1
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A simple cut and stretch assay to detect antimicrobial resistance genes on bacterial plasmids by single-molecule fluorescence microscopy. Sci Rep 2022; 12:9301. [PMID: 35660772 PMCID: PMC9166776 DOI: 10.1038/s41598-022-13315-w] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2022] [Accepted: 05/17/2022] [Indexed: 11/21/2022] Open
Abstract
Antimicrobial resistance (AMR) is a fast-growing threat to global health. The genes conferring AMR to bacteria are often located on plasmids, circular extrachromosomal DNA molecules that can be transferred between bacterial strains and species. Therefore, effective methods to characterize bacterial plasmids and detect the presence of resistance genes can assist in managing AMR, for example, during outbreaks in hospitals. However, existing methods for plasmid analysis either provide limited information or are expensive and challenging to implement in low-resource settings. Herein, we present a simple assay based on CRISPR/Cas9 excision and DNA combing to detect antimicrobial resistance genes on bacterial plasmids. Cas9 recognizes the gene of interest and makes a double-stranded DNA cut, causing the circular plasmid to linearize. The change in plasmid configuration from circular to linear, and hence the presence of the AMR gene, is detected by stretching the plasmids on a glass surface and visualizing by fluorescence microscopy. This single-molecule imaging based assay is inexpensive, fast, and in addition to detecting the presence of AMR genes, it provides detailed information on the number and size of plasmids in the sample. We demonstrate the detection of several β-lactamase-encoding genes on plasmids isolated from clinical samples. Furthermore, we demonstrate that the assay can be performed using standard microbiology and clinical laboratory equipment, making it suitable for low-resource settings.
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2
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Vaidyanathan S, Weerakoon-Ratnayake KM, Uba FI, Hu B, Kaufman D, Choi J, Park S, Soper SA. Thermoplastic nanofluidic devices for identifying abasic sites in single DNA molecules. LAB ON A CHIP 2021; 21:1579-1589. [PMID: 33651049 PMCID: PMC8293902 DOI: 10.1039/d0lc01038c] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/08/2023]
Abstract
DNA damage can take many forms such as double-strand breaks and/or the formation of abasic (apurinic/apyrimidinic; AP) sites. The presence of AP sites can be used to determine therapeutic efficacy of many drugs, such as doxorubicin. While there are different assays to search for DNA damage, they are fraught with limitations, such as the need for large amounts of DNA secured from millions of cells. This is challenging due to the growing importance of using liquid biopsies as a source of biomarkers for many in vitro diagnostic assays. To accommodate the mass limits imposed by the use of liquid biopsies, we report a single-molecule DNA damage assay that uses plastic nanofluidic chips to stretch DNA to near its full contour length when the channel dimensions (width and depth) are near the persistence length (∼50 nm) of double-stranded (ds) DNA. The nanofluidic chip consisted of input funnels for high loading efficiency of single DNA molecules, entropic traps to store the DNA and simultaneously load a series of nanochannels for high throughput processing, and an array of stretching nanochannels to read the AP sites. Single dsDNA molecules, which were labeled with an intercalating dye and a biotinylated aldehyde reactive probe (bARP), could be parked in the stretching nanochannels, where the AP sites were read directly using a dual-color fluorescence microscope equipped with an EMCCD camera. One color of the microscope was used to read the DNA length and the second color detected the AP sites. The nanofluidic chip was made from thermoplastics via nanoimprint lithography, which obviated the need for direct writing the devices in glass or quartz using focused ion beam milling. We show that we can read the frequency of AP sites in single dsDNA molecules with the frequency of AP sites determined by associating fluorescently-labeled streptavidin with bARP through a biotin/streptavidin complex.
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Affiliation(s)
- Swarnagowri Vaidyanathan
- Bioengineering Program, The University of Kansas, Lawrence, KS 66045, USA and Center of BioModular Multiscale Systems for Precision Medicine, Lawrence, KS 66047, USA
| | - Kumuditha M Weerakoon-Ratnayake
- Center of BioModular Multiscale Systems for Precision Medicine, Lawrence, KS 66047, USA and Department of Chemistry, The University of Kansas, Lawrence, KS 66045, USA
| | - Franklin I Uba
- Department of Chemistry, University of North Carolina at Chapel Hill, NC 27599, USA
| | - Bo Hu
- Department of Biomedical Engineering, The University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - David Kaufman
- Center of BioModular Multiscale Systems for Precision Medicine, Lawrence, KS 66047, USA and Department of Pathology and Laboratory Medicine, The University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Junseo Choi
- Center of BioModular Multiscale Systems for Precision Medicine, Lawrence, KS 66047, USA and Mechanical & Industrial Engineering, Louisiana State University, Baton Rouge, LA 70803, USA
| | - Sunggook Park
- Center of BioModular Multiscale Systems for Precision Medicine, Lawrence, KS 66047, USA and Mechanical & Industrial Engineering, Louisiana State University, Baton Rouge, LA 70803, USA
| | - Steven A Soper
- Bioengineering Program, The University of Kansas, Lawrence, KS 66045, USA and Center of BioModular Multiscale Systems for Precision Medicine, Lawrence, KS 66047, USA and Department of Chemistry, The University of Kansas, Lawrence, KS 66045, USA and Department of Cancer Biology and KU Cancer Center, The University of Kansas Medical Center, Kansas City, KS 66106, USA. and Department of Mechanical Engineering, The University of Kansas, Lawrence, KS 66045, USA
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3
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Varapula D, LaBouff E, Raseley K, Uppuluri L, Ehrlich GD, Noh M, Xiao M. A micropatterned substrate for on-surface enzymatic labelling of linearized long DNA molecules. Sci Rep 2019; 9:15059. [PMID: 31636335 PMCID: PMC6803683 DOI: 10.1038/s41598-019-51507-z] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2019] [Accepted: 10/02/2019] [Indexed: 12/22/2022] Open
Abstract
Optical mapping of linearized DNA molecules is a promising new technology for sequence assembly and scaffolding, large structural variant detection, and diagnostics. This is currently achieved either using nanochannel confinement or by stretching single DNA molecules on a solid surface. While the first method necessitates DNA labelling before linearization, the latter allows for modification post-linearization, thereby affording increased process flexibility. Each method is constrained by various physical and chemical limitations. One of the most common techniques for linearization of DNA uses a hydrophobic surface and a receding meniscus, termed molecular combing. Here, we report the development of a microfabricated surface that can not only comb the DNA molecules efficiently but also provides for sequence-specific enzymatic fluorescent DNA labelling. By modifying a glass surface with two contrasting functionalities, such that DNA binds selectively to one of the two regions, we can control DNA extension, which is known to be critical for sequence-recognition by an enzyme. Moreover, the surface modification provides enzymatic access to the DNA backbone, as well as minimizing non-specific fluorescent dye adsorption. These enhancements make the designed surface suitable for large-scale and high-resolution single DNA molecule studies.
