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Matsuoka H. ELECTROCHEMISTRY 2016; 84:107-115. [DOI: 10.5796/electrochemistry.84.107] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022] Open
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2
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Esnault C, Renodon-Cornière A, Takahashi M, Casse N, Delorme N, Louarn G, Fleury F, Pilard JF, Chénais B. Assessment of DNA binding to human Rad51 protein by using quartz crystal microbalance and atomic force microscopy: effects of ADP and BRC4-28 peptide inhibitor. Chemphyschem 2014; 15:3753-60. [PMID: 25208912 DOI: 10.1002/cphc.201402451] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2014] [Indexed: 11/06/2022]
Abstract
The interaction of human Rad51 protein (HsRad51) with single-stranded deoxyribonucleic acid (ssDNA) was investigated by using quartz crystal microbalance (QCM) monitoring and atomic force microscopy (AFM) visualization. Gold surfaces for QCM and AFM were modified by electrografting of the in situ generated aryldiazonium salt from the sulfanilic acid to obtain the organic layer Au-ArSO3 H. The Au-ArSO3 H layer was activated by using a solution of PCl5 in CH2 Cl2 to give a Au-ArSO2 Cl layer. The modified surface was then used to immobilize long ssDNA molecules. The results obtained showed that the presence of adenosine diphosphate promotes the protein autoassociation rather than nucleation around DNA. In addition, when the BRC4-28 peptide inhibitor was used, both QCM and AFM confirmed the inhibitory effect of BRC4-28 toward HsRad51 autoassociation. Altogether these results show the suitability of this modified surface to investigate the kinetics and structure of DNA-protein interactions and for the screening of inhibitors.
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Affiliation(s)
- Charles Esnault
- Institut des Molécules et Matériaux du Mans (IMMM), UMR CNRS 6283, Université du Maine, Av. Olivier Messiaen, 72085 Le Mans Cedex 9 (France)
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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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Li BS, Wei B, Goh MC. Direct visualization of the formation of RecA/dsDNA complexes at the single-molecule level. Micron 2012; 43:1073-5. [PMID: 22633148 DOI: 10.1016/j.micron.2012.04.016] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2011] [Revised: 03/20/2012] [Accepted: 04/29/2012] [Indexed: 10/28/2022]
Abstract
The assembly of RecA on linear dsDNA with ATPγS in the reaction was elucidated using atomic force microscopy (AFM) on a single-molecule level. It was found that assembly generally (∼95%) proceeded from a single nucleation site that started from one end of the DNA strand. About 5% of the complexes were formed starting either from both ends or from the middle of dsDNA strand. In all these cases, the RecA coating was contiguous for each region suggesting the binding of RecA to DNA is cooperative. The AFM observation provides direct experimental evidence to show how RecA binds to linear dsDNA in the presence of ATPγS.
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Affiliation(s)
- Bing Shi Li
- School of Chemistry and Chemical Engineering, Shenzhen University, University of Toronto, M5S 3H6 Toronto, Ontario, Canada.
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Ahmed T, Kilina S, Das T, Haraldsen JT, Rehr JJ, Balatsky AV. Electronic fingerprints of DNA bases on graphene. NANO LETTERS 2012; 12:927-931. [PMID: 22257137 DOI: 10.1021/nl2039315] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
Abstract
We calculate the electronic local density of states (LDOS) of DNA nucleotide bases (A,C,G,T), deposited on graphene. We observe significant base-dependent features in the LDOS in an energy range within a few electronvolts of the Fermi level. These features can serve as electronic fingerprints for the identification of individual bases in scanning tunneling spectroscopy (STS) experiments that perform image and site dependent spectroscopy on biomolecules. Thus the fingerprints of DNA-graphene hybrid structures may provide an alternative route to DNA sequencing using STS.
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Affiliation(s)
- Towfiq Ahmed
- Department of Physics, University of Washington, Seattle, Washington 98195, USA.
