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Shi X, Li H, Yao S, Ding Y, Lin X, Xu H, Liu Y, Zhao C, Zhang T, Wang J. A CRISPR/Cas12a-assisted bacteria quantification platform combined with magnetic covalent organic frameworks and hybridization chain reaction. Food Chem 2024; 440:138196. [PMID: 38104450 DOI: 10.1016/j.foodchem.2023.138196] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2023] [Revised: 12/05/2023] [Accepted: 12/10/2023] [Indexed: 12/19/2023]
Abstract
The total bacterial count is an important indicator of food contamination in food safety supervision and management. Recently, the CRISPR/Cas12a system integrated with nucleic acid amplification has increasingly shown tremendous potential in microorganism detection. However, a general quantification strategy for total bacteria count based on the CRISPR/Cas12a system has not yet been developed. Herein, we established a sensitive bacterial quantification strategy based on the CRISPR/Cas12a system combined with magnetic covalent organic frameworks (MCOFs) and hybridization chain reaction (HCR). MCOFs acted as a carrier, adsorbing the ssDNA as HCR trigger sequence through π-π stacking. Then, the HCR circuit produces DNA duplexes containing the PAM sequences that activate the trans-cleavage activity of Cas12a for further signal amplification. Under the optimal conditions, the proposed method can quantify total bacteria in 50 min with a minimum detection concentration of 10 CFU/mL. The successful applications in food samples confirmed the feasibility and broad application prospects.
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Affiliation(s)
- Xuening Shi
- School of Public Health, Jilin University, Changchun 130021, China; State Key Laboratory for Diagnosis and Treatment of Severe Zoonotic Infectious Diseases, Jilin University, Changchun 130021,China.
| | - Hang Li
- School of Public Health, Jilin University, Changchun 130021, China.
| | - Shuo Yao
- School of Public Health, Jilin University, Changchun 130021, China.
| | - Yukun Ding
- School of Public Health, Jilin University, Changchun 130021, China.
| | - Xiuzhu Lin
- State Key Laboratory of Integrated Optoelectronics, College of Electronic Science and Engineering, Jilin University, Changchun 130012, China.
| | - Hui Xu
- School of Public Health, Jilin University, Changchun 130021, China.
| | - Yi Liu
- School of Public Health, Jilin University, Changchun 130021, China.
| | - Chao Zhao
- School of Public Health, Jilin University, Changchun 130021, China.
| | - Tong Zhang
- State Key Laboratory of Integrated Optoelectronics, College of Electronic Science and Engineering, Jilin University, Changchun 130012, China.
| | - Juan Wang
- School of Public Health, Jilin University, Changchun 130021, China; State Key Laboratory for Diagnosis and Treatment of Severe Zoonotic Infectious Diseases, Jilin University, Changchun 130021,China.
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2
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Hou J, Li N, Zhang W, Zhang W. Exploring the impact of PEGylation on the cell-nanomicelle interactions by AFM-based single-molecule force spectroscopy and force tracing. Acta Biomater 2023; 157:310-320. [PMID: 36535567 DOI: 10.1016/j.actbio.2022.12.020] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2022] [Revised: 11/15/2022] [Accepted: 12/12/2022] [Indexed: 12/23/2022]
Abstract
PEGylation has been considered the gold standard method for the modification of various drug delivery systems since the last century. However, the impact of PEGylation on the dynamic interaction between drug carriers and cell membranes has not been quantitatively clarified. Herein, the cellular binding and receptor-mediated endocytosis of a model PEGylated polypeptide nanomicelle were systematically investigated at the single-particle level using AFM-based single-molecule force spectroscopy (SMFS) and force tracing. A self-assembled elastin-like polypeptide (ELP) nanomicelle, which is capable of cross-linking, gastrin-releasing peptide (GRP) modification, and PEGylation was prepared. The cross-linked ELP-based nanomicelles exhibited outstanding stability in a broad temperature range of 4-40 °C, which facilitate the drug loading, as well as our cell-nanomicelle study at the single particle level. The unbinding force between the cross-linked ELP-based nanomicelles and the GRP receptor (GRPR)-containing cell (PC-3) membranes was quantitatively measured by AFM-SMFS. It is found that the PEGylated GRP-displaying nanomicelles exhibit the highest unbinding force, indicating the enhanced specific binding effect of PEGylation. Furthermore, the receptor-mediated endocytosis of the cross-linked ELP-based nanomicelles was monitored with the help of force tracing based on AFM-SMFS. Our results show that PEGylation decreases the endocytic force, duration, and engulfment depth of the PEGylated GRP-displaying nanomicelles, but increases their endocytic velocity, which results from the elimination of non-specific interactions during endocytosis. These observations demonstrate the diverse and complex roles of PEGylation on the interaction of polypeptide nanomicelles to cell membranes and may shed light on the rational design of organic polymer-based drug delivery systems aiming for active and passive targeting strategies. STATEMENT OF SIGNIFICANCE: A self-assembled elastin-like polypeptide (ELP) nanomicelle, which can be easily cross-linked, gastrin-releasing peptide (GRP) modified, and PEGylated, is designed. The AFM-SMFS experiment shows that PEGylation can enhance specific binding of the nanomicelles to the receptors on cell membranes. The force tracing experiment indicates that PEGylation decreases the endocytic force as well as engulfment depth of the nanomicelles through the elimination of non-specific interactions. PEGylation can benefit the drug delivery systems aiming at active targeting, while might not be an ideal modification for drug carriers designed for passive targeting, whose cellular uptake mainly depends on non-specific interactions.
