sharma R, Lubart Q, Kk S, Ghaeidamini M, Dorfman KD, Esbjörner EK, Westerlund F. Probing physical properties of single amyloid fibrils using nanofluidic channels. NANOSCALE 2023; 15:18737-18744. [PMID: 37953701 DOI: 10.1039/d3nr02740f] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/14/2023]
Abstract
Amyloid fibril formation is central to the pathology of many diseases, including neurodegenerative disorders such as Alzheimer's and Parkinson's disease. Amyloid fibrils can also have functional and scaffolding roles, for example in bacterial biofilms, and have also been exploited as useful biomaterials. Despite being linear protein homopolymers, amyloid fibrils can exhibit significant structural and morphological polymorphism, making it relevant to study them on the single fibril level. We here introduce the concept of nanofluidic channel analysis to the study of single, fluorescently-labeled amyloid fibrils in solution, monitoring the extension and emission intensity of individual fibrils confined in nanochannels with a depth of 300 nm and a width that gradually increases from 300 to 3000 nm. The change in fibril extension with channel width permitted accurate determination of the persistence length of individual fibrils using Odijk's theory for strongly confined polymers. The technique was applied to amyloid fibrils prepared from the Alzheimer's related peptide amyloid-β(1-42) and the Parkinson's related protein α-synuclein, obtaining mean persistence lengths of 5.9 ± 4.5 μm and 3.0 ± 1.6 μm, respectively. The broad distributions of fibril persistence lengths indicate that amyloid fibril polymorphism can manifest in their physical properties. Interestingly, the α-synuclein fibrils had lower persistence lengths than the amyloid-β(1-42) fibrils, despite being thicker. Furthermore, there was no obvious within-sample correlation between the fluorescence emission intensity per unit length of the labelled fibrils and their persistence lengths, suggesting that stiffness may not be proportional to thickness. We foresee that the nanofluidics methodology established here will be a useful tool to study amyloid fibrils on the single fibril level to gain information on heterogeneity in their physical properties and interactions.
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Affiliation(s)
- Nima Sasanian
- Division of Chemical Biology, Department of Life Sciences, Chalmers University of Technology, Kemivägen 10, 412 96 Gothenburg, Sweden.
| | - Rajhans Sharma
- Division of Chemical Biology, Department of Life Sciences, Chalmers University of Technology, Kemivägen 10, 412 96 Gothenburg, Sweden.
| | - Quentin Lubart
- Division of Chemical Biology, Department of Life Sciences, Chalmers University of Technology, Kemivägen 10, 412 96 Gothenburg, Sweden.
| | - Sriram Kk
- Division of Chemical Biology, Department of Life Sciences, Chalmers University of Technology, Kemivägen 10, 412 96 Gothenburg, Sweden.
| | - Marziyeh Ghaeidamini
- Division of Chemical Biology, Department of Life Sciences, Chalmers University of Technology, Kemivägen 10, 412 96 Gothenburg, Sweden.
| | - Kevin D Dorfman
- Department of Chemical Engineering and Materials Science, University of Minnesota-Twin Cities, 421 Washington Ave SE, Minneapolis, Minnesota 55455, USA
| | - Elin K Esbjörner
- Division of Chemical Biology, Department of Life Sciences, Chalmers University of Technology, Kemivägen 10, 412 96 Gothenburg, Sweden.
| | - Fredrik Westerlund
- Division of Chemical Biology, Department of Life Sciences, Chalmers University of Technology, Kemivägen 10, 412 96 Gothenburg, Sweden.
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6
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Lee JH, Chiu JHC, Ginga NJ, Ahmed T, Thouless MD, Liu Y, Takayama S. Super-resolution imaging of linearized chromatin in tunable nanochannels. NANOSCALE HORIZONS 2023; 8:1043-1053. [PMID: 37221952 DOI: 10.1039/d3nh00096f] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/25/2023]
Abstract
Nanofluidic linearization and optical mapping of naked DNA have been reported in the research literature, and implemented in commercial instruments. However, the resolution with which DNA features can be resolved is still inherently limited by both Brownian motion and diffraction-limited optics. Direct analysis of native chromatin is further hampered by difficulty in electrophoretic manipulation, which is routinely used for DNA analysis. This paper describes the development of a three-layer, tunable, nanochannel system that enables non-electrophoretic linearization and immobilization of native chromatin. Furthermore, through careful selection of self-blinking fluorescent dyes and the design of the nanochannel system, we achieve direct stochastic optical reconstruction microscopy (dSTORM) super-resolution imaging of the linearized chromatin. As an initial demonstration, rDNA chromatin extracted from Tetrahymena is analyzed by multi-color imaging of total DNA, newly synthesized DNA, and newly synthesized histone H3. Our analysis reveals a relatively even distribution of newly synthesized H3 across two halves of the rDNA chromatin with palindromic symmetry, supporting dispersive nucleosome segregation. As a proof-of-concept study, our work achieves super-resolution imaging of native chromatin fibers linearized and immobilized in tunable nanochannels. It opens up a new avenue for collecting long-range and high-resolution epigenetic information as well as genetic information.
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Affiliation(s)
- Ji-Hoon Lee
- Wallace H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology and Emory University School of Medicine, Atlanta, GA 30332, USA.
- The Parker H. Petit Institute of Bioengineering and Bioscience, Georgia Institute of Technology, Atlanta, GA 30332, USA
| | - Joyce Han-Ching Chiu
- Wallace H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology and Emory University School of Medicine, Atlanta, GA 30332, USA.
- The Parker H. Petit Institute of Bioengineering and Bioscience, Georgia Institute of Technology, Atlanta, GA 30332, USA
| | - Nicholas J Ginga
- Department of Mechanical and Aerospace Engineering, University of Alabama in Huntsville, Huntsville, AL 35899, USA
| | - Tasdiq Ahmed
- Wallace H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology and Emory University School of Medicine, Atlanta, GA 30332, USA.
- The Parker H. Petit Institute of Bioengineering and Bioscience, Georgia Institute of Technology, Atlanta, GA 30332, USA
| | - M D Thouless
- Department of Mechanical Engineering and Department of Materials Science and Engineering, University of Michigan, Ann Arbor, MI 48109, USA
| | - Yifan Liu
- Department of Biochemistry and Molecular Medicine, University of Southern California Keck School of Medicine, Los Angeles, CA 90033, USA.
| | - Shuichi Takayama
- Wallace H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology and Emory University School of Medicine, Atlanta, GA 30332, USA.
- The Parker H. Petit Institute of Bioengineering and Bioscience, Georgia Institute of Technology, Atlanta, GA 30332, USA
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7
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Rau S, Huynh T, Larsen A, Kounovsky-Shafer KL. Concentration of lambda concatemers using a 3D printed device. Electrophoresis 2023; 44:744-751. [PMID: 36799437 PMCID: PMC10121831 DOI: 10.1002/elps.202200200] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2022] [Revised: 11/18/2022] [Accepted: 02/15/2023] [Indexed: 02/18/2023]
Abstract
Identifying significant variations in genomes can be cumbersome, as the variations span a multitude of base pairs and can make genome assembly difficult. However, large DNA molecules that span the variation aid in assembly. Due to the DNA molecule's large size, routine molecular biology techniques can break DNA. Therefore, a method is required to concentrate large DNA. A bis-acrylamide roadblock was cured in a proof-of-principle 3D printed device to concentrate DNA at the interface between the roadblock and solution. Lambda concatemer DNA was stained with YOYO-1 and loaded into the 3D printed device. A dynamic range of voltages and acrylamide concentrations were tested to determine how much DNA was concentrated and recovered. The fluorescence of the original solution and the concentrated solution was measured, the recovery was 37% of the original sample, and the volume decreased by a factor of 3 of the original volume.
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Affiliation(s)
- Samantha Rau
- Department of Chemistry, University of Nebraska - Kearney, Kearney, NE, USA
| | - Thi Huynh
- Department of Chemistry, University of Nebraska - Kearney, Kearney, NE, USA
| | - Alex Larsen
- Department of Chemistry, University of Nebraska - Kearney, Kearney, NE, USA
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8
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Jin X, Kim YT, Jo K. DNA Visualization Using Fluorescent Proteins. Methods Mol Biol 2023; 2564:223-246. [PMID: 36107345 DOI: 10.1007/978-1-0716-2667-2_11] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
DNA binding fluorescent proteins are a powerful tool for single-molecule visualization. In this chapter, we discuss a protocol for the synthesis of DNA binding fluorescent proteins and visualization of single DNA molecules. This chapter includes stepwise methods for molecular cloning, reversible staining, two-color staining, sequence-specific staining, and microscopic visualization of single DNA molecules in a microfluidic device. This content will be useful for DNA characterization using DNA binding fluorescent proteins and its visualization at the single-molecule level.
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Affiliation(s)
- Xuelin Jin
- College of Agriculture, Yanbian University, Yanji, Jilin Province, China.
| | - Y Tehee Kim
- Department of Chemistry and Program of Integrated Biotechnology, Sogang University, Seoul, Korea
| | - Kyubong Jo
- Department of Chemistry and Program of Integrated Biotechnology, Sogang University, Seoul, Korea.
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9
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Kim T, Kim S, Noh C, Hwang H, Shin J, Won N, Lee S, Kim D, Jang Y, Hong SJ, Park J, Kim SJ, Jang S, Lim KI, Jo K. Counting DNA molecules on a microchannel surface for quantitative analysis. Talanta 2023; 252:123826. [DOI: 10.1016/j.talanta.2022.123826] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2022] [Revised: 08/02/2022] [Accepted: 08/07/2022] [Indexed: 12/30/2022]
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10
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Jin Y, Bae J, Kim TY, Hwang H, Kim T, Yu M, Oh H, Hashiya K, Bando T, Sugiyama H, Jo K. Twelve Colors of Streptavidin–Fluorescent Proteins (SA-FPs): A Versatile Tool to Visualize Genetic Information in Single-Molecule DNA. Anal Chem 2022; 94:16927-16935. [DOI: 10.1021/acs.analchem.2c04344] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Affiliation(s)
- Yu Jin
- Department of Chemistry and Program of Integrated Biotechnology, Sogang University, Seoul 04107, Korea
| | - Jaeyoung Bae
- Department of Chemistry and Program of Integrated Biotechnology, Sogang University, Seoul 04107, Korea
| | - Tehee Yurie Kim
- Department of Chemistry and Program of Integrated Biotechnology, Sogang University, Seoul 04107, Korea
| | - Hyeseung Hwang
- Department of Chemistry and Program of Integrated Biotechnology, Sogang University, Seoul 04107, Korea
| | - Taesoo Kim
- Department of Chemistry and Program of Integrated Biotechnology, Sogang University, Seoul 04107, Korea
| | - Myungheon Yu
- Department of Chemistry and Program of Integrated Biotechnology, Sogang University, Seoul 04107, Korea
| | - Hyesoo Oh
- Department of Chemistry and Program of Integrated Biotechnology, Sogang University, Seoul 04107, Korea
| | - Kaori Hashiya
- Department of Chemistry, Graduate School of Science, Kyoto University, Sakyo-Ku, Kyoto 606-8502, Japan
| | - Toshikazu Bando
- Department of Chemistry, Graduate School of Science, Kyoto University, Sakyo-Ku, Kyoto 606-8502, Japan
| | - Hiroshi Sugiyama
- Department of Chemistry, Graduate School of Science, Kyoto University, Sakyo-Ku, Kyoto 606-8502, Japan
| | - Kyubong Jo
- Department of Chemistry and Program of Integrated Biotechnology, Sogang University, Seoul 04107, Korea
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11
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Kim YT, Oh H, Seo MJ, Lee DH, Shin J, Bong S, Heo S, Hapsari ND, Jo K. 21 Fluorescent Protein-Based DNA Staining Dyes. Molecules 2022; 27:5248. [PMID: 36014487 PMCID: PMC9412447 DOI: 10.3390/molecules27165248] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2022] [Revised: 08/10/2022] [Accepted: 08/12/2022] [Indexed: 11/22/2022] Open
Abstract
Fluorescent protein-DNA-binding peptides or proteins (FP-DBP) are a powerful means to stain and visualize large DNA molecules on a fluorescence microscope. Here, we constructed 21 kinds of FP-DBPs using various colors of fluorescent proteins and two DNA-binding motifs. From the database of fluorescent proteins (FPbase.org), we chose bright FPs, such as RRvT, tdTomato, mNeonGreen, mClover3, YPet, and mScarlet, which are four to eight times brighter than original wild-type GFP. Additionally, we chose other FPs, such as mOrange2, Emerald, mTurquoise2, mStrawberry, and mCherry, for variations in emitting wavelengths. For DNA-binding motifs, we used HMG (high mobility group) as an 11-mer peptide or a 36 kDa tTALE (truncated transcription activator-like effector). Using 21 FP-DBPs, we attempted to stain DNA molecules and then analyzed fluorescence intensities. Most FP-DBPs successfully visualized DNA molecules. Even with the same DNA-binding motif, the order of FP and DBP affected DNA staining in terms of brightness and DNA stretching. The DNA staining pattern by FP-DBPs was also affected by the FP types. The data from 21 FP-DBPs provided a guideline to develop novel DNA-binding fluorescent proteins.