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6
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Li BS, Goh MC. Direct evidence of the role of ATPγS in the binding of single-stranded binding protein (Escherichia coli) and RecA to single-stranded DNA. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2010; 26:14755-14758. [PMID: 20722443 DOI: 10.1021/la102347b] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/29/2023]
Abstract
To gain insight into the influence of ATPγS on the competitive binding of RecA and single-stranded binding protein (SSB) on single-stranded DNA (ssDNA), AFM imaging was used to examine the three-dimensional structures of the different complexes formed by the binding of the two proteins on ssDNA in the presence and absence of ATPγS. In the presence of ATPγS, RecA attaches to ssDNA, displacing SSB, to form continuous binding regions that caused considerable elongation of the strand. When ATPγS is absent, RecA could not compete with SSB and only binds at a few sites that correspond to the vacancy in ssDNA left when SSB unbinds. These results provide direct evidence that, while SSB binding affinity to DNA is substantially higher than that of RecA, the presence of ATPγS is sufficient to alter the events and enable RecA coating of DNA.
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Affiliation(s)
- Bing Shi Li
- Department of Chemistry and Institute for Optical Sciences, University of Toronto, Toronto, Ontario, M5S 3H6 Canada.
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7
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Smeets RMM, Kowalczyk SW, Hall AR, Dekker NH, Dekker C. Translocation of RecA-coated double-stranded DNA through solid-state nanopores. NANO LETTERS 2009; 9:3089-3096. [PMID: 19053490 DOI: 10.1021/nl803189k] [Citation(s) in RCA: 94] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/27/2023]
Abstract
We report translocation of double-stranded DNA (dsDNA) molecules that are coated with RecA protein through solid-state nanopores. Translocation measurements show current-blockade events with a wide variety in time duration (10-4-10-1 s) and conductance blockade values (3-14 nS). Large blockades (11.4+/-0.7 nS) are identified as being caused by translocations of RecA-dsDNA filaments. We confirm these results through a variety of methods, including changing molecular length and using an optical tweezer system to deliver bead-functionalized molecules to the nanopore. We further distinguish two different regimes of translocation: a low-voltage regime (<150 mV) in which the event rate increases exponentially with voltage, and a high-voltage regime in which it remains constant. Our results open possibilities for a variety of future experiments with (partly) protein-coated DNA molecules, which is interesting for both fundamental science and genomic screening applications.
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Affiliation(s)
- R M M Smeets
- KaVli Institute of Nanoscience, Delft University of Technology, Lorentzweg 1, 2628 CJ Delft, The Netherlands
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Chen YY, Wu CC, Hsu JL, Peng HL, Chang HY, Yew TR. Surface rigidity change of Escherichia coli after filamentous bacteriophage infection. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2009; 25:4607-4614. [PMID: 19366225 DOI: 10.1021/la8036346] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/27/2023]
Abstract
In this study, the feasibility using atomic force microscopy (AFM) to study the interaction between bacteriophages (phages) and bacteria in situ was demonstrated here. Filamentous phage M13 specifically infects the male Escherichia coli, which expresses F-pili. After infection, E. coli become fragile and grows at a slower rate. AFM provides a powerful tool for investigating these changes in a near-physiological environment. Using high-resolution AFM in phosphate-buffered saline, the damage to the lipopolysaccharide (LPS) layer on the outer membrane of the M13 phage-infected E. coli was observed. The membrane became smoother and more featureless compared to those that were not infected. Besides, the force-distance (f-d) curves were measured to reveal the surface rigidity change in E. coli after M13 phage infection. The effective spring constant and Young's modulus of E. coli decreased after M13 phage infection. Furthermore, the AFM tip was pressed against E. coli to study the response of E. coli under load before and after M13 phage infection. The results showed that after infection E. coli became less rigid and the membrane was also damaged. However, the stiffness changes, including the spring constant and Young's modulus of E. coli, are negligible after M13 phage infection compared with those in previous reports, which may be one of the reasons that E. coli still can maintain its viability after filamentous phage infection.
