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Kannappan S, Jo K, Kim KK, Lee JH. Utilizing peptide-anchored DNA templates for novel programmable nanoparticle assemblies in biological macromolecules: A review. Int J Biol Macromol 2024; 256:128427. [PMID: 38016615 DOI: 10.1016/j.ijbiomac.2023.128427] [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: 10/19/2023] [Revised: 11/23/2023] [Accepted: 11/23/2023] [Indexed: 11/30/2023]
Abstract
Biological macromolecules such as proteins and DNA are known to self-assemble into various structural moieties with distinct functions. While nucleic acids are the structural building blocks, peptides exemplify diversity as tailorable biochemical units. Thus, combining the scaffold properties of the biomacromolecule DNA and the functionality of peptides could evolve into a powerful method to obtain tailorable nano assemblies. In this review, we discuss the assembly of non-DNA-coated colloidal NPs on DNA/peptide templates using functional anchors. We begin with strategies for directly attaching metallic NPs to DNA templates to ascertain the functional role of DNA as a scaffold. Followed by methods to assemble peptides onto DNA templates to emphasize the functional versatility of biologically abundant DNA-binding peptides. Next, we focus on studies corroborating peptide self-assembling into macromolecular templates onto which NPs can attach to emphasize the properties of NP-binding peptides. Finally, we discuss the assembly of NPs on a DNA template with a focus on the bifunctional DNA-binding peptides with NP-binding affinity (peptide anchors). This review aims to highlight the immense potential of combining the functional power of DNA scaffolds and tailorable functionalities of peptides for NP assembly and the need to utilize them effectively to obtain tailorable hierarchical NP assemblies.
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Affiliation(s)
- Shrute Kannappan
- Department of Precision Medicine, School of Medicine, Sungkyunkwan University (SKKU), Suwon 16419, Republic of Korea; Research Center for Advanced Materials Technology, Sungkyunkwan University (SKKU), Suwon 16419, Republic of Korea
| | - Kyubong Jo
- Department of Chemistry, Sogang University, Mapo-gu, Seoul 04107, Republic of Korea.
| | - Kyeong Kyu Kim
- Department of Precision Medicine, School of Medicine, Sungkyunkwan University (SKKU), Suwon 16419, Republic of Korea; Department of Metabiohealth, Sungkyunkwan University (SKKU), Suwon 16419, Republic of Korea.
| | - Jung Heon Lee
- Research Center for Advanced Materials Technology, Sungkyunkwan University (SKKU), Suwon 16419, Republic of Korea; Department of Metabiohealth, Sungkyunkwan University (SKKU), Suwon 16419, Republic of Korea; School of Advanced Materials Science and Engineering, Sungkyunkwan University (SKKU), Suwon 16419, Republic of Korea.
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2
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Jin X, Kim YT, Jo K. DNA Visualization Using Fluorescent Proteins. Methods Mol Biol 2023; 2564:223-246. [PMID: 36107345 DOI: 10.1007/978-1-0716-2667-2_11] [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] [Indexed: 06/15/2023]
Abstract
DNA binding fluorescent proteins are a powerful tool for single-molecule visualization. In this chapter, we discuss a protocol for the synthesis of DNA binding fluorescent proteins and visualization of single DNA molecules. This chapter includes stepwise methods for molecular cloning, reversible staining, two-color staining, sequence-specific staining, and microscopic visualization of single DNA molecules in a microfluidic device. This content will be useful for DNA characterization using DNA binding fluorescent proteins and its visualization at the single-molecule level.
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Affiliation(s)
- Xuelin Jin
- College of Agriculture, Yanbian University, Yanji, Jilin Province, China.
| | - Y Tehee Kim
- Department of Chemistry and Program of Integrated Biotechnology, Sogang University, Seoul, Korea
| | - Kyubong Jo
- Department of Chemistry and Program of Integrated Biotechnology, Sogang University, Seoul, Korea.
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Kim YT, Oh H, Seo MJ, Lee DH, Shin J, Bong S, Heo S, Hapsari ND, Jo K. 21 Fluorescent Protein-Based DNA Staining Dyes. Molecules 2022; 27:5248. [PMID: 36014487 PMCID: PMC9412447 DOI: 10.3390/molecules27165248] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2022] [Revised: 08/10/2022] [Accepted: 08/12/2022] [Indexed: 11/22/2022] Open
Abstract
Fluorescent protein-DNA-binding peptides or proteins (FP-DBP) are a powerful means to stain and visualize large DNA molecules on a fluorescence microscope. Here, we constructed 21 kinds of FP-DBPs using various colors of fluorescent proteins and two DNA-binding motifs. From the database of fluorescent proteins (FPbase.org), we chose bright FPs, such as RRvT, tdTomato, mNeonGreen, mClover3, YPet, and mScarlet, which are four to eight times brighter than original wild-type GFP. Additionally, we chose other FPs, such as mOrange2, Emerald, mTurquoise2, mStrawberry, and mCherry, for variations in emitting wavelengths. For DNA-binding motifs, we used HMG (high mobility group) as an 11-mer peptide or a 36 kDa tTALE (truncated transcription activator-like effector). Using 21 FP-DBPs, we attempted to stain DNA molecules and then analyzed fluorescence intensities. Most FP-DBPs successfully visualized DNA molecules. Even with the same DNA-binding motif, the order of FP and DBP affected DNA staining in terms of brightness and DNA stretching. The DNA staining pattern by FP-DBPs was also affected by the FP types. The data from 21 FP-DBPs provided a guideline to develop novel DNA-binding fluorescent proteins.
