1
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Lee D, Woo Y, Lim JS, Park I, Park SK, Park JW. Quantification of a Neurological Protein in a Single Cell Without Amplification. ACS OMEGA 2022; 7:20165-20171. [PMID: 35722002 PMCID: PMC9201896 DOI: 10.1021/acsomega.2c02009] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/01/2022] [Accepted: 05/25/2022] [Indexed: 06/15/2023]
Abstract
Proteins are key biomolecules that not only play various roles in the living body but also are used as biomarkers. If these proteins can be quantified at the level of a single cell, understanding the role of proteins will be deepened and diagnosing diseases and abnormality will be further upgraded. In this study, we quantified a neurological protein in a single cell using atomic force microscopy (AFM). After capturing specifically disrupted-in-schizophrenia 1 (DISC1) in a single cell onto a microspot immobilizing the corresponding antibody on the surface, force mapping with AFM was followed to visualize individual DISC1. Although a large variation of the number of DISC1 in a cell was observed, the average number is 4.38 × 103, and the number agrees with the ensemble-averaged value. The current AFM approach for the quantitative analysis of proteins in a single cell should be useful to study molecular behavior of proteins in depth and to follow physiological change of individual cells in response to external stimuli.
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Affiliation(s)
- Donggyu Lee
- Department
of Life Sciences, Pohang University of Science
and Technology, 77 Cheongam-Ro, Nam-Gu, Pohang 37673, Republic of Korea
| | - Youngsik Woo
- Department
of Life Sciences, Pohang University of Science
and Technology, 77 Cheongam-Ro, Nam-Gu, Pohang 37673, Republic of Korea
| | - Ji-seon Lim
- Department
of Chemistry, Pohang University of Science
and Technology, 77 Cheongam-Ro,
Nam-Gu, Pohang 37673, Republic of Korea
| | - Ikbum Park
- Analysis
and Assessment Research Center, Research
Institute of Industrial Science and Technology, 67 Cheongam-Ro, Nam-Gu, Pohang 37673, Republic
of Korea
| | - Sang Ki Park
- Department
of Life Sciences, 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
- Institute
of Convergence Science, Yonsei University, 50 Yonsei-ro, Seodaemun-gu, Seoul 03722, Republic
of Korea
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2
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Shim WC, Woo S, Park JW. Nanoscale Force-Mapping-Based Quantification of Low-Abundance Methylated DNA. NANO LETTERS 2022; 22:1324-1330. [PMID: 35080393 DOI: 10.1021/acs.nanolett.1c04637] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Methylation changes at cytosine-guanine dinucleotide (CpG) sites in genes are closely related to cancer development. Thus, detection and quantification of low-abundance methylated DNA is critical for early diagnosis. Here, we report an atomic force microscopy (AFM)-based quantification method for DNA that contains methyl-CpG at a specific site, without any treatment to the target DNA such as chemical labeling, fluorescence tagging, or amplification. We employed AFM-tip-tethered methyl-CpG-binding proteins to probe surface-captured methylated DNA. We observed a linear correlation (R2 = 0.982) between the input copy number and detected copy number, in the low copy number regime (10 or fewer; subattomolar concentrations). For a mixture of methylated and nonmethylated DNA that resembles clinical samples, we were still able to quantify the methylated DNA. These results highlight the potential of our force-mapping-based quantification method for wide applications in early detection of diseases associated with methylated DNA.