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Affiliation(s)
- Yi-Yang Chen
- Department of Materials Science and Engineering, National Tsing-Hua University, Hsinchu, Taiwan
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9
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Guo C, Song Y, Wang L, Sun L, Sun Y, Peng C, Liu Z, Yang T, Li Z. Atomic Force Microscopic Study of Low Temperature Induced Disassembly of RecA−dsDNA Filaments. J Phys Chem B 2008; 112:1022-7. [DOI: 10.1021/jp077233y] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Cunlan Guo
- State Key Laboratory of Electroanalytical Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun, Jilin 130022, People's Republic of China, and Graduate School of the Chinese Academy of Sciences, Beijing 100039, People's Republic of China
| | - Yonghai Song
- State Key Laboratory of Electroanalytical Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun, Jilin 130022, People's Republic of China, and Graduate School of the Chinese Academy of Sciences, Beijing 100039, People's Republic of China
| | - Li Wang
- State Key Laboratory of Electroanalytical Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun, Jilin 130022, People's Republic of China, and Graduate School of the Chinese Academy of Sciences, Beijing 100039, People's Republic of China
| | - Lanlan Sun
- State Key Laboratory of Electroanalytical Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun, Jilin 130022, People's Republic of China, and Graduate School of the Chinese Academy of Sciences, Beijing 100039, People's Republic of China
| | - Yujing Sun
- State Key Laboratory of Electroanalytical Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun, Jilin 130022, People's Republic of China, and Graduate School of the Chinese Academy of Sciences, Beijing 100039, People's Republic of China
| | - Chongyang Peng
- State Key Laboratory of Electroanalytical Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun, Jilin 130022, People's Republic of China, and Graduate School of the Chinese Academy of Sciences, Beijing 100039, People's Republic of China
| | - Zhelin Liu
- State Key Laboratory of Electroanalytical Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun, Jilin 130022, People's Republic of China, and Graduate School of the Chinese Academy of Sciences, Beijing 100039, People's Republic of China
| | - Tao Yang
- State Key Laboratory of Electroanalytical Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun, Jilin 130022, People's Republic of China, and Graduate School of the Chinese Academy of Sciences, Beijing 100039, People's Republic of China
| | - Zhuang Li
- State Key Laboratory of Electroanalytical Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun, Jilin 130022, People's Republic of China, and Graduate School of the Chinese Academy of Sciences, Beijing 100039, People's Republic of China
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Affiliation(s)
- Karel Klepárník
- Institute of Analytical Chemistry, Academy of Sciences of the Czech Republic, Veveří 97, CZ-602 00 Brno, Czech Republic
| | - Petr Boček
- Institute of Analytical Chemistry, Academy of Sciences of the Czech Republic, Veveří 97, CZ-602 00 Brno, Czech Republic
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11
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Bui MPN, Baek TJ, Seong GH. Gold nanoparticle aggregation-based highly sensitive DNA detection using atomic force microscopy. Anal Bioanal Chem 2007; 388:1185-90. [PMID: 17534606 DOI: 10.1007/s00216-007-1354-4] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2007] [Revised: 05/03/2007] [Accepted: 05/08/2007] [Indexed: 11/30/2022]
Abstract
The potential ability of atomic force microscopy (AFM) as a quantitative bioanalysis tool is demonstrated by using gold nanoparticles as a size enhancer in a DNA hybridization reaction. Two sets of probe DNA were functionalized on gold nanoparticles and sandwich hybridization occurred between two probe DNAs and target DNA, resulting in aggregation of the nanoparticles. At high concentrations of target DNA in the range from 100 nM to 10 microM, the aggregation of gold nanoparticles was determined by monitoring the color change with UV-vis spectroscopy. The absorption spectra broadened after the exposure of DNA-gold nanoparticles to target DNA and a new absorption band at wavelengths >600 nm was observed. However, no differences were observed in the absorption spectra of the gold nanoparticles at low concentrations of target DNA (10 pM to 10 nM) due to insufficient aggregation. AFM was used as a biosensing tool over this range of target DNA concentrations in order to monitor the aggregation of gold nanoparticles and to quantify the concentration of target DNA. Based on the AFM images, we successfully evaluated particle number and size at low concentrations of target DNA. The calibration curve obtained when mean particle aggregate diameter was plotted against concentration of target DNA showed good linearity over the range 10 pM to 10 nM, the working range for quantitative target DNA analysis. This AFM-based DNA detection technique was three orders of magnitude more sensitive than a DNA detection method based on UV-vis spectroscopy.