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Affiliation(s)
- Yurie Tehee Kim
- Department of Chemistry, Sogang University, 35 Baekbeom-ro, Mapogu, Seoul 04107, Korea
| | - Hyesoo Oh
- Department of Chemistry, Sogang University, 35 Baekbeom-ro, Mapogu, Seoul 04107, Korea
| | - Myung Jun Seo
- Department of Chemistry, Sogang University, 35 Baekbeom-ro, Mapogu, Seoul 04107, Korea
| | - Dong Hyeun Lee
- Department of Chemistry, Sogang University, 35 Baekbeom-ro, Mapogu, Seoul 04107, Korea
| | - Jieun Shin
- Department of Chemistry, Sogang University, 35 Baekbeom-ro, Mapogu, Seoul 04107, Korea
| | - Serang Bong
- Department of Chemistry, Sogang University, 35 Baekbeom-ro, Mapogu, Seoul 04107, Korea
| | - Sujeong Heo
- Department of Chemistry, Sogang University, 35 Baekbeom-ro, Mapogu, Seoul 04107, Korea
| | - Natalia Diyah Hapsari
- Department of Chemistry, Sogang University, 35 Baekbeom-ro, Mapogu, Seoul 04107, Korea
- Chemistry Education Program, Department of Mathematics and Science Education, Sanata Dharma University, Yogyakarta 55282, Indonesia
| | - Kyubong Jo
- Department of Chemistry, Sogang University, 35 Baekbeom-ro, Mapogu, Seoul 04107, Korea
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Xie M, Hu Y, Yin J, Zhao Z, Chen J, Chao J. DNA Nanotechnology-Enabled Fabrication of Metal Nanomorphology. RESEARCH (WASHINGTON, D.C.) 2022; 2022:9840131. [PMID: 35935136 PMCID: PMC9275100 DOI: 10.34133/2022/9840131] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/02/2022] [Accepted: 05/24/2022] [Indexed: 11/09/2022]
Abstract
In recent decades, DNA nanotechnology has grown into a highly innovative and widely established field. DNA nanostructures have extraordinary structural programmability and can accurately organize nanoscale materials, especially in guiding the synthesis of metal nanomaterials, which have unique advantages in controlling the growth morphology of metal nanomaterials. This review started with the evolution in DNA nanotechnology and the types of DNA nanostructures. Next, a DNA-based nanofabrication technology, DNA metallization, was introduced. In this section, we systematically summarized the DNA-oriented synthesis of metal nanostructures with different morphologies and structures. Furthermore, the applications of metal nanostructures constructed from DNA templates in various fields including electronics, catalysis, sensing, and bioimaging were figured out. Finally, the development prospects and challenges of metal nanostructures formed under the morphology control by DNA nanotechnology were discussed.
