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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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2
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Gautam D, Pandey S, Chen J. Effect of Flow Rate and Ionic Strength on the Stabilities of YOYO-1 and YO-PRO-1 Intercalated in DNA Molecules. J Phys Chem B 2023; 127:2450-2456. [PMID: 36917775 PMCID: PMC10088364 DOI: 10.1021/acs.jpcb.3c00777] [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] [Indexed: 03/16/2023]
Abstract
Single-molecule DNA studies have improved our understanding of the DNAs' structure and their interactions with other molecules. A variety of DNA labeling dyes are available for single-molecule studies, among which the bis-intercalating dye YOYO-1 and mono-intercalating dye YO-PRO-1 are widely used. They have an extraordinarily strong affinity toward DNA and are bright with a high quantum yield (>0.5) when bound to DNAs. However, it is still not clear how these dyes behave in DNA molecules under higher ionic strength and strong buffer flow. Here, we have studied the effect of ionic strength and flow rate of buffer on their binding in single DNA molecules. The larger the flow rate and the higher the ionic strength, the faster the intercalated dyes are washed away from the DNAs. In the buffer with 1 M ionic strength, YOYO-1 and YO-PRO-1 are mostly washed away from DNA within 2 min of moderate buffer flow.
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Affiliation(s)
- Dinesh Gautam
- Department of Chemistry and Biochemistry, Nanoscale & Quantum Phenomena Institute, Ohio University, Athens, OH 45701, USA
| | - Srijana Pandey
- Department of Chemistry and Biochemistry, Nanoscale & Quantum Phenomena Institute, Ohio University, Athens, OH 45701, USA
| | - Jixin Chen
- Department of Chemistry and Biochemistry, Nanoscale & Quantum Phenomena Institute, Ohio University, Athens, OH 45701, USA
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3
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Ström OE, Beech JP, Tegenfeldt JO. High-Throughput Separation of Long DNA in Deterministic Lateral Displacement Arrays. MICROMACHINES 2022; 13:1754. [PMID: 36296107 PMCID: PMC9611613 DOI: 10.3390/mi13101754] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/13/2022] [Revised: 10/06/2022] [Accepted: 10/09/2022] [Indexed: 06/16/2023]
Abstract
Length-based separation of DNA remains as relevant today as when gel electrophoresis was introduced almost 100 years ago. While new, long-read genomics technologies have revolutionised accessibility to powerful genomic data, the preparation of samples has not proceeded at the same pace, with sample preparation often constituting a considerable bottleneck, both in time and difficulty. Microfluidics holds great potential for automated, sample-to-answer analysis via the integration of preparatory and analytical steps, but for this to be fully realised, more versatile, powerful and integrable unit operations, such as separation, are essential. We demonstrate the displacement and separation of DNA with a throughput that is one to five orders of magnitude greater than other microfluidic techniques. Using a device with a small footprint (23 mm × 0.5 mm), and with feature sizes in the micrometre range, it is considerably easier to fabricate than parallelized nano-array-based approaches. We show the separation of 48.5 kbp and 166 kbp DNA strands achieving a significantly improved throughput of 760 ng/h, compared to previous work and the separation of low concentrations of 48.5 kbp DNA molecules from a massive background of sub 10 kbp fragments. We show that the extension of DNA molecules at high flow velocities, generally believed to make the length-based separation of long DNA difficult, does not place the ultimate limitation on our method. Instead, we explore the effects of polymer rotations and intermolecular interactions at extremely high DNA concentrations and postulate that these may have both negative and positive influences on the separation depending on the detailed experimental conditions.
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Liang J, Koo B, Wu Y, Manna S, Noble JM, Patel M, Park JH, Kozak D, Wang Y, Zheng J. Characterization of Complex Drug Formulations Using Cryogenic Scanning Electron Microscopy (Cryo-SEM). Curr Protoc 2022; 2:e406. [PMID: 35384403 DOI: 10.1002/cpz1.406] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
The physicochemical properties of complex drug formulations, including liposomes, suspensions, and emulsions, are important for understanding drug release mechanisms, quality control, and regulatory assessment. It is ideal to characterize these complex drug formulations in their native hydrated state. This article describes the characterization of complex drug formulations in a frozen-hydrated state using cryogenic scanning electron microscopy (cryo-SEM). In comparison to other techniques, such as optical microscopy or room-temperature scanning electron microscopy, cryo-SEM combines the advantage of studying hydrated samples with high-resolution imaging capability. Detailed information regarding cryo-fixation, cryo-fracture, freeze-etching, sputter-coating, and cryo-SEM imaging is included in this article. A multivesicular liposomal complex drug formulation is used to illustrate the impact of different cryogenic sample preparation conditions. In addition to drug formulations, this approach can also be applied to biological samples (e.g., cells, bacteria) and soft-matter samples (e.g., hydrogels). © Published 2022. This article is a U.S. Government work and is in the public domain in the USA. Basic Protocol 1: Cryo-fixation to preserve the native structure of samples using planchettes Alternate Protocol: Cryo-fixation to preserve the native structure of biological samples on sapphire disks Basic Protocol 2: Sample preparation for cross-sectional cryo-SEM imaging Basic Protocol 3: Cryo-SEM imaging and microanalysis.
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Affiliation(s)
- Jing Liang
- Division of Therapeutic Performance, Office of Research and Standards, Office of Generic Drugs, Center for Drug Evaluation and Research, Food and Drug Administration, Silver Spring, Maryland.,Division of Biology, Chemistry and Materials Science, Office of Science and Engineering Laboratories, Center for Devices and Radiological Health, Food and Drug Administration, Silver Spring, Maryland
| | - Bonhye Koo
- Division of Therapeutic Performance, Office of Research and Standards, Office of Generic Drugs, Center for Drug Evaluation and Research, Food and Drug Administration, Silver Spring, Maryland.,Division of Biology, Chemistry and Materials Science, Office of Science and Engineering Laboratories, Center for Devices and Radiological Health, Food and Drug Administration, Silver Spring, Maryland
| | - Yong Wu
- Division of Biology, Chemistry and Materials Science, Office of Science and Engineering Laboratories, Center for Devices and Radiological Health, Food and Drug Administration, Silver Spring, Maryland
| | - Soumyarwit Manna
- Division of Therapeutic Performance, Office of Research and Standards, Office of Generic Drugs, Center for Drug Evaluation and Research, Food and Drug Administration, Silver Spring, Maryland.,Division of Biology, Chemistry and Materials Science, Office of Science and Engineering Laboratories, Center for Devices and Radiological Health, Food and Drug Administration, Silver Spring, Maryland
| | - Jade M Noble
- Division of Therapeutic Performance, Office of Research and Standards, Office of Generic Drugs, Center for Drug Evaluation and Research, Food and Drug Administration, Silver Spring, Maryland.,Division of Biology, Chemistry and Materials Science, Office of Science and Engineering Laboratories, Center for Devices and Radiological Health, Food and Drug Administration, Silver Spring, Maryland
| | - Mehulkumar Patel
- Division of Biology, Chemistry and Materials Science, Office of Science and Engineering Laboratories, Center for Devices and Radiological Health, Food and Drug Administration, Silver Spring, Maryland
| | - Jin H Park
- Division of Therapeutic Performance, Office of Research and Standards, Office of Generic Drugs, Center for Drug Evaluation and Research, Food and Drug Administration, Silver Spring, Maryland.,Division of Biology, Chemistry and Materials Science, Office of Science and Engineering Laboratories, Center for Devices and Radiological Health, Food and Drug Administration, Silver Spring, Maryland
| | - Darby Kozak
- Division of Therapeutic Performance, Office of Research and Standards, Office of Generic Drugs, Center for Drug Evaluation and Research, Food and Drug Administration, Silver Spring, Maryland
| | - Yan Wang
- Division of Therapeutic Performance, Office of Research and Standards, Office of Generic Drugs, Center for Drug Evaluation and Research, Food and Drug Administration, Silver Spring, Maryland
| | - Jiwen Zheng
- Division of Biology, Chemistry and Materials Science, Office of Science and Engineering Laboratories, Center for Devices and Radiological Health, Food and Drug Administration, Silver Spring, Maryland
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KK S, Lin YL, Sewunet T, Wrande M, Sandegren L, Giske CG, Westerlund F. A Parallelized Nanofluidic Device for High-Throughput Optical DNA Mapping of Bacterial Plasmids. MICROMACHINES 2021; 12:1234. [PMID: 34683285 PMCID: PMC8538381 DOI: 10.3390/mi12101234] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/14/2021] [Revised: 10/05/2021] [Accepted: 10/08/2021] [Indexed: 12/03/2022]
Abstract
Optical DNA mapping (ODM) has developed into an important technique for DNA analysis, where single DNA molecules are sequence-specifically labeled and stretched, for example, in nanofluidic channels. We have developed an ODM assay to analyze bacterial plasmids-circular extrachromosomal DNA that often carry genes that make bacteria resistant to antibiotics. As for most techniques, the next important step is to increase throughput and automation. In this work, we designed and fabricated a nanofluidic device that, together with a simple automation routine, allows parallel analysis of up to 10 samples at the same time. Using plasmids encoding extended-spectrum beta-lactamases (ESBL), isolated from Escherichiacoli and Klebsiellapneumoniae, we demonstrate the multiplexing capabilities of the device when it comes to both many samples in parallel and different resistance genes. As a final example, we combined the device with a novel protocol for rapid cultivation and extraction of plasmids from fecal samples collected from patients. This combined protocol will make it possible to analyze many patient samples in one device already on the day the sample is collected, which is an important step forward for the ODM analysis of plasmids in clinical diagnostics.
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Affiliation(s)
- Sriram KK
- Division of Chemical Biology, Department of Biology and Biological Engineering, Chalmers University of Technology, 412 96 Gothenburg, Sweden; (S.K.); (Y.-L.L.)
| | - Yii-Lih Lin
- Division of Chemical Biology, Department of Biology and Biological Engineering, Chalmers University of Technology, 412 96 Gothenburg, Sweden; (S.K.); (Y.-L.L.)
| | - Tsegaye Sewunet
- Division of Clinical Microbiology, Department of Laboratory Medicine, Karolinska Institute, 141 52 Stockholm, Sweden; (T.S.); (C.G.G.)
| | - Marie Wrande
- Department of Medical Biochemistry and Microbiology, Uppsala University, 752 37 Uppsala, Sweden; (M.W.); (L.S.)
| | - Linus Sandegren
- Department of Medical Biochemistry and Microbiology, Uppsala University, 752 37 Uppsala, Sweden; (M.W.); (L.S.)
| | - Christian G. Giske
- Division of Clinical Microbiology, Department of Laboratory Medicine, Karolinska Institute, 141 52 Stockholm, Sweden; (T.S.); (C.G.G.)
