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Song Y, Ma Z, Zhang W. Manipulation of a Single Polymer Chain: From the Nanomechanical Properties to Dynamic Structure Evolution. Macromolecules 2022. [DOI: 10.1021/acs.macromol.2c00076] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Yu Song
- State Key Laboratory of Supramolecular Structure and Materials, College of Chemistry, Jilin University, Changchun 130012, P. R. China
| | - Ziwen Ma
- State Key Laboratory of Supramolecular Structure and Materials, College of Chemistry, Jilin University, Changchun 130012, P. R. China
| | - Wenke Zhang
- State Key Laboratory of Supramolecular Structure and Materials, College of Chemistry, Jilin University, Changchun 130012, P. R. China
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Qian L, Zhang K, Guo X, Zhou J, Yu M. Single-Chain Mechanical Properties of Gelatin: A Single-Molecule Study. Polymers (Basel) 2022; 14:869. [PMID: 35267692 PMCID: PMC8912665 DOI: 10.3390/polym14050869] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2022] [Revised: 02/18/2022] [Accepted: 02/21/2022] [Indexed: 01/27/2023] Open
Abstract
Gelatin is an important natural biological resource with a wide range of applications in the pharmaceutical, industrial and food industries. We investigated the single-chain behaviors of gelatin by atomic force microscopy (AFM)-based single-molecule force spectroscopy (SMFS), and found that gelatin exists as long chains by fitting with the M-FJC model. By comparing the single-chain elasticity in a nonpolar organic solvent (nonane) and DI water, it was surprising to find that there was almost no difference in the single-chain elasticity of gelatin in nonane and DI water. Considering the specificity of gelatin solubility and the solvent size effect of nonane molecules, when a single gelatin chain is pulled into loose nonane, dehydration does not occur due to strong binding water interactions. Gelatin chains can only interact with water molecules at high temperatures; therefore, no further interaction of single gelatin chains with water molecules occurred at the experimental temperature. This eventually led to almost no difference in the single-chain F-E curves under the two conditions. It is expected that our study will enable the deep exploration of the interaction between water molecules and gelatin and provide a theoretical basis and experimental foundation for the design of gelatin-based materials with more functionalities.
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Affiliation(s)
- Lu Qian
- School of Materials Science and Engineering, South China University of Technology, Guangzhou 510000, China;
| | - Kai Zhang
- School of Mechanical Engineering, Sichuan University, Chengdu 610065, China; (K.Z.); (X.G.); (J.Z.)
| | - Xin Guo
- School of Mechanical Engineering, Sichuan University, Chengdu 610065, China; (K.Z.); (X.G.); (J.Z.)
| | - Junyu Zhou
- School of Mechanical Engineering, Sichuan University, Chengdu 610065, China; (K.Z.); (X.G.); (J.Z.)
| | - Miao Yu
- School of Mechanical Engineering, Sichuan University, Chengdu 610065, China; (K.Z.); (X.G.); (J.Z.)
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Mishra S, Jeon J, Kang JK, Song SH, Kim TY, Ban C, Choi H, Kim Y, Kim M, Park JW. Direct Detection of Low Abundance Genes of Single Point Mutation. NANO LETTERS 2021; 21:9061-9068. [PMID: 34672610 DOI: 10.1021/acs.nanolett.1c02728] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
Cell-free DNA (cfDNA) analysis, specifically circulating tumor DNA (ctDNA) analysis, provides enormous opportunities for noninvasive early assessment of cancers. To date, PCR-based methods have led this field. However, the limited sensitivity/specificity of PCR-based methods necessitates the search for new methods. Here, we describe a direct approach to detect KRAS G12D mutated genes in clinical ctDNA samples with the utmost LOD and sensitivity/specificity. In this study, MutS protein was immobilized on the tip of an atomic force microscope (AFM), and the protein sensed the mismatched sites of the duplex formed between the capture probe on the surface and mutated DNA. A noteworthy LOD (3 copies, 0.006% allele frequency) was achieved, along with superb sensitivity/specificity (100%/100%). These observations demonstrate that force-based AFM, in combination with the protein found in nature and properly designed capture probes/blockers, represents an exciting new avenue for ctDNA analysis.