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Affiliation(s)
- Jue Hou
- State Key Laboratory of Supramolecular Structure and Materials, Center for Supramolecular Chemical Biology, College of Chemistry, Jilin University, Changchun, 130012, PR China
| | - Nan Li
- State Key Laboratory of Supramolecular Structure and Materials, Center for Supramolecular Chemical Biology, College of Chemistry, Jilin University, Changchun, 130012, PR China
| | - Wei Zhang
- State Key Laboratory of Supramolecular Structure and Materials, Center for Supramolecular Chemical Biology, College of Chemistry, Jilin University, Changchun, 130012, PR China; College of Chemistry, Jilin University, Changchun 130012, PR China.
| | - Wenke Zhang
- State Key Laboratory of Supramolecular Structure and Materials, Center for Supramolecular Chemical Biology, College of Chemistry, Jilin University, Changchun, 130012, PR China.
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3
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Li N, Xu Z, Zheng S, Dai H, Wang L, Tian Y, Dong Z, Jiang L. Superamphiphilic TiO 2 Composite Surface for Protein Antifouling. ADVANCED MATERIALS (DEERFIELD BEACH, FLA.) 2021; 33:e2003559. [PMID: 33984172 DOI: 10.1002/adma.202003559] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/25/2020] [Revised: 03/18/2021] [Indexed: 06/12/2023]
Abstract
Unwanted protein adsorption deteriorates fouling processes and reduces analytical device performance. Wettability plays an important role in protein adsorption by affecting interactions between proteins and surfaces. However, the principles of protein adsorption are not completely understood, and surface coatings that exhibit resistance to protein adsorption and long-term stability still need to be developed. Here, a nanostructured superamphiphilic TiO2 composite (TiO2 /SiO2 ) coating that can effectively prevent nonspecific protein adsorption on water/solid interfaces is reported. The confined water on the superamphiphilic surface enables a low adhesion force and the formation of an energy barrier that plays a key role in preventing protein adsorption. This adaptive design protects the capillary wall from fouling in a harsh environment during the bioanalysis of capillary electrophoresis and is further extended to applications in multifunctional microfluidics for liquid transportation. This facile approach is not only perfectly applied in channels with complicated configurations but may also offer significant insights into the design of advanced superwetting materials to control biomolecule adhesion in biomedical devices, microfluidics, and biological assays.
