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Noh C, Kang Y, Heo S, Kim T, Kim H, Chang J, Sundharbaabu PR, Shim S, Lim KI, Lee JH, Jo K. Scanning Electron Microscopy Imaging of Large DNA Molecules Using a Metal-Free Electro-Stain Composed of DNA-Binding Proteins and Synthetic Polymers. Adv Sci (Weinh) 2024:e2309702. [PMID: 38704672 DOI: 10.1002/advs.202309702] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/11/2023] [Revised: 04/19/2024] [Indexed: 05/06/2024]
Abstract
This paper presents the first scanning electron microscopy (SEM)-based DNA imaging in biological samples. This novel approach incorporates a metal-free electro-stain reagent, formulated by combining DNA-binding proteins and synthetic polymers to enhance the visibility of 2-nm-thick DNA under SEM. Notably, DNA molecules stain with proteins and polymers appear as dark lines under SEM. The resulting DNA images exhibit a thickness of 15.0±4.0 nm. As SEM is the primary platform, it integrates seamlessly with various chemically functionalized large surfaces with the aid of microfluidic devices. The approach allows high-resolution imaging of various DNA structures including linear, circular, single-stranded DNA and RNA, originating from nuclear and mitochondrial genomes. Furthermore, quantum dots are successfully visualized as bright labels that are sequence-specifically incorporated into DNA molecules, which highlights the potential for SEM-based optical DNA mapping. In conclusion, DNA imaging using SEM with the novel electro-stain offers electron microscopic resolution with the ease of optical microscopy.
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Affiliation(s)
- Chanyoung Noh
- Department of Chemistry, Sogang University, Seoul, 04107, South Korea
| | - Yoonjung Kang
- Department of Chemistry, Sogang University, Seoul, 04107, South Korea
| | - Sujung Heo
- Department of Chemistry, Sogang University, Seoul, 04107, South Korea
| | - Taesoo Kim
- Department of Chemistry, Sogang University, Seoul, 04107, South Korea
| | - Hayeon Kim
- Department of Chemistry, Sogang University, Seoul, 04107, South Korea
| | - Junhyuck Chang
- School of Advanced Materials Science and Engineering, Department of MetaBioHealth Sungkyunkwan University (SKKU), Suwon, 16419, South Korea
| | - Priyannth Ramasami Sundharbaabu
- School of Advanced Materials Science and Engineering, Department of MetaBioHealth Sungkyunkwan University (SKKU), Suwon, 16419, South Korea
| | - Sanghee Shim
- Department of Chemistry, Korea University, Seoul, 02841, South Korea
| | - Kwang-Il Lim
- Department of Chemical and Biological Engineering, Sookmyung Women's University, Seoul, 04312, South Korea
| | - Jung Heon Lee
- School of Advanced Materials Science and Engineering, Department of MetaBioHealth Sungkyunkwan University (SKKU), Suwon, 16419, South Korea
| | - Kyubong Jo
- Department of Chemistry, Sogang University, Seoul, 04107, South Korea
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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] [What about the content of this article? (0)] [Affiliation(s)] [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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3
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Kim Y, Noh C, Yu M, Bae M, Jo K. Negative nanopore sequencing for mapping biochemical processes on DNA molecules. Chem Commun (Camb) 2023. [PMID: 37435665 DOI: 10.1039/d3cc02112b] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/13/2023]
Abstract
Nanopore sequencing maps biochemical processes on DNA by detecting negative peaks in the sequence alignment profile. Protein-bound DNA and single-strand broken DNA cannot pass through nanopores, resulting in unaligned regions in the genome MAP. This novel approach provides a clear representation of genomic biochemical events.
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Affiliation(s)
- YoonYi Kim
- Department of Chemistry, Sogang University, Seoul 04107, Korea.
| | - Chanyoung Noh
- Department of Chemistry, Sogang University, Seoul 04107, Korea.
| | - Myungheon Yu
- Department of Chemistry, Sogang University, Seoul 04107, Korea.
| | - Minji Bae
- Department of Chemistry, Sogang University, Seoul 04107, Korea.
| | - Kyubong Jo
- Department of Chemistry, Sogang University, Seoul 04107, Korea.
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Bong S, Park CB, Cho SG, Bae J, Hapsari N, Jin X, Heo S, Lee JE, Hashiya K, Bando T, Sugiyama H, Jung KH, Sung B, Jo K. AT-specific DNA visualization revisits the directionality of bacteriophage λ DNA ejection. Nucleic Acids Res 2023; 51:5634-5646. [PMID: 37158237 PMCID: PMC10287942 DOI: 10.1093/nar/gkad340] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2022] [Revised: 03/14/2023] [Accepted: 04/21/2023] [Indexed: 05/10/2023] Open
Abstract
In this study, we specifically visualized DNA molecules at their AT base pairs after in vitro phage ejection. Our AT-specific visualization revealed that either end of the DNA molecule could be ejected first with a nearly 50% probability. This observation challenges the generally accepted theory of Last In First Out (LIFO), which states that the end of the phage λ DNA that enters the capsid last during phage packaging is the first to be ejected, and that both ends of the DNA are unable to move within the extremely condensed phage capsid. To support our observations, we conducted computer simulations that revealed that both ends of the DNA molecule are randomized, resulting in the observed near 50% probability. Additionally, we found that the length of the ejected DNA by LIFO was consistently longer than that by First In First Out (FIFO) during in vitro phage ejection. Our simulations attributed this difference in length to the stiffness difference of the remaining DNA within the phage capsid. In conclusion, this study demonstrates that a DNA molecule within an extremely dense phage capsid exhibits a degree of mobility, allowing it to switch ends during ejection.