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Affiliation(s)
- Yurie Tehee Kim
- Department of Chemistry, Sogang University, 35 Baekbeom-ro, Mapogu, Seoul 04107, Korea
| | - Hyesoo Oh
- Department of Chemistry, Sogang University, 35 Baekbeom-ro, Mapogu, Seoul 04107, Korea
| | - Myung Jun Seo
- Department of Chemistry, Sogang University, 35 Baekbeom-ro, Mapogu, Seoul 04107, Korea
| | - Dong Hyeun Lee
- Department of Chemistry, Sogang University, 35 Baekbeom-ro, Mapogu, Seoul 04107, Korea
| | - Jieun Shin
- Department of Chemistry, Sogang University, 35 Baekbeom-ro, Mapogu, Seoul 04107, Korea
| | - Serang Bong
- Department of Chemistry, Sogang University, 35 Baekbeom-ro, Mapogu, Seoul 04107, Korea
| | - Sujeong Heo
- Department of Chemistry, Sogang University, 35 Baekbeom-ro, Mapogu, Seoul 04107, Korea
| | - Natalia Diyah Hapsari
- Department of Chemistry, Sogang University, 35 Baekbeom-ro, Mapogu, Seoul 04107, Korea
- Chemistry Education Program, Department of Mathematics and Science Education, Sanata Dharma University, Yogyakarta 55282, Indonesia
| | - Kyubong Jo
- Department of Chemistry, Sogang University, 35 Baekbeom-ro, Mapogu, Seoul 04107, Korea
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12
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Waghchoure AP, Reddy JP, Bhosale RS. Fluorescence based miniaturized microfluidic and nanofluidic systems for biomedical applications. PROGRESS IN MOLECULAR BIOLOGY AND TRANSLATIONAL SCIENCE 2022; 186:217-243. [PMID: 35033286 DOI: 10.1016/bs.pmbts.2021.07.029] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Over the last two decades miniaturized microfluidic and nanofluidic systems with fluorescence setup emerged as a powerful technological platform for diverse biomedical applications. Bio-macromolecules such as nucleic acids and proteins are the core cellular components, their single molecule analysis allow us to understand biological processes, disease creation and progression, and development of novel treatment policies. Design and development of foolproof treatment methods requires rigorously analysis of nucleic acids and proteins such as length quantifications, sequence profiling, sequence mapping, analysis of conformational changes, analysis and recognition of epigenetic changes, and their interactions with other biomolecules. Miniaturized microfluidic and nanofluidic systems with fluorescence spectroscopy enable worldwide researchers to perform nucleic acids and proteins extractions and single molecule analysis from the trace amount of biological samples. In the present chapter we mostly highlighted over one decade applications of microfluidic and nanofluidic systems for single cell micro ribonucleic acid (miRNA) isolation and detection, deoxyribonucleic acid (DNA) mapping, DNA barcoding, identification of epigenetic mark on single DNA molecule, DNA-protein interactions study, protein sensing, protein sequencing, protein binding kinetics and many other applications. We also presented the recently reported microfluidic platform for the preparation of reproducible unisize aggregation induced emission (AIE) active nanomaterials and their biological applications.
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Affiliation(s)
| | - J Prakasha Reddy
- Department of Chemistry, Indrashil University, Rajpur, Mehsana, Gujarat, India.
| | - Rajesh S Bhosale
- Department of Chemistry, Indrashil University, Rajpur, Mehsana, Gujarat, India.
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13
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Torstensson E, Goyal G, Johnning A, Westerlund F, Ambjörnsson T. Combining dense and sparse labeling in optical DNA mapping. PLoS One 2021; 16:e0260489. [PMID: 34843574 PMCID: PMC8629184 DOI: 10.1371/journal.pone.0260489] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2021] [Accepted: 11/10/2021] [Indexed: 11/19/2022] Open
Abstract
Optical DNA mapping (ODM) is based on fluorescent labeling, stretching and imaging of single DNA molecules to obtain sequence-specific fluorescence profiles, DNA barcodes. These barcodes can be mapped to theoretical counterparts obtained from DNA reference sequences, which in turn allow for DNA identification in complex samples and for detecting structural changes in individual DNA molecules. There are several types of DNA labeling schemes for ODM and for each labeling type one or several types of match scoring methods are used. By combining the information from multiple labeling schemes one can potentially improve mapping confidence; however, combining match scores from different labeling assays has not been implemented yet. In this study, we introduce two theoretical methods for dealing with analysis of DNA molecules with multiple label types. In our first method, we convert the alignment scores, given as output from the different assays, into p-values using carefully crafted null models. We then combine the p-values for different label types using standard methods to obtain a combined match score and an associated combined p-value. In the second method, we use a block bootstrap approach to check for the uniqueness of a match to a database for all barcodes matching with a combined p-value below a predefined threshold. For obtaining experimental dual-labeled DNA barcodes, we introduce a novel assay where we cut plasmid DNA molecules from bacteria with restriction enzymes and the cut sites serve as sequence-specific markers, which together with barcodes obtained using the established competitive binding labeling method, form a dual-labeled barcode. All experimental data in this study originates from this assay, but we point out that our theoretical framework can be used to combine data from all kinds of available optical DNA mapping assays. We test our multiple labeling frameworks on barcodes from two different plasmids and synthetically generated barcodes (combined competitive-binding- and nick-labeling). It is demonstrated that by simultaneously using the information from all label types, we can substantially increase the significance when we match experimental barcodes to a database consisting of theoretical barcodes for all sequenced plasmids.
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Affiliation(s)
- Erik Torstensson
- Department of Astronomy and Theoretical Physics, Lund University, Lund, Sweden
| | - Gaurav Goyal
- Department of Biology and Biological Engineering, Chalmers University of Technology, Gothenburg, Sweden
| | - Anna Johnning
- Department of Mathematical Sciences, Chalmers University of Technology and the University of Gothenburg, Gothenburg, Sweden
- Systems and Data Analysis, Fraunhofer-Chalmers Centre, Gothenburg, Sweden
- Centre for Antibiotic Resistance Research, CARe, University of Gothenburg, Gothenburg, Sweden
| | - Fredrik Westerlund
- Department of Biology and Biological Engineering, Chalmers University of Technology, Gothenburg, Sweden
| | - Tobias Ambjörnsson
- Department of Astronomy and Theoretical Physics, Lund University, Lund, Sweden
- * E-mail:
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14
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Bucci G, Gadelrab K, Spakowitz AJ. Free Energy and Dynamics of Annihilation of Topological Defects in Nanoconfined DNA. Macromolecules 2021. [DOI: 10.1021/acs.macromol.1c01164] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Giovanna Bucci
- Robert Bosch LLC, 384 Santa Trinita Ave, Sunnyvale, California 94085, United States
| | - Karim Gadelrab
- Robert Bosch LLC, 1 Kendall Square, Suite 7-101, Cambridge, Massachusetts 02139, United States
| | - Andrew J. Spakowitz
- Department of Chemical Engineering, Stanford University, Stanford, California 94305, United States
- Department of Materials Science and Engineering, Stanford University, Stanford, California 94305, United States
- Department of Applied Physics, Stanford University, Stanford, California 94305, United States
- Biophysics Program, Stanford University, Stanford, California 94305, United States
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15
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Silvestri A, Di Trani N, Canavese G, Motto Ros P, Iannucci L, Grassini S, Wang Y, Liu X, Demarchi D, Grattoni A. Silicon Carbide-Gated Nanofluidic Membrane for Active Control of Electrokinetic Ionic Transport. MEMBRANES 2021; 11:535. [PMID: 34357186 PMCID: PMC8303522 DOI: 10.3390/membranes11070535] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/19/2021] [Revised: 07/06/2021] [Accepted: 07/12/2021] [Indexed: 11/16/2022]
Abstract
Manipulation of ions and molecules by external control at the nanoscale is highly relevant to biomedical applications. We report a biocompatible electrode-embedded nanofluidic channel membrane designed for electrofluidic applications such as ionic field-effect transistors for implantable drug-delivery systems. Our nanofluidic membrane includes a polysilicon electrode electrically isolated by amorphous silicon carbide (a-SiC). The nanochannel gating performance was experimentally investigated based on the current-voltage (I-V) characteristics, leakage current, and power consumption in potassium chloride (KCl) electrolyte. We observed significant modulation of ionic diffusive transport of both positively and negatively charged ions under physical confinement of nanochannels, with low power consumption. To study the physical mechanism associated with the gating performance, we performed electrochemical impedance spectroscopy. The results showed that the flat band voltage and density of states were significantly low. In light of its remarkable performance in terms of ionic modulation and low power consumption, this new biocompatible nanofluidic membrane could lead to a new class of silicon implantable nanofluidic systems for tunable drug delivery and personalized medicine.
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Affiliation(s)
- Antonia Silvestri
- Department of Electronics and Telecommunications, Polytechnic of Turin, 10129 Turin, Italy; (A.S.); (P.M.R.); (D.D.)
- Department of Nanomedicine, Houston Methodist Research Institute, Houston, TX 77030, USA; (N.D.T.); (Y.W.); (X.L.)
| | - Nicola Di Trani
- Department of Nanomedicine, Houston Methodist Research Institute, Houston, TX 77030, USA; (N.D.T.); (Y.W.); (X.L.)
| | - Giancarlo Canavese
- Department of Applied Science and Technology, Polytechnic of Turin, 10129 Turin, Italy; (G.C.); (L.I.); (S.G.)
| | - Paolo Motto Ros
- Department of Electronics and Telecommunications, Polytechnic of Turin, 10129 Turin, Italy; (A.S.); (P.M.R.); (D.D.)
| | - Leonardo Iannucci
- Department of Applied Science and Technology, Polytechnic of Turin, 10129 Turin, Italy; (G.C.); (L.I.); (S.G.)
| | - Sabrina Grassini
- Department of Applied Science and Technology, Polytechnic of Turin, 10129 Turin, Italy; (G.C.); (L.I.); (S.G.)
| | - Yu Wang
- Department of Nanomedicine, Houston Methodist Research Institute, Houston, TX 77030, USA; (N.D.T.); (Y.W.); (X.L.)
| | - Xuewu Liu
- Department of Nanomedicine, Houston Methodist Research Institute, Houston, TX 77030, USA; (N.D.T.); (Y.W.); (X.L.)
| | - Danilo Demarchi
- Department of Electronics and Telecommunications, Polytechnic of Turin, 10129 Turin, Italy; (A.S.); (P.M.R.); (D.D.)
| | - Alessandro Grattoni
- Department of Nanomedicine, Houston Methodist Research Institute, Houston, TX 77030, USA; (N.D.T.); (Y.W.); (X.L.)