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Affiliation(s)
- Ning Li
- CAS Key Laboratory of Bio-Inspired Materials and Interface Sciences, Technical Institute of Physics and Chemistry, Chinese Academy of Sciences, Beijing, 100190, P. R. China
- Key Laboratory of Bio-Inspired Smart Interfacial Science and Technology of Ministry of Education, Beijing Advanced Innovation Center for Biomedical Engineering, School of Chemistry, Beihang University, Beijing, 100191, P. R. China
| | - Zhe Xu
- Key Laboratory of Bio-Inspired Smart Interfacial Science and Technology of Ministry of Education, Beijing Advanced Innovation Center for Biomedical Engineering, School of Chemistry, Beihang University, Beijing, 100191, P. R. China
| | - Shuang Zheng
- CAS Key Laboratory of Bio-Inspired Materials and Interface Sciences, Technical Institute of Physics and Chemistry, Chinese Academy of Sciences, Beijing, 100190, P. R. China
| | - Haoyu Dai
- CAS Key Laboratory of Bio-Inspired Materials and Interface Sciences, Technical Institute of Physics and Chemistry, Chinese Academy of Sciences, Beijing, 100190, P. R. China
| | - Li Wang
- Key Laboratory of Bio-Inspired Smart Interfacial Science and Technology of Ministry of Education, Beijing Advanced Innovation Center for Biomedical Engineering, School of Chemistry, Beihang University, Beijing, 100191, P. R. China
| | - Ye Tian
- CAS Key Laboratory of Bio-Inspired Materials and Interface Sciences, Technical Institute of Physics and Chemistry, Chinese Academy of Sciences, Beijing, 100190, P. R. China
| | - Zhichao Dong
- CAS Key Laboratory of Bio-Inspired Materials and Interface Sciences, Technical Institute of Physics and Chemistry, Chinese Academy of Sciences, Beijing, 100190, P. R. China
| | - Lei Jiang
- CAS Key Laboratory of Bio-Inspired Materials and Interface Sciences, Technical Institute of Physics and Chemistry, Chinese Academy of Sciences, Beijing, 100190, P. R. China
- Key Laboratory of Bio-Inspired Smart Interfacial Science and Technology of Ministry of Education, Beijing Advanced Innovation Center for Biomedical Engineering, School of Chemistry, Beihang University, Beijing, 100191, P. R. China
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4
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Bocanegra R, Ismael Plaza GA, Pulido CR, Ibarra B. DNA replication machinery: Insights from in vitro single-molecule approaches. Comput Struct Biotechnol J 2021; 19:2057-2069. [PMID: 33995902 PMCID: PMC8085672 DOI: 10.1016/j.csbj.2021.04.013] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2021] [Revised: 04/03/2021] [Accepted: 04/03/2021] [Indexed: 11/16/2022] Open
Abstract
The replisome is the multiprotein molecular machinery that replicates DNA. The replisome components work in precise coordination to unwind the double helix of the DNA and replicate the two strands simultaneously. The study of DNA replication using in vitro single-molecule approaches provides a novel quantitative understanding of the dynamics and mechanical principles that govern the operation of the replisome and its components. ‘Classical’ ensemble-averaging methods cannot obtain this information. Here we describe the main findings obtained with in vitro single-molecule methods on the performance of individual replisome components and reconstituted prokaryotic and eukaryotic replisomes. The emerging picture from these studies is that of stochastic, versatile and highly dynamic replisome machinery in which transient protein-protein and protein-DNA associations are responsible for robust DNA replication.
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Affiliation(s)
- Rebeca Bocanegra
- IMDEA Nanociencia, Faraday 9, Campus Cantoblanco, 28049 Madrid, Spain
| | - G A Ismael Plaza
- IMDEA Nanociencia, Faraday 9, Campus Cantoblanco, 28049 Madrid, Spain
| | - Carlos R Pulido
- IMDEA Nanociencia, Faraday 9, Campus Cantoblanco, 28049 Madrid, Spain
| | - Borja Ibarra
- IMDEA Nanociencia, Faraday 9, Campus Cantoblanco, 28049 Madrid, Spain
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5
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Atomic force spectroscopic and SPR kinetic analysis of long circular and short ssDNA molecules interacting with single-stranded DNA-binding protein. MONATSHEFTE FUR CHEMIE 2017. [DOI: 10.1007/s00706-017-2022-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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6
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Wang C, Hu R, Morrissey JJ, Kharasch ED, Singamaneni S. Single Molecule Force Spectroscopy to Compare Natural versus Artificial Antibody-Antigen Interaction. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2017; 13:10.1002/smll.201604255. [PMID: 28322497 PMCID: PMC5776662 DOI: 10.1002/smll.201604255] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/24/2016] [Revised: 01/23/2017] [Indexed: 05/07/2023]
Abstract
Biorecognition is central to various biological processes and finds numerous applications in virtually all areas of chemistry, biology, and medicine. Artificial antibodies, produced by imprinting synthetic polymers, are designed to mimic the biological recognition capability of natural antibodies, while exhibiting superior thermal, chemical, and environmental stability compared to their natural counterparts. The binding affinity of the artificial antibodies to their antigens characterizes the biorecognition ability of these synthetic nanoconstructs and their ability to replace natural recognition elements. However, a quantitative study of the binding affinity of an artificial antibody to an antigen, especially at the molecular level, is still lacking. In this study, using atomic force microscopy-based force spectroscopy, the authors show that the binding affinity of an artificial antibody to an antigen (hemoglobin) is weaker than that of natural antibody. The fine difference in the molecular interactions manifests into a significant difference in the bioanalytical parameters of biosensors based on these recognition elements.