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Affiliation(s)
- Serang Bong
- Department of Chemistry, Sogang University, Seoul 04107, Korea
| | - Chung Bin Park
- Department of Chemistry, Sogang University, Seoul 04107, Korea
| | - Shin-Gyu Cho
- Department of Life Science, Sogang University, Seoul 04107, Korea
| | - Jaeyoung Bae
- Department of Chemistry, Sogang University, Seoul 04107, Korea
| | - Natalia Diyah Hapsari
- Department of Chemistry, Sogang University, Seoul 04107, Korea
- Chemistry Education Program, Department of Mathematics and Science Education, Sanata Dharma University, Yogyakarta 55282, Indonesia
| | - Xuelin Jin
- Department of Chemistry, Sogang University, Seoul 04107, Korea
- College of Agriculture, Yanbian University, Yanji133000, China
| | - Sujung Heo
- Department of Chemistry, Sogang University, Seoul 04107, Korea
| | - Ji-eun Lee
- Department of Life Science, Sogang University, Seoul 04107, Korea
| | - Kaori Hashiya
- Department of Chemistry, Graduate School of Science, Kyoto University, Sakyo-Ku, Kyoto606-8502, Japan
| | - Toshikazu Bando
- Department of Chemistry, Graduate School of Science, Kyoto University, Sakyo-Ku, Kyoto606-8502, Japan
| | - Hiroshi Sugiyama
- Department of Chemistry, Graduate School of Science, Kyoto University, Sakyo-Ku, Kyoto606-8502, Japan
| | - Kwang-Hwan Jung
- Department of Life Science, Sogang University, Seoul 04107, Korea
| | - Bong June Sung
- Department of Chemistry, Sogang University, Seoul 04107, Korea
| | - Kyubong Jo
- Department of Chemistry, Sogang University, Seoul 04107, Korea
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Lee Y, Cho CH, Noh C, Yang JH, Park SI, Lee YM, West JA, Bhattacharya D, Jo K, Yoon HS. Origin of minicircular mitochondrial genomes in red algae. Nat Commun 2023; 14:3363. [PMID: 37291154 PMCID: PMC10250338 DOI: 10.1038/s41467-023-39084-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2021] [Accepted: 05/30/2023] [Indexed: 06/10/2023] Open
Abstract
Eukaryotic organelle genomes are generally of conserved size and gene content within phylogenetic groups. However, significant variation in genome structure may occur. Here, we report that the Stylonematophyceae red algae contain multipartite circular mitochondrial genomes (i.e., minicircles) which encode one or two genes bounded by a specific cassette and a conserved constant region. These minicircles are visualized using fluorescence microscope and scanning electron microscope, proving the circularity. Mitochondrial gene sets are reduced in these highly divergent mitogenomes. Newly generated chromosome-level nuclear genome assembly of Rhodosorus marinus reveals that most mitochondrial ribosomal subunit genes are transferred to the nuclear genome. Hetero-concatemers that resulted from recombination between minicircles and unique gene inventory that is responsible for mitochondrial genome stability may explain how the transition from typical mitochondrial genome to minicircles occurs. Our results offer inspiration on minicircular organelle genome formation and highlight an extreme case of mitochondrial gene inventory reduction.
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Affiliation(s)
- Yongsung Lee
- Department of Biological Sciences, Sungkyunkwan University, Suwon, 16419, Korea
| | - Chung Hyun Cho
- Department of Biological Sciences, Sungkyunkwan University, Suwon, 16419, Korea
| | - Chanyoung Noh
- Department of Chemistry, Sogang University, Seoul, 04107, Korea
| | - Ji Hyun Yang
- Department of Biological Sciences, Sungkyunkwan University, Suwon, 16419, Korea
| | - Seung In Park
- Department of Biological Sciences, Sungkyunkwan University, Suwon, 16419, Korea
| | - Yu Min Lee
- Department of Biological Sciences, Sungkyunkwan University, Suwon, 16419, Korea
| | - John A West
- School of Biosciences 2, University of Melbourne, Parkville, Victoria, 3010, Australia
| | - Debashish Bhattacharya
- Department of Biochemistry and Microbiology, Rutgers University, New Brunswick, 08901, USA
| | - Kyubong Jo
- Department of Chemistry, Sogang University, Seoul, 04107, Korea.
| | - Hwan Su Yoon
- Department of Biological Sciences, Sungkyunkwan University, Suwon, 16419, Korea.
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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] [What about the content of this article? (0)] [Affiliation(s)] [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 T, Kim S, Noh C, Hwang H, Shin J, Won N, Lee S, Kim D, Jang Y, Hong SJ, Park J, Kim SJ, Jang S, Lim KI, Jo K. Counting DNA molecules on a microchannel surface for quantitative analysis. Talanta 2023; 252:123826. [DOI: 10.1016/j.talanta.2022.123826] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2022] [Revised: 08/02/2022] [Accepted: 08/07/2022] [Indexed: 12/30/2022]
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8
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Jin Y, Bae J, Kim TY, Hwang H, Kim T, Yu M, Oh H, Hashiya K, Bando T, Sugiyama H, Jo K. Twelve Colors of Streptavidin–Fluorescent Proteins (SA-FPs): A Versatile Tool to Visualize Genetic Information in Single-Molecule DNA. Anal Chem 2022; 94:16927-16935. [DOI: 10.1021/acs.analchem.2c04344] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Affiliation(s)
- Yu Jin
- Department of Chemistry and Program of Integrated Biotechnology, Sogang University, Seoul 04107, Korea
| | - Jaeyoung Bae
- Department of Chemistry and Program of Integrated Biotechnology, Sogang University, Seoul 04107, Korea
| | - Tehee Yurie Kim
- Department of Chemistry and Program of Integrated Biotechnology, Sogang University, Seoul 04107, Korea
| | - Hyeseung Hwang
- Department of Chemistry and Program of Integrated Biotechnology, Sogang University, Seoul 04107, Korea
| | - Taesoo Kim
- Department of Chemistry and Program of Integrated Biotechnology, Sogang University, Seoul 04107, Korea
| | - Myungheon Yu
- Department of Chemistry and Program of Integrated Biotechnology, Sogang University, Seoul 04107, Korea
| | - Hyesoo Oh
- Department of Chemistry and Program of Integrated Biotechnology, Sogang University, Seoul 04107, Korea
| | - Kaori Hashiya
- Department of Chemistry, Graduate School of Science, Kyoto University, Sakyo-Ku, Kyoto 606-8502, Japan
| | - Toshikazu Bando
- Department of Chemistry, Graduate School of Science, Kyoto University, Sakyo-Ku, Kyoto 606-8502, Japan
| | - Hiroshi Sugiyama
- Department of Chemistry, Graduate School of Science, Kyoto University, Sakyo-Ku, Kyoto 606-8502, Japan
| | - Kyubong Jo
- Department of Chemistry and Program of Integrated Biotechnology, Sogang University, Seoul 04107, Korea
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9
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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] [What about the content of this article? (0)] [Affiliation(s)] [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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Kang Y, Cheon NY, Cha J, Kim A, Kim HI, Lee L, Kim KO, Jo K, Lee JY. High-throughput single-molecule imaging system using nanofabricated trenches and fluorescent DNA-binding proteins. Biotechnol Bioeng 2020; 117:1640-1648. [PMID: 32162675 DOI: 10.1002/bit.27331] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2020] [Revised: 03/02/2020] [Accepted: 03/11/2020] [Indexed: 12/18/2022]
Abstract
DNA curtain is a high-throughput system, integrating a lipid bilayer, fluorescence imaging, and microfluidics to probe protein-DNA interactions in real-time and has provided in-depth understanding of DNA metabolism. Especially, the microfluidic platform of a DNA curtain is highly suitable for a biochip. In the DNA curtain, DNA molecules are aligned along chromium nanobarriers, which are fabricated on a slide surface, and visualized using an intercalating dye, YOYO-1. Although the chromium barriers confer precise geometric alignment of DNA, reuse of the slides is limited by wear of the barriers during cleaning. YOYO-1 is rapidly photobleached and causes photocleavage of DNA under continuous laser illumination, restricting DNA observation to a brief time window. To address these challenges, we developed a new nanopatterned slide, upon which carved nanotrenches serve as diffusion barriers. The nanotrenches were robust under harsh cleaning conditions, facilitating the maintenance of surface cleanliness that is essential to slide reuse. We also stained DNA with a fluorescent protein with a DNA-binding motif, fluorescent protein-DNA binding peptide (FP-DBP). FP-DBP was slowly photobleached and did not cause DNA photocleavage. This new DNA curtain system enables a more stable and repeatable investigation of real-time protein-DNA interactions and will serve as a good platform for lab-on-a-chip.