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Affiliation(s)
- Dharma Varapula
- School of Biomedical Engineering, Drexel University, Philadelphia, PA, 19104, USA
| | - Eric LaBouff
- School of Biomedical Engineering, Drexel University, Philadelphia, PA, 19104, USA
- Department of Microbiology and Immunology, Drexel University College of Medicine, Philadelphia, PA, 19102, USA
- Center for Genomic Sciences and Center for Advanced Microbial Processing, Institute of Molecular Medicine and Infectious Disease, Drexel University College of Medicine, Philadelphia, PA, 19102, USA
| | - Kaitlin Raseley
- School of Biomedical Engineering, Drexel University, Philadelphia, PA, 19104, USA
| | - Lahari Uppuluri
- Department of Mechanical Engineering and Mechanics, Drexel University, Philadelphia, PA, 19104, USA
| | - Garth D Ehrlich
- Department of Microbiology and Immunology, Drexel University College of Medicine, Philadelphia, PA, 19102, USA
- Center for Genomic Sciences and Center for Advanced Microbial Processing, Institute of Molecular Medicine and Infectious Disease, Drexel University College of Medicine, Philadelphia, PA, 19102, USA
- Department of Otolaryngology Head and Neck Surgery, Drexel University College of Medicine, Philadelphia, PA, 19102, USA
| | - Moses Noh
- Department of Mechanical Engineering and Mechanics, Drexel University, Philadelphia, PA, 19104, USA
| | - Ming Xiao
- School of Biomedical Engineering, Drexel University, Philadelphia, PA, 19104, USA.
- Center for Genomic Sciences and Center for Advanced Microbial Processing, Institute of Molecular Medicine and Infectious Disease, Drexel University College of Medicine, Philadelphia, PA, 19102, USA.
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4
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Giri D, Li Z, Ashraf KM, Collinson MM, Higgins DA. Molecular Combing of λ-DNA using Self-Propelled Water Droplets on Wettability Gradient Surfaces. ACS APPLIED MATERIALS & INTERFACES 2016; 8:24265-24272. [PMID: 27541167 DOI: 10.1021/acsami.6b08607] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
Surface wettability gradients were used to elongate and align double stranded λ-DNA. Gradients were prepared by vapor phase deposition of octyltrichlorosilane (C8-silane) and fluorinated octyltrichlorosilane (F-silane) precursors. Gradient formation was confirmed by water contact angle and ellipsometric film thickness measurements. Placement of a droplet of aqueous DNA solution on the hydrophobic end of each gradient led to spontaneous motion of the droplet toward the hydrophilic end and deposition of the DNA. Fluorescence imaging of surface-adsorbed YOYO-1 labeled DNA molecules revealed that they are elongated and aligned perpendicular to the droplet-surface contact line at all positions along the gradient, consistent with a dominant role played by surface tension forces in elongating the DNA. The density of adsorbed DNA was found to be greatest on the C8-silane gradient at its hydrophobic end. DNA density decreased toward the hydrophilic end, while the length of the elongated DNA was less dependent on position. The elongation of DNA molecules by spontaneous droplet motion on chemical gradient surfaces has possible applications in DNA barcoding and studies of DNA-protein interactions.
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Affiliation(s)
- Dipak Giri
- Department of Chemistry, Kansas State University , Manhattan, Kansas 66506-0401, United States
| | - Zi Li
- Department of Chemistry, Kansas State University , Manhattan, Kansas 66506-0401, United States
| | - Kayesh M Ashraf
- Department of Chemistry, Virginia Commonwealth University , Richmond, Virginia 23284-2006, United States
| | - Maryanne M Collinson
- Department of Chemistry, Virginia Commonwealth University , Richmond, Virginia 23284-2006, United States
| | - Daniel A Higgins
- Department of Chemistry, Kansas State University , Manhattan, Kansas 66506-0401, United States
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5
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Direct and precise length measurement of single, stretched DNA fragments by dynamic molecular combing and STED nanoscopy. Anal Bioanal Chem 2016; 408:6453-9. [DOI: 10.1007/s00216-016-9764-9] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2016] [Revised: 06/25/2016] [Accepted: 07/04/2016] [Indexed: 11/25/2022]
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6
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Chakraborty S, Noonan PS, Monserud J, Schwartz DK. Structure-Specific Liquid Crystal Anchoring Induced by the Molecular Combing of Short Oligonucleotides. ACS APPLIED MATERIALS & INTERFACES 2015; 7:26874-26879. [PMID: 26562585 DOI: 10.1021/acsami.5b09335] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
Surface-immobilized oligonucleotides were "combed" by meniscus motion and exposed to a nematic liquid crystal (LC). Although the oligonucleotides were as short as 16 bases, they were apparently oriented by this process and, in turn, successfully biased the orientation of the adjacent LC material. Single-stranded DNA (ssDNA) induced LC orientation in the combing direction, while hybridized double-stranded DNA (dsDNA) rotated the azimuthal LC orientation by ∼30° from the combing direction. The sensitivity of the chiral response to mixed ssDNA/dsDNA surfaces was characterized by employing complementary DNA that was longer than the immobilized DNA, resulting in single-stranded overhangs of various lengths. A rotated LC orientation was observed even when more than 70% of the DNA was single-stranded, and the transition from the rotated to nonrotated response was apparently discontinuous as a function of ssDNA surface coverage. These phenomena represent a sensitive DNA hybridization detection strategy that can potentially comprise a multiplexed assay.