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Affiliation(s)
- Congzhou Wang
- Department of Mechanical Engineering and Materials Science, Institute of Materials Science and Engineering, Washington University in St. Louis, Saint Louis, MO 63130, USA
| | - Rong Hu
- Department of Anesthesiology, Washington University in St. Louis, St. Louis, MO, 63110, USA
- Department of Anesthesiology, Shanghai Ninth People’s Hospital Affiliated to Shanghai Jiao Tong University, School of Medicine, Shanghai, China
| | - Jeremiah J. Morrissey
- Department of Anesthesiology, Washington University in St. Louis, St. Louis, MO, 63110, USA
- Siteman Cancer Center, Washington University in St. Louis, St. Louis, MO, 63110, USA
| | - Evan D. Kharasch
- Department of Anesthesiology, Washington University in St. Louis, St. Louis, MO, 63110, USA
- Siteman Cancer Center, Washington University in St. Louis, St. Louis, MO, 63110, USA
- Department of Biochemistry and Molecular Biophysics, Washington University in St. Louis, St. Louis, MO, 63110, USA
- The Center for Clinical Pharmacology, St. Louis College of Pharmacy and Washington University School of Medicine, St. Louis, MO, 63110 USA
| | - Srikanth Singamaneni
- Department of Mechanical Engineering and Materials Science, Institute of Materials Science and Engineering, Washington University in St. Louis, Saint Louis, MO 63130, USA
- Siteman Cancer Center, Washington University in St. Louis, St. Louis, MO, 63110, USA
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7
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Yu M, Qian L, Cui S. Reentrant Variation of Single-Chain Elasticity of Polyelectrolyte Induced by Monovalent Salt. J Phys Chem B 2017; 121:4257-4264. [DOI: 10.1021/acs.jpcb.7b00696] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Affiliation(s)
- Miao Yu
- Key Laboratory of Advanced
Technologies of Materials (Ministry of Education), Southwest Jiaotong University, Chengdu 610031, China
| | - Lu Qian
- Key Laboratory of Advanced
Technologies of Materials (Ministry of Education), Southwest Jiaotong University, Chengdu 610031, China
| | - Shuxun Cui
- Key Laboratory of Advanced
Technologies of Materials (Ministry of Education), Southwest Jiaotong University, Chengdu 610031, China
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8
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Kou X, Zhang W, Zhang W. Quantifying the Interactions between PEI and Double-Stranded DNA: Toward the Understanding of the Role of PEI in Gene Delivery. ACS APPLIED MATERIALS & INTERFACES 2016; 8:21055-21062. [PMID: 27435435 DOI: 10.1021/acsami.6b06399] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
Poly(ethylene imine) (PEI) is one of the most efficient nonviral vectors, and its binding mode/strength with double-stranded DNA (dsDNA), which is still not clear, is a core area of transfection studies. In this work we used the atomic force microscopy (AFM)-based single molecule force spectroscopy (SMFS) to detect the interaction between branched PEI and dsDNA quantitatively by using a long chain DNA as a probe. Our results indicate that PEI binds to phosphoric acid skeletons of dsDNA mainly via electrostatic interactions, no obvious groove-binding or intercalation has happened. The interaction strength is about 24-25 pN, and it remains unchanged at pH 5.0 and 7.4, which correspond to the pH values in lysosomes and in the cytoplasmic matrix, respectively. However, the interaction is found to be sensitive to the ionic strength of the environment. In addition, the unbinding force shows no obvious loading rate dependence indicative of equilibrium binding/unbinding.