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Affiliation(s)
- Yujin Kang
- School of Life Sciences, Ulsan National Institute of Science and Technology, Ulsan, Republic of Korea
| | - Na Young Cheon
- School of Life Sciences, Ulsan National Institute of Science and Technology, Ulsan, Republic of Korea
| | - Jongjin Cha
- Department of Physics and Astronomy, Seoul National University, Seoul, Republic of Korea
| | - Ayoung Kim
- School of Life Sciences, Ulsan National Institute of Science and Technology, Ulsan, Republic of Korea
| | - Hyung-Il Kim
- UNIST Central Research Facilities (UCRF), Ulsan National Institute of Science and Technology, Ulsan, Republic of Korea
| | - Luda Lee
- UNIST Central Research Facilities (UCRF), Ulsan National Institute of Science and Technology, Ulsan, Republic of Korea
| | - Kang O Kim
- UNIST Central Research Facilities (UCRF), Ulsan National Institute of Science and Technology, Ulsan, Republic of Korea
| | - Kyubong Jo
- Department of Chemistry and Integrated Biotechnology, Sogang University, Seoul, Republic of Korea
| | - Ja Yil Lee
- School of Life Sciences, Ulsan National Institute of Science and Technology, Ulsan, Republic of Korea.,Center for Genomic Integrity, Institute for Basic Science, Ulsan, Republic of Korea
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Jo K. Fluorescent Protein as a DNA Staining Dye. Biophys J 2020. [DOI: 10.1016/j.bpj.2019.11.590] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022] Open
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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 2020; 16:e1905821. [PMID: 31898870 DOI: 10.1002/smll.201905821] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [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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13
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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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14
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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] [What about the content of this article? (0)] [Affiliation(s)] [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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15
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Jang YH, Jin X, Shankar P, Lee JH, Jo K, Lim KI. Molecular-Level Interactions between Engineered Materials and Cells. Int J Mol Sci 2019; 20:E4142. [PMID: 31450647 PMCID: PMC6747072 DOI: 10.3390/ijms20174142] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2019] [Revised: 08/19/2019] [Accepted: 08/21/2019] [Indexed: 12/13/2022] Open
Abstract
Various recent experimental observations indicate that growing cells on engineered materials can alter their physiology, function, and fate. This finding suggests that better molecular-level understanding of the interactions between cells and materials may guide the design and construction of sophisticated artificial substrates, potentially enabling control of cells for use in various biomedical applications. In this review, we introduce recent research results that shed light on molecular events and mechanisms involved in the interactions between cells and materials. We discuss the development of materials with distinct physical, chemical, and biological features, cellular sensing of the engineered materials, transfer of the sensing information to the cell nucleus, subsequent changes in physical and chemical states of genomic DNA, and finally the resulting cellular behavior changes. Ongoing efforts to advance materials engineering and the cell-material interface will eventually expand the cell-based applications in therapies and tissue regenerations.
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Affiliation(s)
- Yoon-Ha Jang
- Department of Chemical and Biological Engineering, Sookmyung Women's University, Seoul 04310, Korea
| | - Xuelin Jin
- Department of Chemistry and Integrated Biotechnology, Sogang University, Seoul 04107, Korea
| | - Prabakaran Shankar
- School of Advanced Materials Science and Engineering, Sungkyunkwan University (SKKU), Suwon 16419, Korea
| | - Jung Heon Lee
- School of Advanced Materials Science and Engineering, Sungkyunkwan University (SKKU), Suwon 16419, Korea.
| | - Kyubong Jo
- Department of Chemistry and Integrated Biotechnology, Sogang University, Seoul 04107, Korea.
| | - Kwang-Il Lim
- Department of Chemical and Biological Engineering, Sookmyung Women's University, Seoul 04310, Korea.
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16
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Lee S, Kawamoto Y, Vaijayanthi T, Park J, Bae J, Kim-Ha J, Sugiyama H, Jo K. TAMRA-polypyrrole for A/T sequence visualization on DNA molecules. Nucleic Acids Res 2019; 46:e108. [PMID: 29931115 PMCID: PMC6182132 DOI: 10.1093/nar/gky531] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2018] [Accepted: 05/29/2018] [Indexed: 01/23/2023] Open
Abstract
Fluorophore-linked, sequence-specific DNA binding reagents can visualize sequence information on a large DNA molecule. In this paper, we synthesized newly designed TAMRA-linked polypyrrole to visualize adenine and thymine base pairs. A fluorescent image of the stained DNA molecule generates an intensity profile based on A/T frequency, revealing a characteristic sequence composition pattern. Computer-aided comparison of this intensity pattern with the genome sequence allowed us to determine the DNA sequence on a visualized DNA molecule from possible intensity profile pattern candidates for a given genome. Moreover, TAMRA-polypyrrole offers robust advantages for single DNA molecule detection: no fluorophore-mediated photocleavage and no structural deformation, since it exhibits a sequence-specific pattern alone without the use of intercalating dyes such as YOYO-1. Accordingly, we were able to identify genomic DNA fragments from Escherichia coli cells by aligning them to the genomic A/T frequency map based on TAMRA-polypyrrole-generated intensity profiles. Furthermore, we showed band and interband patterns of polytene chromosomal DNA stained with TAMRA-polypyrrole because it prefers to bind AT base pairs.