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Affiliation(s)
- Saonti Chakraborty
- Department of Chemical and Biological Engineering University of Colorado Boulder , Boulder, Colorado 80309, United States
| | - Patrick S Noonan
- Department of Chemical and Biological Engineering University of Colorado Boulder , Boulder, Colorado 80309, United States
| | - Jon Monserud
- Department of Chemical and Biological Engineering University of Colorado Boulder , Boulder, Colorado 80309, United States
| | - Daniel K Schwartz
- Department of Chemical and Biological Engineering University of Colorado Boulder , Boulder, Colorado 80309, United States
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7
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Torchinsky D, Ebenstein Y. Sizing femtogram amounts of dsDNA by single-molecule counting. Nucleic Acids Res 2015; 44:e17. [PMID: 26365235 PMCID: PMC4737178 DOI: 10.1093/nar/gkv904] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2015] [Accepted: 08/31/2015] [Indexed: 12/20/2022] Open
Abstract
Modern molecular-biology applications raise renewed interest in sizing minute-amounts of DNA. In this work we utilize single-molecule imaging with in situ size calibration to accurately analyze the size and mass distribution of DNA samples. We exploit the correlation between DNA length and its fluorescence intensity after staining in order to assess the length of individual DNA fragments by fluorescence microscopy. Synthetic reference DNA standards are added to the investigated sample before staining and serve as internal size calibrators, supporting a robust assay for accurate DNA sizing. Our results demonstrate the ability to reconstruct the exact length distribution in a complex DNA sample by sizing a subset containing only femtogram amounts of DNA, thus, outperforming microfluidic gel electrophoresis which is the currently accepted gold standard. This assay may find useful applications for genetic analysis where the exact size distribution of DNA molecules is critical and the availability of genetic material is limited.
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Affiliation(s)
- Dmitry Torchinsky
- Raymond and Beverly Sackler Faculty of Exact Sciences, School of Chemistry, Tel Aviv University, Tel Aviv 6997801, Israel
| | - Yuval Ebenstein
- Raymond and Beverly Sackler Faculty of Exact Sciences, School of Chemistry, Tel Aviv University, Tel Aviv 6997801, Israel
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8
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Whitfield CJ, Turley AT, Tuite EM, Connolly BA, Pike AR. Enzymatic Method for the Synthesis of Long DNA Sequences with Multiple Repeat Units. Angew Chem Int Ed Engl 2015; 54:8971-4. [DOI: 10.1002/anie.201502971] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2015] [Indexed: 11/09/2022]
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9
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Whitfield CJ, Turley AT, Tuite EM, Connolly BA, Pike AR. Enzymatic Method for the Synthesis of Long DNA Sequences with Multiple Repeat Units. Angew Chem Int Ed Engl 2015. [DOI: 10.1002/ange.201502971] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
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10
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Deen J, Sempels W, De Dier R, Vermant J, Dedecker P, Hofkens J, Neely RK. Combing of genomic DNA from droplets containing picograms of material. ACS NANO 2015; 9:809-816. [PMID: 25561163 PMCID: PMC4344373 DOI: 10.1021/nn5063497] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/06/2014] [Accepted: 01/05/2015] [Indexed: 05/30/2023]
Abstract
Deposition of linear DNA molecules is a critical step in many single-molecule genomic approaches including DNA mapping, fiber-FISH, and several emerging sequencing technologies. In the ideal situation, the DNA that is deposited for these experiments is absolutely linear and uniformly stretched, thereby enabling accurate distance measurements. However, this is rarely the case, and furthermore, current approaches for the capture and linearization of DNA on a surface tend to require complex surface preparation and large amounts of starting material to achieve genomic-scale mapping. This makes them technically demanding and prevents their application in emerging fields of genomics, such as single-cell based analyses. Here we describe a simple and extremely efficient approach to the deposition and linearization of genomic DNA molecules. We employ droplets containing as little as tens of picograms of material and simply drag them, using a pipet tip, over a polymer-coated coverslip. In this report we highlight one particular polymer, Zeonex, which is remarkably efficient at capturing DNA. We characterize the method of DNA capture on the Zeonex surface and find that the use of droplets greatly facilitates the efficient deposition of DNA. This is the result of a circulating flow in the droplet that maintains a high DNA concentration at the interface of the surface/solution. Overall, our approach provides an accessible route to the study of genomic structural variation from samples containing no more than a handful of cells.