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Affiliation(s)
- Woo Cheol Shim
- Department of Chemistry, Pohang University of Science and Technology, 77 Cheongam-Ro, Nam-Gu, Pohang 37673, Republic of Korea
| | - Sungwook Woo
- 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
- Institute of Convergence Science, Yonsei University, 50 Yonsei-ro, Seodaemun-gu, Seoul, 03722, Republic of Korea
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3
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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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4
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Kim ES, Kim JS, Chakrabarty N, Yun CH. Covalent Positioning of Single DNA Molecules for Nanopatterning. NANOMATERIALS 2021; 11:nano11071725. [PMID: 34209077 PMCID: PMC8307146 DOI: 10.3390/nano11071725] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/30/2021] [Revised: 06/26/2021] [Accepted: 06/28/2021] [Indexed: 11/16/2022]
Abstract
Bottom-up micropatterning or nanopatterning can be viewed as the localization of target molecules to the desired area of a surface. A majority of these processes rely on the physical adsorption of ink-like molecules to the paper-like surface, resulting in unstable immobilization of the target molecules owing to their noncovalent linkage to the surface. Herein, successive single nick-sealing facilitated the covalent immobilization of individual DNA molecules at defined positions on a dendron-coated silicon surface using atomic force microscopy. The covalently-patterned ssDNA was visualized when the streptavidin-coated gold nanoparticles bound to the biotinylated DNA. The successive covalent positioning of the target DNA under ambient conditions may facilitate the bottom-up construction of DNA-based durable nanostructures, nanorobots, or memory system.
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Affiliation(s)
- Eung-Sam Kim
- Department of Biological Sciences, Research Center of Ecomimetics and Center for Next Generation Sensor Research and Development, Chonnam National University, Gwangju 61186, Korea
- Correspondence: ; Tel.: +82-62-530-3416; Fax: +82-62-530-3409
| | - Jung Sook Kim
- Department of Chemistry, Division of Integrative Biosciences and Biotechnology, Pohang University of Science and Technology, Pohang 37673, Korea;
| | - Nishan Chakrabarty
- School of Biological Sciences and Biotechnology, Chonnam National University, Gwangju 61186, Korea; (N.C.); (C.-H.Y.)
| | - Chul-Ho Yun
- School of Biological Sciences and Biotechnology, Chonnam National University, Gwangju 61186, Korea; (N.C.); (C.-H.Y.)
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5
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Yadavalli VK, Ehrhardt CJ. Atomic force microscopy as a biophysical tool for nanoscale forensic investigations. Sci Justice 2020; 61:1-12. [PMID: 33357821 DOI: 10.1016/j.scijus.2020.10.004] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/20/2020] [Revised: 09/30/2020] [Accepted: 10/04/2020] [Indexed: 01/23/2023]
Abstract
The atomic force microscope (AFM) has found its way to the arsenal of tools available to the forensic practitioner for the analysis of samples at the nano and microscales. As a non-destructive probing tool that requires minimal sample preparation, the AFM is very attractive, particularly in the case of minimal or precious sample. To date, the use of the AFM has primarily been in the arena of imaging where it has been complementary to other microscopic examination tools. Forensic applications in the visual examination of evidence such as blood stains, questioned documents, and hair samples have been reported. While a number of reviews have focused on the use of AFM as an imaging tool for forensic analyses, here we not only discuss these works, but also point to a versatile enhancement in the capabilities of this nanoscale tool - namely its use for force spectroscopy. In this mode, the AFM can determine elastic moduli, adhesion forces, energy dissipation, and the interaction forces between cognate ligands, that can be spatially mapped to provide a unique spatial visualization of properties. Our goals in this review are to provide a context for this capability of the AFM, explain its workings, cover some exemplary works pertaining to forensic sciences, and present a critical analysis on the advantages and disadvantages of this modality. Equipped with this high-resolution tool, imaging and biophysical analysis by the AFM can provide a unique complement to other tools available to the researcher for the analysis and characterization of forensic evidence.
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Affiliation(s)
- Vamsi K Yadavalli
- Department of Chemical and Life Science Engineering, Virginia Commonwealth University, Richmond, VA 23284, USA.