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12
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Escudé C, Roulon T, Lyonnais S, Le Cam E. Multiple topological labeling for imaging single plasmids. Anal Biochem 2007; 362:55-62. [PMID: 17250797 DOI: 10.1016/j.ab.2006.12.028] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2006] [Revised: 12/06/2006] [Accepted: 12/13/2006] [Indexed: 11/18/2022]
Abstract
Sequence-specific labeling methods for double-stranded DNA are required for mapping protein binding sites or specific DNA structures on circular DNA molecules by high-resolution imaging techniques such as electron and atomic force microscopies. Site-specific labeling can be achieved by ligating a DNA fragment to a stem-loop-triplex-forming oligonucleotide, thereby forming a topologically linked complex. The superhelicity of the plasmid is not altered and the process can be applied to two different target sites simultaneously, using DNA fragments of different sizes. Observation of the labeled plasmids by electron microscopy revealed that, under conditions where the triple helices were stable, the two labels were located at 339+/-34 bp from one another, in agreement with the distance between the two target sequences for triple helix formation (350 bp). Under conditions where the triple helices were not stable, the short DNA fragments could slide away from their target site. The concomitant attachment of two different stable labels makes it possible, for the first time to our knowledge, to label a circular DNA molecule and obtain information on its direction. In addition to its potential applications as a tool for structural investigations of single DNA molecules and their interactions with proteins, this DNA labeling method may also prove useful in biotechnology and gene therapy.
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Affiliation(s)
- Christophe Escudé
- Département Régulations, Développement et Diversité Moléculaire, USM 0503 Muséum National d'Histoire Naturelle, INSERM U565, CNRS UMR5153, Case postale 26, 43 Rue Cuvier, 75231 Paris Cedex 05, France.
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Kim NH, Baek TJ, Park HG, Seong GH. Highly Sensitive Biomolecule Detection on a Quartz Crystal Microbalance Using Gold Nanoparticles as Signal Amplification Probes. ANAL SCI 2007; 23:177-81. [PMID: 17297229 DOI: 10.2116/analsci.23.177] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
We report here a novel strategy for the high-sensitive detection of target biomolecules with very low concentrations on a quartz crystal microbalance (QCM) device using gold nanoparticles as signal enhancement probes. By employing a streptavidin-biotin interaction as a model system, we could prepare biotin-conjugated gold nanoparticles maintaining good dispersion and long-term stability by controlling the biotin density on the surface of gold nanoparticles that have been investigated by UV-vis spectra and AFM images. These results showed that 10 microM N-(6-[biotinamido]hexyl)-3'-(2'-pyridyldithio)propionamide (biotin-HPDP) was the critical concentration to prevent the nonspecific aggregation of gold nanoparticles in this system. For sensing streptavidin target molecules by QCM, biotinylated BSA was absorbed on the Au surface of the QCM electrode and subsequent coupling of the target streptavidin to the biotin in the sensing interface followed. Amplification of the sensing process was performed by the interaction of the target streptavidin on the sensing surface with gold nanoparticles modified with 10 microM biotin-HPDP. The biotinylated gold nanoparticles were used as signal amplification probes to improve the detection limit, which was 50 ng/ml, of the streptavidin detection system without signal enhancement, and the calibration curve determined for the net frequency changes showed good linearity over a wide range from 1 ng/ml to 10 microg/ml for the quantitative streptavidin target molecule analysis. In addition, the measured dissipation changes suggested that the layer of biotin-BSA adsorbed on the Au electrode and the streptavidin layer assembled on the biotin-BSA surface were highly compact and rigid. On the other hand, the structure formed by the biotinylated gold nanoparticles on the streptavidin layer was flexible and dissipative, being elongated outward from the sensing surface.