- Clinical Microbiology, Karolinska University Hospital, 171 76 Stockholm, Sweden
| | - Fredrik Westerlund
- Division of Chemical Biology, Department of Biology and Biological Engineering, Chalmers University of Technology, 412 96 Gothenburg, Sweden; (S.K.); (Y.-L.L.)
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6
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Jiang K, Rocha S, Kumar R, Westerlund F, Wittung-Stafshede P. C-terminal truncation of α-synuclein alters DNA structure from extension to compaction. Biochem Biophys Res Commun 2021; 568:43-47. [PMID: 34175689 DOI: 10.1016/j.bbrc.2021.06.059] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2021] [Accepted: 06/15/2021] [Indexed: 11/25/2022]
Abstract
Parkinson's disease (PD) is linked to aggregation of the protein α-synuclein (aS) into amyloid fibers. aS is proposed to regulate synaptic activity and may also play a role in gene regulation via interaction with DNA in the cell nucleus. Here, we address the role of the negatively-charged C-terminus in the interaction between aS and DNA using single-molecule techniques. Using nanofluidic channels, we demonstrate that truncation of the C-terminus of aS induces differential effects on DNA depending on the extent of the truncation. The DNA extension increases for full-length aS and the (1-119)aS variant, but decreases about 25% upon binding to the (1-97)aS variant. Atomic force microscopy imaging showed full protein coverage of the DNA at high aS concentration. The characterization of biophysical properties of DNA when in complex with aS variants may provide important insights into the role of such interactions in PD, especially since C-terminal aS truncations have been found in clinical samples from PD patients.
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Affiliation(s)
- Kai Jiang
- Department of Biology and Biological Engineering, Chalmers University of Technology, 412 96, Gothenburg, Sweden
| | - Sandra Rocha
- Department of Biology and Biological Engineering, Chalmers University of Technology, 412 96, Gothenburg, Sweden
| | - Ranjeet Kumar
- Department of Biology and Biological Engineering, Chalmers University of Technology, 412 96, Gothenburg, Sweden
| | - Fredrik Westerlund
- Department of Biology and Biological Engineering, Chalmers University of Technology, 412 96, Gothenburg, Sweden.
| | - Pernilla Wittung-Stafshede
- Department of Biology and Biological Engineering, Chalmers University of Technology, 412 96, Gothenburg, Sweden.
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7
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Lin YL, Sewunet T, KK S, Giske CG, Westerlund F. Optical maps of plasmids as a proxy for clonal spread of MDR bacteria: a case study of an outbreak in a rural Ethiopian hospital. J Antimicrob Chemother 2021; 75:2804-2811. [PMID: 32653928 PMCID: PMC7678893 DOI: 10.1093/jac/dkaa258] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2020] [Revised: 04/24/2020] [Accepted: 05/14/2020] [Indexed: 01/09/2023] Open
Abstract
Objectives MDR bacteria have become a prevailing health threat worldwide. We here aimed to use optical DNA mapping (ODM) as a rapid method to trace nosocomial spread of bacterial clones and gene elements. We believe that this method has the potential to be a tool of pivotal importance for MDR control. Methods Twenty-four Escherichia coli samples of ST410 from three different wards were collected at an Ethiopian hospital and their plasmids were analysed by ODM. Plasmids were specifically digested with Cas9 targeting the antibiotic resistance genes, stained by competitive binding and confined in nanochannels for imaging. The resulting intensity profiles (barcodes) for each plasmid were compared to identify potential clonal spread of resistant bacteria. Results ODM demonstrated that a large fraction of the patients carried bacteria with a plasmid of the same origin, carrying the ESBL gene blaCTX-M-15, suggesting clonal spread. The results correlate perfectly with core genome (cg)MLST data, where bacteria with the same plasmid also had very similar cgMLST profiles. Conclusions ODM is a rapid discriminatory method for identifying plasmids and antibiotic resistance genes. Long-range deletions/insertions, which are challenging for short-read next-generation sequencing, can be easily identified and used to trace bacterial clonal spread. We propose that plasmid typing can be a useful tool to identify clonal spread of MDR bacteria. Furthermore, the simplicity of the method enables possible future application in low- and middle-income countries.
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Affiliation(s)
- Yii-Lih Lin
- Department of Biology and Biological Engineering, Chalmers University of Technology, Gothenburg, Sweden
| | - Tsegaye Sewunet
- Division of Clinical Microbiology, Department of Laboratory Medicine, Karolinska Institutet, Stockholm, Sweden
- School of Laboratory Sciences, Department of Microbiology, Jimma University, Jimma, Ethiopia
| | - Sriram KK
- Department of Biology and Biological Engineering, Chalmers University of Technology, Gothenburg, Sweden
| | - Christian G Giske
- Division of Clinical Microbiology, Department of Laboratory Medicine, Karolinska Institutet, Stockholm, Sweden
- Clinical Microbiology, Karolinska University Hospital, Stockholm, Sweden
| | - Fredrik Westerlund
- Department of Biology and Biological Engineering, Chalmers University of Technology, Gothenburg, Sweden
- Corresponding author. E-mail:
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8
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Jiang K, Humbert N, K K S, Rouzina I, Mely Y, Westerlund F. The HIV-1 nucleocapsid chaperone protein forms locally compacted globules on long double-stranded DNA. Nucleic Acids Res 2021; 49:4550-4563. [PMID: 33872352 PMCID: PMC8096146 DOI: 10.1093/nar/gkab236] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2020] [Revised: 03/09/2021] [Accepted: 03/22/2021] [Indexed: 01/14/2023] Open
Abstract
The nucleocapsid (NC) protein plays key roles in Human Immunodeficiency Virus 1 (HIV-1) replication, notably by condensing and protecting the viral RNA genome and by chaperoning its reverse transcription into double-stranded DNA (dsDNA). Recent findings suggest that integration of viral dsDNA into the host genome, and hence productive infection, is linked to a small subpopulation of viral complexes where reverse transcription was completed within the intact capsid. Therefore, the synthesized dsDNA has to be tightly compacted, most likely by NC, to prevent breaking of the capsid in these complexes. To investigate NC’s ability to compact viral dsDNA, we here characterize the compaction of single dsDNA molecules under unsaturated NC binding conditions using nanofluidic channels. Compaction is shown to result from accumulation of NC at one or few compaction sites, which leads to small dsDNA condensates. NC preferentially initiates compaction at flexible regions along the dsDNA, such as AT-rich regions and DNA ends. Upon further NC binding, these condensates develop into a globular state containing the whole dsDNA molecule. These findings support NC’s role in viral dsDNA compaction within the mature HIV-1 capsid and suggest a possible scenario for the gradual dsDNA decondensation upon capsid uncoating and NC loss.
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Affiliation(s)
- Kai Jiang
- Division of Chemical Biology, Department of Biology and Biological Engineering, Chalmers University of Technology, Gothenburg SE 412 96, Sweden
| | - Nicolas Humbert
- Laboratoire de Bioimagerie et Pathologies, UMR 7021 CNRS, Université de Strasbourg, Faculté de Pharmacie, Illkirch F 67401, France
| | - Sriram K K
- Division of Chemical Biology, Department of Biology and Biological Engineering, Chalmers University of Technology, Gothenburg SE 412 96, Sweden
| | - Ioulia Rouzina
- Department of Chemistry and Biochemistry, The Ohio State University, Center for Retroviral Research, and Center for RNA Biology, Columbus, OH 43210, USA
| | - Yves Mely
- Laboratoire de Bioimagerie et Pathologies, UMR 7021 CNRS, Université de Strasbourg, Faculté de Pharmacie, Illkirch F 67401, France
| | - Fredrik Westerlund
- Division of Chemical Biology, Department of Biology and Biological Engineering, Chalmers University of Technology, Gothenburg SE 412 96, Sweden
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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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10
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Ferreira C, Bikkarolla SK, Frykholm K, Pohjanen S, Brito M, Lameiras C, Nunes OC, Westerlund F, Manaia CM. Polyphasic characterization of carbapenem-resistant Klebsiella pneumoniae clinical isolates suggests vertical transmission of the blaKPC-3 gene. PLoS One 2021; 16:e0247058. [PMID: 33635888 PMCID: PMC7909683 DOI: 10.1371/journal.pone.0247058] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2020] [Accepted: 01/30/2021] [Indexed: 11/18/2022] Open
Abstract
Carbapenem-resistant Klebsiella pneumoniae are a major global threat in healthcare facilities. The propagation of carbapenem resistance determinants can occur through vertical transmission, with genetic elements being transmitted by the host bacterium, or by horizontal transmission, with the same genetic elements being transferred among distinct bacterial hosts. This work aimed to track carbapenem resistance transmission by K. pneumoniae in a healthcare facility. The study involved a polyphasic approach based on conjugation assays, resistance phenotype and genotype analyses, whole genome sequencing, and plasmid characterization by pulsed field gel electrophoresis and optical DNA mapping. Out of 40 K. pneumoniae clinical isolates recovered over two years, five were carbapenem- and multidrug-resistant and belonged to multilocus sequence type ST147. These isolates harboured the carbapenemase encoding blaKPC-3 gene, integrated in conjugative plasmids of 140 kbp or 55 kbp, belonging to replicon types incFIA/incFIIK or incN/incFIIK, respectively. The two distinct plasmids encoding the blaKPC-3 gene were associated with distinct genetic lineages, as confirmed by optical DNA mapping and whole genome sequence analyses. These results suggested vertical (bacterial strain-based) transmission of the carbapenem-resistance genetic elements. Determination of the mode of transmission of antibiotic resistance in healthcare facilities, only possible based on polyphasic approaches as described here, is essential to control resistance propagation.