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Affiliation(s)
- Jochem Deen
- Department of Chemistry, KU Leuven, Celestijnenlaan 200F, Heverlee 3001, Belgium
| | - Wouter Sempels
- Department of Chemistry, KU Leuven, Celestijnenlaan 200F, Heverlee 3001, Belgium
| | - Raf De Dier
- Department of Chemical Engineering, KU Leuven, Willem de Croylaan 46, Heverlee 3001, Belgium
| | - Jan Vermant
- Department of Chemical Engineering, KU Leuven, Willem de Croylaan 46, Heverlee 3001, Belgium
- Department of Materials, ETH Zürich, Vladimir Prelog Weg 5, CH 8093 Zürich, Switzerland
| | - Peter Dedecker
- Department of Chemistry, KU Leuven, Celestijnenlaan 200F, Heverlee 3001, Belgium
| | - Johan Hofkens
- Department of Chemistry, KU Leuven, Celestijnenlaan 200F, Heverlee 3001, Belgium
- Department of Chemistry, University of Copenhagen, Universitetsparken 5, 2100 Copenhagen, Denmark
| | - Robert K. Neely
- Department of Chemistry, KU Leuven, Celestijnenlaan 200F, Heverlee 3001, Belgium
- School of Chemistry, University of Birmingham, Edgbaston, Birmingham B15 2TT, United Kingdom
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11
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Wei Q, Luo W, Chiang S, Kappel T, Mejia C, Tseng D, Chan RYL, Yan E, Qi H, Shabbir F, Ozkan H, Feng S, Ozcan A. Imaging and sizing of single DNA molecules on a mobile phone. ACS NANO 2014; 8:12725-33. [PMID: 25494442 DOI: 10.1021/nn505821y] [Citation(s) in RCA: 114] [Impact Index Per Article: 11.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/06/2023]
Abstract
DNA imaging techniques using optical microscopy have found numerous applications in biology, chemistry and physics and are based on relatively expensive, bulky and complicated set-ups that limit their use to advanced laboratory settings. Here we demonstrate imaging and length quantification of single molecule DNA strands using a compact, lightweight and cost-effective fluorescence microscope installed on a mobile phone. In addition to an optomechanical attachment that creates a high contrast dark-field imaging setup using an external lens, thin-film interference filters, a miniature dovetail stage and a laser-diode for oblique-angle excitation, we also created a computational framework and a mobile phone application connected to a server back-end for measurement of the lengths of individual DNA molecules that are labeled and stretched using disposable chips. Using this mobile phone platform, we imaged single DNA molecules of various lengths to demonstrate a sizing accuracy of <1 kilobase-pairs (kbp) for 10 kbp and longer DNA samples imaged over a field-of-view of ∼2 mm2.
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Affiliation(s)
- Qingshan Wei
- Electrical Engineering Department, University of California , Los Angeles, California 90095, United States
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12
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Yu H, Shan X, Wang S, Chen H, Tao N. Plasmonic imaging and detection of single DNA molecules. ACS NANO 2014; 8:3427-3433. [PMID: 24593238 DOI: 10.1021/nn4062885] [Citation(s) in RCA: 62] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/03/2023]
Abstract
The capability of imaging and detecting single DNA molecules is critical in the study, analysis, and applications of DNA. Fluorescence imaging is a widely used method, but it suffers from blinking and photobleaching, and fluorescence tags may block or affect binding sites on DNA. We report on label-free imaging of single DNA molecules with a differential plasmonic imaging technique. The technique produces high contrast images due to the scattering of surface plasmonic waves by the molecules and the removal of background noises and interference patterns, allowing for quantitative analysis of individual DNA molecules. Simulation of the images based on a scattering model shows good agreement with the experiment. We further demonstrate optical mapping of single DNA molecules.
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Affiliation(s)
- Hui Yu
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University , Nanjing 210093, China
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13
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Sriram KK, Yeh JW, Lin YL, Chang YR, Chou CF. Direct optical mapping of transcription factor binding sites on field-stretched λ-DNA in nanofluidic devices. Nucleic Acids Res 2014; 42:e85. [PMID: 24753422 PMCID: PMC4041428 DOI: 10.1093/nar/gku254] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Mapping transcription factor (TF) binding sites along a DNA backbone is crucial in understanding the regulatory circuits that control cellular processes. Here, we deployed a method adopting bioconjugation, nanofluidic confinement and fluorescence single molecule imaging for direct mapping of TF (RNA polymerase) binding sites on field-stretched single DNA molecules. Using this method, we have mapped out five of the TF binding sites of E. coli RNA polymerase to bacteriophage λ-DNA, where two promoter sites and three pseudo-promoter sites are identified with the corresponding binding frequency of 45% and 30%, respectively. Our method is quick, robust and capable of resolving protein-binding locations with high accuracy (∼ 300 bp), making our system a complementary platform to the methods currently practiced. It is advantageous in parallel analysis and less prone to false positive results over other single molecule mapping techniques such as optical tweezers, atomic force microscopy and molecular combing, and could potentially be extended to general mapping of protein–DNA interaction sites.
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Affiliation(s)
- K K Sriram
- Nano Science and Technology Program, Taiwan International Graduate Program, Institute of Physics, Academia Sinica, 128, Sec. 2, Academia Road, Nankang, Taipei 11529, Taiwan Department of Engineering and System Science, National Tsing Hua University, ESS New Building, 101, Sec. 2, Kuang-Fu Road, Hsinchu 30013, Taiwan Institute of Physics, Academia Sinica, 128, Sec. 2, Academia Road, Nankang, Taipei 11529, Taiwan
| | - Jia-Wei Yeh
- Institute of Physics, Academia Sinica, 128, Sec. 2, Academia Road, Nankang, Taipei 11529, Taiwan
| | - Yii-Lih Lin
- Nano Science and Technology Program, Taiwan International Graduate Program, Institute of Physics, Academia Sinica, 128, Sec. 2, Academia Road, Nankang, Taipei 11529, Taiwan Institute of Physics, Academia Sinica, 128, Sec. 2, Academia Road, Nankang, Taipei 11529, Taiwan Department of Chemistry, National Taiwan University, 1, Sec. 4, Roosevelt Road, Daan, Taipei 10617, Taiwan
| | - Yi-Ren Chang
- Institute of Physics, Academia Sinica, 128, Sec. 2, Academia Road, Nankang, Taipei 11529, Taiwan
| | - Chia-Fu Chou
- Institute of Physics, Academia Sinica, 128, Sec. 2, Academia Road, Nankang, Taipei 11529, Taiwan Research Centre for Applied Sciences, Academia Sinica, 128, Sec. 2, Academia Road, Nankang, Taipei 11529, Taiwan Genomic Research Centre, Academia Sinica, 128, Sec. 2, Academia Road, Nankang, Taipei 11529, Taiwan
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14
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Zarkov A, Stoynov S, Nedelcheva-Veleva M. Novel glass slide preparation system for single DNA molecules analysis. BIOTECHNOL BIOTEC EQ 2014; 28:112-117. [PMID: 26019496 PMCID: PMC4434140 DOI: 10.1080/13102818.2014.901687] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/31/2022] Open
Abstract
Here we propose an easy to build up and apply glass slide preparation system for single DNA molecules stretching. It is based on fast and simple coating of a solid glass with a cocktail of acrylic monomers that are easily polymerized via ultraviolet illumination. The acrylated slides are used to successfully stretch DNA molecules in a broader pH range compared to that of the commonly used amino-silanes. Moreover, the single DNA molecules that are stretched on the acrylated slides give a brighter and more photostable signal when visualized under a fluorescent microscope.