| | - Christopher J Ehrhardt
- Department of Forensic Science, Virginia Commonwealth University, Richmond, VA 23284, USA
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6
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Oh YJ, Koehler M, Lee Y, Mishra S, Park JW, Hinterdorfer P. Ultra-Sensitive and Label-Free Probing of Binding Affinity Using Recognition Imaging. NANO LETTERS 2019; 19:612-617. [PMID: 30560669 DOI: 10.1021/acs.nanolett.8b04883] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Abstract
Reliable quantification of binding affinity is important in biotechnology and pharmacology and increasingly coupled with a demand for ultrasensitivity, nanoscale resolution, and minute sample amounts. Standard techniques are not able to meet these criteria. This study provides a new platform based on atomic force microscopy (AFM)-derived recognition imaging to determine affinity by visualizing single molecular bindings on nanosize dendrons. Using DNA hybridization as a demonstrator, an AFM sensor adorned with a cognate binding strand senses and localizes target DNAs at nanometer resolution. To overcome the limitations of speed and resolution, the AFM cantilever is sinusoidally oscillated close to resonance conditions at small amplitudes. The equilibrium dissociation constant of capturing DNA duplexes was obtained, yielding 2.4 × 10-10 M. Our label-free single-molecular biochemical analysis approach evidences the utility of recognition imaging and analysis in quantifying biomolecular interactions of just a few hundred molecules.
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Affiliation(s)
- Yoo Jin Oh
- Institute of Biophysics , Johannes Kepler University Linz , Gruberstrasse 40 , A-4020 Linz , Austria
| | - Melanie Koehler
- Institute of Biophysics , Johannes Kepler University Linz , Gruberstrasse 40 , A-4020 Linz , Austria
| | - Yoonhee Lee
- Department of Chemistry , Pohang University of Science and Technology , 77 Cheongam-Ro , Nam-Gu, Pohang 37673 , Republic of Korea
| | - Sourav Mishra
- 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
| | - Peter Hinterdorfer
- Institute of Biophysics , Johannes Kepler University Linz , Gruberstrasse 40 , A-4020 Linz , Austria
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7
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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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8
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Walder R, Van Patten WJ, Adhikari A, Perkins TT. Going Vertical To Improve the Accuracy of Atomic Force Microscopy Based Single-Molecule Force Spectroscopy. ACS NANO 2018; 12:198-207. [PMID: 29244486 DOI: 10.1021/acsnano.7b05721] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
Single-molecule force spectroscopy (SMFS) is a powerful technique to characterize the energy landscape of individual proteins, the mechanical properties of nucleic acids, and the strength of receptor-ligand interactions. Atomic force microscopy (AFM)-based SMFS benefits from ongoing progress in improving the precision and stability of cantilevers and the AFM itself. Underappreciated is that the accuracy of such AFM studies remains hindered by inadvertently stretching molecules at an angle while measuring only the vertical component of the force and extension, degrading both measurements. This inaccuracy is particularly problematic in AFM studies using double-stranded DNA and RNA due to their large persistence length (p ≈ 50 nm), often limiting such studies to other SMFS platforms (e.g., custom-built optical and magnetic tweezers). Here, we developed an automated algorithm that aligns the AFM tip above the DNA's attachment point to a coverslip. Importantly, this algorithm was performed at low force (10-20 pN) and relatively fast (15-25 s), preserving the connection between the tip and the target molecule. Our data revealed large uncorrected lateral offsets for 100 and 650 nm DNA molecules [24 ± 18 nm (mean ± standard deviation) and 180 ± 110 nm, respectively]. Correcting this offset yielded a 3-fold improvement in accuracy and precision when characterizing DNA's overstretching transition. We also demonstrated high throughput by acquiring 88 geometrically corrected force-extension curves of a single individual 100 nm DNA molecule in ∼40 min and versatility by aligning polyprotein- and PEG-based protein-ligand assays. Importantly, our software-based algorithm was implemented on a commercial AFM, so it can be broadly adopted. More generally, this work illustrates how to enhance AFM-based SMFS by developing more sophisticated data-acquisition protocols.