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Affiliation(s)
- Catarina Ferreira
- CBQF - Centro de Biotecnologia e Química Fina – Laboratório Associado, Escola Superior de Biotecnologia, Universidade Católica Portuguesa, Porto, Portugal
| | - Santosh K. Bikkarolla
- Division of Chemical Biology, Department of Biology and Biological Engineering, Chalmers University of Technology, Gothenburg, Sweden
| | - Karolin Frykholm
- Division of Chemical Biology, Department of Biology and Biological Engineering, Chalmers University of Technology, Gothenburg, Sweden
| | - Saga Pohjanen
- Division of Chemical Biology, Department of Biology and Biological Engineering, Chalmers University of Technology, Gothenburg, Sweden
| | | | | | - Olga C. Nunes
- LEPABE - Laboratory for Process Engineering, Environment, Biotechnology and Energy, Faculty of Engineering, University of Porto, Porto, Portugal
| | - Fredrik Westerlund
- Division of Chemical Biology, Department of Biology and Biological Engineering, Chalmers University of Technology, Gothenburg, Sweden
- * E-mail: (CMM); (FW)
| | - Célia M. Manaia
- CBQF - Centro de Biotecnologia e Química Fina – Laboratório Associado, Escola Superior de Biotecnologia, Universidade Católica Portuguesa, Porto, Portugal
- * E-mail: (CMM); (FW)
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11
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Abstract
The DNA of our cells is constantly exposed to various types of damaging agents. One of the most critical types of damage is when both strands of the DNA break, and thus such breaks need to be efficiently repaired. It is known that CtIP promotes nucleases in DNA break repair. Here we show that CtIP can also hold the two DNA strands together in solution when DNA is free to move, using novel methodology that allows the monitoring of thousands of single DNA molecules in nanofabricated devices. DNA bridging likely facilitates the enzymatic repair steps and identifies novel CtIP functions that are crucial for repairing broken DNA. The early steps of DNA double-strand break (DSB) repair in human cells involve the MRE11-RAD50-NBS1 (MRN) complex and its cofactor, phosphorylated CtIP. The roles of these proteins in nucleolytic DSB resection are well characterized, but their role in bridging the DNA ends for efficient and correct repair is much less explored. Here we study the binding of phosphorylated CtIP, which promotes the endonuclease activity of MRN, to single long (∼50 kb) DNA molecules using nanofluidic channels and compare it to the yeast homolog Sae2. CtIP bridges DNA in a manner that depends on the oligomeric state of the protein, and truncated mutants demonstrate that the bridging depends on CtIP regions distinct from those that stimulate the nuclease activity of MRN. Sae2 is a much smaller protein than CtIP, and its bridging is significantly less efficient. Our results demonstrate that the nuclease cofactor and structural functions of CtIP may depend on the same protein population, which may be crucial for CtIP functions in both homologous recombination and microhomology-mediated end-joining.
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12
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Affiliation(s)
- Zixue Ma
- Department of Chemical Engineering and Materials Science, University of Minnesota, Twin Cities, 421 Washington Avenue SE, Minneapolis, Minnesota 55455, United States
| | - Kevin D. Dorfman
- Department of Chemical Engineering and Materials Science, University of Minnesota, Twin Cities, 421 Washington Avenue SE, Minneapolis, Minnesota 55455, United States
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13
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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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14
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Optical DNA Mapping Combined with Cas9-Targeted Resistance Gene Identification for Rapid Tracking of Resistance Plasmids in a Neonatal Intensive Care Unit Outbreak. mBio 2019; 10:mBio.00347-19. [PMID: 31289171 PMCID: PMC6747713 DOI: 10.1128/mbio.00347-19] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023] Open
Abstract
This study presents how a novel method, based on visualizing single plasmids using sequence-specific fluorescent labeling, could be used to analyze the genetic dynamics of an outbreak of resistant bacteria in a neonatal intensive care unit at a Swedish hospital. Plasmids are a central reason for the rapid global spread of bacterial resistance to antibiotics. In a single experimental procedure, this method replaces many traditional plasmid analysis techniques that together provide limited details and are slow to perform. The method is much faster than long-read whole-genome sequencing and offers direct genetic comparison of patient samples. We could conclude that no transfer of resistance plasmids had occurred between different bacteria during the outbreak and that secondary cases of ESBL-producing Enterobacteriaceae carriage were instead likely due to influx of new strains. We believe that the method offers potential in improving surveillance and infection control of resistant bacteria in hospitals. The global spread of antibiotic resistance among Enterobacteriaceae is largely due to multidrug resistance plasmids that can transfer between different bacterial strains and species. Horizontal gene transfer of resistance plasmids can complicate hospital outbreaks and cause problems in epidemiological tracing, since tracing is usually based on bacterial clonality. We have developed a method, based on optical DNA mapping combined with Cas9-assisted identification of resistance genes, which is used here to characterize plasmids during an extended-spectrum β-lactamase (ESBL)-producing Enterobacteriaceae outbreak at a Swedish neonatal intensive care unit. The outbreak included 17 neonates initially colonized with ESBL-producing Klebsiella pneumoniae (ESBL-KP), some of which were found to carry additional ESBL-producing Escherichia coli (ESBL-EC) in follow-up samples. We demonstrate that all ESBL-KP isolates contained two plasmids with the blaCTX-M-15 gene located on the smaller one (~80 kbp). The same ESBL-KP clone was present in follow-up samples for up to 2 years in some patients, and the plasmid carrying the blaCTX-M-15 gene was stable throughout this time period. However, extensive genetic rearrangements within the second plasmid were observed in the optical DNA maps for several of the ESBL-KP isolates. Optical mapping also demonstrated that even though other bacterial clones and species carrying blaCTX-M group 1 genes were found in some neonates, no transfer of resistance plasmids had occurred. The data instead pointed toward unrelated acquisition of ESBL-producing Enterobacteriaceae (EPE). In addition to revealing important information about the specific outbreak, the method presented is a promising tool for surveillance and infection control in clinical settings.
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15
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Ferreira C, Bogas D, Bikarolla SK, Varela AR, Frykholm K, Linheiro R, Nunes OC, Westerlund F, Manaia CM. Genetic variation in the conjugative plasmidome of a hospital effluent multidrug resistant Escherichia coli strain. CHEMOSPHERE 2019; 220:748-759. [PMID: 30611073 DOI: 10.1016/j.chemosphere.2018.12.130] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/05/2018] [Revised: 11/23/2018] [Accepted: 12/18/2018] [Indexed: 06/09/2023]
Abstract
Bacteria harboring conjugative plasmids have the potential for spreading antibiotic resistance through horizontal gene transfer. It is described that the selection and dissemination of antibiotic resistance is enhanced by stressors, like metals or antibiotics, which can occur as environmental contaminants. This study aimed at unveiling the composition of the conjugative plasmidome of a hospital effluent multidrug resistant Escherichia coli strain (H1FC54) under different mating conditions. To meet this objective, plasmid pulsed field gel electrophoresis, optical mapping analyses and DNA sequencing were used in combination with phenotype analysis. Strain H1FC54 was observed to harbor five plasmids, three of which were conjugative and two of these, pH1FC54_330 and pH1FC54_140, contained metal and antibiotic resistance genes. Transconjugants obtained in the absence or presence of tellurite (0.5 μM or 5 μM), arsenite (0.5 μM, 5 μM or 15 μM) or ceftazidime (10 mg/L) and selected in the presence of sodium azide (100 mg/L) and tetracycline (16 mg/L) presented distinct phenotypes, associated with the acquisition of different plasmid combinations, including two co-integrate plasmids, of 310 kbp and 517 kbp. The variable composition of the conjugative plasmidome, the formation of co-integrates during conjugation, as well as the transfer of non-transferable plasmids via co-integration, and the possible association between antibiotic, arsenite and tellurite tolerance was demonstrated. These evidences bring interesting insights into the comprehension of the molecular and physiological mechanisms that underlie antibiotic resistance propagation in the environment.
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Affiliation(s)
- Catarina Ferreira
- Universidade Católica Portuguesa, CBQF - Centro de Biotecnologia e Química Fina, Laboratório Associado, Escola Superior de Biotecnologia, Rua Arquiteto Lobão Vital, 172, 4200-374, Porto, Portugal
| | - Diana Bogas
- Universidade Católica Portuguesa, CBQF - Centro de Biotecnologia e Química Fina, Laboratório Associado, Escola Superior de Biotecnologia, Rua Arquiteto Lobão Vital, 172, 4200-374, Porto, Portugal
| | - Santosh K Bikarolla
- Division of Chemical Biology, Department of Biology and Biological Engineering, Chalmers University of Technology, Kemivagen 10, SE-412 96, Gothenburg, Sweden
| | - Ana Rita Varela
- Universidade Católica Portuguesa, CBQF - Centro de Biotecnologia e Química Fina, Laboratório Associado, Escola Superior de Biotecnologia, Rua Arquiteto Lobão Vital, 172, 4200-374, Porto, Portugal; LEPABE - Laboratory for Process Engineering, Environment, Biotechnology and Energy, Faculty of Engineering, University of Porto, Rua Dr. Roberto Frias, 4200-465, Porto, Portugal
| | - Karolin Frykholm
- Division of Chemical Biology, Department of Biology and Biological Engineering, Chalmers University of Technology, Kemivagen 10, SE-412 96, Gothenburg, Sweden
| | - Raquel Linheiro
- Universidade Católica Portuguesa, CBQF - Centro de Biotecnologia e Química Fina, Laboratório Associado, Escola Superior de Biotecnologia, Rua Arquiteto Lobão Vital, 172, 4200-374, Porto, Portugal
| | - Olga C Nunes
- LEPABE - Laboratory for Process Engineering, Environment, Biotechnology and Energy, Faculty of Engineering, University of Porto, Rua Dr. Roberto Frias, 4200-465, Porto, Portugal
| | - Fredrik Westerlund
- Division of Chemical Biology, Department of Biology and Biological Engineering, Chalmers University of Technology, Kemivagen 10, SE-412 96, Gothenburg, Sweden
| | - Célia M Manaia
- Universidade Católica Portuguesa, CBQF - Centro de Biotecnologia e Química Fina, Laboratório Associado, Escola Superior de Biotecnologia, Rua Arquiteto Lobão Vital, 172, 4200-374, Porto, Portugal.