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15
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Dorfman KD, King SB, Olson DW, Thomas JDP, Tree DR. Beyond gel electrophoresis: microfluidic separations, fluorescence burst analysis, and DNA stretching. Chem Rev 2013; 113:2584-667. [PMID: 23140825 PMCID: PMC3595390 DOI: 10.1021/cr3002142] [Citation(s) in RCA: 141] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Affiliation(s)
- Kevin D. Dorfman
- Department of Chemical Engineering and Materials Science, University of Minnesota — Twin Cities, 421 Washington Ave. SE, Minneapolis, MN 55455, Phone: 1-612-624-5560. Fax: 1-612-626-7246
| | - Scott B. King
- Department of Chemical Engineering and Materials Science, University of Minnesota — Twin Cities, 421 Washington Ave. SE, Minneapolis, MN 55455, Phone: 1-612-624-5560. Fax: 1-612-626-7246
| | - Daniel W. Olson
- Department of Chemical Engineering and Materials Science, University of Minnesota — Twin Cities, 421 Washington Ave. SE, Minneapolis, MN 55455, Phone: 1-612-624-5560. Fax: 1-612-626-7246
| | - Joel D. P. Thomas
- Department of Chemical Engineering and Materials Science, University of Minnesota — Twin Cities, 421 Washington Ave. SE, Minneapolis, MN 55455, Phone: 1-612-624-5560. Fax: 1-612-626-7246
| | - Douglas R. Tree
- Department of Chemical Engineering and Materials Science, University of Minnesota — Twin Cities, 421 Washington Ave. SE, Minneapolis, MN 55455, Phone: 1-612-624-5560. Fax: 1-612-626-7246
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16
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Zarkov A, Vasilev A, Deligeorgiev T, Stoynov S, Nedelcheva-Veleva M. Novel Fluorescent Dyes for Single DNA Molecule Techniques. Mol Imaging 2013. [DOI: 10.2310/7290.2012.00018] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Affiliation(s)
- Alexander Zarkov
- From the Institute of Molecular Biology “Roumen Tsanev,” Bulgarian Academy of Sciences, and Faculty of Chemistry, University of Sofia, Sofia, Bulgaria
| | - Aleksey Vasilev
- From the Institute of Molecular Biology “Roumen Tsanev,” Bulgarian Academy of Sciences, and Faculty of Chemistry, University of Sofia, Sofia, Bulgaria
| | - Todor Deligeorgiev
- From the Institute of Molecular Biology “Roumen Tsanev,” Bulgarian Academy of Sciences, and Faculty of Chemistry, University of Sofia, Sofia, Bulgaria
| | - Stoyno Stoynov
- From the Institute of Molecular Biology “Roumen Tsanev,” Bulgarian Academy of Sciences, and Faculty of Chemistry, University of Sofia, Sofia, Bulgaria
| | - Marina Nedelcheva-Veleva
- From the Institute of Molecular Biology “Roumen Tsanev,” Bulgarian Academy of Sciences, and Faculty of Chemistry, University of Sofia, Sofia, Bulgaria
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17
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Cabin-Flaman A, Monnier AF, Coffinier Y, Audinot JN, Gibouin D, Wirtz T, Boukherroub R, Migeon HN, Bensimon A, Jannière L, Ripoll C, Norris V. Combed single DNA molecules imaged by secondary ion mass spectrometry. Anal Chem 2011; 83:6940-7. [PMID: 21851091 DOI: 10.1021/ac201685t] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Studies of replication, recombination, and rearrangements at the level of individual molecules of DNA are often limited by problems of resolution or of perturbations caused by the modifications that are needed for imaging. The Combing-Imaging by Secondary Ion Mass Spectrometry (SIMS) (CIS) method helps solve these problems by combining DNA combing, cesium flooding, and quantitative imaging via the NanoSIMS 50. We show here that CIS can reveal, on the 50 nm scale, individual DNA fibers labeled with different, nonradioactive isotopes and, moreover, that it can quantify these isotopes so as to detect and measure the length of one or more short nucleic acid fragments associated with a longer fiber.
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Affiliation(s)
- Armelle Cabin-Flaman
- Equipe Assemblages Moléculaires: Modélisation et Imagerie SIMS, Laboratoire MERCI EA 3829, Faculté des Sciences de l'Université de Rouen, Mont Saint Aignan, France
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18
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Vasdekis AE, Laporte GP. Enhancing single molecule imaging in optofluidics and microfluidics. Int J Mol Sci 2011; 12:5135-56. [PMID: 21954349 PMCID: PMC3179156 DOI: 10.3390/ijms12085135] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2011] [Revised: 05/23/2011] [Accepted: 07/25/2011] [Indexed: 12/25/2022] Open
Abstract
Microfluidics and optofluidics have revolutionized high-throughput analysis and chemical synthesis over the past decade. Single molecule imaging has witnessed similar growth, due to its capacity to reveal heterogeneities at high spatial and temporal resolutions. However, both resolution types are dependent on the signal to noise ratio (SNR) of the image. In this paper, we review how the SNR can be enhanced in optofluidics and microfluidics. Starting with optofluidics, we outline integrated photonic structures that increase the signal emitted by single chromophores and minimize the excitation volume. Turning then to microfluidics, we review the compatible functionalization strategies that reduce noise stemming from non-specific interactions and architectures that minimize bleaching and blinking.