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Affiliation(s)
- Sourav Mishra
- Department of Chemistry, Pohang University of Science and Technology, 77 Cheongam-Ro, Nam-Gu, Pohang 37673, Republic of Korea
| | - Jinseong Jeon
- Department of Chemistry, Pohang University of Science and Technology, 77 Cheongam-Ro, Nam-Gu, Pohang 37673, Republic of Korea
| | - Jun-Kyu Kang
- Cancer Genomics Research Laboratory, Cancer Research Institute, Seoul National University, Seoul 03080, Republic of Korea
- Department of Molecular Medicine and Biopharmaceutical Sciences, Graduate School of Convergence Science and Technology, Seoul National University, Seoul 03080, Republic of Korea
| | - Sang-Hyun Song
- Cancer Genomics Research Laboratory, Cancer Research Institute, Seoul National University, Seoul 03080, Republic of Korea
- Department of Molecular Medicine and Biopharmaceutical Sciences, Graduate School of Convergence Science and Technology, Seoul National University, Seoul 03080, Republic of Korea
| | - Tae-You Kim
- Cancer Genomics Research Laboratory, Cancer Research Institute, Seoul National University, Seoul 03080, Republic of Korea
- Department of Molecular Medicine and Biopharmaceutical Sciences, Graduate School of Convergence Science and Technology, Seoul National University, Seoul 03080, Republic of Korea
- Department of Internal Medicine, Seoul National University Hospital, Seoul 03080, Republic of Korea
| | - Changill Ban
- Department of Chemistry, Pohang University of Science and Technology, 77 Cheongam-Ro, Nam-Gu, Pohang 37673, Republic of Korea
- Institute of Convergence Science, Yonsei University, 50 Yonsei-ro, Seodaemun-gu, Seoul 03722, Republic of Korea
| | - Hayoung Choi
- Catholic Genetic Laboratory Center, Seoul St. Mary's Hospital, College of Medicine, The Catholic University of Korea, Seoul 06591, Republic of Korea
| | - Yonggoo Kim
- Catholic Genetic Laboratory Center, Seoul St. Mary's Hospital, College of Medicine, The Catholic University of Korea, Seoul 06591, Republic of Korea
- Department of Laboratory Medicine, College of Medicine, The Catholic University of Korea, Seoul 06591, Republic of Korea
| | - Myungshin Kim
- Catholic Genetic Laboratory Center, Seoul St. Mary's Hospital, College of Medicine, The Catholic University of Korea, Seoul 06591, Republic of Korea
- Department of Laboratory Medicine, College of Medicine, The Catholic University of Korea, Seoul 06591, Republic of Korea
| | - Joon Won Park
- Department of Chemistry, Pohang University of Science and Technology, 77 Cheongam-Ro, Nam-Gu, Pohang 37673, Republic of Korea
- Institute of Convergence Science, Yonsei University, 50 Yonsei-ro, Seodaemun-gu, Seoul 03722, Republic of Korea
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Riechers SL, Petrik N, Loring JS, Murphy MK, Pearce CI, Kimmel GA, Rosso KM. Integrated atomic force microscopy and x-ray irradiation for in situ characterization of radiation-induced processes. THE REVIEW OF SCIENTIFIC INSTRUMENTS 2021; 92:113701. [PMID: 34852514 DOI: 10.1063/5.0054646] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/20/2021] [Accepted: 10/11/2021] [Indexed: 06/13/2023]
Abstract
Understanding radiation-induced chemical and physical transformations at material interfaces is important across diverse fields, but experimental approaches are often limited to either ex situ observations or in situ electron microscopy or synchrotron-based methods, in which cases the radiation type and dose are inextricably tied to the imaging basis itself. In this work, we overcome this limitation by demonstrating integration of an x-ray source with an atomic force microscope to directly monitor radiolytically driven interfacial chemistry at the nanoscale. We illustrate the value of in situ observations by examining effects of radiolysis on material adhesion forces in aqueous solution as well as examining the production of alkali nitrates at the interface between an alkali halide crystal surface and air. For the examined salt-air interface, direct visualization under flexible experimental conditions greatly extends prior observations by enabling the transformation process to be followed comprehensively from source-to-sink with mass balance quantitation. Our novel rad-atomic force microscope opens doors into understanding the dynamics of radiolytically driven mass transfer and surface alteration at the nanoscale in real-time.
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Affiliation(s)
- Shawn L Riechers
- Pacific Northwest National Laboratory, Richland, Washington 99352, USA
| | - Nikolai Petrik
- Pacific Northwest National Laboratory, Richland, Washington 99352, USA
| | - John S Loring
- Pacific Northwest National Laboratory, Richland, Washington 99352, USA
| | - Mark K Murphy
- Pacific Northwest National Laboratory, Richland, Washington 99352, USA
| | - Carolyn I Pearce
- Pacific Northwest National Laboratory, Richland, Washington 99352, USA
| | - Greg A Kimmel
- Pacific Northwest National Laboratory, Richland, Washington 99352, USA
| | - Kevin M Rosso
- Pacific Northwest National Laboratory, Richland, Washington 99352, USA
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Ramphal IA, Hagerman ME. Nanoscale morphology, tribology and electrical properties of polyaniline/graphene oxide/LAPONITE® composites investigated using atomic force microscopy. NANOSCALE 2019; 11:20876-20883. [PMID: 31657821 DOI: 10.1039/c9nr05713g] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Polyaniline composites with graphene and graphene oxide have received broad interest for applications in charge separation and storage in electrical devices. Syntheses via in situ polymerization of aniline in colloidal dispersions of graphene oxide have afforded nanocomposites of polyaniline intercalated within graphene oxide nanosheets. The simultaneous inclusion of LAPONITE® nanoparticles has improved aqueous phase processability and thin film formation. Mechanical, morphological and conductivity studies including atomic force microscopy and scanning electron microscopy were employed to study the host-guest interactions and heterointerfaces that govern self-assembly. Adhesion and conductivity values within graphene oxide/polyaniline/LAPONITE® (GOPL) nanocomposites were tuned by varying the weight ratios of polyaniline : graphene oxide. These studies inform ongoing work to use GOPL nanomaterials for clean energy harvesting and storage applications.