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16
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Annealing of ssDNA and compaction of dsDNA by the HIV-1 nucleocapsid and Gag proteins visualized using nanofluidic channels. Q Rev Biophys 2019; 52:e2. [DOI: 10.1017/s0033583518000124] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Abstract
The nucleocapsid protein NC is a crucial component in the human immunodeficiency virus type 1 life cycle. It functions both in its processed mature form and as part of the polyprotein Gag that plays a key role in the formation of new viruses. NC can protect nucleic acids (NAs) from degradation by compacting them to a dense coil. Moreover, through its NA chaperone activity, NC can also promote the most stable conformation of NAs. Here, we explore the balance between these activities for NC and Gag by confining DNA–protein complexes in nanochannels. The chaperone activity is visualized as concatemerization and circularization of long DNA via annealing of short single-stranded DNA overhangs. The first ten amino acids of NC are important for the chaperone activity that is almost completely absent for Gag. Gag condenses DNA more efficiently than mature NC, suggesting that additional residues of Gag are involved. Importantly, this is the first single DNA molecule study of full-length Gag and we reveal important differences to the truncated Δ-p6 Gag that has been used before. In addition, the study also highlights how nanochannels can be used to study reactions on ends of long single DNA molecules, which is not trivial with competing single DNA molecule techniques.
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17
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Wu S, Jeffet J, Grunwald A, Sharim H, Gilat N, Torchinsky D, Zheng Q, Zirkin S, Xu L, Ebenstein Y. Microfluidic DNA combing for parallel single-molecule analysis. NANOTECHNOLOGY 2019; 30:045101. [PMID: 30485249 DOI: 10.1088/1361-6528/aaeddc] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
DNA combing is a widely used method for stretching and immobilising DNA molecules on a surface. Fluorescent labelling of genomic information enables high-resolution optical analysis of DNA at the single-molecule level. Despite its simplicity, the application of DNA combing in diagnostic workflows is still limited, mainly due to difficulties in analysing multiple small-volume DNA samples in parallel. Here, we report a simple and versatile microfluidic DNA combing technology (μDC), which allows manipulating, stretching and imaging of multiple, microliter scale DNA samples by employing a manifold of parallel microfluidic channels. Using DNA molecules with repetitive units as molecular rulers, we demonstrate that the μDC technology allows uniform stretching of DNA molecules. The stretching ratio remains consistent along individual molecules as well as between different molecules in the various channels, allowing simultaneous quantitative analysis of different samples loaded into parallel channels. Furthermore, we demonstrate the application of μDC to characterise UVB-induced DNA damage levels in human embryonic kidney cells and the spatial correlation between DNA damage sites. Our results point out the potential application of μDC for quantitative and comparative single-molecule studies of genomic features. The extremely simple design of μDC makes it suitable for integration into other microfluidic platforms to facilitate high-throughput DNA analysis in biological research and medical point-of-care applications.
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Affiliation(s)
- Shuyi Wu
- Center for Nano and Micro Mechanics, School of Aerospace Engineering, Tsinghua University, Beijing, People's Republic of China
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18
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Öz R, Kk S, Westerlund F. A nanofluidic device for real-time visualization of DNA-protein interactions on the single DNA molecule level. NANOSCALE 2019; 11:2071-2078. [PMID: 30644945 DOI: 10.1039/c8nr09023h] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Single DNA molecule techniques have revolutionized our understanding of DNA-protein interactions. Traditional techniques for such studies have the major drawback that the DNA molecule studied is attached to a bead or a surface. Stretching of DNA molecules in nanofluidic channels has enabled single-molecule studies of DNA-protein interactions without the need of tethering the molecule to a foreign entity. This in turn allows for studying reactions along the whole extension of the molecule, including the free DNA ends. However, existing studies either rely on measurements where all components are mixed before introduction into the nanochannels or where passive diffusion brings the reagents to the confined DNA molecule. We here present a new generation of nanofluidic devices, where active exchange of the local environment within the nanofluidic channel is possible, while keeping the DNA molecule stretched and in confinement. To demonstrate the functionality of this novel device we added different analytes, such as SDS, spermidine and DNase I, to YOYO-1 stained DNA and studied the response in real time. We also performed a FRET-based reaction, where two different analytes were added sequentially to the same DNA molecule. We believe that this design will enable in situ mapping of complex biochemical processes, involving multiple proteins and cofactors, on single DNA molecules as well as other biomacromolecules.
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Affiliation(s)
- Robin Öz
- Department of Biology and Biological Engineering, Chalmers University of Technology, Gothenburg, Sweden.
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19
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Jiang K, Rocha S, Westling A, Kesarimangalam S, Dorfman KD, Wittung-Stafshede P, Westerlund F. Alpha-Synuclein Modulates the Physical Properties of DNA. Chemistry 2018; 24:15685-15690. [PMID: 30102440 PMCID: PMC6217799 DOI: 10.1002/chem.201803933] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2018] [Indexed: 11/06/2022]
Abstract
Fundamental research on Parkinson's disease (PD) most often focuses on the ability of α-synuclein (aS) to form oligomers and amyloids, and how such species promote brain cell death. However, there are indications that aS also plays a gene-regulatory role in the cell nucleus. Here, the interaction between monomeric aS and DNA in vitro has been investigated with single-molecule techniques. Using a nanofluidic channel system, it was discovered that aS binds to DNA and by studying the DNA-protein complexes at different confinements we determined that aS binding increases the persistence length of DNA from 70 to 90 nm at high coverage. By atomic force microscopy it was revealed that at low protein-to-DNA ratio, the aS binding occurs as small protein clusters scattered along the DNA; at high protein-to-DNA ratio, the DNA is fully covered by protein. As DNA-aS interactions may play roles in PD, it is of importance to characterize biophysical properties of such complexes in detail.
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Affiliation(s)
- Kai Jiang
- Department of Biology and Biological Engineering, Chalmers University of Technology, Gothenburg, Sweden
| | - Sandra Rocha
- Department of Biology and Biological Engineering, Chalmers University of Technology, Gothenburg, Sweden
| | - Alvina Westling
- Department of Biology and Biological Engineering, Chalmers University of Technology, Gothenburg, Sweden
| | - Sriram Kesarimangalam
- Department of Biology and Biological Engineering, Chalmers University of Technology, Gothenburg, Sweden
| | - Kevin D Dorfman
- Department of Chemical Engineering and Materials Science, University of Minnesota-Twin Cities, Minneapolis, Minnesota, USA
| | | | - Fredrik Westerlund
- Department of Biology and Biological Engineering, Chalmers University of Technology, Gothenburg, Sweden
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20
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Abstract
Long-read genomic applications, such as genome mapping in nanochannels, require long DNA that is free of small-DNA impurities. We have developed a chip-based system based on entropic trapping that can simultaneously concentrate and purify a long DNA sample under the alternating application of an applied pressure (for sample injection) and an electric field (for filtration and concentration). In contrast, short DNA tends to pass through the filter owing to its comparatively weak entropic penalty for entering the nanoslit. The single-stage prototype developed here, which operates in a continuous pulsatile manner, achieves selectivities of up to 3.5 for λ-phage DNA (48.5 kilobase pairs) compared to a 2 kilobase pair standard based on experimental data for the fraction filtered using pure samples of each species. The device is fabricated in fused silica using standard clean-room methods, making it compatible for integration with long-read genomics technologies.
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Affiliation(s)
- Pranav Agrawal
- Department of Chemical Engineering and Materials Science, University of Minnesota - Twin Cities, 421 Washington Ave. SE, Minneapolis, MN 55455, USA.
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21
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Gupta D, Bhandari AB, Dorfman KD. Evaluation of Blob Theory for the Diffusion of DNA in Nanochannels. Macromolecules 2018; 51:1748-1755. [PMID: 29599567 DOI: 10.1021/acs.macromol.7b02270] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
We have measured the diffusivity of λ-DNA molecules in approximately square nanochannels with effective sizes ranging from 117 nm to 260 nm at moderate ionic strength. The experimental results do not agree with the non-draining scaling predicted by blob theory. Rather, the data are consistent with the predictions of previous simulations of the Kirkwood diffusivity of a discrete wormlike chain model, without the need for any fitting parameters.
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Affiliation(s)
- Damini Gupta
- Department of Chemical Engineering and Materials Science, University of Minnesota - Twin Cities, 421 Washington Ave SE, Minneapolis, Minnesota 55455, 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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22
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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 both 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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23
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Vasilev AA, Kandinska MI, Stoyanov SS, Yordanova SB, Sucunza D, Vaquero JJ, Castaño OD, Baluschev S, Angelova SE. Halogen-containing thiazole orange analogues - new fluorogenic DNA stains. Beilstein J Org Chem 2017; 13:2902-2914. [PMID: 29564018 PMCID: PMC5753173 DOI: 10.3762/bjoc.13.283] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2017] [Accepted: 12/15/2017] [Indexed: 12/20/2022] Open
Abstract
Novel asymmetric monomeric monomethine cyanine dyes 5a–d, which are analogues of the commercial dsDNA fluorescence binder thiazole orange (TO), have been synthesized. The synthesis was achieved by using a simple, efficient and environmetally benign synthetic procedure to obtain these cationic dyes in good to excellent yields. Interactions of the new derivatives of TO with dsDNA have been investigated by absorption and fluorescence spectroscopy. The longest wavelength absorption bands in the UV–vis spectra of the target compounds are in the range of 509–519 nm and these are characterized by high molar absorptivities (63000–91480 L·mol−1·cm−1). All investigated dyes from the series are either not fluorescent or their fluorescence is quite low, but they become strongly fluorescent after binding to dsDNA. The influence of the substituents attached to the chromophores was investigated by combination of spectroscopic (UV–vis and fluorescence spectroscopy) and theoretical (DFT and TDDFT calculations) methods.