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Affiliation(s)
- Robert Walder
- JILA, National Institute of Standards and Technology , and University of Colorado, Boulder, Colorado 80309, United States
| | - William J Van Patten
- JILA, National Institute of Standards and Technology , and University of Colorado, Boulder, Colorado 80309, United States
| | - Ayush Adhikari
- JILA, National Institute of Standards and Technology , and University of Colorado, Boulder, Colorado 80309, United States
| | - Thomas T Perkins
- JILA, National Institute of Standards and Technology , and University of Colorado, Boulder, Colorado 80309, United States
- Department of Molecular, Cellular, and Developmental Biology, University of Colorado , Boulder, Colorado 80309, United States
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9
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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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10
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Kim Y, Kim W, Park JW. Principles and Applications of Force Spectroscopy Using Atomic Force Microscopy. B KOREAN CHEM SOC 2016. [DOI: 10.1002/bkcs.11022] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Affiliation(s)
- Youngkyu Kim
- Department of Chemistry; Pohang University of Science and Technology; Pohang 37673 Korea
| | - Woong Kim
- Department of Chemistry; Pohang University of Science and Technology; Pohang 37673 Korea
| | - Joon Won Park
- Department of Chemistry; Pohang University of Science and Technology; Pohang 37673 Korea
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11
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Koo H, Park I, Lee Y, Kim HJ, Jung JH, Lee JH, Kim Y, Kim JH, Park JW. Visualization and Quantification of MicroRNA in a Single Cell Using Atomic Force Microscopy. J Am Chem Soc 2016; 138:11664-71. [PMID: 27529574 DOI: 10.1021/jacs.6b05048] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
MicroRNAs (miRNAs) play critical roles in controlling various cellular processes, and the expression levels of individual miRNAs can be considerably altered in pathological conditions such as cancer. Accurate quantification of miRNA at the single-cell level will lead to a better understanding of miRNA function. Here, we present a direct and sensitive method for miRNA detection using atomic force microscopy (AFM). A hybrid binding domain (HBD)-tethered tip enabled mature miRNAs, but not premature miRNAs, to be located individually on an adhesion force map. By scanning several sections of a micrometer-sized DNA spot, we were able to quantify the copy number of miR-134 in a single neuron and demonstrate that the expression was increased upon cell activation. Moreover, we visualized individual miR-134s on fixed neurons after membrane removal and observed 2-4 miR-134s in the area of 1.0 × 1.0 μm(2) of soma. The number increased to 8-14 in stimulated neurons, and this change matches the ensemble-averaged increase in copy number. These findings indicate that miRNAs can be reliably quantified at the single cell level with AFM and that their distribution can be mapped at nanometric lateral resolution without modification or amplification. Furthermore, the analysis of miRNAs, mRNAs, and proteins in the same sample or region by scanning sequentially with different AFM tips would let us accurately understand the post-transcriptional regulation of biological processes.
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Affiliation(s)
- Hyunseo Koo
- Department of Chemistry, ‡Division of Integrative Biosciences and Biotechnology, and §Department of Life Sciences, Pohang University of Science and Technology , 77 Cheongam-Ro, Nam-Gu, Pohang 37673, Korea
| | - Ikbum Park
- Department of Chemistry, ‡Division of Integrative Biosciences and Biotechnology, and §Department of Life Sciences, Pohang University of Science and Technology , 77 Cheongam-Ro, Nam-Gu, Pohang 37673, Korea
| | - Yoonhee Lee
- Department of Chemistry, ‡Division of Integrative Biosciences and Biotechnology, and §Department of Life Sciences, Pohang University of Science and Technology , 77 Cheongam-Ro, Nam-Gu, Pohang 37673, Korea
| | - Hyun Jin Kim
- Department of Chemistry, ‡Division of Integrative Biosciences and Biotechnology, and §Department of Life Sciences, Pohang University of Science and Technology , 77 Cheongam-Ro, Nam-Gu, Pohang 37673, Korea
| | - Jung Hoon Jung
- Department of Chemistry, ‡Division of Integrative Biosciences and Biotechnology, and §Department of Life Sciences, Pohang University of Science and Technology , 77 Cheongam-Ro, Nam-Gu, Pohang 37673, Korea
| | - Joo Han Lee