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Affiliation(s)
- Mo Xie
- State Key Laboratory of Organic Electronics and Information Displays & Jiangsu Key Laboratory for Biosensors, Institute of Advanced Materials (IAM), Jiangsu National Synergetic Innovation Center for Advanced Materials (SICAM), Nanjing University of Posts and Telecommunications, 9 Wenyuan Road, Nanjing 210023, China
| | - Yang Hu
- State Key Laboratory of Organic Electronics and Information Displays & Jiangsu Key Laboratory for Biosensors, Institute of Advanced Materials (IAM), Jiangsu National Synergetic Innovation Center for Advanced Materials (SICAM), Nanjing University of Posts and Telecommunications, 9 Wenyuan Road, Nanjing 210023, China
| | - Jue Yin
- State Key Laboratory of Organic Electronics and Information Displays & Jiangsu Key Laboratory for Biosensors, Institute of Advanced Materials (IAM), Jiangsu National Synergetic Innovation Center for Advanced Materials (SICAM), Nanjing University of Posts and Telecommunications, 9 Wenyuan Road, Nanjing 210023, China
| | - Ziwei Zhao
- State Key Laboratory of Organic Electronics and Information Displays & Jiangsu Key Laboratory for Biosensors, Institute of Advanced Materials (IAM), Jiangsu National Synergetic Innovation Center for Advanced Materials (SICAM), Nanjing University of Posts and Telecommunications, 9 Wenyuan Road, Nanjing 210023, China
| | - Jing Chen
- The Interdisciplinary Research Center, Shanghai Synchrotron Radiation Facility, Zhangjiang Laboratory, Shanghai Advanced Research Institute, Chinese Academy of Sciences, Shanghai 201210, China
| | - Jie Chao
- State Key Laboratory of Organic Electronics and Information Displays & Jiangsu Key Laboratory for Biosensors, Institute of Advanced Materials (IAM), Jiangsu National Synergetic Innovation Center for Advanced Materials (SICAM), Nanjing University of Posts and Telecommunications, 9 Wenyuan Road, Nanjing 210023, China
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Lee JW, Chae S, Oh S, Kim SH, Meeseepong M, Choi KH, Jeon J, Lee NE, Song SY, Lee JH, Choi JY. Bio-essential Inorganic Molecular Nanowires as a Bioactive Muscle Extracellular-Matrix-Mimicking Material. ACS APPLIED MATERIALS & INTERFACES 2021; 13:39135-39141. [PMID: 34374274 DOI: 10.1021/acsami.1c12440] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
Many physiochemical properties of the extracellular matrix (ECM) of muscle tissues, such as nanometer scale dimension, nanotopography, negative charge, and elasticity, must be carefully reproduced to fabricate scaffold materials mimicking muscle tissues. Hence, we developed a muscle tissue ECM-mimicking scaffold using Mo6S3I6 inorganic molecular wires (IMWs). Composed of bio-essential elements and having a nanofibrous structure with a diameter of ∼1 nm and a negative surface charge with high stability, Mo6S3I6 IMWs are ideal for mimicking natural ECM molecules. Once Mo6S3I6 IMWs were patterned on a polydimethylsiloxane surface with an elasticity of 1877.1 ± 22.2 kPa, that is, comparable to that of muscle tissues, the proliferation and α-tubulin expression of myoblasts enhanced significantly. Additionally, the repetitive one-dimensional patterns of Mo6S3I6 IMWs induced the alignment and stretching of myoblasts with enhanced α-tubulin expression and differentiation into myocytes. This study demonstrates that Mo6S3I6 IMWs are promising for mimicking the ECM of muscle tissues.
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Affiliation(s)
- Jin Woong Lee
- School of Advanced Materials Science & Engineering, Sungkyunkwan University (SKKU), Suwon 16419, Republic of Korea
- Research Center for Advanced Materials Technology, Sungkyunkwan University, Suwon 16419, Republic of Korea
| | - Sudong Chae
- School of Advanced Materials Science & Engineering, Sungkyunkwan University (SKKU), Suwon 16419, Republic of Korea
| | - Seungbae Oh
- School of Advanced Materials Science & Engineering, Sungkyunkwan University (SKKU), Suwon 16419, Republic of Korea
| | - Si Hyun Kim
- SKKU Advanced Institute of Nanotechnology (SAINT), Sungkyunkwan University, Suwon 16419, Republic of Korea
| | - Montri Meeseepong
- SKKU Advanced Institute of Nanotechnology (SAINT), Sungkyunkwan University, Suwon 16419, Republic of Korea
| | - Kyung Hwan Choi
- SKKU Advanced Institute of Nanotechnology (SAINT), Sungkyunkwan University, Suwon 16419, Republic of Korea
| | - Jiho Jeon
- SKKU Advanced Institute of Nanotechnology (SAINT), Sungkyunkwan University, Suwon 16419, Republic of Korea
| | - Nae-Eung Lee
- School of Advanced Materials Science & Engineering, Sungkyunkwan University (SKKU), Suwon 16419, Republic of Korea
- Research Center for Advanced Materials Technology, Sungkyunkwan University, Suwon 16419, Republic of Korea
- SKKU Advanced Institute of Nanotechnology (SAINT), Sungkyunkwan University, Suwon 16419, Republic of Korea
- Biomedical Institute for Convergence at SKKU (BICS), Sungkyunkwan University, Suwon 16419, Republic of Korea
| | - Si Young Song
- Department of Orthopaedic Surgery, Hallym University Dongtan Sacred Heart Hospital, Hwaseong 18450, Republic of Korea
| | - Jung Heon Lee
- School of Advanced Materials Science & Engineering, Sungkyunkwan University (SKKU), Suwon 16419, Republic of Korea
- Research Center for Advanced Materials Technology, Sungkyunkwan University, Suwon 16419, Republic of Korea
- SKKU Advanced Institute of Nanotechnology (SAINT), Sungkyunkwan University, Suwon 16419, Republic of Korea
- Biomedical Institute for Convergence at SKKU (BICS), Sungkyunkwan University, Suwon 16419, Republic of Korea
| | - Jae-Young Choi
- School of Advanced Materials Science & Engineering, Sungkyunkwan University (SKKU), Suwon 16419, Republic of Korea