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Affiliation(s)
- Nam Hyun Kim
- Department of Applied Chemistry, Hanyang University, Ansan, South Korea
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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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Li BS, Sattin BD, Goh MC. Direct and real-time visualization of the disassembly of a single RecA-DNA-ATPgammaS complex using AFM imaging in fluid. NANO LETTERS 2006; 6:1474-8. [PMID: 16834432 DOI: 10.1021/nl060862j] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/10/2023]
Abstract
RecA disassembly from circular double-stranded DNA (dsDNA) was studied by atomic force microscopy (AFM) imaging in fluid on a single molecule scale. The RecA/DNA complex was formed in the presence of ATPgammaS, and the disassembly was then initiated by buffer exchange to rinse off ATPgammaS. Performing AFM imaging in fluid allowed direct and real-time visualization of the disassembly of RecA from dsDNA in solution. It was found that RecA disassembly commenced from multiple sites both in deionized water and in buffer; the areas where RecA dissociated showed the appearance of "gaps" in the filamentous structure. RecA further disassembled either through the already existing "gaps" or by generation of new gaps. The disassembly was slower in buffer than in deionized water, suggesting that ions also contribute to the stabilization of the complex. RecA hexamers and monomers were observed in deionized water and in buffer, respectively, during the disassembly process.
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Affiliation(s)
- Bing Shi Li
- Department of Chemistry and Institute for Optical Sciences, University of Toronto, Ontario, Canada
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16
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Hilal N, Bowen W, Alkhatib L, Ogunbiyi O. A Review of Atomic Force Microscopy Applied to Cell Interactions with Membranes. Chem Eng Res Des 2006. [DOI: 10.1205/cherd05053] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
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18
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Shi WX, Larson RG. Atomic force microscopic study of aggregation of RecA-DNA nucleoprotein filaments into left-handed supercoiled bundles. NANO LETTERS 2005; 5:2476-81. [PMID: 16351198 DOI: 10.1021/nl051783v] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/05/2023]
Abstract
RecA and its complexes with double-stranded DNA (dsDNA) and single-stranded DNA (ssDNA) are responsible for homologous recombination and DNA repair. In this study, we have observed, by atomic force microscopy (AFM), two-filament left-handed superhelices of RecA-dsDNA filaments that further interwind into four- or six-filament bundles, in addition to previously reported left-handed bundles of three or six filaments. Also revealed are four-filament bundles formed by further interwinding of two intrafilament superhelices of individual filaments. Pitches of superhelices of RecA-DNA filaments are similar to each other regardless the number of component filaments, and those formed on Phix174 RFII dsDNA and pNEB206A dsDNA are measured as 339.3 +/- 6.2 nm (690 counts of pitch/2) and 321.6 +/- 11.7 nm (101 counts of pitch/2), respectively, consistent with earlier measurements made by electron microscopy with a much smaller sample size. The study of these structures provides insight into the self-interactions of RecA and RecA-like proteins, which are present in all living cells, and into the general phenomenon of bundling, which is relevant to both biological and nonbiological filaments.
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Affiliation(s)
- Wei-Xian Shi
- Department of Chemical Engineering, University of Michigan, 3074 H.H. Dow, 2300 Hayward Street, Ann Arbor, MI 48109-2136, USA
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Umemura K, Okada T, Kuroda R. Cooperativity and intermediate structures of single-stranded DNA binding-assisted RecA-single-stranded DNA complex formation studied by atomic force microscopy. SCANNING 2005; 27:35-43. [PMID: 15712756 DOI: 10.1002/sca.4950270107] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
The formation of a complex between RecA protein and single-stranded (ss) DNA was studied systematically by atomic force microscopy (AFM) by varying incubation time and the molecular ratio of RecA protein to single-stranded DNA binding (SSB) protein. New intermediate structures, such as small circular, tangled, and protruded structures in the absence of SSB and sharply turned structures in the presence of SSB, were clearly identified at the early stage of complex formation. These structures have probably resulted from competitive binding of RecA and SSB to DNA. After long incubation, only fully covered RecA-ssDNA and totally RecA-free SSB-ssDNA complexes were present regardless of RecA concentrations. Together with intermediate structures which consisted of only two parts, that is, ssDNA covered by SSB and by RecA proteins, the observation suggested strong neighbor cooperative binding of RecA to ssDNA assisted by SSB.