- Department of Surgery, Houston Methodist Research Institute, Houston, TX 77030, USA
- Department of Radiation Oncology, Houston Methodist Research Institute, Houston, TX 77030, USA
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16
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Uppuluri L, Jadhav T, Wang Y, Xiao M. Multicolor Whole-Genome Mapping in Nanochannels for Genetic Analysis. Anal Chem 2021; 93:9808-9816. [PMID: 34232611 DOI: 10.1021/acs.analchem.1c01373] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
Analysis of structural variations (SVs) is important to understand mutations underlying genetic disorders and pathogenic conditions. However, characterizing SVs using short-read, high-throughput sequencing technology is difficult. Although long-read sequencing technologies are being increasingly employed in characterizing SVs, their low throughput and high costs discourage widespread adoption. Sequence motif-based optical mapping in nanochannels is useful in whole-genome mapping and SV detection, but it is not possible to precisely locate the breakpoints or estimate the copy numbers. We present here a universal multicolor mapping strategy in nanochannels combining conventional sequence-motif labeling system with Cas9-mediated target-specific labeling of any 20-base sequences (20mers) to create custom labels and detect new features. The sequence motifs are labeled with green fluorophores and the 20mers are labeled with red fluorophores. Using this strategy, it is possible to not only detect the SVs but also utilize custom labels to interrogate the features not accessible to motif-labeling, locate breakpoints, and precisely estimate copy numbers of genomic repeats. We validated our approach by quantifying the D4Z4 copy numbers, a known biomarker for facioscapulohumeral muscular dystrophy (FSHD) and estimating the telomere length, a clinical biomarker for assessing disease risk factors in aging-related diseases and malignant cancers. We also demonstrate the application of our methodology in discovering transposable long non-interspersed Elements 1 (LINE-1) insertions across the whole genome.
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Affiliation(s)
- Lahari Uppuluri
- School of Biomedical Engineering, Science and Health Systems, Drexel University, 3141 Chestnut Street, Philadelphia, Pennsylvania 19104, United States
| | - Tanaya Jadhav
- School of Biomedical Engineering, Science and Health Systems, Drexel University, 3141 Chestnut Street, Philadelphia, Pennsylvania 19104, United States
| | - Yilin Wang
- School of Biomedical Engineering, Science and Health Systems, Drexel University, 3141 Chestnut Street, Philadelphia, Pennsylvania 19104, United States
| | - Ming Xiao
- School of Biomedical Engineering, Science and Health Systems, Drexel University, 3141 Chestnut Street, Philadelphia, Pennsylvania 19104, United States.,Center for Genomic Sciences, Institute of Molecular Medicine and Infectious Disease, Drexel University, 3141 Chestnut Street, Philadelphia, Pennsylvania 19104, United States
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17
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Jeffet J, Margalit S, Michaeli Y, Ebenstein Y. Single-molecule optical genome mapping in nanochannels: multidisciplinarity at the nanoscale. Essays Biochem 2021; 65:51-66. [PMID: 33739394 PMCID: PMC8056043 DOI: 10.1042/ebc20200021] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2021] [Revised: 02/24/2021] [Accepted: 02/26/2021] [Indexed: 12/12/2022]
Abstract
The human genome contains multiple layers of information that extend beyond the genetic sequence. In fact, identical genetics do not necessarily yield identical phenotypes as evident for the case of two different cell types in the human body. The great variation in structure and function displayed by cells with identical genetic background is attributed to additional genomic information content. This includes large-scale genetic aberrations, as well as diverse epigenetic patterns that are crucial for regulating specific cell functions. These genetic and epigenetic patterns operate in concert in order to maintain specific cellular functions in health and disease. Single-molecule optical genome mapping is a high-throughput genome analysis method that is based on imaging long chromosomal fragments stretched in nanochannel arrays. The access to long DNA molecules coupled with fluorescent tagging of various genomic information presents a unique opportunity to study genetic and epigenetic patterns in the genome at a single-molecule level over large genomic distances. Optical mapping entwines synergistically chemical, physical, and computational advancements, to uncover invaluable biological insights, inaccessible by sequencing technologies. Here we describe the method's basic principles of operation, and review the various available mechanisms to fluorescently tag genomic information. We present some of the recent biological and clinical impact enabled by optical mapping and present recent approaches for increasing the method's resolution and accuracy. Finally, we discuss how multiple layers of genomic information may be mapped simultaneously on the same DNA molecule, thus paving the way for characterizing multiple genomic observables on individual DNA molecules.
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Affiliation(s)
- Jonathan Jeffet
- Raymond and Beverly Sackler Faculty of Exact Sciences, Center for Nanoscience and Nanotechnology, Center for Light Matter Interaction, Tel Aviv University, Tel Aviv 6997801, Israel
| | - Sapir Margalit
- Raymond and Beverly Sackler Faculty of Exact Sciences, Center for Nanoscience and Nanotechnology, Center for Light Matter Interaction, Tel Aviv University, Tel Aviv 6997801, Israel
| | - Yael Michaeli
- Raymond and Beverly Sackler Faculty of Exact Sciences, Center for Nanoscience and Nanotechnology, Center for Light Matter Interaction, Tel Aviv University, Tel Aviv 6997801, Israel
| | - Yuval Ebenstein
- Raymond and Beverly Sackler Faculty of Exact Sciences, Center for Nanoscience and Nanotechnology, Center for Light Matter Interaction, Tel Aviv University, Tel Aviv 6997801, Israel
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18
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Nikoubashman A. Ordering, phase behavior, and correlations of semiflexible polymers in confinement. J Chem Phys 2021; 154:090901. [DOI: 10.1063/5.0038052] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023] Open
Affiliation(s)
- Arash Nikoubashman
- Institute of Physics, Johannes Gutenberg University Mainz, Staudingerweg 7, 55128 Mainz, Germany
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19
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Bucci G, Spakowitz AJ. Systematic Approach toward Accurate and Efficient DNA Sequencing via Nanoconfinement. ACS Macro Lett 2020; 9:1184-1191. [PMID: 35653210 DOI: 10.1021/acsmacrolett.0c00423] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Coarse-grained modeling tools are employed to simulate the mechanics of DNA loading within a nanoscale confinement and predict semiflexible polymer conformations within the confinement, providing design recommendations for DNA-sequencing devices. A workflow is developed to quantify competing requirements of efficiency and accuracy and extract metrics that guide design optimization. The mean first-passage time for DNA loading is calculated as a function of the nanochannel geometry and the applied electric field. We analyze the interplay between the free energy of confinement and the electric potential energy in achieving high-throughput, base-pair detection. The single-read probability is investigated as informative metrics for sequencing accuracy and for sensing-strategy design. High cost, low throughput, and low accuracy have so far limited the adoption of nanochannel analysis and other long-read technologies. Our work directly addresses these limitations with a systematic approach that is scalable to long molecules and complex geometries.
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Affiliation(s)
- Giovanna Bucci
- Robert Bosch LLC, 384 Santa Trinita Avenue, Sunnyvale, California 94085, United States
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20
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Yuan Y, Chung CYL, Chan TF. Advances in optical mapping for genomic research. Comput Struct Biotechnol J 2020; 18:2051-2062. [PMID: 32802277 PMCID: PMC7419273 DOI: 10.1016/j.csbj.2020.07.018] [Citation(s) in RCA: 55] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2020] [Revised: 07/08/2020] [Accepted: 07/24/2020] [Indexed: 12/28/2022] Open
Abstract
Recent advances in optical mapping have allowed the construction of improved genome assemblies with greater contiguity. Optical mapping also enables genome comparison and identification of large-scale structural variations. Association of these large-scale genomic features with biological functions is an important goal in plant and animal breeding and in medical research. Optical mapping has also been used in microbiology and still plays an important role in strain typing and epidemiological studies. Here, we review the development of optical mapping in recent decades to illustrate its importance in genomic research. We detail its applications and algorithms to show its specific advantages. Finally, we discuss the challenges required to facilitate the optimization of optical mapping and improve its future development and application.
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Key Words
- 3D, three-dimensional
- DBG, de Bruijn graph
- DLS, direct label and strain
- DNA, deoxyribonucleic acid
- Genome assembly
- Hi-C, high-throughput chromosome conformation capture
- Mb, million base pair
- Next generation sequencing
- OLC, overlap-layout-consensus
- Optical mapping
- PCR, polymerase chain reaction
- PacBio, Pacific Biosciences
- SRS, short-read sequencing
- SV, structural variation
- Structural variation
- bp, base pair
- kb, kilobase pair
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Affiliation(s)
- Yuxuan Yuan
- School of Life Sciences, The Chinese University of Hong Kong, Hong Kong SAR, China
- State Key Laboratory for Agrobiotechnology, The Chinese University of Hong Kong, Hong Kong SAR, China
- AoE Centre for Genomic Studies on Plant-Environment Interaction for Sustainable Agriculture and Food Security, The Chinese University of Hong Kong, Hong Kong SAR, China
| | - Claire Yik-Lok Chung
- School of Life Sciences, The Chinese University of Hong Kong, Hong Kong SAR, China
- State Key Laboratory for Agrobiotechnology, The Chinese University of Hong Kong, Hong Kong SAR, China
| | - Ting-Fung Chan
- School of Life Sciences, The Chinese University of Hong Kong, Hong Kong SAR, China
- State Key Laboratory for Agrobiotechnology, The Chinese University of Hong Kong, Hong Kong SAR, China
- AoE Centre for Genomic Studies on Plant-Environment Interaction for Sustainable Agriculture and Food Security, The Chinese University of Hong Kong, Hong Kong SAR, China
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21
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Müller V, Nyblom M, Johnning A, Wrande M, Dvirnas A, KK S, Giske CG, Ambjörnsson T, Sandegren L, Kristiansson E, Westerlund F. Cultivation-Free Typing of Bacteria Using Optical DNA Mapping. ACS Infect Dis 2020; 6:1076-1084. [PMID: 32294378 PMCID: PMC7304876 DOI: 10.1021/acsinfecdis.9b00464] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2019] [Indexed: 01/06/2023]
Abstract
A variety of pathogenic bacteria can infect humans, and rapid species identification is crucial for the correct treatment. However, the identification process can often be time-consuming and depend on the cultivation of the bacterial pathogen(s). Here, we present a stand-alone, enzyme-free, optical DNA mapping assay capable of species identification by matching the intensity profiles of large DNA molecules to a database of fully assembled bacterial genomes (>10 000). The assay includes a new data analysis strategy as well as a general DNA extraction protocol for both Gram-negative and Gram-positive bacteria. We demonstrate that the assay is capable of identifying bacteria directly from uncultured clinical urine samples, as well as in mixtures, with the potential to be discriminative even at the subspecies level. We foresee that the assay has applications both within research laboratories and in clinical settings, where the time-consuming step of cultivation can be minimized or even completely avoided.