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Affiliation(s)
- Andreas E. Vasdekis
- Optics Laboratory, School of Engineering, Ecole Polytechnique Fédérale de Lausanne (EPFL), Lausanne CH-1015, Switzerland; E-Mail:
| | - Gregoire P.J. Laporte
- Optics Laboratory, School of Engineering, Ecole Polytechnique Fédérale de Lausanne (EPFL), Lausanne CH-1015, Switzerland; E-Mail:
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19
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Rodríguez-Pérez JC, Hamley IW, Squires AM. Infrared Linear Dichroism Spectroscopy on Amyloid Fibrils Aligned by Molecular Combing. Biomacromolecules 2011; 12:1810-21. [DOI: 10.1021/bm200167n] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
| | - Ian W. Hamley
- Department of Chemistry, University of Reading, Reading, RG6 6AD, United Kingdom
| | - Adam M. Squires
- Department of Chemistry, University of Reading, Reading, RG6 6AD, United Kingdom
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20
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Lei S, Yang Y, Zeng Q, Wang C. Combined SPM investigation on the interfacial structure of a phthalocyanine/conjugated polymer composite film. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2011; 27:3496-3501. [PMID: 21341779 DOI: 10.1021/la104219z] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/30/2023]
Abstract
The morphology of the composite film of organic semiconductors determines the properties and performances of devices to a large extent. In this work, we present a combined AFM and STM study on the interfacial structures of CuPcOC8 and CuPcOC8/PmPV composite films on graphite surface. For CuPcOC8 thin films, the face-on epitaxial growth of CuPcOC8 could persist within 3 to 5 monolayers and the formation of π-π stacked columns will occur with edge-on configuration when the film thickness further increases. For the CuPcOC8/PmPV composite film with 1:1 weight ratio, STM results reveal a preferential adsorption of PmPV on graphite surface, while AFM results indicate the phase segregation in the upper layer. STM also reveals in the molecular scale good compatibility of CuPcOC8 with PmPV.
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Affiliation(s)
- Shengbin Lei
- Key Laboratory of Microsystems and Microstructures Manufacturing, Ministry of Education & The Academy of Fundamental and Interdisciplinary Science, Harbin Institute of Technology, Harbin, 150080, PR China.
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21
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Hirose T, Sugiyama S. A simple DNA Characterization method using fiber-fluorescence in situ hybridization performed without DNA fragmentation. Photochem Photobiol 2011; 87:470-3. [PMID: 21366598 DOI: 10.1111/j.1751-1097.2010.00854.x] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
Abstract
We performed high-resolution fluorescence imaging of lambda phage DNA molecules hybridized with fluorescent-labeled DNA and peptide nucleic acid probes. In this method, the target DNA and probe were mixed, rapidly denatured and then subjected to liquid hybridization conditions. The hybridized DNA sample was then spotted onto a nontreated glass substrate and subjected to molecular combing. The resultant continuous fluorescence signal of intact lambda DNA shows that the fluorescent-labeled probes bound to the predicted sites but in a pattern that was clearly different to the beads-on-a-string pattern typical for fiber-fluorescence in situ hybridization. The key changes to the conventional method are hybridization of the free target DNA in liquid and lowering the denaturation temperature. The method described here allows the rapid and direct visualization of the specific binding sites of intact DNA molecules without damaging the DNA fibers and causing fragmentation of the fluorescence signal. This technique should be a useful tool in studies of genetics and also large-scale DNA sequencing projects.
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Affiliation(s)
- Tamaki Hirose
- Nanobiotechnology Laboratory, National Food Research Institute, National Agriculture and Food Research Organization, Tsukuba, Ibaraki, Japan
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22
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Vasdekis AE, O’Neil CP, Hubbell JA, Psaltis D. Microfluidic Assays for DNA Manipulation Based on a Block Copolymer Immobilization Strategy. Biomacromolecules 2010; 11:827-31. [DOI: 10.1021/bm901453u] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Andreas E. Vasdekis
- Optics Laboratory, School of Engineering and Laboratory of Regenerative Medicine and Pharmacobiology, Institute of Bioengineering, Ecole Polytechnique Fédérale de Lausanne (EPFL), Switzerland
| | - Conlin P. O’Neil
- Optics Laboratory, School of Engineering and Laboratory of Regenerative Medicine and Pharmacobiology, Institute of Bioengineering, Ecole Polytechnique Fédérale de Lausanne (EPFL), Switzerland
| | - Jeffrey A. Hubbell
- Optics Laboratory, School of Engineering and Laboratory of Regenerative Medicine and Pharmacobiology, Institute of Bioengineering, Ecole Polytechnique Fédérale de Lausanne (EPFL), Switzerland
| | - Demetri Psaltis
- Optics Laboratory, School of Engineering and Laboratory of Regenerative Medicine and Pharmacobiology, Institute of Bioengineering, Ecole Polytechnique Fédérale de Lausanne (EPFL), Switzerland
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23
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A new DNA combing method for biochemical analysis. Anal Biochem 2010; 400:145-7. [PMID: 20085744 DOI: 10.1016/j.ab.2010.01.021] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2009] [Revised: 01/06/2010] [Accepted: 01/14/2010] [Indexed: 11/23/2022]
Abstract
A simple molecular combing method for analysis of biochemical reactions, called the moving droplet method, has been developed. In this method, small droplets containing DNA molecules run down a sloped glass substrate, and this creates a moving interface among the air, droplet, and substrate that stretches the DNA molecules. This method requires a much smaller volume of sample solution than other established combing methods, allowing wider application in various fields. Using this method, lambdaDNA molecules were stretched and absorbed to a glass substrate, and single-molecule analysis of DNA synthesis by DNA polymerases was performed.