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Affiliation(s)
- K Umemura
- Joint Research Center for Atom Technology, Ibaraki
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Wicaksono DHB, Ebihara T, Funabashi H, Mie M, Yanagida Y, Aizawa M, Kobatake E. On-chip biosensing of estrogen receptor-α at single molecular level. Biosens Bioelectron 2004; 19:1573-9. [PMID: 15142590 DOI: 10.1016/j.bios.2003.12.028] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2003] [Revised: 12/11/2003] [Accepted: 12/11/2003] [Indexed: 11/20/2022]
Abstract
A novel method for detecting interaction between DNA and DNA-binding protein at single molecular level has been proposed. In this study, estrogen receptor-alpha (ER-alpha) was used for biosensing as the proof-example. A 518 bp-long (ca. 176 nm) DNA probe labeled with streptavidin at its 5'-terminus was prepared by inserting a consensus oligonucleotide sequence that binds to ER-alpha. A solution containing ER-alpha was dropped onto the Ni-treated mica substrate on which the DNA prove was previously immobilized, and it was observed by AFM. Specific binding of ER-alpha could be observed by measuring the distance between the site where binding occur, to the streptavidin label.
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Affiliation(s)
- Dedy H B Wicaksono
- Department of Biological Information, Graduate School of Bioscience and Biotechnology, Tokyo Institute of Technology, 4259 Nagatsuta, Midori-ku, Yokohama 226-8501, Japan
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21
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Wang L, Wang E. Controlled rearrangement of adsorbed undecanol films on mica surfaces induced by an atomic force microscopy tip. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2004; 20:2677-2682. [PMID: 15835136 DOI: 10.1021/la0354842] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
An undecanol film adsorbed on a mica surface was found to rearrange and spread in a position-controlled way induced by a tapping mode atomic force microscopy (AFM) probe. AFM images of varying scanning times showed that before forming an ordered monolayer the undecanol molecules were adsorbed on the mica surface in the disordered and disorganized status. With the proceeding of scanning, these undecanol molecules gradually formed an ordered and flat film. Such behavior was caused by the formation of a stable film and had never been reported for other alcohols.
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Affiliation(s)
- Li Wang
- State Key Laboratory of Electroanalytical Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun 130022, China
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22
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Santos NC, Castanho MARB. An overview of the biophysical applications of atomic force microscopy. Biophys Chem 2004; 107:133-49. [PMID: 14962595 DOI: 10.1016/j.bpc.2003.09.001] [Citation(s) in RCA: 126] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2002] [Revised: 07/30/2003] [Accepted: 09/04/2003] [Indexed: 11/27/2022]
Abstract
The potentialities of the atomic force microscopy (AFM) make it a tool of undeniable value for the study of biologically relevant samples. AFM is progressively becoming a usual benchtop technique. In average, more than one paper is published every day on AFM biological applications. This figure overcomes materials science applications, showing that 17 years after its invention, AFM has completely crossed the limits of its traditional areas of application. Its potential to image the structure of biomolecules or bio-surfaces with molecular or even sub-molecular resolution, study samples under physiological conditions (which allows to follow in situ the real time dynamics of some biological events), measure local chemical, physical and mechanical properties of a sample and manipulate single molecules should be emphasized.
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Affiliation(s)
- Nuno C Santos
- Instituto de Bioquímica/Instituto de Medicina Molecular, Faculdade de Medicina de Lisboa, Av. Prof. Egas Moniz, 1649-028 Lisbon, Portugal.
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23
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Mukhopadhyay R, Srivatsan SG, Verma S. Surface trapping and AFM detection of DNA topological intermediates generated from an oxidative chemical nuclease. Biochem Biophys Res Commun 2003; 308:165-9. [PMID: 12890496 DOI: 10.1016/s0006-291x(03)01351-2] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Abstract
Direct observation of DNA topological intermediates generated from a 'chemical nuclease' treatment has been made by atomic force microscopy (AFM). The intermediates were trapped at the mica-water interface and imaging was carried out in the dynamic force mode. Complete conversion from supercoiled circular state to relaxed circular/linear state has been observed over a time scale of 8 min. Implication of such studies in complementing gel electrophoresis data has been predicted.