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Poturnayová A, Buríková M, Bízik J, Hianik T. DNA Aptamers in the Detection of Leukemia Cells by the Thickness Shear Mode Acoustics Method. Chemphyschem 2019; 20:545-554. [PMID: 30552789 DOI: 10.1002/cphc.201801126] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2018] [Revised: 12/13/2018] [Indexed: 12/11/2022]
Abstract
By using the thickness shear mode acoustics method (TSM) and single-molecule force spectroscopy (SMFS) we studied the interactions between DNA aptamers (sgc8c) specific to the protein tyrosine kinase 7 (PTK7), which is localized in the membranes of leukemia lymphoblastics (MOLT-4), and lymphocyte (Jurkat) cell lines, as well with PTK7-negative U266 myeloid leukemia cells. The TSM method allowed the development of a highly sensitive, label-free biosensor for the detection leukemia cells with a limit of detection of (195±20) cells/mL. SMFS approved the high selectivity of the sgc8c aptamers to the PTK7 receptors at the cell surface and allowed determining the binding probability of the aptamers to the PTK7 receptors at different cell lines.
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Affiliation(s)
- Alexandra Poturnayová
- Department of Nuclear Physics and Biophysics Faculty of Mathematics, Physics and Informatics, Comenius University Mlynská dolina F1, 842 48, Bratislava, Slovakia.,Institute of Animal Biochemistry and Genetics, Center of Biosciences SAS Dúbravská cesta 9, 840 05, Bratislava, Slovakia
| | - Monika Buríková
- Cancer Research Institute, Biomedical Research Center SAS, Dúbravská cesta 9, 840 05, Bratislava, Slovakia
| | - Jozef Bízik
- Cancer Research Institute, Biomedical Research Center SAS, Dúbravská cesta 9, 840 05, Bratislava, Slovakia
| | - Tibor Hianik
- Department of Nuclear Physics and Biophysics Faculty of Mathematics, Physics and Informatics, Comenius University Mlynská dolina F1, 842 48, Bratislava, Slovakia
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Mishra S, Lee Y, Park JW. Direct Quantification of Trace Amounts of a Chronic Myeloid Leukemia Biomarker Using Locked Nucleic Acid Capture Probes. Anal Chem 2018; 90:12824-12831. [PMID: 30272952 DOI: 10.1021/acs.analchem.8b03350] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Molecular monitoring is indispensable for the clinical management of chronic myeloid leukemia (CML) patients. Real-time quantitative polymerase chain reaction (RT-qPCR) is the gold standard for the quantitative assessment of BCR-ABL transcript levels, which are critical in clinical decision-making. However, the frequent recurrence of the disease after drug discontinuation for 60% of patients has necessitated more sensitive and specific techniques to detect residual BCR-ABL transcripts. Here, we describe a quantification method for the detection of BCR-ABL targets at very low concentrations (<10 copies/sample) in the presence of a million copies of normal BCR and ABL genes. In this method, a fully modified locked nucleic acid (LNA) and a LNA/DNA chimera were used as capture probes, and the quantitative imaging mode of atomic force microscopy (AFM) was employed. Targets with one of the major breakpoints (found in more than 95% of CML patients), b3a2 and b2a2, were quantified. The BCR-ABL target captured on a miniaturized LNA-probe spot was scanned at nanometric resolution, and the samples containing one to ten copies of the BCR-ABL genes were examined. It was observed that the highest sensitivity, i.e., the detection of a single copy of the target gene, could be achieved through multiple runs, and the observed cluster number was well correlative (adjusted R2 = 0.999) to the target copy number in the sample solution. This observation clearly demonstrates that the LNA-based platform is effective in quantifying BCR-ABL targets with extremely low copy numbers, highlighting the potential applicability of AFM for use in the direct quantification of such targets without amplification or labeling.