- SKKU Advanced Institute of Nanotechnology (SAINT), Sungkyunkwan University, Suwon 16419, Republic of Korea
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Portable Au Nanoparticle-Based Colorimetric Sensor Strip for Rapid On-Site Detection of Cd2+ Ions in Potable Water. BIOCHIP JOURNAL 2021. [DOI: 10.1007/s13206-021-00029-w] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
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Lee B, Yoon S, Lee JW, Kim Y, Chang J, Yun J, Ro JC, Lee JS, Lee JH. Statistical Characterization of the Morphologies of Nanoparticles through Machine Learning Based Electron Microscopy Image Analysis. ACS NANO 2020; 14:17125-17133. [PMID: 33231065 DOI: 10.1021/acsnano.0c06809] [Citation(s) in RCA: 42] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/06/2023]
Abstract
Although transmission electron microscopy (TEM) may be one of the most efficient techniques available for studying the morphological characteristics of nanoparticles, analyzing them quantitatively in a statistical manner is exceedingly difficult. Herein, we report a method for mass-throughput analysis of the morphologies of nanoparticles by applying a genetic algorithm to an image analysis technique. The proposed method enables the analysis of over 150,000 nanoparticles with a high precision of 99.75% and a low false discovery rate of 0.25%. Furthermore, we clustered nanoparticles with similar morphological shapes into several groups for diverse statistical analyses. We determined that at least 1,500 nanoparticles are necessary to represent the total population of nanoparticles at a 95% credible interval. In addition, the number of TEM measurements and the average number of nanoparticles in each TEM image should be considered to ensure a satisfactory representation of nanoparticles using TEM images. Moreover, the statistical distribution of polydisperse nanoparticles plays a key role in accurately estimating their optical properties. We expect this method to become a powerful tool and aid in expanding nanoparticle-related research into the statistical domain for use in big data analysis.
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Affiliation(s)
- Byoungsang Lee
- School of Advanced Materials Science and Engineering, Sungkyunkwan University (SKKU), Suwon 16419, South Korea
| | - Seokyoung Yoon
- SKKU Advanced Institute of Nanotechnology (SAINT), Sungkyunkwan University (SKKU), Suwon 16419, South Korea
| | - Jin Woong Lee
- School of Advanced Materials Science and Engineering, Sungkyunkwan University (SKKU), Suwon 16419, South Korea
| | - Yunchul Kim
- School of Advanced Materials Science and Engineering, Sungkyunkwan University (SKKU), Suwon 16419, South Korea
| | - Junhyuck Chang
- School of Advanced Materials Science and Engineering, Sungkyunkwan University (SKKU), Suwon 16419, South Korea
| | - Jaesub Yun
- Department of Systems Management Engineering, Sungkyunkwan University (SKKU), Suwon 16419, South Korea
| | - Jae Chul Ro
- School of Advanced Materials Science and Engineering, Sungkyunkwan University (SKKU), Suwon 16419, South Korea
| | - Jong-Seok Lee
- Department of Systems Management Engineering, Sungkyunkwan University (SKKU), Suwon 16419, South Korea
| | - Jung Heon Lee
- School of Advanced Materials Science and Engineering, Sungkyunkwan University (SKKU), Suwon 16419, South Korea
- SKKU Advanced Institute of Nanotechnology (SAINT), Sungkyunkwan University (SKKU), Suwon 16419, South Korea
- Biomedical Institute for Convergence at SKKU (BICS), Sungkyunkwan University (SKKU), Suwon 16419, South Korea
- Institute of Quantum Biophysics (IQB), Sungkyunkwan University (SKKU), Suwon 16419, South Korea
- Research Center for Advanced Materials Technology, Sungkyunkwan University (SKKU), Suwon 16419, South Korea
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Kim KI, Yoon S, Chang J, Lee S, Cho HH, Jeong SH, Jo K, Lee JH. Multifunctional Heterogeneous Carbon Nanotube Nanocomposites Assembled by DNA-Binding Peptide Anchors. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2020; 16:e1905821. [PMID: 31898870 DOI: 10.1002/smll.201905821] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/10/2019] [Revised: 12/13/2019] [Indexed: 05/25/2023]
Abstract
Although carbon nanotubes (CNTs) are remarkable materials with many exceptional characteristics, their poor chemical functionality limits their potential applications. Herein, a strategy is proposed for functionalizing CNTs, which can be achieved with any functional group (FG) without degrading their intrinsic structure by using a deoxyribonucleic acid (DNA)-binding peptide (DBP) anchor. By employing a DBP tagged with a certain FG, such as thiol, biotin, and carboxyl acid, it is possible to introduce any FG with a controlled density on DNA-wrapped CNTs. Additionally, different types of FGs can be introduced on CNTs simultaneously, using DBPs tagged with different FGs. This method can be used to prepare CNT nanocomposites containing different types of nanoparticles (NPs), such as Au NPs, magnetic NPs, and quantum dots. The CNT nanocomposites decorated with these NPs can be used as reusable catalase-like nanocomposites with exceptional catalytic activities, owing to the synergistic effects of all the components. Additionally, the unique DBP-DNA interaction allows the on-demand detachment of the NPs attached to the CNT surface; further, it facilitates a CNT chirality-specific NP attachment and separation using the sequence-specific programmable characteristics of oligonucleotides. The proposed method provides a novel chemistry platform for constructing new functional CNTs suitable for diverse applications.