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Affiliation(s)
- Seonghyun Lee
- Department of Chemistry and Program of Integrated Biotechnology, Sogang University, Seoul 04107, Republic of Korea
| | - Yusuke Kawamoto
- Department of Chemistry, Graduate School of Science, Kyoto University, Sakyo-Ku, Kyoto 606-8502, Japan
| | - Thangavel Vaijayanthi
- Department of Chemistry, Graduate School of Science, Kyoto University, Sakyo-Ku, Kyoto 606-8502, Japan
| | - Jihyun Park
- Department of Chemistry and Program of Integrated Biotechnology, Sogang University, Seoul 04107, Republic of Korea
| | - Jaeyoung Bae
- Department of Chemistry and Program of Integrated Biotechnology, Sogang University, Seoul 04107, Republic of Korea
| | - Jeongsil Kim-Ha
- Department of Integrative Bioscience and Biotechnology, College of Life Sciences, Sejong University, Seoul 05006, Republic of Korea
| | - Hiroshi Sugiyama
- Department of Chemistry, Graduate School of Science, Kyoto University, Sakyo-Ku, Kyoto 606-8502, Japan
| | - Kyubong Jo
- Department of Chemistry and Program of Integrated Biotechnology, Sogang University, Seoul 04107, Republic of Korea
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Park J, Lee S, Won N, Shin E, Kim SH, Chun MY, Gu J, Jung GY, Lim KI, Jo K. Single-molecule DNA visualization using AT-specific red and non-specific green DNA-binding fluorescent proteins. Analyst 2019; 144:921-927. [PMID: 30310901 DOI: 10.1039/c8an01426d] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
The recent advances in the single cell genome analysis are generating a considerable amount of novel insights into complex biological systems. However, there are still technical challenges because each cell has a single copy of DNA to be amplified in most single cell genome analytical methods. In this paper, we present a novel approach to directly visualize a genomic map on a large DNA molecule instantly stained with red and green DNA-binding fluorescent proteins without DNA amplification. For this visualization, we constructed a few types of fluorescent protein-fused DNA-binding proteins: H-NS (histone-like nucleoid-structuring protein), DNA-binding domain of BRCA1 (breast cancer 1), high mobility group-1 (HMG), and lysine tryptophan (KW) repeat motif. Because H-NS and HMG preferentially bind A/T-rich regions, we combined A/T specific binder (H-NS-mCherry and HMG-mCherry as red color) and a non-specific complementary DNA binder (BRCA1-eGFP and 2(KW)2-eGFP repeat as green color) to produce a sequence-specific two-color DNA physical map for efficient optical identification of single DNA molecules.
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Affiliation(s)
- Jihyun Park
- Department of Chemistry and Interdisciplinary Program of Integrated Biotech, Sogang University, 1 Shinsudong, Mapogu, Seoul, 04107, Korea.
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Lee S, Jo K. Tamra-Polypyrrole for A/T Sequence Visualization on DNA Molecules. Biophys J 2019. [DOI: 10.1016/j.bpj.2018.11.1947] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022] Open
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19
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Jin X, Jo K. A Novel Approach for Single Molecule Observation of DNA Loops Formed by ToxR-RNA Polymerase Complex, LacI, and DmpR. Biophys J 2019. [DOI: 10.1016/j.bpj.2018.11.1504] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022] Open
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20
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Lee S, Lee Y, Kim Y, Wang C, Park J, Jung GY, Chen Y, Chang R, Ikeda S, Sugiyama H, Jo K. Nanochannel-Confined TAMRA-Polypyrrole Stained DNA Stretching by Varying the Ionic Strength from Micromolar to Millimolar Concentrations. Polymers (Basel) 2018; 11:E15. [PMID: 30959999 PMCID: PMC6401831 DOI: 10.3390/polym11010015] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2018] [Revised: 12/17/2018] [Accepted: 12/17/2018] [Indexed: 12/19/2022] Open
Abstract
Large DNA molecules have been utilized as a model system to investigate polymer physics. However, DNA visualization via intercalating dyes has generated equivocal results due to dye-induced structural deformation, particularly unwanted unwinding of the double helix. Thus, the contour length increases and the persistence length changes so unpredictably that there has been a controversy. In this paper, we used TAMRA-polypyrrole to stain single DNA molecules. Since this staining did not change the contour length of B-form DNA, we utilized TAMRA-polypyrrole stained DNA as a tool to measure the persistence length by changing the ionic strength. Then, we investigated DNA stretching in nanochannels by varying the ionic strength from 0.06 mM to 47 mM to evaluate several polymer physics theories proposed by Odijk, de Gennes and recent papers to deal with these regimes.
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Affiliation(s)
- Seonghyun Lee
- Department of Chemistry and Integrated Biotechnology, Sogang University, Seoul 04107, Korea.
| | - Yelin Lee
- Department of Chemistry and Integrated Biotechnology, Sogang University, Seoul 04107, Korea.
| | - Yongkyun Kim
- Department of Chemistry and Integrated Biotechnology, Sogang University, Seoul 04107, Korea.
| | - Cong Wang
- Department of Mechanical Engineering, Sogang University, Seoul 04107, Korea.
| | - Jungyul Park
- Department of Mechanical Engineering, Sogang University, Seoul 04107, Korea.
| | - Gun Young Jung
- School of Material Science and Engineering, GIST, Gwangju 61005, Korea.
| | - Yenglong Chen
- Institute of Physics, Academia Sinica and Department of Chemical Engineering, National Tsing-Hua University and Department of Physics, National Taiwan University, Taipei 10617, Taiwan.
| | - Rakwoo Chang
- Department of Chemistry, Kwangwoon University, Seoul 01897, Korea.
| | - Shuji Ikeda
- Department of Chemistry, Graduate School of Science, Kyoto University, Sakyo-Ku, Kyoto 606-8501, Japan.
| | - Hiroshi Sugiyama
- Department of Chemistry, Graduate School of Science, Kyoto University, Sakyo-Ku, Kyoto 606-8501, Japan.
| | - Kyubong Jo
- Department of Chemistry and Integrated Biotechnology, Sogang University, Seoul 04107, Korea.
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Gubu A, Li L, Ning Y, Zhang X, Lee S, Feng M, Li Q, Lei X, Jo K, Tang X. Bioorthogonal Metabolic DNA Labelling using Vinyl Thioether-Modified Thymidine and o-Quinolinone Quinone Methide. Chemistry 2018; 24:5895-5900. [PMID: 29443432 DOI: 10.1002/chem.201705917] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2017] [Indexed: 12/12/2022]
Abstract
Bioorthogonal metabolic DNA labeling with fluorochromes is a powerful strategy to visualize DNA molecules and their functions. Here, we report the development of a new DNA metabolic labeling strategy enabled by the catalyst-free bioorthogonal ligation using vinyl thioether modified thymidine and o-quinolinone quinone methide. With the newly designed vinyl thioether-modified thymidine (VTdT), we added labeling tags on cellular DNA, which could further be linked to fluorochromes in cells. Therefore, we successfully visualized the DNA localization within cells as well as single DNA molecules without other staining reagents. In addition, we further characterized this bioorthogonal DNA metabolic labeling using DNase I digestion, MS characterization of VTdT as well as VTdT-oQQF conjugate in cell nuclei or mitochondria. This technique provides a powerful strategy to study DNA in cells, which paves the way to achieve future spatiotemporal deciphering of DNA synthesis and functions.