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Affiliation(s)
- Sourav Mishra
- Department of Chemistry , Pohang University of Science and Technology , 77 Cheongam-Ro , Nam-Gu, Pohang 37673 , Republic of Korea
| | - Yoonhee Lee
- Department of Chemistry , Pohang University of Science and Technology , 77 Cheongam-Ro , Nam-Gu, Pohang 37673 , Republic of Korea
| | - Joon Won Park
- Department of Chemistry , Pohang University of Science and Technology , 77 Cheongam-Ro , Nam-Gu, Pohang 37673 , Republic of Korea
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Bae YI, Hwang I, Kim I, Kim K, Park JW. Force Measurement for the Interaction between Cucurbit[7]uril and Mica and Self-Assembled Monolayer in the Presence of Zn 2+ Studied with Atomic Force Microscopy. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2017; 33:11884-11892. [PMID: 28946747 DOI: 10.1021/acs.langmuir.7b02168] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
Force spectroscopy with atomic force microscopy (AFM) revealed that cucurbit[7]uril (CB[7]) strongly binds to a mica surface in the presence of cations. Indeed, Zn2+ was observed to facilitate the self-assembly of CB[7] on the mica surface, whereas monocations, such as Na+, were less effective. The progression of the process and the cation-mediated self-assembled monolayer were characterized using AFM, and the observed height of the layer agrees well with the calculated CB[7] value (9.1 Å). We utilized force-based AFM to further study the interaction of CB[7] with guest molecules. To this end, CB[7] was immobilized on a glass substrate, and aminomethylferrocene (am-Fc) was conjugated onto an AFM tip. The single-molecule interaction between CB[7] and am-Fc was monitored by collecting the unbinding force curves. The force histogram showed single ruptures and a unimodal distribution, and the most probable unbinding force value was 101 pN in deionized water and 86 pN in phosphate-buffered saline buffer. The results indicate that the unbinding force was larger than that of streptavidin-biotin measured under the same conditions, whereas the dissociation constant was smaller by 1 order of magnitude (0.012 s-1 vs 0.13 s-1). Furthermore, a high-resolution adhesion force map showed a part of the CB[7] cavities on the surface.
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Affiliation(s)
- Young-In Bae
- Department of Chemistry, ‡Center for Self-Assembly and Complexity (CSC), Institute for Basic Science (IBS), and §Division of Advanced Materials Science, Pohang University of Science and Technology , 77 Cheongam-Ro, Nam-Gu, Pohang 37673, Korea
| | - Ilha Hwang
- Department of Chemistry, ‡Center for Self-Assembly and Complexity (CSC), Institute for Basic Science (IBS), and §Division of Advanced Materials Science, Pohang University of Science and Technology , 77 Cheongam-Ro, Nam-Gu, Pohang 37673, Korea
| | - Ikjin Kim
- Department of Chemistry, ‡Center for Self-Assembly and Complexity (CSC), Institute for Basic Science (IBS), and §Division of Advanced Materials Science, Pohang University of Science and Technology , 77 Cheongam-Ro, Nam-Gu, Pohang 37673, Korea
| | - Kimoon Kim
- Department of Chemistry, ‡Center for Self-Assembly and Complexity (CSC), Institute for Basic Science (IBS), and §Division of Advanced Materials Science, Pohang University of Science and Technology , 77 Cheongam-Ro, Nam-Gu, Pohang 37673, Korea
| | - Joon Won Park
- Department of Chemistry, ‡Center for Self-Assembly and Complexity (CSC), Institute for Basic Science (IBS), and §Division of Advanced Materials Science, Pohang University of Science and Technology , 77 Cheongam-Ro, Nam-Gu, Pohang 37673, Korea
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Kasas S, Dietler G. DNA-protein interactions explored by atomic force microscopy. Semin Cell Dev Biol 2017; 73:231-239. [PMID: 28716606 DOI: 10.1016/j.semcdb.2017.07.015] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2017] [Revised: 07/12/2017] [Accepted: 07/13/2017] [Indexed: 11/30/2022]
Abstract
DNA-protein interactions play an important role in all living organisms on Earth. The advent of atomic force microscopy permitted for the first time to follow and to characterize interaction forces between these two molecular species. After a short description of the AFM and its imaging modes we review, in a chronological order some of the studies that we think importantly contributed to the field.
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Affiliation(s)
- S Kasas
- Laboratoire de Physique de la Matière Vivante, Ecole Polytechnique Fédérale de Lausanne (EPFL), 1015 Lausanne, Switzerland; Plateforme de Morphologie, Faculté de Médecine, Université de Lausanne, Bugnion 9, 1005 Lausanne, Switzerland.
| | - G Dietler
- Laboratoire de Physique de la Matière Vivante, Ecole Polytechnique Fédérale de Lausanne (EPFL), 1015 Lausanne, Switzerland
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