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Affiliation(s)
- Vilhelm Müller
- Department of Biology
and Biological Engineering, Chalmers University
of Technology, Kemivägen 10, 412 96 Gothenburg, Sweden
| | - My Nyblom
- Department of Biology
and Biological Engineering, Chalmers University
of Technology, Kemivägen 10, 412 96 Gothenburg, Sweden
| | - Anna Johnning
- Department of Mathematical
Sciences, Chalmers University of Technology
and the University of Gothenburg, 412 96 Gothenburg, Sweden
- Systems and Data Analysis, Fraunhofer-Chalmers
Centre, Chalmers Science
Park, 412 88 Gothenburg, Sweden
- Centre for Antibiotic Resistance Research,
CARe, University of Gothenburg, Box 440, 405 30 Gothenburg, Sweden
| | - Marie Wrande
- Department of Medical
Biochemistry and Microbiology, Uppsala University, Husargatan 3, Box
582, 751 23 Uppsala, Sweden
| | - Albertas Dvirnas
- Department of Astronomy and Theoretical Physics, Lund University, Sölvegatan 14A, 223 62 Lund, Sweden
| | - Sriram KK
- Department of Biology
and Biological Engineering, Chalmers University
of Technology, Kemivägen 10, 412 96 Gothenburg, Sweden
| | - Christian G. Giske
- Department of Laboratory Medicine, Karolinska
Institutet, Alfred Nobels
Allé 8, 141 86 Stockholm, Sweden
- Department of Clinical
Microbiology, Karolinska University Hospital, 171 76 Stockholm, Sweden
| | - Tobias Ambjörnsson
- Department of Astronomy and Theoretical Physics, Lund University, Sölvegatan 14A, 223 62 Lund, Sweden
| | - Linus Sandegren
- Department of Medical
Biochemistry and Microbiology, Uppsala University, Husargatan 3, Box
582, 751 23 Uppsala, Sweden
| | - Erik Kristiansson
- Department of Mathematical
Sciences, Chalmers University of Technology
and the University of Gothenburg, 412 96 Gothenburg, Sweden
- Centre for Antibiotic Resistance Research,
CARe, University of Gothenburg, Box 440, 405 30 Gothenburg, Sweden
| | - Fredrik Westerlund
- Department of Biology
and Biological Engineering, Chalmers University
of Technology, Kemivägen 10, 412 96 Gothenburg, Sweden
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22
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Benková Z, Rišpanová L, Cifra P. Conformation of Flexible and Semiflexible Chains Confined in Nanoposts Array of Various Geometries. Polymers (Basel) 2020; 12:E1064. [PMID: 32384748 PMCID: PMC7284769 DOI: 10.3390/polym12051064] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2020] [Revised: 04/27/2020] [Accepted: 04/29/2020] [Indexed: 01/17/2023] Open
Abstract
The conformation and distribution of a flexible and semiflexible chain confined in an array of nanoposts arranged in parallel way in a square-lattice projection of their cross-section was investigated using coarse-grained molecular dynamics simulations. The geometry of the nanopost array was varied at the constant post diameter dp and the ensuing modifications of the chain conformation were compared with the structural behavior of the chain in the series of nanopost arrays with the constant post separation Sp as well as with the constant distance between two adjacent post walls (passage width) wp. The free energy arguments based on an approximation of the array of nanopost to a composite of quasi-channels of diameter dc and quasi-slits of height wp provide semiqualitative explanations for the observed structural behavior of both chains. At constant post separation and passage width, the occupation number displays a monotonic decrease with the increasing geometry ratio dc/wp or volume fraction of posts, while a maximum is observed at constant post diameter. The latter finding is attributed to a relaxed conformation of the chains at small dc/wp ratio, which results from a combination of wide interstitial volumes and wide passage apertures. This maximum is approximately positioned at the same dc/wp value for both flexible and semiflexible chains. The chain expansion from a single interstitial volume into more interstitial volumes also starts at the same value of dc/wp ratio for both chains. The dependence of the axial chain extension on the dc/wp ratio turns out to be controlled by the diameter of the interstitial space and by the number of monomers in the individual interstitial volumes. If these two factors act in the same way on the axial extension of chain fragments in interstitial volumes the monotonic increase of the axial chain extension with the dc/wp in the nanopost arrays is observed. At constant wp, however, these two factors act in opposite way and the axial chain extension plotted against the dc/wp ratio exhibits a maximum. In the case of constant post diameter, the characteristic hump in the single chain structure factor whose position correlates with the post separation is found only in the structure factor of the flexible chain confined in the nanopost array of certain value of Sp. The structure factor of the flexible chain contains more information on the monomer organization and mutual correlations than the structure factor of the semiflexible chain. The stiffer chain confined in the nanopost array is composed of low number of statistical segments important for the presence of respective hierarchical regimes in the structure factor.
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Affiliation(s)
- Zuzana Benková
- Polymer Institute, Slovak Academy of Sciences, Dúbravská cesta 9, 845 41 Bratislava, Slovakia; (L.R.); (P.C.)
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23
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Melnychuk N, Egloff S, Runser A, Reisch A, Klymchenko AS. Light‐Harvesting Nanoparticle Probes for FRET‐Based Detection of Oligonucleotides with Single‐Molecule Sensitivity. Angew Chem Int Ed Engl 2020. [DOI: 10.1002/ange.201913804] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Affiliation(s)
- Nina Melnychuk
- Laboratoire de Bioimagerie et PathologiesUMR 7021 CNRSFaculté de PharmacieUniversité de Strasbourg 74, Route du Rhin 67401 Illkirch France
| | - Sylvie Egloff
- Laboratoire de Bioimagerie et PathologiesUMR 7021 CNRSFaculté de PharmacieUniversité de Strasbourg 74, Route du Rhin 67401 Illkirch France
| | - Anne Runser
- Laboratoire de Bioimagerie et PathologiesUMR 7021 CNRSFaculté de PharmacieUniversité de Strasbourg 74, Route du Rhin 67401 Illkirch France
| | - Andreas Reisch
- Laboratoire de Bioimagerie et PathologiesUMR 7021 CNRSFaculté de PharmacieUniversité de Strasbourg 74, Route du Rhin 67401 Illkirch France
| | - Andrey S. Klymchenko
- Laboratoire de Bioimagerie et PathologiesUMR 7021 CNRSFaculté de PharmacieUniversité de Strasbourg 74, Route du Rhin 67401 Illkirch France
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24
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Melnychuk N, Egloff S, Runser A, Reisch A, Klymchenko AS. Light‐Harvesting Nanoparticle Probes for FRET‐Based Detection of Oligonucleotides with Single‐Molecule Sensitivity. Angew Chem Int Ed Engl 2020; 59:6811-6818. [DOI: 10.1002/anie.201913804] [Citation(s) in RCA: 50] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2019] [Revised: 12/30/2019] [Indexed: 12/27/2022]
Affiliation(s)
- Nina Melnychuk
- Laboratoire de Bioimagerie et PathologiesUMR 7021 CNRSFaculté de PharmacieUniversité de Strasbourg 74, Route du Rhin 67401 Illkirch France
| | - Sylvie Egloff
- Laboratoire de Bioimagerie et PathologiesUMR 7021 CNRSFaculté de PharmacieUniversité de Strasbourg 74, Route du Rhin 67401 Illkirch France
| | - Anne Runser
- Laboratoire de Bioimagerie et PathologiesUMR 7021 CNRSFaculté de PharmacieUniversité de Strasbourg 74, Route du Rhin 67401 Illkirch France
| | - Andreas Reisch
- Laboratoire de Bioimagerie et PathologiesUMR 7021 CNRSFaculté de PharmacieUniversité de Strasbourg 74, Route du Rhin 67401 Illkirch France
| | - Andrey S. Klymchenko
- Laboratoire de Bioimagerie et PathologiesUMR 7021 CNRSFaculté de PharmacieUniversité de Strasbourg 74, Route du Rhin 67401 Illkirch France
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25
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Jin X, Hapsari ND, Lee S, Jo K. DNA binding fluorescent proteins as single-molecule probes. Analyst 2020; 145:4079-4095. [DOI: 10.1039/d0an00218f] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
DNA binding fluorescent proteins are useful probes for a broad range of biological applications.
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Affiliation(s)
- Xuelin Jin
- Department of Chemistry and Interdisciplinary Program of Integrated Biotechnology
- Sogang University
- Seoul
- Republic of Korea
| | - Natalia Diyah Hapsari
- Department of Chemistry and Interdisciplinary Program of Integrated Biotechnology
- Sogang University
- Seoul
- Republic of Korea
- Chemistry Education Program
| | - Seonghyun Lee
- Department of Chemistry and Interdisciplinary Program of Integrated Biotechnology
- Sogang University
- Seoul
- Republic of Korea
| | - Kyubong Jo
- Department of Chemistry and Interdisciplinary Program of Integrated Biotechnology
- Sogang University
- Seoul
- Republic of Korea
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26
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Müller V, Dvirnas A, Andersson J, Singh V, Kk S, Johansson P, Ebenstein Y, Ambjörnsson T, Westerlund F. Enzyme-free optical DNA mapping of the human genome using competitive binding. Nucleic Acids Res 2019; 47:e89. [PMID: 31165870 PMCID: PMC6735870 DOI: 10.1093/nar/gkz489] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2019] [Revised: 05/03/2019] [Accepted: 05/22/2019] [Indexed: 01/24/2023] Open
Abstract
Optical DNA mapping (ODM) allows visualization of long-range sequence information along single DNA molecules. The data can for example be used for detecting long range structural variations, for aiding DNA sequence assembly of complex genomes and for mapping epigenetic marks and DNA damage across the genome. ODM traditionally utilizes sequence specific marks based on nicking enzymes, combined with a DNA stain, YOYO-1, for detection of the DNA contour. Here we use a competitive binding approach, based on YOYO-1 and netropsin, which highlights the contour of the DNA molecules, while simultaneously creating a continuous sequence specific pattern, based on the AT/GC variation along the detected molecule. We demonstrate and validate competitive-binding-based ODM using bacterial artificial chromosomes (BACs) derived from the human genome and then turn to DNA extracted from white blood cells. We generalize our findings with in-silico simulations that show that we can map a vast majority of the human genome. Finally, we demonstrate the possibility of combining competitive binding with enzymatic labeling by mapping DNA damage sites induced by the cytotoxic drug etoposide to the human genome. Overall, we demonstrate that competitive-binding-based ODM has the potential to be used both as a standalone assay for studies of the human genome, as well as in combination with enzymatic approaches, some of which are already commercialized.