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Affiliation(s)
- Xiaolong Kou
- State Key Laboratory of Supramolecular Structure and Materials, College of Chemistry, Jilin University , Changchun 130012, People's Republic of China
| | - Wei Zhang
- State Key Laboratory of Supramolecular Structure and Materials, College of Chemistry, Jilin University , Changchun 130012, People's Republic of China
| | - Wenke Zhang
- State Key Laboratory of Supramolecular Structure and Materials, College of Chemistry, Jilin University , Changchun 130012, People's Republic of China
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9
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Kuo TY, Tseng WH, Chen CH. Force Spectroscopy of Metal-Crown Ether Multivalency: Effect of Local Environments on Energy Landscape and Sensing Kinetics. Angew Chem Int Ed Engl 2015. [DOI: 10.1002/ange.201503948] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
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10
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Kuo TY, Tseng WH, Chen CH. Force Spectroscopy of Metal-Crown Ether Multivalency: Effect of Local Environments on Energy Landscape and Sensing Kinetics. Angew Chem Int Ed Engl 2015; 54:9213-7. [DOI: 10.1002/anie.201503948] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2015] [Indexed: 11/09/2022]
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11
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Kim DH, Lee JE, Xu ZY, Geem KR, Kwon Y, Park JW, Hwang I. Cytosolic targeting factor AKR2A captures chloroplast outer membrane-localized client proteins at the ribosome during translation. Nat Commun 2015; 6:6843. [PMID: 25880450 DOI: 10.1038/ncomms7843] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2014] [Accepted: 03/04/2015] [Indexed: 01/30/2023] Open
Abstract
In eukaryotic cells, organellar proteome biogenesis is pivotal for cellular function. Chloroplasts contain a complex proteome, the biogenesis of which includes post-translational import of nuclear-encoded proteins. However, the mechanisms determining when and how nascent chloroplast-targeted proteins are sorted in the cytosol are unknown. Here, we establish the timing and mode of interaction between ankyrin repeat-containing protein 2 (AKR2A), the cytosolic targeting factor of chloroplast outer membrane (COM) proteins, and its interacting partners during translation at the single-molecule level. The targeting signal of a nascent AKR2A client protein residing in the ribosomal exit tunnel induces AKR2A binding to ribosomal RPL23A. Subsequently, RPL23A-bound AKR2A binds to the targeting signal when it becomes exposed from ribosomes. Failure of AKR2A binding to RPL23A in planta severely disrupts protein targeting to the COM; thus, AKR2A-mediated targeting of COM proteins is coupled to their translation, which in turn is crucial for biogenesis of the entire chloroplast proteome.
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Affiliation(s)
- Dae Heon Kim
- Department of Life Sciences, Pohang University of Science and Technology, Pohang 790-784, Korea
| | - Jae-Eun Lee
- Department of Chemistry, Pohang University of Science and Technology, Pohang 790-784, Korea
| | - Zheng-Yi Xu
- Department of Life Sciences, Pohang University of Science and Technology, Pohang 790-784, Korea
| | - Kyoung Rok Geem
- Department of Life Sciences, Pohang University of Science and Technology, Pohang 790-784, Korea
| | - Yun Kwon
- Department of Life Sciences, Pohang University of Science and Technology, Pohang 790-784, Korea
| | - Joon Won Park
- Department of Chemistry, Pohang University of Science and Technology, Pohang 790-784, Korea
| | - Inhwan Hwang
- Department of Life Sciences, Pohang University of Science and Technology, Pohang 790-784, Korea.,Division of Integrative Biosciences and Biotechnology, Pohang University of Science and Technology, Pohang 790-784, Korea
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12
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Chakraborty K, Bandyopadhyay S. Correlated Conformational Motions of the KH Domains of Far Upstream Element Binding Protein Complexed with Single-Stranded DNA Oligomers. J Phys Chem B 2015; 119:10998-1009. [DOI: 10.1021/acs.jpcb.5b01687] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Affiliation(s)
- Kaushik Chakraborty
- Molecular Modeling Laboratory,
Department of Chemistry, Indian Institute of Technology, Kharagpur - 721302, India
| | - Sanjoy Bandyopadhyay
- Molecular Modeling Laboratory,
Department of Chemistry, Indian Institute of Technology, Kharagpur - 721302, India
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13
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Rezgui R, Lestini R, Kühn J, Fave X, McLeod L, Myllykallio H, Alexandrou A, Bouzigues C. Differential interaction kinetics of a bipolar structure-specific endonuclease with DNA flaps revealed by single-molecule imaging. PLoS One 2014; 9:e113493. [PMID: 25412080 PMCID: PMC4239081 DOI: 10.1371/journal.pone.0113493] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2014] [Accepted: 10/23/2014] [Indexed: 11/18/2022] Open
Abstract
As DNA repair enzymes are essential for preserving genome integrity, understanding their substrate interaction dynamics and the regulation of their catalytic mechanisms is crucial. Using single-molecule imaging, we investigated the association and dissociation kinetics of the bipolar endonuclease NucS from Pyrococcus abyssi (Pab) on 5′ and 3′-flap structures under various experimental conditions. We show that association of the PabNucS with ssDNA flaps is largely controlled by diffusion in the NucS-DNA energy landscape and does not require a free 5′ or 3′ extremity. On the other hand, NucS dissociation is independent of the flap length and thus independent of sliding on the single-stranded portion of the flapped DNA substrates. Our kinetic measurements have revealed previously unnoticed asymmetry in dissociation kinetics from these substrates that is markedly modulated by the replication clamp PCNA. We propose that the replication clamp PCNA enhances the cleavage specificity of NucS proteins by accelerating NucS loading at the ssDNA/dsDNA junctions and by minimizing the nuclease interaction time with its DNA substrate. Our data are also consistent with marked reorganization of ssDNA and nuclease domains occurring during NucS catalysis, and indicate that NucS binds its substrate directly at the ssDNA-dsDNA junction and then threads the ssDNA extremity into the catalytic site. The powerful techniques used here for probing the dynamics of DNA-enzyme binding at the single-molecule have provided new insight regarding substrate specificity of NucS nucleases.