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24
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Gross P, Farge G, Peterman EJG, Wuite GJL. Combining optical tweezers, single-molecule fluorescence microscopy, and microfluidics for studies of DNA-protein interactions. Methods Enzymol 2010; 475:427-53. [PMID: 20627167 DOI: 10.1016/s0076-6879(10)75017-5] [Citation(s) in RCA: 71] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
The technically challenging field of single-molecule biophysics has established itself in the last decade by granting access to detailed information about the fate of individual biomolecules, unattainable in traditional biochemical assays. The appeal of single-molecule methods lies in the directness of the information obtained from individual biomolecules. Technological improvements in single-molecule methods have made it possible to combine optical tweezers, fluorescence microscopy, and microfluidic flow systems. Such a combination of techniques has opened new possibilities to study complex biochemical reactions on the single-molecule level. In this chapter, we provide general considerations for the development of a combined optical trapping, fluorescence microscopy, and microfluidics instrument, along with methods to solve technical issues that are critical for designing successful experiments. Finally, we present several experiments to illustrate the power of this combination of techniques.
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Affiliation(s)
- Peter Gross
- Department of Physics and Astronomy and Laser Centre, VU University, De Boelelaan, Amsterdam, The Netherlands
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25
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Lee JK, Jäckel F, Moerner WE, Bao Z. Micrometer-sized DNA-single-fluorophore-DNA supramolecule: synthesis and single-molecule characterization. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2009; 5:2418-23. [PMID: 19517486 DOI: 10.1002/smll.200900494] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/20/2023]
Abstract
The synthesis of single-fluorophore-bis(micrometer-sized DNA) triblock supramolecules and the optical and structural characterization of the construct at the single-molecule level is reported. A fluorophore-bis(oligodeoxynucleotide) triblock is synthesized via the amide-coupling reaction. Subsequent protocols of DNA hybridization/ligation are developed to form the supramolecular triblock structure with lambda-DNA fragments on the micrometer length scale. The successful synthesis of the micrometer-sized DNA-single-fluorophore-DNA supramolecule is confirmed by agarose gel electrophoresis with fluorescence imaging under UV excitation. Single triblock structures are directly imaged by combined scanning force microscopy and single-molecule fluorescence microscopy, and provide unambiguous confirmation of the existence of the single fluorophore inserted in the middle of the long DNA. This type of triblock structure is a step closer to providing a scaffold for single-molecule electronic devices after metallization of the DNAs.
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Affiliation(s)
- Jungkyu K Lee
- Department of Chemistry, Stanford University, Stanford, CA 94305-5080, USA
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26
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Lü J, Ye M, Duan N, Li B. Enzymatic digestion of single DNA molecules anchored on nanogold-modified surfaces. NANOSCALE RESEARCH LETTERS 2009; 4:1029-1034. [PMID: 20596481 PMCID: PMC2893842 DOI: 10.1007/s11671-009-9350-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/09/2009] [Accepted: 05/14/2009] [Indexed: 05/29/2023]
Abstract
To study enzyme-DNA interactions at single molecular level, both the attachment points and the immediate surroundings of surfaces must be carefully considered such that they do not compromise the structural information and biological properties of the sample under investigation. The present work demonstrates the feasibility of enzymatic digestion of single DNA molecules attached to nanoparticle-modified surfaces. With Nanogold linking DNA to the mica surface by electrostatic interactions, advantageous conditions with fewer effects on the length and topography of DNA are obtained, and an appropriate environment for the activities of DNA is created. We demonstrate that by using Dip-Pen Nanolithography, individual DNA molecules attached to modified mica surfaces can be efficiently digested by DNase I.
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Affiliation(s)
- Junhong Lü
- Shanghai Institute of Applied Physics, Chinese Academy of Sciences, P,O, Box 800-204, Shanghai, 201800, China.
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27
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van Mameren J, Peterman EJG, Wuite GJL. See me, feel me: methods to concurrently visualize and manipulate single DNA molecules and associated proteins. Nucleic Acids Res 2008; 36:4381-9. [PMID: 18586820 PMCID: PMC2490750 DOI: 10.1093/nar/gkn412] [Citation(s) in RCA: 81] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Direct visualization of DNA and proteins allows researchers to investigate DNA–protein interactions with great detail. Much progress has been made in this area as a result of increasingly sensitive single-molecule fluorescence techniques. At the same time, methods that control the conformation of DNA molecules have been improving constantly. The combination of both techniques has appealed to researchers ever since single-molecule measurements have become possible and indeed first implementations of such combined approaches have proven useful in the study of several DNA-binding proteins in real time. Here, we describe the technical state-of-the-art of various integrated manipulation-and-visualization methods. We first discuss methods that allow only little control over the DNA conformation, such as DNA combing. We then describe DNA flow-stretching approaches that allow more control, and end with the full control on position and extension obtained by manipulating DNA with optical tweezers. The advantages and limitations of the various techniques are discussed, as well as several examples of applications to biophysical or biochemical questions. We conclude with an outlook describing potential future technical developments in combining fluorescence microscopy with DNA micromanipulation technology.
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Affiliation(s)
- Joost van Mameren
- Department of Physics and Astronomy and Laser Centre, VU University, De Boelelaan 1081, 1081 HV, Amsterdam, The Netherlands
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28
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Engstler M, Pfohl T, Herminghaus S, Boshart M, Wiegertjes G, Heddergott N, Overath P. Hydrodynamic flow-mediated protein sorting on the cell surface of trypanosomes. Cell 2007; 131:505-15. [PMID: 17981118 DOI: 10.1016/j.cell.2007.08.046] [Citation(s) in RCA: 291] [Impact Index Per Article: 17.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2007] [Revised: 06/19/2007] [Accepted: 08/27/2007] [Indexed: 11/30/2022]
Abstract
The unicellular parasite Trypanosoma brucei rapidly removes host-derived immunoglobulin (Ig) from its cell surface, which is dominated by a single type of glycosylphosphatidylinositol-anchored variant surface glycoprotein (VSG). We have determined the mechanism of antibody clearance and found that Ig-VSG immune complexes are passively sorted to the posterior cell pole, where they are endocytosed. The backward movement of immune complexes requires forward cellular motility but is independent of endocytosis and of actin function. We suggest that the hydrodynamic flow acting on swimming trypanosomes causes directional movement of Ig-VSG immune complexes in the plane of the plasma membrane, that is, immunoglobulins attached to VSG function as molecular sails. Protein sorting by hydrodynamic forces helps to protect trypanosomes against complement-mediated immune destruction in culture and possibly in infected mammals but likewise may be of functional significance at the surface of other cell types such as epithelial cells lining blood vessels.