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Affiliation(s)
- Vilhelm Müller
- Department of Biology and Biological Engineering, Chalmers University of Technology, Gothenburg, Sweden
| | - Albertas Dvirnas
- Department of Astronomy and Theoretical Physics, Lund University, Lund, Sweden
| | - John Andersson
- Department of Biology and Biological Engineering, Chalmers University of Technology, Gothenburg, Sweden
| | - Vandana Singh
- Department of Biology and Biological Engineering, Chalmers University of Technology, Gothenburg, Sweden
| | - Sriram Kk
- Department of Biology and Biological Engineering, Chalmers University of Technology, Gothenburg, Sweden
| | - Pegah Johansson
- Clinical Chemistry, Sahlgrenska University Hospital, Gothenburg, Sweden
| | - Yuval Ebenstein
- School of Chemistry, Center for Nanoscience and Nanotechnology, Center for Light-Matter Interaction, Raymond and Beverly Sackler Faculty of Exact Sciences, Tel Aviv University, Tel Aviv, Israel
| | - Tobias Ambjörnsson
- Department of Astronomy and Theoretical Physics, Lund University, Lund, Sweden
| | - Fredrik Westerlund
- Department of Biology and Biological Engineering, Chalmers University of Technology, Gothenburg, Sweden
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27
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Shin E, Kim W, Lee S, Bae J, Kim S, Ko W, Seo HS, Lim S, Lee HS, Jo K. Truncated TALE-FP as DNA Staining Dye in a High-salt Buffer. Sci Rep 2019; 9:17197. [PMID: 31748571 PMCID: PMC6868158 DOI: 10.1038/s41598-019-53722-0] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2018] [Accepted: 11/05/2019] [Indexed: 01/19/2023] Open
Abstract
Large DNA molecules are a promising platform for in vitro single-molecule biochemical analysis to investigate DNA-protein interactions by fluorescence microscopy. For many studies, intercalating fluorescent dyes have been primary DNA staining reagents, but they often cause photo-induced DNA breakage as well as structural deformation. As a solution, we previously developed several fluorescent-protein DNA-binding peptides or proteins (FP-DBP) for reversibly staining DNA molecules without structural deformation or photo-induced damage. However, they cannot stain DNA in a condition similar to a physiological salt concentration that most biochemical reactions require. Given these concerns, here we developed a salt-tolerant FP-DBP: truncated transcription activator-like effector (tTALE-FP), which can stain DNA up to 100 mM NaCl. Moreover, we found an interesting phenomenon that the tTALE-FP stained DNA evenly in 1 × TE buffer but showed AT-rich specific patterns from 40 mM to 100 mM NaCl. Using an assay based on fluorescence resonance energy transfer, we demonstrated that this binding pattern is caused by a higher DNA binding affinity of tTALE-FP for AT-rich compared to GC-rich regions. Finally, we used tTALE-FP in a single molecule fluorescence assay to monitor real-time restriction enzyme digestion of single DNA molecules. Altogether, our results demonstrate that this protein can provide a useful alternative as a DNA stain over intercalators.
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Affiliation(s)
- Eunji Shin
- Department of Chemistry and Interdisciplinary Program of Integrated Biotech, Sogang University, 1 Shinsudong, Mapogu, Seoul, 04107, Korea
| | - Woojung Kim
- Department of Chemistry and Interdisciplinary Program of Integrated Biotech, Sogang University, 1 Shinsudong, Mapogu, Seoul, 04107, Korea
| | - Seonghyun Lee
- Department of Chemistry and Interdisciplinary Program of Integrated Biotech, Sogang University, 1 Shinsudong, Mapogu, Seoul, 04107, Korea
| | - Jaeyoung Bae
- Department of Chemistry and Interdisciplinary Program of Integrated Biotech, Sogang University, 1 Shinsudong, Mapogu, Seoul, 04107, Korea
| | - Sanggil Kim
- Department of Chemistry and Interdisciplinary Program of Integrated Biotech, Sogang University, 1 Shinsudong, Mapogu, Seoul, 04107, Korea
| | - Wooseok Ko
- Department of Chemistry and Interdisciplinary Program of Integrated Biotech, Sogang University, 1 Shinsudong, Mapogu, Seoul, 04107, Korea
| | - Ho Seong Seo
- Research Division for Biotechnology, Korea Atomic Energy Research Institute, Jeongeup, 580-185, Korea
| | - Sangyong Lim
- Research Division for Biotechnology, Korea Atomic Energy Research Institute, Jeongeup, 580-185, Korea
| | - Hyun Soo Lee
- Department of Chemistry and Interdisciplinary Program of Integrated Biotech, Sogang University, 1 Shinsudong, Mapogu, Seoul, 04107, Korea.
| | - Kyubong Jo
- Department of Chemistry and Interdisciplinary Program of Integrated Biotech, Sogang University, 1 Shinsudong, Mapogu, Seoul, 04107, Korea.
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Chen P, Jing X, Ren J, Cao H, Hao P, Li X. Modelling BioNano optical data and simulation study of genome map assembly. Bioinformatics 2019; 34:3966-3974. [PMID: 29893801 PMCID: PMC6247929 DOI: 10.1093/bioinformatics/bty456] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2017] [Accepted: 06/07/2018] [Indexed: 11/12/2022] Open
Abstract
Motivation The launch of the BioNano next-generation mapping system has greatly enhanced the performance of physical map construction, thus rapidly expanding the application of optical mapping in genome research. Data biases have profound implications for downstream applications. However, very little is known about the properties and biases of BioNano data, and the very factors that contribute to whole-genome optical map assembly. Results We generated BioNano molecule data from eight organisms with diverse base compositions. We first characterized the properties/biases of BioNano molecule data, i.e. molecule length distribution, false labelling signal, variation of optical resolution and coverage distribution bias, and their inducing factors such as chimeric molecules, fragile sites and DNA molecule stretching. Second, we developed the BioNano Molecule SIMulator (BMSIM), a novel computer simulation program for optical data. BMSIM, is of great use for future genome mapping projects. Third, we evaluated the experimental variables that impact whole-genome optical map assembly. Specifically, the effects of coverage depth, molecule length, false-positive and false-negative labelling signals, chimeric molecules and nicking enzyme and nick site density were investigated. Our simulation study provides the empirical findings on how to control experimental variables and gauge analytical parameters to maximize benefit and minimize cost on whole-genome optical map assembly. Availability and implementation BMSIM is freely available on: https://github.com/pingchen09990102/BMSIM. Supplementary information Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Ping Chen
- Key Laboratory of Synthetic Biology, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Xinyun Jing
- Key Laboratory of Synthetic Biology, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, China
| | - Jian Ren
- Ultravision Technology, Beijing, China
| | - Han Cao
- BioNano Genomics, San Diego, CA, USA
| | - Pei Hao
- University of Chinese Academy of Sciences, Beijing, China.,Key Laboratory of Molecular Virology and Immunology, Institute Pasteur of Shanghai, Chinese Academy of Sciences, Shanghai, China
| | - Xuan Li
- Key Laboratory of Synthetic Biology, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, China.,University of Chinese Academy of Sciences, Beijing, China
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29
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Varapula D, LaBouff E, Raseley K, Uppuluri L, Ehrlich GD, Noh M, Xiao M. A micropatterned substrate for on-surface enzymatic labelling of linearized long DNA molecules. Sci Rep 2019; 9:15059. [PMID: 31636335 PMCID: PMC6803683 DOI: 10.1038/s41598-019-51507-z] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2019] [Accepted: 10/02/2019] [Indexed: 12/22/2022] Open
Abstract
Optical mapping of linearized DNA molecules is a promising new technology for sequence assembly and scaffolding, large structural variant detection, and diagnostics. This is currently achieved either using nanochannel confinement or by stretching single DNA molecules on a solid surface. While the first method necessitates DNA labelling before linearization, the latter allows for modification post-linearization, thereby affording increased process flexibility. Each method is constrained by various physical and chemical limitations. One of the most common techniques for linearization of DNA uses a hydrophobic surface and a receding meniscus, termed molecular combing. Here, we report the development of a microfabricated surface that can not only comb the DNA molecules efficiently but also provides for sequence-specific enzymatic fluorescent DNA labelling. By modifying a glass surface with two contrasting functionalities, such that DNA binds selectively to one of the two regions, we can control DNA extension, which is known to be critical for sequence-recognition by an enzyme. Moreover, the surface modification provides enzymatic access to the DNA backbone, as well as minimizing non-specific fluorescent dye adsorption. These enhancements make the designed surface suitable for large-scale and high-resolution single DNA molecule studies.
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Affiliation(s)
- Dharma Varapula
- School of Biomedical Engineering, Drexel University, Philadelphia, PA, 19104, USA
| | - Eric LaBouff
- School of Biomedical Engineering, Drexel University, Philadelphia, PA, 19104, USA
- Department of Microbiology and Immunology, Drexel University College of Medicine, Philadelphia, PA, 19102, USA
- Center for Genomic Sciences and Center for Advanced Microbial Processing, Institute of Molecular Medicine and Infectious Disease, Drexel University College of Medicine, Philadelphia, PA, 19102, USA
| | - Kaitlin Raseley
- School of Biomedical Engineering, Drexel University, Philadelphia, PA, 19104, USA
| | - Lahari Uppuluri
- Department of Mechanical Engineering and Mechanics, Drexel University, Philadelphia, PA, 19104, USA
| | - Garth D Ehrlich
- Department of Microbiology and Immunology, Drexel University College of Medicine, Philadelphia, PA, 19102, USA
- Center for Genomic Sciences and Center for Advanced Microbial Processing, Institute of Molecular Medicine and Infectious Disease, Drexel University College of Medicine, Philadelphia, PA, 19102, USA
- Department of Otolaryngology Head and Neck Surgery, Drexel University College of Medicine, Philadelphia, PA, 19102, USA
| | - Moses Noh
- Department of Mechanical Engineering and Mechanics, Drexel University, Philadelphia, PA, 19104, USA
| | - Ming Xiao
- School of Biomedical Engineering, Drexel University, Philadelphia, PA, 19104, USA.
- Center for Genomic Sciences and Center for Advanced Microbial Processing, Institute of Molecular Medicine and Infectious Disease, Drexel University College of Medicine, Philadelphia, PA, 19102, USA.
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30
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Chuang HM, Reifenberger JG, Bhandari AB, Dorfman KD. Extension distribution for DNA confined in a nanochannel near the Odijk regime. J Chem Phys 2019; 151:114903. [PMID: 31542006 DOI: 10.1063/1.5121305] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
Abstract
DNA confinement in a nanochannel typically is understood via mapping to the confinement of an equivalent neutral polymer by hard walls. This model has proven to be effective for confinement in relatively large channels where hairpin formation is frequent. An analysis of existing experimental data for Escherichia coli DNA extension in channels smaller than the persistence length, combined with an additional dataset for λ-DNA confined in a 34 nm wide channel, reveals a breakdown in this approach as the channel size approaches the Odijk regime of strong confinement. In particular, the predicted extension distribution obtained from the asymptotic solution to the weakly correlated telegraph model for a confined wormlike chain deviates significantly from the experimental distribution obtained for DNA confinement in the 34 nm channel, and the discrepancy cannot be resolved by treating the alignment fluctuations or the effective channel size as fitting parameters. We posit that the DNA-wall electrostatic interactions, which are sensible throughout a significant fraction of the channel cross section in the Odijk regime, are the source of the disagreement between theory and experiment. Dimensional analysis of the wormlike chain propagator in channel confinement reveals the importance of a dimensionless parameter, reflecting the magnitude of the DNA-wall electrostatic interactions relative to thermal energy, which has not been considered explicitly in the prevailing theories for DNA confinement in a nanochannel.
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Affiliation(s)
- Hui-Min Chuang
- Department of Chemical Engineering and Materials Science, University of Minnesota - Twin Cities, 421 Washington Ave. SE, Minneapolis, Minnesota 55455, USA
| | - Jeffrey G Reifenberger
- Bionano Genomics, Inc., 9640 Towne Centre Drive, Suite 100, San Diego, California 92121, USA
| | - Aditya Bikram Bhandari
- Department of Chemical Engineering and Materials Science, University of Minnesota - Twin Cities, 421 Washington Ave. SE, Minneapolis, Minnesota 55455, USA
| | - Kevin D Dorfman
- Department of Chemical Engineering and Materials Science, University of Minnesota - Twin Cities, 421 Washington Ave. SE, Minneapolis, Minnesota 55455, USA
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31
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Lee S, Kawamoto Y, Vaijayanthi T, Park J, Bae J, Kim-Ha J, Sugiyama H, Jo K. TAMRA-polypyrrole for A/T sequence visualization on DNA molecules. Nucleic Acids Res 2019; 46:e108. [PMID: 29931115 PMCID: PMC6182132 DOI: 10.1093/nar/gky531] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2018] [Accepted: 05/29/2018] [Indexed: 01/23/2023] Open
Abstract
Fluorophore-linked, sequence-specific DNA binding reagents can visualize sequence information on a large DNA molecule. In this paper, we synthesized newly designed TAMRA-linked polypyrrole to visualize adenine and thymine base pairs. A fluorescent image of the stained DNA molecule generates an intensity profile based on A/T frequency, revealing a characteristic sequence composition pattern. Computer-aided comparison of this intensity pattern with the genome sequence allowed us to determine the DNA sequence on a visualized DNA molecule from possible intensity profile pattern candidates for a given genome. Moreover, TAMRA-polypyrrole offers robust advantages for single DNA molecule detection: no fluorophore-mediated photocleavage and no structural deformation, since it exhibits a sequence-specific pattern alone without the use of intercalating dyes such as YOYO-1. Accordingly, we were able to identify genomic DNA fragments from Escherichia coli cells by aligning them to the genomic A/T frequency map based on TAMRA-polypyrrole-generated intensity profiles. Furthermore, we showed band and interband patterns of polytene chromosomal DNA stained with TAMRA-polypyrrole because it prefers to bind AT base pairs.