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Affiliation(s)
- Aleksey A Vasilev
- Department of Pharmaceutical and Applied Organic Chemistry, Faculty of Chemistry and Pharmacy, Sofia University "St. Kliment Ohridski", 1 James Bourchier Blvd., 1164 Sofia, Bulgaria
| | - Meglena I Kandinska
- Department of Organic Chemistry and Pharmacognosy, Faculty of Chemistry and Pharmacy, Sofia University "St. Kliment Ohridski", 1 James Bourchier Blvd., 1164 Sofia, Bulgaria
| | - Stanimir S Stoyanov
- Department of Organic Chemistry and Pharmacognosy, Faculty of Chemistry and Pharmacy, Sofia University "St. Kliment Ohridski", 1 James Bourchier Blvd., 1164 Sofia, Bulgaria
| | - Stanislava B Yordanova
- Department of Organic Chemistry and Pharmacognosy, Faculty of Chemistry and Pharmacy, Sofia University "St. Kliment Ohridski", 1 James Bourchier Blvd., 1164 Sofia, Bulgaria
| | - David Sucunza
- Departments of Organic and Physical Chemistry, University of Alcala, 28871-Alcala de Henares, Madrid, Spain
| | - Juan J Vaquero
- Departments of Organic and Physical Chemistry, University of Alcala, 28871-Alcala de Henares, Madrid, Spain
| | - Obis D Castaño
- Departments of Organic and Physical Chemistry, University of Alcala, 28871-Alcala de Henares, Madrid, Spain
| | - Stanislav Baluschev
- Max Planck Institute for Polymer Research, Ackermannweg 10, 55128 Mainz, Germany
| | - Silvia E Angelova
- Departments of Organic and Physical Chemistry, University of Alcala, 28871-Alcala de Henares, Madrid, Spain.,Institute of Organic Chemistry with Centre of Phytochemisty, Bulgarian Academy of Sciences, 1113 Sofia, Bulgaria (permanent address)
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24
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Imamura R, Murata N, Shimanouchi T, Yamashita K, Fukuzawa M, Noda M. A Label-Free Fluorescent Array Sensor Utilizing Liposome Encapsulating Calcein for Discriminating Target Proteins by Principal Component Analysis. SENSORS (BASEL, SWITZERLAND) 2017; 17:E1630. [PMID: 28714873 PMCID: PMC5539792 DOI: 10.3390/s17071630] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/16/2017] [Revised: 07/05/2017] [Accepted: 07/13/2017] [Indexed: 01/10/2023]
Abstract
A new fluorescent arrayed biosensor has been developed to discriminate species and concentrations of target proteins by using plural different phospholipid liposome species encapsulating fluorescent molecules, utilizing differences in permeation of the fluorescent molecules through the membrane to modulate liposome-target protein interactions. This approach proposes a basically new label-free fluorescent sensor, compared with the common technique of developed fluorescent array sensors with labeling. We have confirmed a high output intensity of fluorescence emission related to characteristics of the fluorescent molecules dependent on their concentrations when they leak from inside the liposomes through the perturbed lipid membrane. After taking an array image of the fluorescence emission from the sensor using a CMOS imager, the output intensities of the fluorescence were analyzed by a principal component analysis (PCA) statistical method. It is found from PCA plots that different protein species with several concentrations were successfully discriminated by using the different lipid membranes with high cumulative contribution ratio. We also confirmed that the accuracy of the discrimination by the array sensor with a single shot is higher than that of a single sensor with multiple shots.
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Affiliation(s)
- Ryota Imamura
- Graduate School of Science and Technology, Kyoto Institute of Technology, Matsugasaki, Sakyo-ku, Kyoto 606-8585, Japan.
| | - Naoki Murata
- Graduate School of Science and Technology, Kyoto Institute of Technology, Matsugasaki, Sakyo-ku, Kyoto 606-8585, Japan.
| | - Toshinori Shimanouchi
- Graduate School of Environmental and Life Science, Okayama University, 1-1-1 Tsushima-naka, Kita-ku, Okayama 700-8530, Japan.
| | - Kaoru Yamashita
- Graduate School of Science and Technology, Kyoto Institute of Technology, Matsugasaki, Sakyo-ku, Kyoto 606-8585, Japan.
| | - Masayuki Fukuzawa
- Graduate School of Science and Technology, Kyoto Institute of Technology, Matsugasaki, Sakyo-ku, Kyoto 606-8585, Japan.
| | - Minoru Noda
- Graduate School of Science and Technology, Kyoto Institute of Technology, Matsugasaki, Sakyo-ku, Kyoto 606-8585, Japan.
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25
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Cheong GK, Li X, Dorfman KD. Wall depletion length of a channel-confined polymer. Phys Rev E 2017; 95:022501. [PMID: 28297899 DOI: 10.1103/physreve.95.022501] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2016] [Indexed: 11/07/2022]
Abstract
Numerous experiments have taken advantage of DNA as a model system to test theories for a channel-confined polymer. A tacit assumption in analyzing these data is the existence of a well-defined depletion length characterizing DNA-wall interactions such that the experimental system (a polyelectrolyte in a channel with charged walls) can be mapped to the theoretical model (a neutral polymer with hard walls). We test this assumption using pruned-enriched Rosenbluth method (PERM) simulations of a DNA-like semiflexible polymer confined in a tube. The polymer-wall interactions are modeled by augmenting a hard wall interaction with an exponentially decaying, repulsive soft potential. The free energy, mean span, and variance in the mean span obtained in the presence of a soft wall potential are compared to equivalent simulations in the absence of the soft wall potential to determine the depletion length. We find that the mean span and variance about the mean span have the same depletion length for all soft potentials we tested. In contrast, the depletion length for the confinement free energy approaches that for the mean span only when depletion length no longer depends on channel size. The results have implications for the interpretation of DNA confinement experiments under low ionic strengths.
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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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26
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Jeffet J, Kobo A, Su T, Grunwald A, Green O, Nilsson AN, Eisenberg E, Ambjörnsson T, Westerlund F, Weinhold E, Shabat D, Purohit PK, Ebenstein Y. Super-Resolution Genome Mapping in Silicon Nanochannels. ACS NANO 2016; 10:9823-9830. [PMID: 27646634 DOI: 10.1021/acsnano.6b05398] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/21/2023]
Abstract
Optical genome mapping in nanochannels is a powerful genetic analysis method, complementary to deoxyribonucleic acid (DNA) sequencing. The method is based on detecting a pattern of fluorescent labels attached along individual DNA molecules. When such molecules are extended in nanochannels, the labels create a fluorescent genetic barcode that is used for mapping the DNA molecule to its genomic locus and identifying large-scale variation from the genome reference. Mapping resolution is currently limited by two main factors: the optical diffraction limit and the thermal fluctuations of DNA molecules suspended in the nanochannels. Here, we utilize single-molecule tracking and super-resolution localization in order to improve the mapping accuracy and resolving power of this genome mapping technique and achieve a 15-fold increase in resolving power compared to currently practiced methods. We took advantage of a naturally occurring genetic repeat array and labeled each repeat with custom-designed Trolox conjugated fluorophores for enhanced photostability. This model system allowed us to acquire extremely long image sequences of the equally spaced fluorescent markers along DNA molecules, enabling detailed characterization of nanoconfined DNA dynamics and quantitative comparison to the Odijk theory for confined polymer chains. We present a simple method to overcome the thermal fluctuations in the nanochannels and exploit single-step photobleaching to resolve subdiffraction spaced fluorescent markers along fluctuating DNA molecules with ∼100 bp resolution. In addition, we show how time-averaging over just ∼50 frames of 40 ms enhances mapping accuracy, improves mapping P-value scores by 3 orders of magnitude compared to nonaveraged alignment, and provides a significant advantage for analyzing structural variations between DNA molecules with similar sequence composition.
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Affiliation(s)
- Jonathan Jeffet
- Raymond and Beverly Sackler Faculty of Exact Sciences, Tel Aviv University , Tel Aviv 6997801, Israel
| | - Asaf Kobo
- Raymond and Beverly Sackler Faculty of Exact Sciences, Tel Aviv University , Tel Aviv 6997801, Israel
| | - Tianxiang Su
- School of Engineering and Applied Sciences, Harvard University , Cambridge, Massachusetts 02138, United States
| | - Assaf Grunwald
- Raymond and Beverly Sackler Faculty of Exact Sciences, Tel Aviv University , Tel Aviv 6997801, Israel
| | - Ori Green
- Raymond and Beverly Sackler Faculty of Exact Sciences, Tel Aviv University , Tel Aviv 6997801, Israel
| | - Adam N Nilsson
- Department of Astronomy and Theoretical Physics, Lund University , SE-221 00 Lund, Sweden
| | - Eli Eisenberg
- Raymond and Beverly Sackler Faculty of Exact Sciences, Tel Aviv University , Tel Aviv 6997801, Israel
| | - Tobias Ambjörnsson
- Department of Astronomy and Theoretical Physics, Lund University , SE-221 00 Lund, Sweden
| | - Fredrik Westerlund
- Department of Biology and Biological Engineering, Chalmers University of Technology , SE-412 96 Gothenburg, Sweden
| | - Elmar Weinhold
- Institute of Organic Chemistry, RWTH Aachen University , Aachen D-52056, Germany
| | - Doron Shabat
- Raymond and Beverly Sackler Faculty of Exact Sciences, Tel Aviv University , Tel Aviv 6997801, Israel
| | - Prashant K Purohit
- Department of Mechanical Engineering and Applied Mechanics, University of Pennsylvania , Philadelphia, Pennsylvania 19104, United States
| | - Yuval Ebenstein
- Raymond and Beverly Sackler Faculty of Exact Sciences, Tel Aviv University , Tel Aviv 6997801, Israel
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27
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Rapid identification of intact bacterial resistance plasmids via optical mapping of single DNA molecules. Sci Rep 2016; 6:30410. [PMID: 27460437 PMCID: PMC4961956 DOI: 10.1038/srep30410] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2015] [Accepted: 07/05/2016] [Indexed: 11/08/2022] Open
Abstract
The rapid spread of antibiotic resistance – currently one of the greatest threats to human health according to WHO – is to a large extent enabled by plasmid-mediated horizontal transfer of resistance genes. Rapid identification and characterization of plasmids is thus important both for individual clinical outcomes and for epidemiological monitoring of antibiotic resistance. Toward this aim, we have developed an optical DNA mapping procedure where individual intact plasmids are elongated within nanofluidic channels and visualized through fluorescence microscopy, yielding barcodes that reflect the underlying sequence. The assay rapidly identifies plasmids through statistical comparisons with barcodes based on publicly available sequence repositories and also enables detection of structural variations. Since the assay yields holistic sequence information for individual intact plasmids, it is an ideal complement to next generation sequencing efforts which involve reassembly of sequence reads from fragmented DNA molecules. The assay should be applicable in microbiology labs around the world in applications ranging from fundamental plasmid biology to clinical epidemiology and diagnostics.