- Department of Chemistry, ‡Division of Integrative Biosciences and Biotechnology, and §Department of Life Sciences, Pohang University of Science and Technology , 77 Cheongam-Ro, Nam-Gu, Pohang 37673, Korea
| | - Youngkyu Kim
- Department of Chemistry, ‡Division of Integrative Biosciences and Biotechnology, and §Department of Life Sciences, Pohang University of Science and Technology , 77 Cheongam-Ro, Nam-Gu, Pohang 37673, Korea
| | - Joung-Hun Kim
- Department of Chemistry, ‡Division of Integrative Biosciences and Biotechnology, and §Department of Life Sciences, Pohang University of Science and Technology , 77 Cheongam-Ro, Nam-Gu, Pohang 37673, Korea
| | - Joon Won Park
- Department of Chemistry, ‡Division of Integrative Biosciences and Biotechnology, and §Department of Life Sciences, Pohang University of Science and Technology , 77 Cheongam-Ro, Nam-Gu, Pohang 37673, Korea
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12
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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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Lee Y, Kim Y, Lee D, Roy D, Park JW. Quantification of Fewer than Ten Copies of a DNA Biomarker without Amplification or Labeling. J Am Chem Soc 2016; 138:7075-81. [DOI: 10.1021/jacs.6b02791] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Affiliation(s)
| | | | | | - Dhruvajyoti Roy
- Nanogea Inc., 6162 Bristol Parkway, Culver City, California 90230, United States
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14
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Sokolov I, Zorn G, Nichols JM. A study of molecular adsorption of a cationic surfactant on complex surfaces with atomic force microscopy. Analyst 2016; 141:1017-26. [PMID: 26730682 DOI: 10.1039/c5an01941a] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
The study of molecular adsorption on solid surfaces is of broad interest. However, so far the study has been restricted to idealized flat smooth rigid surfaces which are rarely the case in real world applications. Here we describe a study of molecular adsorption on a complex surface of the submicron fibers of a fibrous membrane of regenerated cellulose in aqueous media. We use a cationic surfactant, cetyltrimethylammonium chloride (CTAC), as the adsorbing molecule. We study the equilibrium adsorption of CTAC molecules on the same area of the fibers by sequentially immersing the membrane in pure water, 1 mM and then a 20 mM solution of CTAC. Atomic force microscopy (AFM) is applied to study the adsorption. The force-volume mode is used to record the force-deformation curves of the adsorbed molecules on the fiber surface. We suggest a model to separate the forces due to the adsorbed molecules from the elastic deformation of the fiber. Interestingly, knowledge of the surface geometry is not required in this model provided the surface is made of elastically homogeneous material. Different models are investigated to estimate the amount of the adsorbed molecules based on the obtained force curves. The exponential steric repulsion model fits the force data the best. The amount of the adsorbed surfactant molecules and its dependence on the concentration are found to be reasonable compared to the data previously measured by means of Raman scattering done on a flat surface of silica.
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Affiliation(s)
- I Sokolov
- Departments of ME, BME, Physics, Tufts University, Medford, MA 02155, USA.
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15
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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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16
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Kim JS, Park YS, Nam HG, Park JW. Imaging a specific mRNA in pollen with atomic force microscopy. RSC Adv 2015. [DOI: 10.1039/c5ra00199d] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Distribution of ammonium transporter mRNA in a sectioned pollen is studied at the higher resolution, and localization of the mRNA in the nucleus of the sperm cells is observed.
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Affiliation(s)
- Jung Sook Kim
- Department of Chemistry
- Pohang University of Science and Technology
- Pohang 790–784
- Republic of Korea
| | - Yu Shin Park
- Center for Core Research Facilities
- DGIST
- Daegu 711–873
- Republic of Korea
| | - Hong Gil Nam
- Center for Plant Aging Research
- Institute for Basic Science (IBS)
- Daegu 711–873
- Republic of Korea
- Department of New Biology
| | - Joon Won Park
- Department of Chemistry
- Pohang University of Science and Technology
- Pohang 790–784
- Republic of Korea
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