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Affiliation(s)
- Amu Gubu
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University, No. 38 Xueyuan Rd., Beijing, P. R. China
| | - Long Li
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University, No. 38 Xueyuan Rd., Beijing, P. R. China
| | - Yan Ning
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University, No. 38 Xueyuan Rd., Beijing, P. R. China
| | - Xiaoyun Zhang
- Beijing National Laboratory for Molecular Sciences, Key Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education, Department of Chemical Biology, College of Chemistry and Molecular Engineering, Synthetic and Functional Biomolecules Center, Peking-Tsinghua Center for Life Sciences, Peking University, P. R. China
| | - Seonghyun Lee
- Department of Chemistry and Interdisciplinary Program of Integrated Biotechnology, Sogang University, Republic of Korea
| | - Mengke Feng
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University, No. 38 Xueyuan Rd., Beijing, P. R. China
| | - Qiang Li
- Beijing National Laboratory for Molecular Sciences, Key Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education, Department of Chemical Biology, College of Chemistry and Molecular Engineering, Synthetic and Functional Biomolecules Center, Peking-Tsinghua Center for Life Sciences, Peking University, P. R. China
| | - Xiaoguang Lei
- Beijing National Laboratory for Molecular Sciences, Key Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education, Department of Chemical Biology, College of Chemistry and Molecular Engineering, Synthetic and Functional Biomolecules Center, Peking-Tsinghua Center for Life Sciences, Peking University, P. R. China
| | - Kyubong Jo
- Department of Chemistry and Interdisciplinary Program of Integrated Biotechnology, Sogang University, Republic of Korea
| | - Xinjing Tang
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University, No. 38 Xueyuan Rd., Beijing, P. R. China
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22
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Lee N, Jo K, Kim K, Yang J, Chang J, Na D. Intra-arterial delivery of human mesenchymal stem cells into the brains of New Zealand white rabbits. Cytotherapy 2017. [DOI: 10.1016/j.jcyt.2017.02.305] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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23
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Lim Y, Jo K, Ha HS, Yim HW, Yoon KH, Lee WC, Son HY, Baek KH, Kang MI. The prevalence of osteoporosis and the rate of bone loss in Korean adults: the Chungju metabolic disease cohort (CMC) study. Osteoporos Int 2017; 28:1453-1459. [PMID: 28083665 DOI: 10.1007/s00198-016-3893-z] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/12/2016] [Accepted: 12/18/2016] [Indexed: 12/23/2022]
Abstract
UNLABELLED Because the rate of bone loss is an important risk factor for fracture, we studied longitudinal changes in bone mineral density (BMD). Although the BMD of the hip decreased over time, spine BMD remained largely stable or increased. Therefore, spine BMD may not be appropriate for assessing BMD change. INTRODUCTION The rate of age-dependent bone loss has been shown to be an important risk factor for fracture. However, longitudinal rates of BMD loss in Korea have not yet been reported. The objective of this study was to evaluate longitudinal changes in BMD in Korea. METHODS This cohort study was performed in a population of individuals 40 years of age or older living in the rural area of Chungju City, Korea. A second BMD examination was conducted approximately 4 years after a baseline examination. A total of 3755 of the 6007 subjects completed the follow-up visit, corresponding to a follow-up rate of 62.51%. RESULTS The age-standardized osteoporosis prevalence was 12.81% in males and 44.35% in females. In males, the average annual BMD loss at the total hip increased from -0.25% per year in their 40s to -1.12% per year in their 80s. In females, the average annual BMD loss at the total hip increased from -0.69% per year in their 40s to -1.51% per year in their 80s. However, the average annual percentage change in spine BMD in females increased from -0.91% per year in their 40s to +1.39% per year in their 80s. CONCLUSIONS A substantial number of subjects had osteoporosis, even though we standardized the prevalence of osteoporosis. In total hip, the mean BMD was decreased during the follow-up period; in addition, the annual percentage loss increased with age. However, spine BMD remained approximately stable or increased over time and therefore may not be appropriate for assessing BMD change.
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Affiliation(s)
- Y Lim
- Division of Endocrinology and Metabolism, Department of Internal Medicine, College of Medicine, The Catholic University of Korea, 222 Banpo-daero Seocho-gu, Seoul, 137-701, South Korea
| | - K Jo
- Division of Endocrinology and Metabolism, Department of Internal Medicine, College of Medicine, The Catholic University of Korea, 222 Banpo-daero Seocho-gu, Seoul, 137-701, South Korea
| | - H-S Ha
- Department of Preventive Medicine, College of Medicine, The Catholic University of Korea, 222 Banpo-daero, Seocho-gu, Seoul, 137-701, South Korea
| | - H-W Yim
- Department of Preventive Medicine, College of Medicine, The Catholic University of Korea, 222 Banpo-daero, Seocho-gu, Seoul, 137-701, South Korea
- Clinical Research Coordinating Center, College of Medicine, The Catholic University of Korea, 222 Banpo-daero, Seocho-gu, Seoul, 137-701, South Korea
| | - K-H Yoon
- Division of Endocrinology and Metabolism, Department of Internal Medicine, College of Medicine, The Catholic University of Korea, 222 Banpo-daero Seocho-gu, Seoul, 137-701, South Korea
| | - W-C Lee
- Department of Preventive Medicine, College of Medicine, The Catholic University of Korea, 222 Banpo-daero, Seocho-gu, Seoul, 137-701, South Korea
| | - H-Y Son
- Division of Endocrinology and Metabolism, Department of Internal Medicine, College of Medicine, The Catholic University of Korea, 222 Banpo-daero Seocho-gu, Seoul, 137-701, South Korea
| | - K H Baek
- Division of Endocrinology and Metabolism, Department of Internal Medicine, College of Medicine, The Catholic University of Korea, 222 Banpo-daero Seocho-gu, Seoul, 137-701, South Korea.
| | - M-I Kang
- Division of Endocrinology and Metabolism, Department of Internal Medicine, College of Medicine, The Catholic University of Korea, 222 Banpo-daero Seocho-gu, Seoul, 137-701, South Korea.
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24
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Kim KI, Lee S, Jin X, Kim SJ, Jo K, Lee JH. DNA Binding Peptide Directed Synthesis of Continuous DNA Nanowires for Analysis of Large DNA Molecules by Scanning Electron Microscope. Small 2017; 13:1601926. [PMID: 27813273 DOI: 10.1002/smll.201601926] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/08/2016] [Revised: 10/04/2016] [Indexed: 06/06/2023]
Abstract
Synthesis of smooth and continuous DNA nanowires, preserving the original structure of native DNA, and allowing its analysis by scanning electron microscope (SEM), is demonstrated. Gold nanoparticles densely assembled on the DNA backbone via thiol-tagged DNA binding peptides work as seeds for metallization of DNA. This method allows whole analysis of DNA molecules with entangled 3D features.