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Affiliation(s)
- Kyung-Il Kim
- School of Advanced Materials Science and Engineering, Sungkyunkwan University (SKKU), Suwon, 16419, Republic of Korea
| | - Seokyoung Yoon
- SKKU Advanced Institute of Nanotechnology (SAINT), Sungkyunkwan University (SKKU), Suwon, 16419, Republic of Korea
| | - Junhyuck Chang
- School of Advanced Materials Science and Engineering, Sungkyunkwan University (SKKU), Suwon, 16419, Republic of Korea
| | - Seonghyun Lee
- Department of Chemistry and Interdisciplinary Program of Integrated Biotechnology, Sogang University, Seoul, 04107, Republic of Korea
| | - Hui Hun Cho
- SKKU Advanced Institute of Nanotechnology (SAINT), Sungkyunkwan University (SKKU), Suwon, 16419, Republic of Korea
| | - Sun Hwan Jeong
- School of Advanced Materials Science and Engineering, Sungkyunkwan University (SKKU), Suwon, 16419, Republic of Korea
| | - Kyubong Jo
- Department of Chemistry and Interdisciplinary Program of Integrated Biotechnology, Sogang University, Seoul, 04107, Republic of Korea
| | - Jung Heon Lee
- School of Advanced Materials Science and Engineering, Sungkyunkwan University (SKKU), Suwon, 16419, Republic of Korea
- SKKU Advanced Institute of Nanotechnology (SAINT), Sungkyunkwan University (SKKU), Suwon, 16419, Republic of Korea
- Biomedical Institute for Convergence at SKKU (BICS), Sungkyunkwan University (SKKU), Suwon, 16419, Republic of Korea
- Research Center for Advanced Materials Technology, Sungkyunkwan University (SKKU), Suwon, 16419, Republic of Korea
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Jin X, Hapsari ND, Lee S, Jo K. DNA binding fluorescent proteins as single-molecule probes. Analyst 2020; 145:4079-4095. [DOI: 10.1039/d0an00218f] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
DNA binding fluorescent proteins are useful probes for a broad range of biological applications.
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Affiliation(s)
- Xuelin Jin
- Department of Chemistry and Interdisciplinary Program of Integrated Biotechnology
- Sogang University
- Seoul
- Republic of Korea
| | - Natalia Diyah Hapsari
- Department of Chemistry and Interdisciplinary Program of Integrated Biotechnology
- Sogang University
- Seoul
- Republic of Korea
- Chemistry Education Program
| | - Seonghyun Lee
- Department of Chemistry and Interdisciplinary Program of Integrated Biotechnology
- Sogang University
- Seoul
- Republic of Korea
| | - Kyubong Jo
- Department of Chemistry and Interdisciplinary Program of Integrated Biotechnology
- Sogang University
- Seoul
- Republic of Korea
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Shin E, Kim W, Lee S, Bae J, Kim S, Ko W, Seo HS, Lim S, Lee HS, Jo K. Truncated TALE-FP as DNA Staining Dye in a High-salt Buffer. Sci Rep 2019; 9:17197. [PMID: 31748571 PMCID: PMC6868158 DOI: 10.1038/s41598-019-53722-0] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2018] [Accepted: 11/05/2019] [Indexed: 01/19/2023] Open
Abstract
Large DNA molecules are a promising platform for in vitro single-molecule biochemical analysis to investigate DNA-protein interactions by fluorescence microscopy. For many studies, intercalating fluorescent dyes have been primary DNA staining reagents, but they often cause photo-induced DNA breakage as well as structural deformation. As a solution, we previously developed several fluorescent-protein DNA-binding peptides or proteins (FP-DBP) for reversibly staining DNA molecules without structural deformation or photo-induced damage. However, they cannot stain DNA in a condition similar to a physiological salt concentration that most biochemical reactions require. Given these concerns, here we developed a salt-tolerant FP-DBP: truncated transcription activator-like effector (tTALE-FP), which can stain DNA up to 100 mM NaCl. Moreover, we found an interesting phenomenon that the tTALE-FP stained DNA evenly in 1 × TE buffer but showed AT-rich specific patterns from 40 mM to 100 mM NaCl. Using an assay based on fluorescence resonance energy transfer, we demonstrated that this binding pattern is caused by a higher DNA binding affinity of tTALE-FP for AT-rich compared to GC-rich regions. Finally, we used tTALE-FP in a single molecule fluorescence assay to monitor real-time restriction enzyme digestion of single DNA molecules. Altogether, our results demonstrate that this protein can provide a useful alternative as a DNA stain over intercalators.
