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Li BS, Huang X, Li H, Xia W, Xue S, Xia Q, Tang BZ. Solvent and Surface/Interface Effect on the Hierarchical Assemblies of Chiral Aggregation-Induced Emitting Molecules. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2019; 35:3805-3813. [PMID: 30767500 DOI: 10.1021/acs.langmuir.8b03358] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
The core of aggregation-induced emitting (AIE) molecules was their aggregation behavior. It was, in essence, a self-assembly process driven by noncovalent interactions, which were governed not only by the chemical structures of the molecules but also by the conditions where the self-assemblies were formed. The self-assemblies of two AIE molecules, tetraphenylethene (TPE) derivatives carrying one valine attachment (TPE-Val) and two valine attachments (TPE-2Val), were studied. Both kinds of molecules self-assembled into supramolecular helical fibers with different handedness upon the addition of poor solvent to their solution. However, when deposited on air/water interface, both kinds of molecules formed aligned elementary helical fibers instead of supramolecular fibers. The lateral solvophobic effect exerted by water molecules caused a shift of the original noncovalent balance between molecules and solvent; thus, the supramolecular helical assemblies were unraveled into aligned helical elementary fibers. Similar elementary assemblies were formed on the surface of 3-aminopropyl triethoxysilane-modified mica, confirming the lateral solvophobic effect on the self-assemblies of the molecules.
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Affiliation(s)
- Bing Shi Li
- College of Chemistry and Environmental Engineering , Shenzhen University , 1066 Xueyuan Avenue , Nanshan, Shenzhen 518055 , China
| | - Xuejiao Huang
- College of Chemistry and Environmental Engineering , Shenzhen University , 1066 Xueyuan Avenue , Nanshan, Shenzhen 518055 , China
| | - Hongkun Li
- College of Chemistry and Environmental Engineering , Shenzhen University , 1066 Xueyuan Avenue , Nanshan, Shenzhen 518055 , China
- The Hong Kong University of Science & Technology (HKUST)-Shenzhen Research Institute , No. 9 Yuexing 1st Road, South Area, Hi-tech Park , Nanshan, Shenzhen 518057 , China
- Laboratory of Advanced Optoelectronic Materials, College of Chemistry, Chemical Engineering and Materials Science , Soochow University , 50 Donghuan Road , Suzhou 215123 , China
| | - Wenjuan Xia
- College of Chemistry and Environmental Engineering , Shenzhen University , 1066 Xueyuan Avenue , Nanshan, Shenzhen 518055 , China
| | - Shan Xue
- College of Chemistry and Environmental Engineering , Shenzhen University , 1066 Xueyuan Avenue , Nanshan, Shenzhen 518055 , China
| | - Qing Xia
- College of Chemistry and Environmental Engineering , Shenzhen University , 1066 Xueyuan Avenue , Nanshan, Shenzhen 518055 , China
| | - Ben Zhong Tang
- The Hong Kong University of Science & Technology (HKUST)-Shenzhen Research Institute , No. 9 Yuexing 1st Road, South Area, Hi-tech Park , Nanshan, Shenzhen 518057 , China
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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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Sanchez H, Reuter M, Yokokawa M, Takeyasu K, Wyman C. Taking it one step at a time in homologous recombination repair. DNA Repair (Amst) 2014; 20:110-118. [PMID: 24636751 DOI: 10.1016/j.dnarep.2014.02.012] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2013] [Revised: 02/07/2014] [Accepted: 02/11/2014] [Indexed: 01/10/2023]
Abstract
The individual steps in the process of homologous recombination are particularly amenable to analysis by single-molecule imaging and manipulation experiments. Over the past 20 years these have provided a wealth of new information on the DNA transactions that make up this vital process. Exciting progress in developing new tools and techniques to analyze more complex components, dynamic reaction steps and molecular coordination continues at a rapid pace. Here we highlight recent results and indicate some emerging techniques likely to produce the next stage of advanced insight into homologous recombination. In this and related fields the future is bright.
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Affiliation(s)
- Humberto Sanchez
- Department of Genetics, Cancer Genomics Center, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Marcel Reuter
- Department of Genetics, Cancer Genomics Center, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Masatoshi Yokokawa
- Graduate School of Pure and Applied Science, University of Tsukuba, Japan
| | | | - Claire Wyman
- Department of Genetics, Cancer Genomics Center, Erasmus University Medical Center, Rotterdam, The Netherlands; Department of Radiation Oncology, Erasmus University Medical Center, Rotterdam, The Netherlands.