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Affiliation(s)
- R Mukhopadhyay
- Department of Biological Sciences and Bioengineering, Indian Institute of Technology Kanpur, Kanpur, Uttar Pradesh 208016, India.
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24
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Seong GH, Yanagida Y, Aizawa M, Kobatake E. Atomic force microscopy identification of transcription factor NFkappaB bound to streptavidin-pin-holding DNA probe. Anal Biochem 2002; 309:241-7. [PMID: 12413457 DOI: 10.1016/s0003-2697(02)00303-2] [Citation(s) in RCA: 18] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
A novel method for identifying DNA-binding proteins from image analysis using AFM was developed. Here, transcription factor NFkappaB, which a well-studied example of transcription activator proteins, was used as a target protein. 5'-biotinlynated double-stranded DNA probe was labeled site specifically through high affinity with streptavidin. When the biotinylated DNA fragments were incubated with the streptavidin at a 1:2 molar ratio of DNA:streptavidin, the overall efficiency of labeling was over 90%. The double-stranded DNA probes were immobilized on a mica surface by the adsorption of streptavidin that attached to the 5'-end of DNA and applied for selection of the target protein NFkappaB in solution and then AFM was used to image the DNA probe-NFkappaB complexes. The length of the distance between 5'-labeled streptavidin and NFkappaB bound on DNA probes from AFM images is 0.64, the normalized position of the NFkappaB binding site, and this result is in close agreement with the expected 299 and 167bp values.
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Affiliation(s)
- Gi Hun Seong
- Department of Biological Information, Graduate School of Bioscience and Biotechnology, Tokyo Institute of Technology, 4259 Nagatsuta, Midori-ku, Yokohama 226-8501, Japan
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25
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Wu A, Li Z, Yu L, Wang H, Wang E. A relocated technique of atomic force microscopy (AFM) samples and its application in molecular biology. Ultramicroscopy 2002; 92:201-7. [PMID: 12213021 DOI: 10.1016/s0304-3991(02)00133-x] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
A kind of simple atomic force microscopy (AFM) relocated technique, which takes advantage of homemade sample locator system, is used for investigating repeatedly imaging of some specific species on the whole substrate (over 1 x 1 cm2) with resolution about 400 nm. As applications of this sample locator system, single extended DNA molecules and plasmid DNA network are shown in different AFM operational modes: tapping mode and contact mode with different tips after the substrates have been moved.
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Affiliation(s)
- Aiguo Wu
- Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Jilin
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26
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Seong GH, Kobatake E, Miura K, Nakazawa A, Aizawa M. Direct atomic force microscopy visualization of integration host factor-induced DNA bending structure of the promoter regulatory region on the Pseudomonas TOL plasmid. Biochem Biophys Res Commun 2002; 291:361-6. [PMID: 11846413 DOI: 10.1006/bbrc.2002.6443] [Citation(s) in RCA: 38] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Atomic force microscopy (AFM) was used to analyze DNA bending induced by integration host factor (IHF). The direct AFM visualization of IHF-DNA complexes on the OP1 promoter regulatory regions on the Pseudomonas TOL plasmid showed that there was no intrinsic DNA bend in the OP1 promoter region, but a sharp DNA bend was induced by binding of IHF to the region between the upstream regulatory sequence and the promoter sequence. The DNA bending angles were distributed with a mean bend angle of 123 degrees. The IHF-DNA complexes were shown to bend at the IHF binding site giving rise to an asymmetric structure. These results provide direct evidence that IHF is required functionally for activation of OP1 transcription and support the DNA-loop model that the sharp DNA bend induced by binding of IHF facilitates the contact between RNA polymerase bound by the promoter sequence and XylR protein attached to the upstream sequence in the OP1 promoter.
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Affiliation(s)
- Gi Hun Seong
- Department of Biological Information, Graduate School of Bioscience and Biotechnology, Tokyo Institute of Technology, 4259 Nagatsuta, Midori-ku, Yokohama 226-8501, Japan
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27
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Affiliation(s)
- Masuo AIZAWA
- Department of Biological Information, Graduate School of Bioscience and Biotechnology, Tokyo Institute of Technology
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