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Frykholm K, Berntsson RPA, Claesson M, de Battice L, Odegrip R, Stenmark P, Westerlund F. DNA compaction by the bacteriophage protein Cox studied on the single DNA molecule level using nanofluidic channels. Nucleic Acids Res 2016; 44:7219-27. [PMID: 27131370 PMCID: PMC5009727 DOI: 10.1093/nar/gkw352] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2015] [Accepted: 03/30/2016] [Indexed: 01/10/2023] Open
Abstract
The Cox protein from bacteriophage P2 forms oligomeric filaments and it has been proposed that DNA can be wound up around these filaments, similar to how histones condense DNA. We here use fluorescence microscopy to study single DNA–Cox complexes in nanofluidic channels and compare how the Cox homologs from phages P2 and WΦ affect DNA. By measuring the extension of nanoconfined DNA in absence and presence of Cox we show that the protein compacts DNA and that the binding is highly cooperative, in agreement with the model of a Cox filament around which DNA is wrapped. Furthermore, comparing microscopy images for the wild-type P2 Cox protein and two mutants allows us to discriminate between compaction due to filament formation and compaction by monomeric Cox. P2 and WΦ Cox have similar effects on the physical properties of DNA and the subtle, but significant, differences in DNA binding are due to differences in binding affinity rather than binding mode. The presented work highlights the use of single DNA molecule studies to confirm structural predictions from X-ray crystallography. It also shows how a small protein by oligomerization can have great impact on the organization of DNA and thereby fulfill multiple regulatory functions.
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Affiliation(s)
- Karolin Frykholm
- Department of Biology and Biological Engineering, Chalmers University of Technology, SE-41296 Gothenburg, Sweden
| | - Ronnie Per-Arne Berntsson
- Department of Biochemistry and Biophysics, Arrhenius Laboratories for Natural Sciences, Stockholm University, SE-10691 Stockholm, Sweden
| | - Magnus Claesson
- Department of Biochemistry and Biophysics, Arrhenius Laboratories for Natural Sciences, Stockholm University, SE-10691 Stockholm, Sweden
| | - Laura de Battice
- Department of Chemistry and Chemical Engineering, Chalmers University of Technology, SE-41296 Gothenburg, Sweden
| | - Richard Odegrip
- Department of Molecular Biosciences, The Wenner-Gren Institute, Arrhenius Laboratories for Natural Sciences, Stockholm University, SE-10691 Stockholm, Sweden
| | - Pål Stenmark
- Department of Biochemistry and Biophysics, Arrhenius Laboratories for Natural Sciences, Stockholm University, SE-10691 Stockholm, Sweden
| | - Fredrik Westerlund
- Department of Biology and Biological Engineering, Chalmers University of Technology, SE-41296 Gothenburg, Sweden
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29
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Rapid visual identification of PCR amplified nucleic acids by centrifugal gel separation: Potential use for molecular point-of-care tests. Biosens Bioelectron 2016; 79:829-34. [PMID: 26774997 DOI: 10.1016/j.bios.2016.01.006] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2015] [Revised: 12/31/2015] [Accepted: 01/04/2016] [Indexed: 11/21/2022]
Abstract
Recently, nucleic acid amplification and detection techniques have progressed based on advances in in microfluidics, microelectronics, and optical systems. Nucleic acids amplification based point-of-care test (POCT) in resource-limited settings requires simple visual detection methods. Several biosensing methods including lateral flow immunoassays (LFIA) were previously used to visually detect nucleic acids. However, prolonged assay time, several washing steps, and a need for specific antibodies limited their use. Here we developed a novel, rapid method to visualize amplified nucleic acids with naked eyes in clinical samples. First, we optimized conditions based on separation using very low centrifugal force and a density medium to detect human papillomavirus (HPV)-16 DNA in cervical specimens. After DNA extraction, HPV16 PCR was performed with biotin-labeled forward primer and Cy3-labeled reverse primer. PCR amplicon was mixed with streptavidin-magnetic beads, introduced into the density medium. After two-minute centrifugation, the result was visually identified. This system showed identical results with commercial HPV real-time PCR for 30 clinical samples and could detect up to 10(2)copies/mL of HPV DNA without any optical instruments. This robust and sensitive visual detection system is suitable for non-specialist personnel and point-of-care diagnosis in low-resource settings.
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30
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Smithe TSC, Iarko V, Muralidhar A, Werner E, Dorfman KD, Mehlig B. Finite-size corrections for confined polymers in the extended de Gennes regime. PHYSICAL REVIEW. E, STATISTICAL, NONLINEAR, AND SOFT MATTER PHYSICS 2015; 92:062601. [PMID: 26764718 PMCID: PMC4714778 DOI: 10.1103/physreve.92.062601] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/12/2015] [Indexed: 06/01/2023]
Abstract
Theoretical results for the extension of a polymer confined to a channel are usually derived in the limit of infinite contour length. But experimental studies and simulations of DNA molecules confined to nanochannels are not necessarily in this asymptotic limit. We calculate the statistics of the span and the end-to-end distance of a semiflexible polymer of finite length in the extended de Gennes regime, exploiting the fact that the problem can be mapped to a one-dimensional weakly self-avoiding random walk. The results thus obtained compare favorably with pruned-enriched Rosenbluth method (PERM) simulations of a three-dimensional discrete wormlike chain model of DNA confined in a nanochannel. We discuss the implications for experimental studies of linear λ-DNA confined to nanochannels at the high ionic strengths used in many experiments.
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Affiliation(s)
- T. St Clere Smithe
- Department of Physics, University of Gothenburg, Origovägen 6B, 412 96 Göteborg, Sweden
| | - V. Iarko
- Department of Physics, University of Gothenburg, Origovägen 6B, 412 96 Göteborg, Sweden
| | - A. Muralidhar
- Department of Chemical Engineering and Materials Science, University of Minnesota – Twin Cities, 421 Washington Avenue SE, Minneapolis, Minnesota 55455, USA
| | - E. Werner
- Department of Physics, University of Gothenburg, Origovägen 6B, 412 96 Göteborg, Sweden
| | - K. D. Dorfman
- Department of Chemical Engineering and Materials Science, University of Minnesota – Twin Cities, 421 Washington Avenue SE, Minneapolis, Minnesota 55455, USA
| | - B. Mehlig
- Department of Physics, University of Gothenburg, Origovägen 6B, 412 96 Göteborg, Sweden
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31
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Iarko V, Werner E, Nyberg LK, Müller V, Fritzsche J, Ambjörnsson T, Beech JP, Tegenfeldt JO, Mehlig K, Westerlund F, Mehlig B. Extension of nanoconfined DNA: Quantitative comparison between experiment and theory. PHYSICAL REVIEW. E, STATISTICAL, NONLINEAR, AND SOFT MATTER PHYSICS 2015; 92:062701. [PMID: 26764721 DOI: 10.1103/physreve.92.062701] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/05/2015] [Indexed: 05/27/2023]
Abstract
The extension of DNA confined to nanochannels has been studied intensively and in detail. However, quantitative comparisons between experiments and model calculations are difficult because most theoretical predictions involve undetermined prefactors, and because the model parameters (contour length, Kuhn length, effective width) are difficult to compute reliably, leading to substantial uncertainties. Here we use a recent asymptotically exact theory for the DNA extension in the "extended de Gennes regime" that allows us to compare experimental results with theory. For this purpose, we performed experiments measuring the mean DNA extension and its standard deviation while varying the channel geometry, dye intercalation ratio, and ionic strength of the buffer. The experimental results agree very well with theory at high ionic strengths, indicating that the model parameters are reliable. At low ionic strengths, the agreement is less good. We discuss possible reasons. In principle, our approach allows us to measure the Kuhn length and the effective width of a single DNA molecule and more generally of semiflexible polymers in solution.
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Affiliation(s)
- V Iarko
- Department of Physics, University of Gothenburg, 412 96 Göteborg, Sweden
| | - E Werner
- Department of Physics, University of Gothenburg, 412 96 Göteborg, Sweden
| | - L K Nyberg
- Department of Biology and Biological Engineering, Chalmers University of Technology, 412 96 Göteborg, Sweden
| | - V Müller
- Department of Biology and Biological Engineering, Chalmers University of Technology, 412 96 Göteborg, Sweden
| | - J Fritzsche
- Department of Applied Physics, Chalmers University of Technology, 412 96 Göteborg, Sweden
| | - T Ambjörnsson
- Department of Astronomy and Theoretical Physics, Lund University, 22 100 Lund, Sweden
| | - J P Beech
- Department of Physics, Division of Solid State Physics, Lund University, 22 100 Lund, Sweden
| | - J O Tegenfeldt
- Department of Physics, Division of Solid State Physics, Lund University, 22 100 Lund, Sweden
- NanoLund, Lund University, 22 100 Lund, Sweden
| | - K Mehlig
- Department of Public Health and Community Medicine, University of Gothenburg, 413 46 Göteborg, Sweden
| | - F Westerlund
- Department of Biology and Biological Engineering, Chalmers University of Technology, 412 96 Göteborg, Sweden
| | - B Mehlig
- Department of Physics, University of Gothenburg, 412 96 Göteborg, Sweden
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32
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Reifenberger JG, Dorfman KD, Cao H. Topological events in single molecules of E. coli DNA confined in nanochannels. Analyst 2015; 140:4887-94. [PMID: 25991508 PMCID: PMC4486629 DOI: 10.1039/c5an00343a] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
We present experimental data concerning potential topological events such as folds, internal backfolds, and/or knots within long molecules of double-stranded DNA when they are stretched by confinement in a nanochannel. Genomic DNA from E. coli was labeled near the 'GCTCTTC' sequence with a fluorescently labeled dUTP analog and stained with the DNA intercalator YOYO. Individual long molecules of DNA were then linearized and imaged using methods based on the NanoChannel Array technology (Irys® System) available from BioNano Genomics. Data were collected on 189 153 molecules of length greater than 50 kilobases. A custom code was developed to search for abnormal intensity spikes in the YOYO backbone profile along the length of individual molecules. By correlating the YOYO intensity spikes with the aligned barcode pattern to the reference, we were able to correlate the bright intensity regions of YOYO with abnormal stretching in the molecule, which suggests these events were either a knot or a region of internal backfolding within the DNA. We interpret the results of our experiments involving molecules exceeding 50 kilobases in the context of existing simulation data for relatively short DNA, typically several kilobases. The frequency of these events is lower than the predictions from simulations, while the size of the events is larger than simulation predictions and often exceeds the molecular weight of the simulated molecules. We also identified DNA molecules that exhibit large, single folds as they enter the nanochannels. Overall, topological events occur at a low frequency (∼7% of all molecules) and pose an easily surmountable obstacle for the practice of genome mapping in nanochannels.