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Affiliation(s)
- Kyung-Il Kim
- 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
| | - Xuelin Jin
- Department of Chemistry and Interdisciplinary Program of Integrated Biotechnology, Sogang University, Seoul, 04107, Republic of Korea
| | - Su Ji Kim
- SKKU Advanced Institute of Nanotechnology (SAINT), 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
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Abstract
Large DNA molecules tethered on the functionalized glass surface have been utilized in polymer physics and biochemistry particularly for investigating interactions between DNA and its binding proteins. Here, we report a method that uses fluorescent microscopy for visualizing large DNA molecules tethered on the surface. First, glass coverslips are biotinylated and passivated by coating with biotinylated polyethylene glycol, which specifically binds biotinylated DNA via avidin protein linkers and significantly reduces undesirable binding from non-specific interactions of proteins or DNA molecules on the surface. Second, the DNA molecules are biotinylated by two different methods depending on their terminals. The blunt ended DNA is tagged with biotinylated dUTP at its 3' hydroxyl terminus, by terminal transferase, while the sticky ended DNA is hybridized with biotinylated complimentary oligonucleotides by DNA ligase. Finally, a microfluidic shear flow makes single DNA molecules stretch to their full contour lengths after being stained with fluorescent protein-DNA binding peptide (FP-DBP).
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Affiliation(s)
- Seonghyun Lee
- Department of Chemistry and Interdisciplinary Program of Integrated Biotechnology, Sogang University
| | - Kyubong Jo
- Department of Chemistry and Interdisciplinary Program of Integrated Biotechnology, Sogang University;
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26
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Kang Y, Lee J, Kim J, Oh Y, Kim D, Lee J, Lim S, Jo K. Analysis of alcohol-induced DNA damage in Escherichia coli by visualizing single genomic DNA molecules. Analyst 2016; 141:4326-31. [PMID: 27186604 DOI: 10.1039/c6an00616g] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Consumption of alcohol injures DNA, and such damage is considered to be a primary cause for the development of cancer and many other diseases essentially due to reactive oxygen species generated from alcohol. To sensitively detect alcohol-induced DNA lesions in a biological system, we introduced a novel analytical platform for visualization of single genomic DNA molecules using E. coli. By fluorescently labelling the DNA lesions, our approach demonstrated, with the highest sensitivity, that we could count the number of DNA lesions induced by alcohol metabolism in a single bacterial cell. Moreover, our results showed a linear relationship between ethanol concentration and the number of DNA lesions: 0.88 lesions per 1% ethanol. Using this approach, we quantitatively analysed the DNA damage induced by exposure to alcoholic beverages such as beer (5% ethanol), rice wine (13%), soju (20%), and whisky (40%).
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Affiliation(s)
- Yujin Kang
- Department of Chemistry and Interdisciplinary Program of Integrated Biotechnology, Sogang University, Seoul 121-742, Korea.
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Jung J, Jang E, Shoaib MA, Jo K, Kim JS. Droplet formation and growth inside a polymer network: A molecular dynamics simulation study. J Chem Phys 2016; 144:134502. [PMID: 27059575 DOI: 10.1063/1.4944965] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Abstract
We present a molecular dynamics simulation study that focuses on the formation and growth of nanoscale droplets inside polymer networks. Droplet formation and growth are investigated by the liquid-vapor phase separation of a dilute Lennard-Jones (LJ) fluid inside regularly crosslinked, polymer networks with varying mesh sizes. In a polymer network with small mesh sizes, droplet formation can be suppressed, the extent of which is dependent on the attraction strength between the LJ particles. When droplets form in a polymer network with intermediate mesh sizes, subsequent growth is significantly slower when compared with that in bulk without a polymer network. Interestingly, droplet growth beyond the initial nucleation stage occurs by different mechanisms depending on the mesh size: droplets grow mainly by diffusion and coalescence inside polymer networks with large mesh sizes (as observed in bulk), whereas Ostwald ripening becomes a more dominant mechanism for droplet growth for small mesh sizes. The analysis of droplet trajectories clearly reveals the obstruction effect of the polymer network on the movement of growing droplets, which leads to Ostwald ripening of droplets. This study suggests how polymer networks can be used to control the growth of nanoscale droplets.
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Affiliation(s)
- Jiyun Jung
- Department of Chemistry and Nanoscience, Ewha Womans University, Seoul 03760, Republic of Korea
| | - Eunseon Jang
- Department of Chemistry and Nanoscience, Ewha Womans University, Seoul 03760, Republic of Korea
| | - Mahbubul Alam Shoaib
- Department of Chemistry and Nanoscience, Ewha Womans University, Seoul 03760, Republic of Korea
| | - Kyubong Jo
- Department of Chemistry and Interdisciplinary Program of Integrated Biotechnology, Sogang University, Seoul 04107, Republic of Korea
| | - Jun Soo Kim
- Department of Chemistry and Nanoscience, Ewha Womans University, Seoul 03760, Republic of Korea
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28
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Lee S, Jo K. DNA Binding Fluorescent Proteins for the Direct Visualization of Large DNA Molecules. Biophys J 2016. [DOI: 10.1016/j.bpj.2015.11.1314] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022] Open
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Lee S, Oh Y, Lee J, Choe S, Lim S, Lee HS, Jo K, Schwartz DC. DNA binding fluorescent proteins for the direct visualization of large DNA molecules. Nucleic Acids Res 2016; 44:e6. [PMID: 26264666 PMCID: PMC4705684 DOI: 10.1093/nar/gkv834] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2015] [Revised: 08/03/2015] [Accepted: 08/06/2015] [Indexed: 12/14/2022] Open
Abstract
Fluorescent proteins that also bind DNA molecules are useful reagents for a broad range of biological applications because they can be optically localized and tracked within cells, or provide versatile labels for in vitro experiments. We report a novel design for a fluorescent, DNA-binding protein (FP-DBP) that completely 'paints' entire DNA molecules, whereby sequence-independent DNA binding is accomplished by linking a fluorescent protein to two small peptides (KWKWKKA) using lysine for binding to the DNA phosphates, and tryptophan for intercalating between DNA bases. Importantly, this ubiquitous binding motif enables fluorescent proteins (Kd = 14.7 μM) to confluently stain DNA molecules and such binding is reversible via pH shifts. These proteins offer useful robust advantages for single DNA molecule studies: lack of fluorophore mediated photocleavage and staining that does not perturb polymer contour lengths. Accordingly, we demonstrate confluent staining of naked DNA molecules presented within microfluidic devices, or localized within live bacterial cells.
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Affiliation(s)
- Seonghyun Lee
- Department of Chemistry and Interdisciplinary Program of Integrated Biotechnology, Sogang University, 1 Shinsudong, Mapogu, Seoul, 121-742, Korea
| | - Yeeun Oh
- Department of Chemistry and Interdisciplinary Program of Integrated Biotechnology, Sogang University, 1 Shinsudong, Mapogu, Seoul, 121-742, Korea
| | - Jungyoon Lee
- Department of Chemistry and Interdisciplinary Program of Integrated Biotechnology, Sogang University, 1 Shinsudong, Mapogu, Seoul, 121-742, Korea
| | - Sojeong Choe
- Department of Chemistry and Interdisciplinary Program of Integrated Biotechnology, Sogang University, 1 Shinsudong, Mapogu, Seoul, 121-742, 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 Biotechnology, Sogang University, 1 Shinsudong, Mapogu, Seoul, 121-742, Korea
| | - Kyubong Jo
- Department of Chemistry and Interdisciplinary Program of Integrated Biotechnology, Sogang University, 1 Shinsudong, Mapogu, Seoul, 121-742, Korea
| | - David C Schwartz
- Laboratory for Molecular and Computational Genomics, Department of Chemistry, Laboratory of Genetics, University of Wisconsin-Madison, Madison, WI 53705, USA
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Lee S, Wang C, Song J, Kim DG, Oh Y, Ko W, Lee J, Park J, Lee HS, Jo K. Investigation of various fluorescent protein–DNA binding peptides for effectively visualizing large DNA molecules. RSC Adv 2016. [DOI: 10.1039/c6ra08683g] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Single-molecule DNA visualization with fluorescent protein DNA binding peptides.