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Affiliation(s)
- Eunji Shin
- Department of Chemistry and Interdisciplinary Program of Integrated Biotech, Sogang University, 1 Shinsudong, Mapogu, Seoul, 04107, Korea
| | - Woojung Kim
- Department of Chemistry and Interdisciplinary Program of Integrated Biotech, Sogang University, 1 Shinsudong, Mapogu, Seoul, 04107, Korea
| | - Seonghyun Lee
- Department of Chemistry and Interdisciplinary Program of Integrated Biotech, Sogang University, 1 Shinsudong, Mapogu, Seoul, 04107, Korea
| | - Jaeyoung Bae
- Department of Chemistry and Interdisciplinary Program of Integrated Biotech, Sogang University, 1 Shinsudong, Mapogu, Seoul, 04107, Korea
| | - Sanggil Kim
- Department of Chemistry and Interdisciplinary Program of Integrated Biotech, Sogang University, 1 Shinsudong, Mapogu, Seoul, 04107, Korea
| | - Wooseok Ko
- Department of Chemistry and Interdisciplinary Program of Integrated Biotech, Sogang University, 1 Shinsudong, Mapogu, Seoul, 04107, Korea
| | - Ho Seong Seo
- Research Division for Biotechnology, Korea Atomic Energy Research Institute, Jeongeup, 580-185, Korea
| | - Sangyong Lim
- Research Division for Biotechnology, Korea Atomic Energy Research Institute, Jeongeup, 580-185, Korea
| | - Hyun Soo Lee
- Department of Chemistry and Interdisciplinary Program of Integrated Biotech, Sogang University, 1 Shinsudong, Mapogu, Seoul, 04107, Korea.
| | - Kyubong Jo
- Department of Chemistry and Interdisciplinary Program of Integrated Biotech, Sogang University, 1 Shinsudong, Mapogu, Seoul, 04107, Korea.
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Kim SH, Oh S, Chae S, Lee JW, Choi KH, Lee KE, Chang J, Shi L, Choi JY, Lee JH. Exceptional Mechanical Properties of Phase-Separation-Free Mo 3Se 3--Chain-Reinforced Hydrogel Prepared by Polymer Wrapping Process. NANO LETTERS 2019; 19:5717-5724. [PMID: 31369273 DOI: 10.1021/acs.nanolett.9b02343] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
As Mo3Se3- chain nanowires have dimensions comparable to those of natural hydrogel chains (molecular-level diameters of ∼0.6 nm and lengths of several micrometers) and excellent mechanical strength and flexibility, they have large potential to reinforce hydrogels and improve their mechanical properties. When a Mo3Se3--chain-nanowire-gelatin composite hydrogel is prepared simply by mixing Mo3Se3- nanowires with gelatin, phase separation of the Mo3Se3- nanowires from the gelatin matrix occurs in the micronetwork, providing only small improvements in their mechanical properties. In contrast, when the surface of the Mo3Se3- nanowire is wrapped with the gelatin polymer, the chemical compatibility of the Mo3Se3- nanowire with the gelatin matrix is significantly improved, which enables the fabrication of a phase-separation-free Mo3Se3--reinforced gelatin hydrogel. The composite gelatin hydrogel exhibits significantly improved mechanical properties, including a tensile strength of 27.6 kPa, fracture toughness of 26.9 kJ/m3, and elastic modulus of 54.8 kPa, which are 367%, 868%, and 378% higher than those of the pure gelatin hydrogel, respectively. Furthermore, the amount of Mo3Se3- nanowires added in the composite hydrogel is as low as 0.01 wt %. The improvements in the mechanical properties are significantly larger than those for other reported composite hydrogels reinforced with one-dimensional materials.