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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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Gallyamov MO. Scanning Force Microscopy as Applied to Conformational Studies in Macromolecular Research. Macromol Rapid Commun 2011; 32:1210-46. [DOI: 10.1002/marc.201100150] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2011] [Revised: 04/06/2011] [Indexed: 01/17/2023]
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Three powerful research tools from single cells into single molecules: AFM, laser tweezers, and Raman spectroscopy. Appl Biochem Biotechnol 2011; 165:485-96. [PMID: 21556902 DOI: 10.1007/s12010-011-9267-2] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2010] [Accepted: 04/18/2011] [Indexed: 01/11/2023]
Abstract
By using three physical techniques (atomic force microscopy (AFM), laser tweezers, and Raman spectroscopy), many excellent works in single-cell/molecule research have been accomplished. In this review, we present a brief introduction to the principles of these three techniques, and their capabilities toward single-cell/molecule research are highlighted. Afterward, the advances in single-cell/molecule research that have been facilitated by these three techniques are described. Following this, their complementary assets for single-cell/molecule research are analyzed, and the necessity of integrating the functions of these three techniques into one instrument is proposed.
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Zhang L, Ju Y, Hosoi A, Fujimoto A. Microwave atomic force microscopy imaging for nanometer-scale electrical property characterization. THE REVIEW OF SCIENTIFIC INSTRUMENTS 2010; 81:123708. [PMID: 21198033 DOI: 10.1063/1.3525058] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/30/2023]
Abstract
We introduce a new type of microscopy which is capable of investigating surface topography and electrical property of conductive and dielectric materials simultaneously on a nanometer scale. The microwave atomic force microscopy is a combination of the principles of the scanning probe microscope and the microwave-measurement technique. As a result, under the noncontact AFM working conditions, we successfully generated a microwave image of a 200-nm Au film coating on a glass wafer substrate with a spatial resolution of 120 nm and a measured voltage difference of 19.2 mV between the two materials.
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Affiliation(s)
- Lan Zhang
- Department of Mechanical Science and Engineering, Nagoya University, Furo-Cho, Chikusa-ku, Nagoya 4648603, Japan
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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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Li BS, Goh MC. Direct visualization of the formation and structure of RecA/dsDNA complexes. Micron 2010; 41:227-31. [DOI: 10.1016/j.micron.2009.10.011] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2009] [Accepted: 10/26/2009] [Indexed: 10/20/2022]
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Hilario J, Kowalczykowski SC. Visualizing protein-DNA interactions at the single-molecule level. Curr Opin Chem Biol 2009; 14:15-22. [PMID: 19945909 DOI: 10.1016/j.cbpa.2009.10.035] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2009] [Revised: 10/25/2009] [Accepted: 10/27/2009] [Indexed: 10/20/2022]
Abstract
Recent advancements in single-molecule methods have allowed researchers to directly observe proteins acting on their DNA targets in real-time. Single-molecule imaging of protein-DNA interactions permits detection of the dynamic behavior of individual complexes that otherwise would be obscured in ensemble experiments. The kinetics of these processes can be monitored directly, permitting identification of unique subpopulations or novel reaction intermediates. Innovative techniques have been developed to isolate and manipulate individual DNA or protein molecules, and to visualize their interactions. The actions of proteins that have been visualized include: duplex DNA unwinding, DNA degradation, DNA packaging, translocation on DNA, sliding, superhelical twisting, and DNA bending, extension, and condensation. These single-molecule studies have provided new insights into nearly all aspects of DNA metabolism. Here we focus primarily on recent advances in fluorescence imaging and mechanical detection of individual protein-DNA complexes, with emphasis on selected proteins involved in DNA recombination: DNA helicases, DNA translocases, and DNA strand exchange proteins.
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Affiliation(s)
- Jovencio Hilario
- Department of Microbiology, University of California, Davis, CA 95616-8665, USA.