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Affiliation(s)
- Seonghyun Lee
- Department of Chemistry and Program of Integrated Biotech
- Sogang University
- Seoul
- Korea
| | - Cong Wang
- Department of Mechanical Engineering
- Sogang University
- Seoul
- Korea
| | - Junghyun Song
- Department of Chemistry and Program of Integrated Biotech
- Sogang University
- Seoul
- Korea
| | - Do-geun Kim
- Department of Chemistry and Program of Integrated Biotech
- Sogang University
- Seoul
- Korea
| | - Yeeun Oh
- Department of Chemistry and Program of Integrated Biotech
- Sogang University
- Seoul
- Korea
| | - Wooseok Ko
- Department of Chemistry and Program of Integrated Biotech
- Sogang University
- Seoul
- Korea
| | - Jinyong Lee
- Department of Chemistry and Program of Integrated Biotech
- Sogang University
- Seoul
- Korea
| | - Jungyul Park
- Department of Mechanical Engineering
- Sogang University
- Seoul
- Korea
| | - Hyun Soo Lee
- Department of Chemistry and Program of Integrated Biotech
- Sogang University
- Seoul
- Korea
| | - Kyubong Jo
- Department of Chemistry and Program of Integrated Biotech
- Sogang University
- Seoul
- Korea
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31
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Abstract
FRET sensors based on fluorescent proteins have been powerful tools for probing protein–protein interactions and structural changes within proteins.
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Affiliation(s)
- Wooseok Ko
- Department of Chemistry
- Sogang University
- Seoul 121-742
- Republic of Korea
| | - Sanggil Kim
- Department of Chemistry
- Sogang University
- Seoul 121-742
- Republic of Korea
| | - Seonghyun Lee
- Department of Chemistry
- Sogang University
- Seoul 121-742
- Republic of Korea
| | - Kyubong Jo
- Department of Chemistry
- Sogang University
- Seoul 121-742
- Republic of Korea
| | - Hyun Soo Lee
- Department of Chemistry
- Sogang University
- Seoul 121-742
- Republic of Korea
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32
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Abstract
We present a single molecule visualization approach for the quantitative analysis of reactive oxygen species (ROS) induced DNA damage, such as base oxidation and single stranded breaks in large DNA molecules. We utilized the Fenton reaction to generate DNA damage with subsequent enzymatic treatment using a mixture of three types of glycosylases to remove oxidized bases, and then fluorescent labeling on damaged lesions via nick translation. This single molecule analytical platform provided the capability to count one or two damaged sites per λ DNA molecule (48.5 kb), which were reliably dependent on the concentrations of hydrogen peroxide and ferrous ion at the micromolar level. More importantly, the labeled damaged sites that were visualized under a microscope provided positional information, which offered the capability of comparing DNA damaged sites with the in silico genomic map to reveal sequence specificity that GTGR is more sensitive to oxidative damage. Consequently, single DNA molecule analysis provides a sensitive analytical platform for ROS-induced DNA damage and suggests an interesting biochemical insight that the genome primarily active during the lysogenic cycle may have less probability for oxidative DNA damage.
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Affiliation(s)
- Jinyong Lee
- Department of Chemistry and Interdisciplinary Program of Integrated Biotechnology, Sogang University, Seoul, 121-742, Korea.
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33
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Lee J, Kim Y, Lee S, Jo K. Visualization of large elongated DNA molecules. Electrophoresis 2015; 36:2057-71. [PMID: 25994517 DOI: 10.1002/elps.201400479] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2014] [Revised: 03/08/2015] [Accepted: 04/27/2015] [Indexed: 12/26/2022]
Abstract
Long and linear DNA molecules are the mainstream single-molecule analytes for a variety of biochemical analysis within microfluidic devices, including functionalized surfaces and nanostructures. However, for biochemical analysis, large DNA molecules have to be unraveled, elongated, and visualized to obtain biochemical and genomic information. To date, elongated DNA molecules have been exploited in the development of a number of genome analysis systems as well as for the study of polymer physics due to the advantage of direct visualization of single DNA molecule. Moreover, each single DNA molecule provides individual information, which makes it useful for stochastic event analysis. Therefore, numerous studies of enzymatic random motions have been performed on a large elongated DNA molecule. In this review, we introduce mechanisms to elongate DNA molecules using microfluidics and nanostructures in the beginning. Secondly, we discuss how elongated DNA molecules have been utilized to obtain biochemical and genomic information by direct visualization of DNA molecules. Finally, we reviewed the approaches used to study the interaction of proteins and large DNA molecules. Although DNA-protein interactions have been investigated for many decades, it is noticeable that there have been significant achievements for the last five years. Therefore, we focus mainly on recent developments for monitoring enzymatic activity on large elongated DNA molecules.
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Affiliation(s)
- Jinyong Lee
- Department of Chemistry and Interdisciplinary Program of Integrated Biotechnology, Sogang University, Mapogu, Seoul, Republic of Korea
| | - Yongkyun Kim
- Department of Chemistry and Interdisciplinary Program of Integrated Biotechnology, Sogang University, Mapogu, Seoul, Republic of Korea
| | - Seonghyun Lee
- Department of Chemistry and Interdisciplinary Program of Integrated Biotechnology, Sogang University, Mapogu, Seoul, Republic of Korea
| | - Kyubong Jo
- Department of Chemistry and Interdisciplinary Program of Integrated Biotechnology, Sogang University, Mapogu, Seoul, Republic of Korea
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Yeom T, Lee J, Lee S, Kang S, Kim KR, Han B, Lee HS, Jo K. Mass spectrometric investigation of the role of the linking polypeptide chain in DNA polymerase I. Analyst 2015; 139:2432-9. [PMID: 24695614 DOI: 10.1039/c4an00107a] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
DNA polymerase I offers great promise for a wide range of biotechnological applications due to its capability to add labeled nucleotides into double-stranded large DNA molecules by using both polymerase and nuclease domains. Accordingly, it is crucially important to thoroughly characterize this enzyme for further developments. Although the enzyme has been thus far characterized using mainly traditional analytical instruments, here we utilized an advanced and convenient means of mass spectrometry to elucidate enzymatic functions and mechanisms by measuring DNA oligomers generated by polymerase and nuclease reactions. Our analysis revealed several novel enzymatic features, including the observation that polymerase readily dissociates from the DNA molecules containing a wide single-stranded section. From this finding, we reasoned a serious situation of DNA break because polymerase domains cannot efficiently repair the wide single-stranded section, which is susceptible to DNA breaks. Furthermore, we deduced a plausible explanation for a paradoxical question as to why two domains of polymerase and 5'-nuclease are linked by a small and flexible polypeptide in polymerase I. The polypeptide link seems to prevent a 5'-nuclease from causing DNA breaks by locating a polymerase domain closely for immediate repair reaction. Here we present experimental evidence to prove our hypothesis via a set of mass spectrometric analyses as well as single DNA molecule observation and bacterial cell growth assay. Consequently, mass spectrometric analysis for DNA polymerase I provides a meaningful biological insight that a polypeptide link can be a molecular leash to control an aggressive domain in order to prevent unmanageable damages.