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Affiliation(s)
- Si Hyun Kim
- SKKU Advanced Institute of Nanotechnology (SAINT) , Sungkyunkwan University (SKKU) , Suwon , Gyeonggi 16419 , Republic of Korea
| | - Seungbae Oh
- School of Advanced Materials Science and Engineering , Sungkyunkwan University (SKKU) , Suwon , Gyeonggi 16419 , Republic of Korea
| | - Sudong Chae
- School of Advanced Materials Science and Engineering , Sungkyunkwan University (SKKU) , Suwon , Gyeonggi 16419 , Republic of Korea
| | - Jin Woong Lee
- School of Advanced Materials Science and Engineering , Sungkyunkwan University (SKKU) , Suwon , Gyeonggi 16419 , Republic of Korea
| | - Kyung Hwan Choi
- SKKU Advanced Institute of Nanotechnology (SAINT) , Sungkyunkwan University (SKKU) , Suwon , Gyeonggi 16419 , Republic of Korea
| | - Kyung Eun Lee
- Biomedical Research Center , Korea Institute of Science and Technology (KIST) , Seoul 02792 , Republic of Korea
| | - Jongwha Chang
- School of Pharmacy , University of Texas , El Paso , Texas 79968 , United States
| | - Liyi Shi
- Research Center of Nanoscience and Nanotechnology , Shanghai University , Shanghai 200444 , China
| | - Jae-Young Choi
- SKKU Advanced Institute of Nanotechnology (SAINT) , Sungkyunkwan University (SKKU) , Suwon , Gyeonggi 16419 , Republic of Korea
- School of Advanced Materials Science and Engineering , Sungkyunkwan University (SKKU) , Suwon , Gyeonggi 16419 , Republic of Korea
| | - Jung Heon Lee
- SKKU Advanced Institute of Nanotechnology (SAINT) , Sungkyunkwan University (SKKU) , Suwon , Gyeonggi 16419 , Republic of Korea
- School of Advanced Materials Science and Engineering , Sungkyunkwan University (SKKU) , Suwon , Gyeonggi 16419 , Republic of Korea
- Biomedical Institute for Convergence at SKKU (BICS) , Sungkyunkwan University (SKKU) , Suwon , Gyeonggi 16419 , Republic of Korea
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Lee JW, Chae S, Oh S, Kim SH, Choi KH, Meeseepong M, Chang J, Kim N, Lee NE, Lee JH, Choi JY. Single-Chain Atomic Crystals as Extracellular Matrix-Mimicking Material with Exceptional Biocompatibility and Bioactivity. NANO LETTERS 2018; 18:7619-7627. [PMID: 30474985 DOI: 10.1021/acs.nanolett.8b03201] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
In this study, Mo3Se3- single-chain atomic crystals (SCACs) with atomically small chain diameters of ∼0.6 nm, large surface areas, and mechanical flexibility were synthesized and investigated as an extracellular matrix (ECM)-mimicking scaffold material for tissue engineering applications. The proliferation of L-929 and MC3T3-E1 cell lines increased up to 268.4 ± 24.4% and 396.2 ± 8.1%, respectively, after 48 h of culturing with Mo3Se3- SCACs. More importantly, this extremely high proliferation was observed when the cells were treated with 200 μg mL-1 of Mo3Se3- SCACs, which is above the cytotoxic concentration of most nanomaterials reported earlier. An ECM-mimicking scaffold film prepared by coating Mo3Se3- SCACs on a glass substrate enabled the cells to adhere to the surface in a highly stretched manner at the initial stage of cell adhesion. Most cells cultured on the ECM-mimicking scaffold film remained alive; in contrast, a substantial number of cells cultured on glass substrates without the Mo3Se3- SCAC coating did not survive. This work not only proves the exceptional biocompatible and bioactive characteristics of the Mo3Se3- SCACs but also suggests that, as an ECM-mimicking scaffold material, Mo3Se3- SCACs can overcome several critical limitations of most other nanomaterials.