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Affiliation(s)
- Markus Engstler
- Institut für Mikrobiologie und Genetik, Technische Universität Darmstadt, Schnittspahnstrasse 10, 64287, Darmstadt, Germany.
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29
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Krogmeier JR, Schaefer I, Seward G, Yantz GR, Larson JW. An integrated optics microfluidic device for detecting single DNA molecules. LAB ON A CHIP 2007; 7:1767-1774. [PMID: 18030399 DOI: 10.1039/b710504e] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/25/2023]
Abstract
A fluorescence-based integrated optics microfluidic device is presented, capable of detecting single DNA molecules in a high throughput and reproducible manner. The device integrates microfluidics for DNA stretching with two optical elements for single molecule detection (SMD): a plano-aspheric refractive lens for fluorescence excitation (illuminator) and a solid parabolic reflective mirror for fluorescence collection (collector). Although miniaturized in size, both optical components were produced and assembled onto the microfluidic device by readily manufacturable fabrication techniques. The optical resolution of the device is determined by the small and relatively low numerical aperture (NA) illuminator lens (0.10 effective NA, 4.0 mm diameter) that delivers excitation light to a diffraction limited 2.0 microm diameter spot at full width half maximum within the microfluidic channel. The collector (0.82 annular NA, 15 mm diameter) reflects the fluorescence over a large collection angle, representing 71% of a hemisphere, toward a single photon counting module in an infinity-corrected scheme. As a proof-of-principle experiment for this simple integrated device, individual intercalated lambda-phage DNA molecules (48.5 kb) were stretched in a mixed elongational-shear microflow, detected, and sized with a fluorescence signal to noise ratio of 9.9 +/-1.0. We have demonstrated that SMD does not require traditional high numerical aperture objective lenses and sub-micron positioning systems conventionally used in many applications. Rather, standard manufacturing processes can be combined in a novel way that promises greater accessibility and affordability for microfluidic-based single molecule applications.
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30
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Xiao M, Phong A, Ha C, Chan TF, Cai D, Leung L, Wan E, Kistler AL, DeRisi JL, Selvin PR, Kwok PY. Rapid DNA mapping by fluorescent single molecule detection. Nucleic Acids Res 2006; 35:e16. [PMID: 17175538 PMCID: PMC1807959 DOI: 10.1093/nar/gkl1044] [Citation(s) in RCA: 86] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
DNA mapping is an important analytical tool in genomic sequencing, medical diagnostics and pathogen identification. Here we report an optical DNA mapping strategy based on direct imaging of individual DNA molecules and localization of multiple sequence motifs on the molecules. Individual genomic DNA molecules were labeled with fluorescent dyes at specific sequence motifs by the action of nicking endonuclease followed by the incorporation of dye terminators with DNA polymerase. The labeled DNA molecules were then stretched into linear form on a modified glass surface and imaged using total internal reflection fluorescence (TIRF) microscopy. By determining the positions of the fluorescent labels with respect to the DNA backbone, the distribution of the sequence motif recognized by the nicking endonuclease can be established with good accuracy, in a manner similar to reading a barcode. With this approach, we constructed a specific sequence motif map of lambda-DNA. We further demonstrated the capability of this approach to rapidly type a human adenovirus and several strains of human rhinovirus.
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Affiliation(s)
- Ming Xiao
- Cardiovascular Research Institute and Center for Human Genetics, University of CaliforniaSan Francisco, CA 94115, USA
- To whom correspondence should be addressed at: 513, Parnassus Avenue, HSW-901A, San Francisco, CA 94143, USA. Tel: +1 41 551 43876; Fax: +1 41 547 62956;
| | - Angie Phong
- Cardiovascular Research Institute and Center for Human Genetics, University of CaliforniaSan Francisco, CA 94115, USA
| | - Connie Ha
- Cardiovascular Research Institute and Center for Human Genetics, University of CaliforniaSan Francisco, CA 94115, USA
| | - Ting-Fung Chan
- Cardiovascular Research Institute and Center for Human Genetics, University of CaliforniaSan Francisco, CA 94115, USA
| | - Dongmei Cai
- Cardiovascular Research Institute and Center for Human Genetics, University of CaliforniaSan Francisco, CA 94115, USA
| | - Lucinda Leung
- Cardiovascular Research Institute and Center for Human Genetics, University of CaliforniaSan Francisco, CA 94115, USA
| | - Eunice Wan
- Cardiovascular Research Institute and Center for Human Genetics, University of CaliforniaSan Francisco, CA 94115, USA
| | - Amy L. Kistler
- Department of Biochemistry and Biophysics, University of CaliforniaSan Francisco, CA 94115, USA
| | - Joseph L. DeRisi
- Department of Biochemistry and Biophysics, University of CaliforniaSan Francisco, CA 94115, USA
| | - Paul R. Selvin
- Department of Physics and Center of Biophysics, University of Illinois at Urbana-ChampaignUrbana, IL 61801, USA
| | - Pui-Yan Kwok
- Cardiovascular Research Institute and Center for Human Genetics, University of CaliforniaSan Francisco, CA 94115, USA
- Department of Dermatology, University of CaliforniaSan Francisco, CA 94115, USA
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