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Affiliation(s)
- Rachid Rezgui
- Laboratoire d'Optique et Biosciences, Ecole Polytechnique, CNRS (Centre National pour la Recherche Scientifique) UMR (Unité Mixte de Recherche) 7645, Inserm (Institut national de la santé et de la recherche médicale) U696, Palaiseau, France
| | - Roxane Lestini
- Laboratoire d'Optique et Biosciences, Ecole Polytechnique, CNRS (Centre National pour la Recherche Scientifique) UMR (Unité Mixte de Recherche) 7645, Inserm (Institut national de la santé et de la recherche médicale) U696, Palaiseau, France
| | - Joëlle Kühn
- Laboratoire d'Optique et Biosciences, Ecole Polytechnique, CNRS (Centre National pour la Recherche Scientifique) UMR (Unité Mixte de Recherche) 7645, Inserm (Institut national de la santé et de la recherche médicale) U696, Palaiseau, France
| | - Xenia Fave
- Laboratoire d'Optique et Biosciences, Ecole Polytechnique, CNRS (Centre National pour la Recherche Scientifique) UMR (Unité Mixte de Recherche) 7645, Inserm (Institut national de la santé et de la recherche médicale) U696, Palaiseau, France
| | - Lauren McLeod
- Laboratoire d'Optique et Biosciences, Ecole Polytechnique, CNRS (Centre National pour la Recherche Scientifique) UMR (Unité Mixte de Recherche) 7645, Inserm (Institut national de la santé et de la recherche médicale) U696, Palaiseau, France
| | - Hannu Myllykallio
- Laboratoire d'Optique et Biosciences, Ecole Polytechnique, CNRS (Centre National pour la Recherche Scientifique) UMR (Unité Mixte de Recherche) 7645, Inserm (Institut national de la santé et de la recherche médicale) U696, Palaiseau, France
| | - Antigoni Alexandrou
- Laboratoire d'Optique et Biosciences, Ecole Polytechnique, CNRS (Centre National pour la Recherche Scientifique) UMR (Unité Mixte de Recherche) 7645, Inserm (Institut national de la santé et de la recherche médicale) U696, Palaiseau, France
| | - Cedric Bouzigues
- Laboratoire d'Optique et Biosciences, Ecole Polytechnique, CNRS (Centre National pour la Recherche Scientifique) UMR (Unité Mixte de Recherche) 7645, Inserm (Institut national de la santé et de la recherche médicale) U696, Palaiseau, France
- * E-mail:
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14
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Liu N, Chen Y, Peng B, Lin Y, Wang Q, Su Z, Zhang W, Li H, Shen J. Single-molecule force spectroscopy study on the mechanism of RNA disassembly in tobacco mosaic virus. Biophys J 2014; 105:2790-800. [PMID: 24359751 DOI: 10.1016/j.bpj.2013.10.005] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2013] [Revised: 09/22/2013] [Accepted: 10/09/2013] [Indexed: 12/17/2022] Open
Abstract
To explore the disassembly mechanism of tobacco mosaic virus (TMV), a model system for virus study, during infection, we have used single-molecule force spectroscopy to mimic and follow the process of RNA disassembly from the protein coat of TMV by the replisome (molecular motor) in vivo, under different pH and Ca(2+) concentrations. Dynamic force spectroscopy revealed the unbinding free-energy landscapes as that at pH 4.7 the disassembly process is dominated by one free-energy barrier, whereas at pH 7.0 the process is dominated by one barrier and that there exists a second barrier. The additional free-energy barrier at longer distance has been attributed to the hindrance of disordered loops within the inner channel of TMV, and the biological function of those protein loops was discussed. The combination of pH increase and Ca(2+) concentration drop could weaken RNA-protein interactions so much that the molecular motor replisome would be able to pull and disassemble the rest of the genetic RNA from the protein coat in vivo. All these facts provide supporting evidence at the single-molecule level, to our knowledge for the first time, for the cotranslational disassembly mechanism during TMV infection under physiological conditions.