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Affiliation(s)
- Jin Woong Lee
- School of Advanced Materials Science & Engineering , Sungkyunkwan University (SKKU) , Suwon 16419 , Republic of Korea
| | - Sudong Chae
- School of Advanced Materials Science & Engineering , Sungkyunkwan University (SKKU) , Suwon 16419 , Republic of Korea
| | - Seoungbae Oh
- School of Advanced Materials Science & Engineering , Sungkyunkwan University (SKKU) , Suwon 16419 , Republic of Korea
| | - Si Hyun Kim
- SKKU Advanced Institute of Nanotechnology (SAINT) , Sungkyunkwan University (SKKU) , Suwon 16419 , Republic of Korea
| | - Kyung Hwan Choi
- SKKU Advanced Institute of Nanotechnology (SAINT) , Sungkyunkwan University (SKKU) , Suwon 16419 , Republic of Korea
| | - Montri Meeseepong
- SKKU Advanced Institute of Nanotechnology (SAINT) , Sungkyunkwan University (SKKU) , Suwon 16419 , Republic of Korea
| | - Jongwha Chang
- School of Pharmacy , University of Texas , El Paso , Texas 79968 , United States
| | - Namsoo Kim
- Department of Metallurgical & Materials Engineering , The University of Texas , El Paso , Texas 79968 , United States
| | - Nae-Eung Lee
- School of Advanced Materials Science & Engineering , Sungkyunkwan University (SKKU) , Suwon 16419 , Republic of Korea
- SKKU Advanced Institute of Nanotechnology (SAINT) , Sungkyunkwan University (SKKU) , Suwon 16419 , Republic of Korea
- Samsung Advanced Institute for Health Sciences & Technology (SAIHST) , Sungkyunkwan University (SKKU) , Suwon 16419 , Republic of Korea
- Biomedical Institute for Convergence at SKKU (BICS) , Sungkyunkwan University (SKKU) , Suwon 16419 , Republic of Korea
| | - Jung Heon Lee
- School of Advanced Materials Science & Engineering , Sungkyunkwan University (SKKU) , Suwon 16419 , Republic of Korea
- SKKU Advanced Institute of Nanotechnology (SAINT) , Sungkyunkwan University (SKKU) , Suwon 16419 , Republic of Korea
- Biomedical Institute for Convergence at SKKU (BICS) , Sungkyunkwan University (SKKU) , Suwon 16419 , Republic of Korea
| | - Jae-Young Choi
- School of Advanced Materials Science & Engineering , Sungkyunkwan University (SKKU) , Suwon 16419 , Republic of Korea
- SKKU Advanced Institute of Nanotechnology (SAINT) , Sungkyunkwan University (SKKU) , Suwon 16419 , Republic of Korea
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Chen Z, Liu C, Cao F, Ren J, Qu X. DNA metallization: principles, methods, structures, and applications. Chem Soc Rev 2018; 47:4017-4072. [DOI: 10.1039/c8cs00011e] [Citation(s) in RCA: 114] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
This review summarizes the research activities on DNA metallization since the concept was first proposed in 1998, covering the principles, methods, structures, and applications.
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Affiliation(s)
- Zhaowei Chen
- Laboratory of Chemical Biology and State Key Laboratory of Rare Earth Resources Utilization
- Changchun Institute of Applied Chemistry
- Chinese Academy of Science
- Changchun
- P. R. China
| | - Chaoqun Liu
- Laboratory of Chemical Biology and State Key Laboratory of Rare Earth Resources Utilization
- Changchun Institute of Applied Chemistry
- Chinese Academy of Science
- Changchun
- P. R. China
| | - Fangfang Cao
- Laboratory of Chemical Biology and State Key Laboratory of Rare Earth Resources Utilization
- Changchun Institute of Applied Chemistry
- Chinese Academy of Science
- Changchun
- P. R. China
| | - Jinsong Ren
- Laboratory of Chemical Biology and State Key Laboratory of Rare Earth Resources Utilization
- Changchun Institute of Applied Chemistry
- Chinese Academy of Science
- Changchun
- P. R. China
| | - Xiaogang Qu
- Laboratory of Chemical Biology and State Key Laboratory of Rare Earth Resources Utilization
- Changchun Institute of Applied Chemistry
- Chinese Academy of Science
- Changchun
- P. R. China
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Yoon S, Lee B, Yun J, Han JG, Lee JS, Lee JH. Systematic study of interdependent relationship on gold nanorod synthesis assisted by electron microscopy image analysis. NANOSCALE 2017; 9:7114-7123. [PMID: 28513707 DOI: 10.1039/c7nr01462g] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/21/2023]
Abstract
Here, we systematically investigated the independent, multiple, and synergic effects of three major components, namely, ascorbic acid (AA), seed, and silver ions (Ag+), on the characteristics of gold nanorods (GNRs), i.e., longitudinal localized surface plasmon resonance (LSPR) peak position, shape, size, and monodispersity. To quantitatively assess the shape and dimensions of GNRs, we used an automated transmission electron microscopy image analysis method using a MATLAB-based code developed in-house and the concept of solidity, which is the ratio between the area of a GNR and the area of its convex hull. The solidity of a straight GNR is close to 1, while it decreases for both dumbbell- and dogbone-shaped GNRs. We found that the LSPR peak position, shape, and monodispersity of the GNRs all altered simultaneously with changes in the amounts of individual components. For example, as the amount of AA increased, both the LSPR peak and solidity decreased, while the polydispersity increased. In contrast, as the amount of seeds increased, both the LSPR and solidity increased, while the monodispersity improved. More importantly, we found that the influence of each component can actually change depending on the composition of the GNR growth solution. For instance, the LSPR peak position red-shifted as the amount of AA increased when the seed content was low, whereas it blue-shifted when the seed content was high.
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Affiliation(s)
- Seokyoung Yoon
- SKKU Advanced Institute of Nanotechnology (SAINT), Sungkyunkwan University (SKKU), Suwon 16419, South Korea.
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