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33
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Frykholm K, Nyberg LK, Lagerstedt E, Noble C, Fritzsche J, Karami N, Ambjörnsson T, Sandegren L, Westerlund F. Fast size-determination of intact bacterial plasmids using nanofluidic channels. LAB ON A CHIP 2015; 15:2739-2743. [PMID: 25997119 DOI: 10.1039/c5lc00378d] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
We demonstrate how nanofluidic channels can be used as a tool to rapidly determine the number and sizes of plasmids in bacterial isolates. Each step can be automated at low cost, opening up opportunities for general use in microbiology labs.
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Affiliation(s)
- K Frykholm
- Department of Biology and Biological Engineering, Chalmers University of Technology, SE-412 96, Gothenburg, Sweden.
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34
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Gupta D, Miller JJ, Muralidhar A, Mahshid S, Reisner W, Dorfman KD. Experimental evidence of weak excluded volume effects for nanochannel confined DNA. ACS Macro Lett 2015; 4:759-763. [PMID: 26664782 PMCID: PMC4671635 DOI: 10.1021/acsmacrolett.5b00340] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
We present experimental demonstration that weak excluded volume effects arise in DNA nanochannel confinement. In particular, by performing measurements of the variance in chain extension as a function of nanochannel dimension for effective channel size ranging from 305 nm to 453 nm, we show that the scaling of the variance in extension with channel size rejects the de Gennes scaling δ2X ~ D1/3 in favor of δ2X ~ D0 using uncertainty at the 95% confidence level. We also show how simulations and confinement spectroscopy can be combined to reduce molecular weight dispersity effects arising from shearing, photocleavage, and nonuniform staining of DNA.
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Affiliation(s)
- Damini Gupta
- Department of Chemical Engineering and Materials Science, University of Minnesota – Twin Cities, 421 Washington Ave SE, Minneapolis, Minnesota 55455, USA
| | - Jeremy J. Miller
- Department of Chemical Engineering and Materials Science, University of Minnesota – Twin Cities, 421 Washington Ave SE, Minneapolis, Minnesota 55455, USA
| | - Abhiram Muralidhar
- Department of Chemical Engineering and Materials Science, University of Minnesota – Twin Cities, 421 Washington Ave SE, Minneapolis, Minnesota 55455, USA
| | - Sara Mahshid
- Physics Department, McGill University, 3600 rue University, Montreal QC H3A 2T8, Canada
| | - Walter Reisner
- Physics Department, McGill University, 3600 rue University, Montreal QC H3A 2T8, Canada
| | - 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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35
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Biebricher AS, Heller I, Roijmans RFH, Hoekstra TP, Peterman EJG, Wuite GJL. The impact of DNA intercalators on DNA and DNA-processing enzymes elucidated through force-dependent binding kinetics. Nat Commun 2015; 6:7304. [PMID: 26084388 PMCID: PMC4557362 DOI: 10.1038/ncomms8304] [Citation(s) in RCA: 124] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2014] [Accepted: 04/27/2015] [Indexed: 11/09/2022] Open
Abstract
DNA intercalators are widely used as fluorescent probes to visualize DNA and DNA transactions in vivo and in vitro. It is well known that they perturb DNA structure and stability, which can in turn influence DNA-processing by proteins. Here we elucidate this perturbation by combining single-dye fluorescence microscopy with force spectroscopy and measuring the kinetics of DNA intercalation by the mono- and bis-intercalating cyanine dyes SYTOX Orange, SYTOX Green, SYBR Gold, YO-PRO-1, YOYO-1 and POPO-3. We show that their DNA-binding affinity is mainly governed by a strongly tension-dependent dissociation rate. These rates can be tuned over a range of seven orders of magnitude by changing DNA tension, intercalating species and ionic strength. We show that optimizing these rates minimizes the impact of intercalators on strand separation and enzymatic activity. These new insights provide handles for the improved use of intercalators as DNA probes with minimal perturbation and maximal efficacy. DNA intercalators, a type of fluorescent probes widely used to visualize DNA, can perturb DNA structure and stability. Here, the authors show how DNA-binding affinity can be tuned using DNA tension, ionic strength and dye species, and how this can be used to minimize DNA structural perturbations.
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Affiliation(s)
- Andreas S Biebricher
- Department of Physics and Astronomy, LaserLaB Amsterdam, VU University Amsterdam, De Boelelaan 1081, Amsterdam 1081HV, The Netherlands
| | - Iddo Heller
- Department of Physics and Astronomy, LaserLaB Amsterdam, VU University Amsterdam, De Boelelaan 1081, Amsterdam 1081HV, The Netherlands
| | - Roel F H Roijmans
- Department of Physics and Astronomy, LaserLaB Amsterdam, VU University Amsterdam, De Boelelaan 1081, Amsterdam 1081HV, The Netherlands
| | - Tjalle P Hoekstra
- Department of Physics and Astronomy, LaserLaB Amsterdam, VU University Amsterdam, De Boelelaan 1081, Amsterdam 1081HV, The Netherlands
| | - Erwin J G Peterman
- Department of Physics and Astronomy, LaserLaB Amsterdam, VU University Amsterdam, De Boelelaan 1081, Amsterdam 1081HV, The Netherlands
| | - Gijs J L Wuite
- Department of Physics and Astronomy, LaserLaB Amsterdam, VU University Amsterdam, De Boelelaan 1081, Amsterdam 1081HV, The Netherlands
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36
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Japaridze A, Benke A, Renevey S, Benadiba C, Dietler G. Influence of DNA Binding Dyes on Bare DNA Structure Studied with Atomic Force Microscopy. Macromolecules 2015. [DOI: 10.1021/ma502537g] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Aleksandre Japaridze
- Laboratory of Physics of Living Matter and ‡Laboratory of Experimental Biophysics, EPFL, 1015 Lausanne, Switzerland
| | - Alexander Benke
- Laboratory of Physics of Living Matter and ‡Laboratory of Experimental Biophysics, EPFL, 1015 Lausanne, Switzerland
| | - Sylvain Renevey
- Laboratory of Physics of Living Matter and ‡Laboratory of Experimental Biophysics, EPFL, 1015 Lausanne, Switzerland
| | - Carine Benadiba
- Laboratory of Physics of Living Matter and ‡Laboratory of Experimental Biophysics, EPFL, 1015 Lausanne, Switzerland
| | - Giovanni Dietler
- Laboratory of Physics of Living Matter and ‡Laboratory of Experimental Biophysics, EPFL, 1015 Lausanne, Switzerland
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37
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Reinhart WF, Reifenberger JG, Gupta D, Muralidhar A, Sheats J, Cao H, Dorfman KD. Distribution of distances between DNA barcode labels in nanochannels close to the persistence length. J Chem Phys 2015; 142:064902. [PMID: 25681938 PMCID: PMC4327924 DOI: 10.1063/1.4907552] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2014] [Accepted: 01/25/2015] [Indexed: 11/14/2022] Open
Abstract
We obtained experimental extension data for barcoded E. coli genomic DNA molecules confined in nanochannels from 40 nm to 51 nm in width. The resulting data set consists of 1 627 779 measurements of the distance between fluorescent probes on 25 407 individual molecules. The probability density for the extension between labels is negatively skewed, and the magnitude of the skewness is relatively insensitive to the distance between labels. The two Odijk theories for DNA confinement bracket the mean extension and its variance, consistent with the scaling arguments underlying the theories. We also find that a harmonic approximation to the free energy, obtained directly from the probability density for the distance between barcode labels, leads to substantial quantitative error in the variance of the extension data. These results suggest that a theory for DNA confinement in such channels must account for the anharmonic nature of the free energy as a function of chain extension.
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Affiliation(s)
- Wesley F Reinhart
- Department of Chemical Engineering and Materials Science, University of Minnesota-Twin Cities, 421 Washington Ave SE, Minneapolis, Minnesota 55455, USA
| | - Jeff G Reifenberger
- BioNano Genomics, 9640 Towne Centre Dr., Ste. 100, San Diego, California 92121, USA
| | - Damini Gupta
- Department of Chemical Engineering and Materials Science, University of Minnesota-Twin Cities, 421 Washington Ave SE, Minneapolis, Minnesota 55455, USA
| | - Abhiram Muralidhar
- Department of Chemical Engineering and Materials Science, University of Minnesota-Twin Cities, 421 Washington Ave SE, Minneapolis, Minnesota 55455, USA
| | - Julian Sheats
- Department of Chemical Engineering and Materials Science, University of Minnesota-Twin Cities, 421 Washington Ave SE, Minneapolis, Minnesota 55455, USA
| | - Han Cao
- BioNano Genomics, 9640 Towne Centre Dr., Ste. 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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38
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Alizadehheidari M, Werner E, Noble C, Reiter-Schad M, Nyberg LK, Fritzsche J, Mehlig B, Tegenfeldt JO, Ambjörnsson T, Persson F, Westerlund F. Nanoconfined Circular and Linear DNA: Equilibrium Conformations and Unfolding Kinetics. Macromolecules 2015. [DOI: 10.1021/ma5022067] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Affiliation(s)
| | - Erik Werner
- Department
of Physics, Gothenburg University, Gothenburg, Sweden
| | | | | | | | | | - Bernhard Mehlig
- Department
of Physics, Gothenburg University, Gothenburg, Sweden
| | | | | | - Fredrik Persson
- Department of Cell and
Molecular Biology, Uppsala University, Uppsala, Sweden
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39
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Dorfman KD, Gupta D, Jain A, Muralidhar A, Tree DR. Hydrodynamics of DNA confined in nanoslits and nanochannels. THE EUROPEAN PHYSICAL JOURNAL. SPECIAL TOPICS 2014; 223:3179-3200. [PMID: 25566349 PMCID: PMC4282777 DOI: 10.1140/epjst/e2014-02326-4] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/01/2023]
Abstract
Modeling the dynamics of a confined, semi exible polymer is a challenging problem, owing to the complicated interplay between the configurations of the chain, which are strongly affected by the length scale for the confinement relative to the persistence length of the chain, and the polymer-wall hydrodynamic interactions. At the same time, understanding these dynamics are crucial to the advancement of emerging genomic technologies that use confinement to stretch out DNA and "read" a genomic signature. In this mini-review, we begin by considering what is known experimentally and theoretically about the friction of a wormlike chain such as DNA confined in a slit or a channel. We then discuss how to estimate the friction coefficient of such a chain, either with dynamic simulations or via Monte Carlo sampling and the Kirk-wood pre-averaging approximation. We then review our recent work on computing the diffusivity of DNA in nanoslits and nanochannels, and conclude with some promising avenues for future work and caveats about our approach.