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Affiliation(s)
- Seonghyun Lee
- Department of Chemistry and Program of Integrated Biotechnology, Sogang University, Seoul 04107, Republic of Korea
| | - Yusuke Kawamoto
- Department of Chemistry, Graduate School of Science, Kyoto University, Sakyo-Ku, Kyoto 606-8502, Japan
| | - Thangavel Vaijayanthi
- Department of Chemistry, Graduate School of Science, Kyoto University, Sakyo-Ku, Kyoto 606-8502, Japan
| | - Jihyun Park
- Department of Chemistry and Program of Integrated Biotechnology, Sogang University, Seoul 04107, Republic of Korea
| | - Jaeyoung Bae
- Department of Chemistry and Program of Integrated Biotechnology, Sogang University, Seoul 04107, Republic of Korea
| | - Jeongsil Kim-Ha
- Department of Integrative Bioscience and Biotechnology, College of Life Sciences, Sejong University, Seoul 05006, Republic of Korea
| | - Hiroshi Sugiyama
- Department of Chemistry, Graduate School of Science, Kyoto University, Sakyo-Ku, Kyoto 606-8502, Japan
| | - Kyubong Jo
- Department of Chemistry and Program of Integrated Biotechnology, Sogang University, Seoul 04107, Republic of Korea
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Park J, Lee S, Won N, Shin E, Kim SH, Chun MY, Gu J, Jung GY, Lim KI, Jo K. Single-molecule DNA visualization using AT-specific red and non-specific green DNA-binding fluorescent proteins. Analyst 2019; 144:921-927. [PMID: 30310901 DOI: 10.1039/c8an01426d] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
The recent advances in the single cell genome analysis are generating a considerable amount of novel insights into complex biological systems. However, there are still technical challenges because each cell has a single copy of DNA to be amplified in most single cell genome analytical methods. In this paper, we present a novel approach to directly visualize a genomic map on a large DNA molecule instantly stained with red and green DNA-binding fluorescent proteins without DNA amplification. For this visualization, we constructed a few types of fluorescent protein-fused DNA-binding proteins: H-NS (histone-like nucleoid-structuring protein), DNA-binding domain of BRCA1 (breast cancer 1), high mobility group-1 (HMG), and lysine tryptophan (KW) repeat motif. Because H-NS and HMG preferentially bind A/T-rich regions, we combined A/T specific binder (H-NS-mCherry and HMG-mCherry as red color) and a non-specific complementary DNA binder (BRCA1-eGFP and 2(KW)2-eGFP repeat as green color) to produce a sequence-specific two-color DNA physical map for efficient optical identification of single DNA molecules.
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Affiliation(s)
- Jihyun Park
- Department of Chemistry and Interdisciplinary Program of Integrated Biotech, Sogang University, 1 Shinsudong, Mapogu, Seoul, 04107, Korea.
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Kim YS, Dincau BM, Kwon YT, Kim JH, Yeo WH. Directly Accessible and Transferrable Nanofluidic Systems for Biomolecule Manipulation. ACS Sens 2019; 4:1417-1423. [PMID: 31062586 DOI: 10.1021/acssensors.9b00470] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Molecular detection and manipulation via nanofluidic systems offers new routes for single-molecule analysis to study epigenetic mechanisms and genetic mutation of disease. For detection of single biological molecule, many types of nanomicrofluidic systems have been utilized. Typically, mechanical tethering, fluidic pressure, chemical interactions, or electrical forces allow controllable attraction, enrichment, confinement, and elongation of target molecules. The currently available methods, however, are unable to offer both molecular manipulation and direct and concurrent assessment of target molecules in the system due to the nature of enclosed channels and associated fluidic components. Here, we introduce a wafer-scale nanofluidic system that incorporates an array of accessible open nanochannels and nano-microtrappers to enrich and elongate target molecules (DNA) via the combination of an electric field and hydrodynamic force. The open nanofluidic system allows easy access, direct observation, and manipulation of molecules in the nanochannels. The presence of a stretched single DNA and the efficacy of the nanofluidic system are studied by fluorescence microscopy and atomic force microscopy. Hybrid integration of the nanodevice fabrication with a material transfer printing technique enables to design a highly flexible and transferrable nanofluidic system after molecular concentration.
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Affiliation(s)
| | - Brian M. Dincau
- School of Engineering and Computer Science, Washington State University, Vancouver, Washington 98686, United States
| | | | - Jong-Hoon Kim
- School of Engineering and Computer Science, Washington State University, Vancouver, Washington 98686, United States
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34
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A simple dialysis device for large DNA molecules. Biotechniques 2019; 66:93-95. [PMID: 30744406 DOI: 10.2144/btn-2018-0133] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
The potential of genomic DNA is realized when new modalities are invented that manipulate large DNAs with minimal breakage or loss of sample. Here, we describe a polydimethylsiloxane-polycarbonate membrane device to remove small molecules from a sample while retaining large DNAs. Dialysis rates dramatically change as DNA size in kb (M) increases and DNA dimensions become comparable to pore size, and chain characteristics go from rod-like to Gaussian. Consequently, we describe empirical rates of dialysis, R, as a function of M as falling into two regimes: DNAs ≤ 1 kb show R(M) ∼e - t/τ M (t = time, τM = time constant), while DNAs ≥1.65 kb slowly passage with R(M) ∼M -1.68; such partitioning potentiates single-molecule imaging.
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35
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Basak R, Liu F, Qureshi S, Gupta N, Zhang C, de Vries R, van Kan JA, Dheen ST, van der Maarel JRC. Linearization and Labeling of Single-Stranded DNA for Optical Sequence Analysis. J Phys Chem Lett 2019; 10:316-321. [PMID: 30615463 DOI: 10.1021/acs.jpclett.8b03465] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Genetic profiling would benefit from linearization of ssDNA through the exposure of the unpaired bases to gene-targeting probes. This is compromised by ssDNA's high flexibility and tendency to form self-annealed structures. Here, we demonstrate that self-annealing can be avoided through controlled coating with a cationic-neutral diblock polypeptide copolymer. Coating does not preclude site-specific binding of fluorescence labeled oligonucleotides. Bottlebrush-coated ssDNA can be linearized by confinement inside a nanochannel or molecular combing. A stretch of 0.32 nm per nucleotide is achieved inside a channel with a cross-section of 100 nm and a 2-fold excess of polypeptide with respect to DNA charge. With combing, the complexes are stretched to a similar extent. Atomic force microscopy of dried complexes on silica revealed that the contour and persistence lengths are close to those of dsDNA in the B-form. Labeling is based on hybridization and not limited by restriction enzymes. Enzyme-free labeling offers new opportunities for the detection of specific sequences.
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Affiliation(s)
- Rajib Basak
- Department of Physics , National University of Singapore , Singapore 117542
| | - Fan Liu
- Department of Physics , National University of Singapore , Singapore 117542
| | - Sarfraz Qureshi
- Department of Physics , National University of Singapore , Singapore 117542
| | - Neelima Gupta
- Department of Anatomy , National University of Singapore , Singapore 117594
| | - Ce Zhang
- Institute of Photonics and Photon-Technology , Northwest University , Xi'an , China 710069
| | - Renko de Vries
- Laboratory of Physical Chemistry and Colloid Science , Wageningen University , 6708 Wageningen , The Netherlands
| | - Jeroen A van Kan
- Department of Physics , National University of Singapore , Singapore 117542
| | - S Thameem Dheen
- Department of Anatomy , National University of Singapore , Singapore 117594
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36
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Krog J, Alizadehheidari M, Werner E, Bikkarolla SK, Tegenfeldt JO, Mehlig B, Lomholt MA, Westerlund F, Ambjörnsson T. Stochastic unfolding of nanoconfined DNA: Experiments, model and Bayesian analysis. J Chem Phys 2019; 149:215101. [PMID: 30525714 DOI: 10.1063/1.5051319] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
Nanochannels provide a means for detailed experiments on the effect of confinement on biomacromolecules, such as DNA. Here we introduce a model for the complete unfolding of DNA from the circular to linear configuration. Two main ingredients are the entropic unfolding force and the friction coefficient for the unfolding process, and we describe the associated dynamics by a non-linear Langevin equation. By analyzing experimental data where DNA molecules are photo-cut and unfolded inside a nanochannel, our model allows us to extract values for the unfolding force as well as the friction coefficient for the first time. In order to extract numerical values for these physical quantities, we employ a recently introduced Bayesian inference framework. We find that the determined unfolding force is in agreement with estimates from a simple Flory-type argument. The estimated friction coefficient is in agreement with theoretical estimates for motion of a cylinder in a channel. We further validate the estimated friction constant by extracting this parameter from DNA's center-of-mass motion before and after unfolding, yielding decent agreement. We provide publically available software for performing the required image and Bayesian analysis.
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Affiliation(s)
- Jens Krog
- MEMPHYS-Center for Biomembrane Physics, Department of Physics, Chemistry, and Pharmacy, University of Southern Denmark, Odense, Denmark
| | | | - Erik Werner
- Department of Physics, Gothenburg University, Gothenburg, Sweden
| | - Santosh Kumar Bikkarolla
- Department of Biology and Biological Engineering, Chalmers University of Technology, Gothenburg, Sweden
| | | | - Bernhard Mehlig
- Department of Physics, Gothenburg University, Gothenburg, Sweden
| | - Michael A Lomholt
- MEMPHYS-Center for Biomembrane Physics, Department of Physics, Chemistry, and Pharmacy, University of Southern Denmark, Odense, Denmark
| | - Fredrik Westerlund
- Department of Biology and Biological Engineering, Chalmers University of Technology, Gothenburg, Sweden
| | - Tobias Ambjörnsson
- Department of Astronomy and Theoretical Physics, Lund University, Lund, Sweden
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37
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Lee S, Lee Y, Kim Y, Wang C, Park J, Jung GY, Chen Y, Chang R, Ikeda S, Sugiyama H, Jo K. Nanochannel-Confined TAMRA-Polypyrrole Stained DNA Stretching by Varying the Ionic Strength from Micromolar to Millimolar Concentrations. Polymers (Basel) 2018; 11:E15. [PMID: 30959999 PMCID: PMC6401831 DOI: 10.3390/polym11010015] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2018] [Revised: 12/17/2018] [Accepted: 12/17/2018] [Indexed: 12/19/2022] Open
Abstract
Large DNA molecules have been utilized as a model system to investigate polymer physics. However, DNA visualization via intercalating dyes has generated equivocal results due to dye-induced structural deformation, particularly unwanted unwinding of the double helix. Thus, the contour length increases and the persistence length changes so unpredictably that there has been a controversy. In this paper, we used TAMRA-polypyrrole to stain single DNA molecules. Since this staining did not change the contour length of B-form DNA, we utilized TAMRA-polypyrrole stained DNA as a tool to measure the persistence length by changing the ionic strength. Then, we investigated DNA stretching in nanochannels by varying the ionic strength from 0.06 mM to 47 mM to evaluate several polymer physics theories proposed by Odijk, de Gennes and recent papers to deal with these regimes.