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Affiliation(s)
- Ningning Liu
- State Key Laboratory of Supramolecular Structure and Materials, College of Chemistry, Jilin University, Changchun, P. R. China; School of Chemistry and Material Science, Liaoning Shihua University, Fushun, P. R. China
| | - Ying Chen
- State Key Laboratory of Supramolecular Structure and Materials, College of Chemistry, Jilin University, Changchun, P. R. China
| | - Bo Peng
- State Key Laboratory of Polymer Physics and Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun, P. R. China
| | - Yuan Lin
- State Key Laboratory of Polymer Physics and Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun, P. R. China
| | - Qian Wang
- State Key Laboratory of Polymer Physics and Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun, P. R. China; Department of Chemistry and Biochemistry, University of South Carolina, Columbia, South Carolina.
| | - Zhaohui Su
- State Key Laboratory of Polymer Physics and Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun, P. R. China
| | - Wenke Zhang
- State Key Laboratory of Supramolecular Structure and Materials, College of Chemistry, Jilin University, Changchun, P. R. China.
| | - Hongbin Li
- State Key Laboratory of Supramolecular Structure and Materials, College of Chemistry, Jilin University, Changchun, P. R. China; Department of Chemistry, University of British Columbia, Vancouver, British Columbia, Canada
| | - Jiacong Shen
- State Key Laboratory of Supramolecular Structure and Materials, College of Chemistry, Jilin University, Changchun, P. R. China
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C-terminal domain swapping of SSB changes the size of the ssDNA binding site. BIOMED RESEARCH INTERNATIONAL 2014; 2014:573936. [PMID: 25162017 PMCID: PMC4137731 DOI: 10.1155/2014/573936] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/26/2014] [Accepted: 07/09/2014] [Indexed: 01/29/2023]
Abstract
Single-stranded DNA-binding protein (SSB) plays an important role in DNA metabolism, including DNA replication, repair, and recombination, and is therefore essential for cell survival. Bacterial SSB consists of an N-terminal ssDNA-binding/oligomerization domain and a flexible C-terminal protein-protein interaction domain. We characterized the ssDNA-binding properties of Klebsiella pneumoniae SSB (KpSSB), Salmonella enterica Serovar Typhimurium LT2 SSB (StSSB), Pseudomonas aeruginosa PAO1 SSB (PaSSB), and two chimeric KpSSB proteins, namely, KpSSBnStSSBc and KpSSBnPaSSBc. The C-terminal domain of StSSB or PaSSB was exchanged with that of KpSSB through protein chimeragenesis. By using the electrophoretic mobility shift assay, we characterized the stoichiometry of KpSSB, StSSB, PaSSB, KpSSBnStSSBc, and KpSSBnPaSSBc, complexed with a series of ssDNA homopolymers. The binding site sizes were determined to be 26 ± 2, 21 ± 2, 29 ± 2, 21 ± 2, and 29 ± 2 nucleotides (nt), respectively. Comparison of the binding site sizes of KpSSB, KpSSBnStSSBc, and KpSSBnPaSSBc showed that the C-terminal domain swapping of SSB changes the size of the binding site. Our observations suggest that not only the conserved N-terminal domain but also the C-terminal domain of SSB is an important determinant for ssDNA binding.
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Xu H, Chen D, Wang S, Zhou Y, Sun J, Zhang W, Zhang X. Macromolecular self-assembly and nanotechnology in China. PHILOSOPHICAL TRANSACTIONS. SERIES A, MATHEMATICAL, PHYSICAL, AND ENGINEERING SCIENCES 2013; 371:20120305. [PMID: 24000357 DOI: 10.1098/rsta.2012.0305] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/02/2023]
Abstract
Macromolecular self-assembly refers to the assembly of synthetic polymers, biomacromolecules and supra-molecular polymers. Through macromolecular self-assembly, the fabrication of ordered structures at different scales, the control of the dynamic assembly process and the integrations of advanced functions can be realized. Macromolecular self-assembly and nanotechnology research in China has developed rapidly, from the early periods of follow-up at low to high level and progress into a stage of innovation and creation. This review selects some representative progresses achieved recently, aiming to reflect the current status of macromolecular self-assembly and nanotechnology research in China.
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Affiliation(s)
- Huaping Xu
- Key Laboratory of Organic Optoelectronics and Molecular Engineering, Department of Chemistry, Tsinghua University, Beijing 100084, People's Republic of China.