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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 USA
| | - Damini Gupta
- Department of Chemical Engineering and Materials Science, University of Minnesota – Twin Cities, 421 Washington Ave. SE, Minneapolis, MN 55455 USA
| | - Aashish Jain
- Department of Chemical Engineering and Materials Science, University of Minnesota – Twin Cities, 421 Washington Ave. SE, Minneapolis, MN 55455 USA
| | - Abhiram Muralidhar
- Department of Chemical Engineering and Materials Science, University of Minnesota – Twin Cities, 421 Washington Ave. SE, Minneapolis, MN 55455 USA
| | - Douglas R. Tree
- Department of Chemical Engineering and Materials Science, University of Minnesota – Twin Cities, 421 Washington Ave. SE, Minneapolis, MN 55455 USA
- Materials Research Laboratory, University of California – Santa Barbara, Santa Barbara, CA 93106 USA
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40
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Nilsson AN, Emilsson G, Nyberg LK, Noble C, Stadler LS, Fritzsche J, Moore ERB, Tegenfeldt JO, Ambjörnsson T, Westerlund F. Competitive binding-based optical DNA mapping for fast identification of bacteria--multi-ligand transfer matrix theory and experimental applications on Escherichia coli. Nucleic Acids Res 2014; 42:e118. [PMID: 25013180 PMCID: PMC4150756 DOI: 10.1093/nar/gku556] [Citation(s) in RCA: 54] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2014] [Revised: 05/29/2014] [Accepted: 06/10/2014] [Indexed: 11/25/2022] Open
Abstract
We demonstrate a single DNA molecule optical mapping assay able to resolve a specific Escherichia coli strain from other strains. The assay is based on competitive binding of the fluorescent dye YOYO-1 and the AT-specific antibiotic netropsin. The optical map is visualized by stretching the DNA molecules in nanofluidic channels. We optimize the experimental conditions to obtain reproducible barcodes containing as much information as possible. We implement a multi-ligand transfer matrix method for calculating theoretical barcodes from known DNA sequences. Our method extends previous theoretical approaches for competitive binding of two types of ligands to many types of ligands and introduces a recursive approach that allows long barcodes to be calculated with standard computer floating point formats. The identification of a specific E. coli strain (CCUG 10979) is based on mapping of 50-160 kilobasepair experimental DNA fragments onto the theoretical genome using the developed theory. Our identification protocol introduces two theoretical constructs: a P-value for a best experiment-theory match and an information score threshold. The developed methods provide a novel optical mapping toolbox for identification of bacterial species and strains. The protocol does not require cultivation of bacteria or DNA amplification, which allows for ultra-fast identification of bacterial pathogens.
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Affiliation(s)
- Adam N. Nilsson
- Department of Astronomy and Theoretical Physics, Lund University, Sölvegatan 14A, 223 62 Lund, Sweden
| | - Gustav Emilsson
- Division of Chemistry and Biochemistry, Department of Chemical and Biological Engineering, Chalmers University of Technology, Kemivägen 10, 412 96 Göteborg, Sweden
| | - Lena K. Nyberg
- Division of Chemistry and Biochemistry, Department of Chemical and Biological Engineering, Chalmers University of Technology, Kemivägen 10, 412 96 Göteborg, Sweden
| | - Charleston Noble
- Department of Astronomy and Theoretical Physics, Lund University, Sölvegatan 14A, 223 62 Lund, Sweden
- Department of Applied Physics, Chalmers University of Technology, Kemivägen 10, 412 96 Göteborg, Sweden
| | - Liselott Svensson Stadler
- Division of Solid State Physics, Department of Physics, Lund University, PO 118, 221 00 Lund, Sweden
| | - Joachim Fritzsche
- Department of Infectious Diseases, Sahlgrenska Academy, University of Gothenburg, Guldhedsgatan 10A, 413 46 Göteborg, Sweden
| | - Edward R. B. Moore
- Division of Solid State Physics, Department of Physics, Lund University, PO 118, 221 00 Lund, Sweden
| | - Jonas O. Tegenfeldt
- Department of Applied Physics, Chalmers University of Technology, Kemivägen 10, 412 96 Göteborg, Sweden
| | - Tobias Ambjörnsson
- Department of Astronomy and Theoretical Physics, Lund University, Sölvegatan 14A, 223 62 Lund, Sweden
| | - Fredrik Westerlund
- Division of Chemistry and Biochemistry, Department of Chemical and Biological Engineering, Chalmers University of Technology, Kemivägen 10, 412 96 Göteborg, Sweden
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41
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Gupta D, Sheats J, Muralidhar A, Miller JJ, Huang DE, Mahshid S, Dorfman KD, Reisner W. Mixed confinement regimes during equilibrium confinement spectroscopy of DNA. J Chem Phys 2014; 140:214901. [PMID: 24908035 PMCID: PMC4048444 DOI: 10.1063/1.4879515] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2014] [Accepted: 05/12/2014] [Indexed: 11/14/2022] Open
Abstract
We have used a combination of fluorescence microscopy experiments and Pruned Enriched Rosenbluth Method simulations of a discrete wormlike chain model to measure the mean extension and the variance in the mean extension of λ-DNA in 100 nm deep nanochannels with widths ranging from 100 nm to 1000 nm in discrete 100 nm steps. The mean extension is only weakly affected by the channel aspect ratio. In contrast, the fluctuations of the chain extension qualitatively differ between rectangular channels and square channels with the same cross-sectional area, owing to the "mixing" of different confinement regimes in the rectangular channels. The agreement between experiment and simulation is very good, using the extension due to intercalation as the only adjustable parameter.
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Affiliation(s)
- Damini Gupta
- Department of Chemical Engineering and Materials Science, University of Minnesota - Twin Cities, 421 Washington Ave SE, Minneapolis, Minnesota 55455, USA
| | - Julian Sheats
- Department of Chemical Engineering and Materials Science, University of Minnesota - Twin Cities, 421 Washington Ave SE, Minneapolis, Minnesota 55455, USA
| | - Abhiram Muralidhar
- Department of Chemical Engineering and Materials Science, University of Minnesota - Twin Cities, 421 Washington Ave SE, Minneapolis, Minnesota 55455, USA
| | - Jeremy J Miller
- Department of Chemical Engineering and Materials Science, University of Minnesota - Twin Cities, 421 Washington Ave SE, Minneapolis, Minnesota 55455, USA
| | - Derek E Huang
- Department of Chemical Engineering and Materials Science, University of Minnesota - Twin Cities, 421 Washington Ave SE, Minneapolis, Minnesota 55455, USA
| | - Sara Mahshid
- Physics Department, McGill University, 3600 rue University, Montreal, Quebec H3A 2T8, Canada
| | - Kevin D Dorfman
- Department of Chemical Engineering and Materials Science, University of Minnesota - Twin Cities, 421 Washington Ave SE, Minneapolis, Minnesota 55455, USA
| | - Walter Reisner
- Physics Department, McGill University, 3600 rue University, Montreal, Quebec H3A 2T8, Canada
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Muralidhar A, Tree DR, Wang Y, Dorfman KD. Interplay between chain stiffness and excluded volume of semiflexible polymers confined in nanochannels. J Chem Phys 2014; 140:084905. [PMID: 24588196 PMCID: PMC3977884 DOI: 10.1063/1.4865965] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2013] [Accepted: 02/05/2014] [Indexed: 11/14/2022] Open
Abstract
The properties of channel-confined semiflexible polymers are determined by a complicated interplay of chain stiffness and excluded volume effects. Using Pruned-Enriched Rosenbluth Method (PERM) simulations, we study the equilibrium properties of channel-confined polymers by systematically controlling chain stiffness and excluded volume. Our calculations of chain extension and confinement free energy for freely jointed chains with and without excluded volume show excellent agreement with theoretical predictions. For ideal wormlike chains, the extension is seen to crossover from Odijk behavior in strong confinement to zero-stretching, bulk-like behavior in weak confinement. In contrast, for self-avoiding wormlike chains, we always observe that the linear scaling of the extension with the contour length is valid in the long-chain limit irrespective of the regime of confinement, owing to the coexistence of stiffness and excluded volume effects. We further propose that the long-chain limit for the extension corresponds to chain lengths wherein the projection of the end-to-end distance along the axis of the channel is nearly equal to the mean span parallel to the axis. For DNA in nanochannels, this limit was identified using PERM simulations out to molecular weights of more than 1 megabase pairs; the molecular weight of λ-DNA is found to exhibit nearly asymptotic fractional extension for channels sizes used commonly in experiments.
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Affiliation(s)
- Abhiram Muralidhar
- Department of Chemical Engineering and Materials Science, University of Minnesota - Twin Cities, 421 Washington Avenue SE, Minneapolis, Minnesota 55455, USA
| | - Douglas R Tree
- Department of Chemical Engineering and Materials Science, University of Minnesota - Twin Cities, 421 Washington Avenue SE, Minneapolis, Minnesota 55455, USA
| | - Yanwei Wang
- Department of Polymer Science and Engineering, Jiangsu Key Laboratory of Advanced Functional Polymer Design and Application, College of Chemistry, Chemical Engineering and Materials Science, Soochow University, 199 Ren-ai Road, Suzhou 215123, People's Republic of China
| | - 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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