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Affiliation(s)
- Seonghyun Lee
- Department of Chemistry and Integrated Biotechnology, Sogang University, Seoul 04107, Korea.
| | - Yelin Lee
- Department of Chemistry and Integrated Biotechnology, Sogang University, Seoul 04107, Korea.
| | - Yongkyun Kim
- Department of Chemistry and Integrated Biotechnology, Sogang University, Seoul 04107, Korea.
| | - Cong Wang
- Department of Mechanical Engineering, Sogang University, Seoul 04107, Korea.
| | - Jungyul Park
- Department of Mechanical Engineering, Sogang University, Seoul 04107, Korea.
| | - Gun Young Jung
- School of Material Science and Engineering, GIST, Gwangju 61005, Korea.
| | - Yenglong Chen
- Institute of Physics, Academia Sinica and Department of Chemical Engineering, National Tsing-Hua University and Department of Physics, National Taiwan University, Taipei 10617, Taiwan.
| | - Rakwoo Chang
- Department of Chemistry, Kwangwoon University, Seoul 01897, Korea.
| | - Shuji Ikeda
- Department of Chemistry, Graduate School of Science, Kyoto University, Sakyo-Ku, Kyoto 606-8501, Japan.
| | - Hiroshi Sugiyama
- Department of Chemistry, Graduate School of Science, Kyoto University, Sakyo-Ku, Kyoto 606-8501, Japan.
| | - Kyubong Jo
- Department of Chemistry and Integrated Biotechnology, Sogang University, Seoul 04107, Korea.
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Krerowicz SJ, Hernandez-Ortiz JP, Schwartz DC. Microscale Objects via Restructuring of Large, Double-Stranded DNA Molecules. ACS APPLIED MATERIALS & INTERFACES 2018; 10:41215-41223. [PMID: 30403478 PMCID: PMC6453721 DOI: 10.1021/acsami.8b18157] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
As the interest in DNA nanotechnology increases, so does the need for larger and more complex DNA structures. In this work, we describe two methods of using large, double-stranded (ds) DNA to self-assemble sequence-specific, nonrepetitive microscale structures. A model system restructures T7 DNA (40 kb) through sequence-specific biotinylation followed by intramolecular binding to a 40 nm diameter neutravidin bead to create T7 "rosettes". This model system informed the creation of "nodal DNA" where "nodes" with single-stranded DNA flaps are attached to a large dsDNA insert so that a complementary oligonucleotide "strap" bridges the two nodes for restructuring to form a DNA "bolo". To do this in high yield, several methodologies were developed, including a protection/deprotection scheme using RNA/RNase H and dialysis chambers, which remove excess straps while retaining large DNA molecules. To assess these restructuring processes, the DNA was adsorbed onto supported lipid bilayers, allowing for a visual assay of their structure using single-molecule fluorescence microscopy. Good agreement between the expected and observed fluorescence intensity measurements of the individual features of restructured DNA for both the DNA rosettes and bolos gives us a high degree of confidence that both processes give sequence-specific restructuring of large, dsDNA molecules to create microscale objects.
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Affiliation(s)
- Samuel J.W. Krerowicz
- Laboratory for Molecular and Computational Genomics, University of Wisconsin-Madison, Madison, Wisconsin 53706, USA
- Department of Chemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706, USA
- Laboratory of Genetics, University of Wisconsin-Madison, Madison, Wisconsin 53706, USA
- UW Biotechnology Center, University of Wisconsin-Madison, Madison, Wisconsin 53706, USA
| | - Juan P. Hernandez-Ortiz
- UW Biotechnology Center, University of Wisconsin-Madison, Madison, Wisconsin 53706, USA
- Departamento de Materiales y Nanotecnología, Universidad Nacional de Colombia- Medellín, Medellín 050034, Colombia
- Colombia/Wisconsin One-Health Consortium, Universidad Nacional de Colombia- Medellín, Medellín 050034, Colombia
| | - David C. Schwartz
- Laboratory for Molecular and Computational Genomics, University of Wisconsin-Madison, Madison, Wisconsin 53706, USA
- Department of Chemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706, USA
- Laboratory of Genetics, University of Wisconsin-Madison, Madison, Wisconsin 53706, USA
- UW Biotechnology Center, University of Wisconsin-Madison, Madison, Wisconsin 53706, USA
- Colombia/Wisconsin One-Health Consortium, Universidad Nacional de Colombia- Medellín, Medellín 050034, Colombia
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Single-molecule DNA-mapping and whole-genome sequencing of individual cells. Proc Natl Acad Sci U S A 2018; 115:11192-11197. [PMID: 30322920 DOI: 10.1073/pnas.1804194115] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023] Open
Abstract
To elucidate cellular diversity and clonal evolution in tissues and tumors, one must resolve genomic heterogeneity in single cells. To this end, we have developed low-cost, mass-producible micro-/nanofluidic chips for DNA extraction from individual cells. These chips have modules that collect genomic DNA for sequencing or map genomic structure directly, on-chip, with denaturation-renaturation (D-R) optical mapping [Marie R, et al. (2013) Proc Natl Acad Sci USA 110:4893-4898]. Processing of single cells from the LS174T colorectal cancer cell line showed that D-R mapping of single molecules can reveal structural variation (SV) in the genome of single cells. In one experiment, we processed 17 fragments covering 19.8 Mb of the cell's genome. One megabase-large fragment aligned well to chromosome 19 with half its length, while the other half showed variable alignment. Paired-end single-cell sequencing supported this finding, revealing a region of complexity and a 50-kb deletion. Sequencing struggled, however, to detect a 20-kb gap that D-R mapping showed clearly in a megabase fragment that otherwise mapped well to the reference at the pericentromeric region of chromosome 4. Pericentromeric regions are complex and show substantial sequence homology between different chromosomes, making mapping of sequence reads ambiguous. Thus, D-R mapping directly, from a single molecule, revealed characteristics of the single-cell genome that were challenging for short-read sequencing.
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41
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Bhandari AB, Reifenberger JG, Chuang HM, Cao H, Dorfman KD. Measuring the wall depletion length of nanoconfined DNA. J Chem Phys 2018; 149:104901. [PMID: 30219022 PMCID: PMC6135644 DOI: 10.1063/1.5040458] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2018] [Accepted: 08/20/2018] [Indexed: 12/14/2022] Open
Abstract
Efforts to study the polymer physics of DNA confined in nanochannels have been stymied by a lack of consensus regarding its wall depletion length. We have measured this quantity in 38 nm wide, square silicon dioxide nanochannels for five different ionic strengths between 15 mM and 75 mM. Experiments used the Bionano Genomics Irys platform for massively parallel data acquisition, attenuating the effect of the sequence-dependent persistence length and finite-length effects by using nick-labeled E. coli genomic DNA with contour length separations of at least 30 µm (88 325 base pairs) between nick pairs. Over 5 × 106 measurements of the fractional extension were obtained from 39 291 labeled DNA molecules. Analyzing the stretching via Odijk's theory for a strongly confined wormlike chain yielded a linear relationship between the depletion length and the Debye length. This simple linear fit to the experimental data exhibits the same qualitative trend as previously defined analytical models for the depletion length but now quantitatively captures the experimental data.
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Affiliation(s)
- Aditya Bikram Bhandari
- Department of Chemical Engineering and Materials Science, University of Minnesota-Twin Cities, 421 Washington Ave. SE, Minneapolis, Minnesota 55455, USA
| | - Jeffrey G Reifenberger
- Bionano Genomics, Inc., 9640 Towne Centre Drive, Suite 100, San Diego, California 92121, USA
| | - Hui-Min Chuang
- Department of Chemical Engineering and Materials Science, University of Minnesota-Twin Cities, 421 Washington Ave. SE, Minneapolis, Minnesota 55455, USA
| | - Han Cao
- Bionano Genomics, Inc., 9640 Towne Centre Drive, Suite 100, San Diego, California 92121, USA
| | - Kevin D Dorfman
- Department of Chemical Engineering and Materials Science, University of Minnesota-Twin Cities, 421 Washington Ave. SE, Minneapolis, Minnesota 55455, USA
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42
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Ödman D, Werner E, Dorfman KD, Doering CR, Mehlig B. Distribution of label spacings for genome mapping in nanochannels. BIOMICROFLUIDICS 2018; 12:034115. [PMID: 30018694 PMCID: PMC6019347 DOI: 10.1063/1.5038417] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/03/2018] [Accepted: 06/06/2018] [Indexed: 05/27/2023]
Abstract
In genome mapping experiments, long DNA molecules are stretched by confining them to very narrow channels, so that the locations of sequence-specific fluorescent labels along the channel axis provide large-scale genomic information. It is difficult, however, to make the channels narrow enough so that the DNA molecule is fully stretched. In practice, its conformations may form hairpins that change the spacings between internal segments of the DNA molecule, and thus the label locations along the channel axis. Here, we describe a theory for the distribution of label spacings that explains the heavy tails observed in distributions of label spacings in genome mapping experiments.
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Affiliation(s)
- D Ödman
- Department of Physics, University of Gothenburg, 41296 Gothenburg, Sweden
| | - E Werner
- Department of Physics, University of Gothenburg, 41296 Gothenburg, Sweden
| | - K D Dorfman
- Department of Chemical Engineering and Materials Science, University of Minnesota, Minneapolis, Minnesota 55455, USA
| | - C R Doering
- Center for the Study of Complex Systems, University of Michigan, Ann Arbor, Michigan 48109-1042, USA
| | - B Mehlig
- Department of Physics, University of Gothenburg, 41296 Gothenburg, Sweden
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43
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Yu M, Hou Y, Song R, Xu X, Yao S. Tunable Confinement for Bridging Single-Cell Manipulation and Single-Molecule DNA Linearization. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2018; 14:e1800229. [PMID: 29575689 DOI: 10.1002/smll.201800229] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/18/2018] [Revised: 02/07/2018] [Indexed: 06/08/2023]
Abstract
DNA linearization by nanoconfinement has offered a new avenue toward large-scale genome mapping. The ability to smoothly interface the widely different length scales from cell manipulation to DNA linearization is critical to the development of single-cell genomic mapping or sequencing technologies. Conventional nanochannel technologies for DNA analysis suffer from complex fabrication procedures, DNA stacking at the nanochannel entrance, and inefficient solution exchange. In this work, a dynamic and tunable confinement strategy is developed to manipulate and linearize genomic-length DNA molecules from a single cell. By leveraging pneumatic microvalve control and elastomeric collapse, an array of nanochannels with confining dimension down to 20 nm and length up to sub-millimeter is created and can be dynamically tuned in size. The curved edges of the microvalve form gradual transitions from microscale to nanoscale confinement, smoothly facilitating DNA entry into the nanochannels. A unified micro/nanofluidic device that integrates single-cell trapping and lysis, DNA extraction, purification, labeling, and linearization is developed based on dynamically controllable nanochannels. Mbp-long DNA molecules are extracted directly from a single cell and in situ linearized in the nanochannels. The device provides a facile and promising platform to achieve the ultimate goal of single-cell, single-genome analysis.