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Label-free detection of single-stranded DNA binding protein based on a cantilever array. Talanta 2013; 109:173-6. [DOI: 10.1016/j.talanta.2013.02.001] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2012] [Revised: 01/29/2013] [Accepted: 02/01/2013] [Indexed: 11/20/2022]
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18
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Ritzefeld M, Walhorn V, Anselmetti D, Sewald N. Analysis of DNA interactions using single-molecule force spectroscopy. Amino Acids 2013; 44:1457-75. [PMID: 23468137 DOI: 10.1007/s00726-013-1474-4] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2013] [Accepted: 02/13/2013] [Indexed: 11/25/2022]
Abstract
Protein-DNA interactions are involved in many biochemical pathways and determine the fate of the corresponding cell. Qualitative and quantitative investigations on these recognition and binding processes are of key importance for an improved understanding of biochemical processes and also for systems biology. This review article focusses on atomic force microscopy (AFM)-based single-molecule force spectroscopy and its application to the quantification of forces and binding mechanisms that lead to the formation of protein-DNA complexes. AFM and dynamic force spectroscopy are exciting tools that allow for quantitative analysis of biomolecular interactions. Besides an overview on the method and the most important immobilization approaches, the physical basics of the data evaluation is described. Recent applications of AFM-based force spectroscopy to investigate DNA intercalation, complexes involving DNA aptamers and peptide- and protein-DNA interactions are given.
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Affiliation(s)
- Markus Ritzefeld
- Organic and Bioorganic Chemistry, Bielefeld University, Bielefeld, Germany
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Jung YJ, Albrecht JA, Kwak JW, Park JW. Direct quantitative analysis of HCV RNA by atomic force microscopy without labeling or amplification. Nucleic Acids Res 2012; 40:11728-36. [PMID: 23074195 PMCID: PMC3526272 DOI: 10.1093/nar/gks953] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
Force-based atomic force microscopy (AFM) was used to detect HCV (hepatitis C virus) RNA directly and to quantitatively analyse it without the need for reverse transcription or amplification. Capture and detection DNA probes were designed. The former was spotted onto a substrate with a conventional microarrayer, and the latter was immobilized on an AFM probe. To control the spacing between the immobilized DNAs on the surface, dendron self-assembly was employed. Force-distance curves showed that the mean force of the specific unbinding events was 32 ± 5 pN, and the hydrodynamic distance of the captured RNA was 30-60 nm. Adhesion force maps were generated with criteria including the mean force value, probability of obtaining the specific curves and hydrodynamic distance. The maps for the samples whose concentrations ranged from 0.76 fM to 6.0 fM showed that cluster number has a linear relationship with RNA concentration, while the difference between the observed number and the calculated one increased at low concentrations. Because the detection limit is expected to be enhanced by a factor of 10 000 when a spot of 1 micron diameter is employed, it is believed that HCV RNA of a few copy numbers can be detected by the use of AFM.
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Affiliation(s)
- Yu Jin Jung
- Nanogea Corporation, 6162 Bristol Parkway, Culver City, CA 90230, USA.
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Kim ES, Kim JS, Lee Y, Choi KY, Park JW. Following the DNA ligation of a single duplex using atomic force microscopy. ACS NANO 2012; 6:6108-6114. [PMID: 22686610 DOI: 10.1021/nn301200k] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/01/2023]
Abstract
Nick-sealing of a single DNA duplex was studied with the use of atomic force microscopy (AFM). To form a nick between a 47 mer DNA and a 24 mer DNA, the complementary 71 mer template DNA immobilized on an AFM tip was hybridized with the 47 mer DNA and brought into contact with the 24 mer DNA on a substrate surface. The AFM tip and substrate surface were modified with dendron molecules to ensure the formation of a single DNA duplex. When a single nick in the DNA duplex was sealed by DNA ligase during a pause, an increase in the unbinding force was observed after the pause. The change from 24.0 ± 4.4 piconewtons (pN) to 62.8 ± 14.6 pN matched well with the resulting DNA length (71 bp). Additionally, a 30 s pause showed a 3-fold higher nick-sealing probability (60%) than a 10 s pause, while the probability did not increase with a 120 s pause. In the presence of free 47 mer DNAs in solution, the single nick-sealing event could be repeated at other positions.
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Affiliation(s)
- Eung-Sam Kim
- School of Interdisciplinary Bioscience and Bioengineering, Pohang University of Science and Technology, San 31 Hyoja-dong, Pohang 790-784, South Korea
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Liu N, Zhang W. Feeling Inter- or Intramolecular Interactions with the Polymer Chain as Probe: Recent Progress in SMFS Studies on Macromolecular Interactions. Chemphyschem 2012; 13:2238-56. [DOI: 10.1002/cphc.201200154] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2012] [Indexed: 01/30/2023]
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