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SONG Y, WANG L, ZHAO S, LIAN W, LI Z. Disassembly of DNA-ligand on mica surface: atomic force microscopy studies. J Microsc 2009; 234:130-6. [DOI: 10.1111/j.1365-2818.2009.03154.x] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
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Gallyamov MO, Qin S, Matyjaszewski K, Khokhlov A, Möller M. Motion of single wandering diblock-macromolecules directed by a PTFE nano-fence: real time SFM observations. Phys Chem Chem Phys 2009; 11:5591-7. [DOI: 10.1039/b819011a] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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Leuba SH, Anand SP, Harp JM, Khan SA. Expedient placement of two fluorescent dyes for investigating dynamic DNA protein interactions in real time. Chromosome Res 2008; 16:451-67. [PMID: 18461484 PMCID: PMC2413326 DOI: 10.1007/s10577-008-1235-5] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Many questions in molecular and cellular biology can be reduced to questions about 'who talks to whom, when and how frequently'. Here, we review approaches we have used with single-pair fluorescence resonance energy transfer (spFRET) to follow the motions between two well-placed fluorescent probes to ask similar questions. We describe two systems. We have used a nucleosomal system in which the naked DNA molecule has the acceptor and donor dyes too far apart for FRET to occur whereas the dyes are close enough in the reconstituted nucleosome for FRET. As these individual nucleosomes were tethered on a surface, we could follow dynamics in the repositioning of these two dyes, inferring that nucleosomes stochastically and reversibly open and close. These results imply that most of the DNA on the nucleosome can be sporadically accessible to regulatory proteins and proteins that track the DNA double helix. In the case of following the binding of recombination protein RecA to double-stranded DNA (dsDNA) and the RecA filament displacement by DNA helicase motor PcrA, the dsDNA template is prepared with the two dyes close enough to each other to generate high FRET. Binding of the RecA molecules to form a filament lengthens the dsDNA molecule 1.5-fold and reduces the FRET accordingly. Once added, DNA motor protein helicase PcrA can displace the RecA filament with concomitant return of the DNA molecule to its original B-form and high FRET state. Thus, appropriately placed fluorescent dyes can be used to monitor conformational changes occurring in DNA and or proteins and provide increased sensitivity for investigating dynamic DNA-protein interactions in real time.
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Affiliation(s)
- Sanford H Leuba
- Department of Cell Biology, University of Pittsburgh School of Medicine and Swanson School of Engineering, Petersen Institute of NanoScience and Engineering and University of Pittsburgh Cancer Institute, Pittsburgh, PA, 15213, USA.
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Liao Y, You J, Shi T, An L, Dutta PK. Phase behavior and dewetting for polymer blend films studied by in situ AFM and XPS: from thin to ultrathin films. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2007; 23:11107-11. [PMID: 17894511 DOI: 10.1021/la701761p] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/17/2023]
Abstract
In this work, the film thickness (l0) effect on the phase and dewetting behaviors of the blend film of poly(methyl methacrylate)/poly(styrene-ran-acrylonitrile) (PMMA/SAN) has been studied by in situ atomic force microscopy (AFM) and X-ray photoelectron spectroscopy (XPS). The thinner film shows the more compatibility of the blend, and the phase separation of the film occurs at l0>5Rg (radius of gyration). An initially time-independent q*, the characteristic wavenumber of the phase image, which is in good agreement of Cahn's linearized theory for the early stage of spinodal decomposition, has been obtained in real space and discussed in detail. For 5Rg>l0>3Rg, a "pseudo-dewetting/(phase separation+wetting)" behavior occurs, where the pseudo-wetting is driven by the concentration fluctuation mechanism. For l0<3Rg, a "real dewetting/(phase separation+wetting)" behavior occurs.
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Affiliation(s)
- Yonggui Liao
- State Key Laboratory of Polymer Physics and Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun 130022, People's Republic of China
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Singleton SF, Roca AI, Lee AM, Xiao J. Probing the structure of RecA-DNA filaments. Advantages of a fluorescent guanine analog. Tetrahedron 2007; 63:3553-3566. [PMID: 17955055 PMCID: PMC2031864 DOI: 10.1016/j.tet.2006.10.092] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
The RecA protein of Escherichia coli plays a crucial roles in DNA recombination and repair, as well as various aspects of bacterial pathogenicity. The formation of a RecA-ATP-ssDNA complex initiates all RecA activities and yet a complete structural and mechanistic description of this filament has remained elusive. An analysis of RecA-DNA interactions was performed using fluorescently labeled oligonucleotides. A direct comparison was made between fluorescein and several fluorescent nucleosides. The fluorescent guanine analog 6-methylisoxanthopterin (6MI) demonstrated significant advantages over the other fluorophores and represents an important new tool for characterizing RecA-DNA interactions.
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Affiliation(s)
- Scott F. Singleton
- Division of Medicinal Chemistry & Natural Products, School of Pharmacy, The University of North Carolina at Chapel Hill, CB 7360, Chapel Hill, NC 27599-7360, USA
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