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Affiliation(s)
- Miao Yu
- Department of Mechanical and Aerospace Engineering, The Hong Kong University of Science and Technology, Kowloon, 999077, Hong Kong, China
| | - Youmin Hou
- Department of Mechanical and Aerospace Engineering, The Hong Kong University of Science and Technology, Kowloon, 999077, Hong Kong, China
| | - Ruyuan Song
- Department of Chemical and Biological Engineering, The Hong Kong University of Science and Technology, Kowloon, 999077, Hong Kong, China
| | - Xiaonan Xu
- Department of Mechanical and Aerospace Engineering, The Hong Kong University of Science and Technology, Kowloon, 999077, Hong Kong, China
| | - Shuhuai Yao
- Department of Mechanical and Aerospace Engineering, The Hong Kong University of Science and Technology, Kowloon, 999077, Hong Kong, China
- Department of Chemical and Biological Engineering, The Hong Kong University of Science and Technology, Kowloon, 999077, Hong Kong, China
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44
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Abstract
The output from whole genome sequencing is a set of contigs, i.e. short non-overlapping DNA sequences (sizes 1-100 kilobasepairs). Piecing the contigs together is an especially difficult task for previously unsequenced DNA, and may not be feasible due to factors such as the lack of sufficient coverage or larger repetitive regions which generate gaps in the final sequence. Here we propose a new method for scaffolding such contigs. The proposed method uses densely labeled optical DNA barcodes from competitive binding experiments as scaffolds. On these scaffolds we position theoretical barcodes which are calculated from the contig sequences. This allows us to construct longer DNA sequences from the contig sequences. This proof-of-principle study extends previous studies which use sparsely labeled DNA barcodes for scaffolding purposes. Our method applies a probabilistic approach that allows us to discard “foreign” contigs from mixed samples with contigs from different types of DNA. We satisfy the contig non-overlap constraint by formulating the contig placement challenge as a combinatorial auction problem. Our exact algorithm for solving this problem reduces computational costs compared to previous methods in the combinatorial auction field. We demonstrate the usefulness of the proposed scaffolding method both for synthetic contigs and for contigs obtained using Illumina sequencing for a mixed sample with plasmid and chromosomal DNA.
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45
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Soh BW, Narsimhan V, Klotz AR, Doyle PS. Knots modify the coil-stretch transition in linear DNA polymers. SOFT MATTER 2018; 14:1689-1698. [PMID: 29423476 DOI: 10.1039/c7sm02195j] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
We perform single-molecule DNA experiments to investigate the relaxation dynamics of knotted polymers and examine the steady-state behavior of knotted polymers in elongational fields. The occurrence of a knot reduces the relaxation time of a molecule and leads to a shift in the molecule's coil-stretch transition to larger strain rates. We measure chain extension and extension fluctuations as a function of strain rate for unknotted and knotted molecules. The curves for knotted molecules can be collapsed onto the unknotted curves by defining an effective Weissenberg number based on the measured knotted relaxation time in the low extension regime, or a relaxation time based on Rouse/Zimm scaling theories in the high extension regime. Because a knot reduces a molecule's relaxation time, we observe that knot untying near the coil-stretch transition can result in dramatic changes in the molecule's conformation. For example, a knotted molecule at a given strain rate can experience a stretch-coil transition, followed by a coil-stretch transition, after the knot partially or fully unties.
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Affiliation(s)
- Beatrice W Soh
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA.
| | - Vivek Narsimhan
- Department of Chemical Engineering, Purdue University, West Lafayette, Indiana 47907, USA
| | - Alexander R Klotz
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA.
| | - Patrick S Doyle
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA.
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46
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Ven K, Vanspauwen B, Pérez-Ruiz E, Leirs K, Decrop D, Gerstmans H, Spasic D, Lammertyn J. Target Confinement in Small Reaction Volumes Using Microfluidic Technologies: A Smart Approach for Single-Entity Detection and Analysis. ACS Sens 2018; 3:264-284. [PMID: 29363316 DOI: 10.1021/acssensors.7b00873] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Over the last decades, the study of cells, nucleic acid molecules, and proteins has evolved from ensemble measurements to so-called single-entity studies. The latter offers huge benefits, not only as biological research tools to examine heterogeneities among individual entities within a population, but also as biosensing tools for medical diagnostics, which can reach the ultimate sensitivity by detecting single targets. Whereas various techniques for single-entity detection have been reported, this review focuses on microfluidic systems that physically confine single targets in small reaction volumes. We categorize these techniques as droplet-, microchamber-, and nanostructure-based and provide an overview of their implementation for studying single cells, nucleic acids, and proteins. We furthermore reflect on the advantages and limitations of these techniques and highlight future opportunities in the field.
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Affiliation(s)
- Karen Ven
- Department
of Biosystems, KU Leuven - University of Leuven, Willem de Croylaan 42, 3001 Leuven, Belgium
| | - Bram Vanspauwen
- Department
of Biosystems, KU Leuven - University of Leuven, Willem de Croylaan 42, 3001 Leuven, Belgium
| | - Elena Pérez-Ruiz
- Department
of Biosystems, KU Leuven - University of Leuven, Willem de Croylaan 42, 3001 Leuven, Belgium
| | - Karen Leirs
- Department
of Biosystems, KU Leuven - University of Leuven, Willem de Croylaan 42, 3001 Leuven, Belgium
| | - Deborah Decrop
- Department
of Biosystems, KU Leuven - University of Leuven, Willem de Croylaan 42, 3001 Leuven, Belgium
| | - Hans Gerstmans
- Department
of Biosystems, KU Leuven - University of Leuven, Willem de Croylaan 42, 3001 Leuven, Belgium
- Department
of Applied biosciences, Ghent University, Valentyn Vaerwyckweg 1 - building
C, 9000 Gent, Belgium
- Department
of Biosystems, KU Leuven - University of Leuven, Kasteelpark Arenberg
21, 3001 Leuven, Belgium
| | - Dragana Spasic
- Department
of Biosystems, KU Leuven - University of Leuven, Willem de Croylaan 42, 3001 Leuven, Belgium
| | - Jeroen Lammertyn
- Department
of Biosystems, KU Leuven - University of Leuven, Willem de Croylaan 42, 3001 Leuven, Belgium
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47
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Reifenberger JG, Cao H, Dorfman KD. Odijk excluded volume interactions during the unfolding of DNA confined in a nanochannel. Macromolecules 2018; 51:1172-1180. [PMID: 29479117 PMCID: PMC5823525 DOI: 10.1021/acs.macromol.7b02466] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
We report experimental data on the unfolding of human and E. coli genomic DNA molecules shortly after injection into a 45 nm nanochannel. The unfolding dynamics are deterministic, consistent with previous experiments and modeling in larger channels, and do not depend on the biological origin of the DNA. The measured entropic unfolding force per friction per unit contour length agrees with that predicted by combining the Odijk excluded volume with numerical calculations of the Kirkwood diffusivity of confined DNA. The time scale emerging from our analysis has implications for genome mapping in nanochannels, especially as the technology moves towards longer DNA, by setting a lower bound for the delay time before making a measurement.
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Affiliation(s)
| | - Han Cao
- BioNano Genomics Inc., 9640 Towne Centre Drive, Suite 100, San Diego, CA 92121
| | - Kevin D. Dorfman
- Department of Chemical Engineering and Materials Science, University of Minnesota – Twin Cities, 421 Washington Ave SE, Minneapolis, Minnesota 55455, USA
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48
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Maschmann A, Masters C, Davison M, Lallman J, Thompson D, Kounovsky-Shafer KL. Determining if DNA Stained with a Cyanine Dye Can Be Digested with Restriction Enzymes. J Vis Exp 2018. [PMID: 29443093 DOI: 10.3791/57141] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023] Open
Abstract
Visualization of DNA for fluorescence microscopy utilizes a variety of dyes such as cyanine dyes. These dyes are utilized due to their high affinity and sensitivity for DNA. In order to determine if the DNA molecules are full length after the completion of the experiment, a method is required to determine if the stained molecules are full length by digesting DNA with restriction enzymes. However, stained DNA may inhibit the enzymes, so a method is needed to determine what enzymes one could use for fluorochrome stained DNA. In this method, DNA is stained with a cyanine dye overnight to allow the dye and DNA to equilibrate. Next, stained DNA is digested with a restriction enzyme, loaded into a gel and electrophoresed. The experimental DNA digest bands are compared to an in silico digest to determine the restriction enzyme activity. If there is the same number of bands as expected, then the reaction is complete. More bands than expected indicate partial digestion and less bands indicate incomplete digestion. The advantage of this method is its simplicity and it uses equipment that a scientist would need for a restriction enzyme assay and gel electrophoresis. A limitation of this method is that the enzymes available to most scientists are commercially available enzymes; however, any restriction enzymes could be used.
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Affiliation(s)
| | - Cody Masters
- Department of Chemistry, University of Nebraska - Kearney
| | | | - Joshua Lallman
- Department of Chemistry, University of Nebraska - Kearney
| | - Drew Thompson
- Department of Chemistry, University of Nebraska - Kearney
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49
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Cheong GK, Li X, Dorfman KD. Evidence for the extended de Gennes regime of a semiflexible polymer in slit confinement. Phys Rev E 2018; 97:022502. [PMID: 29479576 PMCID: PMC5823612 DOI: 10.1103/physreve.97.022502] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
We use off-lattice, pruned-enriched Rosenbluth method (PERM) simulations to compute the confinement free energy of a real wormlike chain of effective width w and persistence length lp in a slit of height H. For slit heights much larger than the persistence length of the polymer and much smaller than the thermal blob size, the excess free energy of the confined chain is consistent with a modified version of the scaling theory for the extended de Gennes regime in a channel that reflects the blob statistics in slit confinement. Explicitly, for channel sizes [Formula: see text], the difference between the confinement free energy of the real chain and that of an ideal chain scales like w/H.
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Affiliation(s)
- Guo Kang Cheong
- Department of Chemical Engineering and Materials Science, University of Minnesota – Twin Cities, 421 Washington Avenue SE, Minneapolis, Minnesota 55455, USA
| | - Xiaolan Li
- Department of Chemical Engineering and Materials Science, University of Minnesota – Twin Cities, 421 Washington Avenue SE, Minneapolis, Minnesota 55455, USA
| | - Kevin D. Dorfman
- Department of Chemical Engineering and Materials Science, University of Minnesota – Twin Cities, 421 Washington Avenue SE, Minneapolis, Minnesota 55455, USA
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50
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Dorfman KD. The Statistical Segment Length of DNA: Opportunities for Biomechanical Modeling in Polymer Physics and Next-Generation Genomics. J Biomech Eng 2018; 140:2653367. [PMID: 28857114 PMCID: PMC5816256 DOI: 10.1115/1.4037790] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2017] [Revised: 08/16/2017] [Indexed: 12/28/2022]
Abstract
The development of bright bisintercalating dyes for deoxyribonucleic acid (DNA) in the 1990s, most notably YOYO-1, revolutionized the field of polymer physics in the ensuing years. These dyes, in conjunction with modern molecular biology techniques, permit the facile observation of polymer dynamics via fluorescence microscopy and thus direct tests of different theories of polymer dynamics. At the same time, they have played a key role in advancing an emerging next-generation method known as genome mapping in nanochannels. The effect of intercalation on the bending energy of DNA as embodied by a change in its statistical segment length (or, alternatively, its persistence length) has been the subject of significant controversy. The precise value of the statistical segment length is critical for the proper interpretation of polymer physics experiments and controls the phenomena underlying the aforementioned genomics technology. In this perspective, we briefly review the model of DNA as a wormlike chain and a trio of methods (light scattering, optical or magnetic tweezers, and atomic force microscopy (AFM)) that have been used to determine the statistical segment length of DNA. We then outline the disagreement in the literature over the role of bisintercalation on the bending energy of DNA, and how a multiscale biomechanical approach could provide an important model for this scientifically and technologically relevant problem.
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Affiliation(s)
- Kevin D. Dorfman
- Department of Chemical Engineering and
Materials Science,
University of Minnesota—Twin Cities,
421 Washington Ave SE,
Minneapolis, MN 55455
e-mail:
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