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Affiliation(s)
- Taeho Yeom
- Department of Chemistry and Interdisciplinary Program of Integrated Biotechnology, Sogang University, Seoul, 121-742, Republic of Korea.
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35
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Lee J, Chang R, Chen YL, Jo K. Single DNA Molecule Swollen and Trapped in Nanoslit. Biophys J 2015. [DOI: 10.1016/j.bpj.2014.11.964] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022] Open
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36
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Abstract
We present nanoslit confined DNA conformations at very low ionic strengths and a theory to explain most measurements for single DNA molecule size under strong nanoslit confinement. Very low ionic strength conditions not only increase the DNA persistence length dramatically, but also cause DNA molecules to swell to the extent that the effective diameter of DNA becomes larger than the nanoslit height. By accounting for these effects, our results and theory provide a reasonable clue for a current controversy regarding the dependence of the DNA conformation on slit height (h), persistence length (p), and effective diameter (w).
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Affiliation(s)
- Jinyong Lee
- Department
of Chemistry and Interdisciplinary Program of Integrated Biotechnology, Sogang University, Seoul, Republic of Korea
| | - Sulhwa Kim
- Department
of Chemistry and Interdisciplinary Program of Integrated Biotechnology, Sogang University, Seoul, Republic of Korea
| | - Huisu Jeong
- School
of Material Science and Engineering, Gwanju Institute of Science and Technology (GIST), Gwangju, Republic of Korea
| | - Gun Young Jung
- School
of Material Science and Engineering, Gwanju Institute of Science and Technology (GIST), Gwangju, Republic of Korea
| | - Rakwoo Chang
- Department
of Chemistry, Kwangwoon University, Seoul, Republic of Korea
| | - Yeng-Long Chen
- Institute of Physics, Academia Sinica, Taipei, Taiwan
- Department
of Physics, National Taiwan University, Taipei, Taiwan
- Department
of Chemical Engineering, National Tsing-Hua University, Hsinchu, Taiwan
| | - Kyubong Jo
- Department
of Chemistry and Interdisciplinary Program of Integrated Biotechnology, Sogang University, Seoul, Republic of Korea
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Kim B, Kim K, Jeon P, Kim S, Kim H, Byun H, Cha J, Hong S, Jo K. Thromboembolic complications in patients with clopidogrel resistance after coil embolization for unruptured intracranial aneurysms. AJNR Am J Neuroradiol 2014; 35:1786-92. [PMID: 24831597 DOI: 10.3174/ajnr.a3955] [Citation(s) in RCA: 45] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
BACKGROUND AND PURPOSE Antiplatelet resistance is known to be associated with symptomatic ischemic complication after endovascular coil embolization. The purpose of our study was to evaluate the relationship between antiplatelet resistance and clinically silent thromboembolic complications using DWI in patients who underwent coil embolization for unruptured intracranial aneurysm. MATERIALS AND METHODS Between October 2011 and May 2013, 58 patients with 62 unruptured aneurysms who were measured for antiplatelet response using VerifyNow assay and underwent elective coil embolization for an unruptured aneurysm with posttreatment DWI were enrolled. Diffusion-positive lesions were classified into 3 groups according to the number of lesions (n=0 [grade 0], n<6 [grade I], and n≥6 [grade II]). The relationship between antiplatelet resistance and diffusion-positive lesions was analyzed. RESULTS Sixty-two endovascular coiling procedures were performed on 58 patients. Clopidogrel resistance was revealed in 23 patients (39.7%) and diffusion-positive lesions were demonstrated in 28 patients (48.3%); these consisted of 19 (32.8%) grade I and 9 (15.5%) grade II lesions. Clopidogrel resistance was not relevant to the development of any diffusion-positive lesion (grade I and II, P=.789) but was associated with the development of multiple diffusion-positive lesions (grade II, P=.002). In the logistic regression prediction model, clopidogrel resistance showed significant correlation with the development of grade II lesions (P=.001). CONCLUSIONS Multiple diffusion-positive lesions (≥6 in number) occurred more frequently in patients with clopidogrel resistance after endovascular coiling for unruptured aneurysms.
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Affiliation(s)
- B Kim
- From the Departments of Radiology (B.K., K.K., P.J., S.K., H.K., H.B., J.C.)
| | - K Kim
- From the Departments of Radiology (B.K., K.K., P.J., S.K., H.K., H.B., J.C.)
| | - P Jeon
- From the Departments of Radiology (B.K., K.K., P.J., S.K., H.K., H.B., J.C.)
| | - S Kim
- From the Departments of Radiology (B.K., K.K., P.J., S.K., H.K., H.B., J.C.)
| | - H Kim
- From the Departments of Radiology (B.K., K.K., P.J., S.K., H.K., H.B., J.C.)
| | - H Byun
- From the Departments of Radiology (B.K., K.K., P.J., S.K., H.K., H.B., J.C.)
| | - J Cha
- From the Departments of Radiology (B.K., K.K., P.J., S.K., H.K., H.B., J.C.)
| | - S Hong
- Neurosurgery (S.H., K.J.), Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Korea
| | - K Jo
- Neurosurgery (S.H., K.J.), Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Korea
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38
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Jo K, Jeong C, Lee S, Shin D, Park J, Park S, Lim Y. A Reusable Proton Range Compensator and Verification of Its Functionality. Int J Radiat Oncol Biol Phys 2014. [DOI: 10.1016/j.ijrobp.2014.05.2619] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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Jeong H, Song H, Pak Y, Kwon IK, Jo K, Lee H, Jung GY. Enhanced light absorption of silicon nanotube arrays for organic/inorganic hybrid solar cells. Adv Mater 2014; 26:3445-50. [PMID: 24550094 DOI: 10.1002/adma.201305394] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/30/2013] [Revised: 01/08/2014] [Indexed: 05/11/2023]
Abstract
By combining nanoimprint lithography technique and a two-step lift-off process, a Si nanotube array is fabricated and applied as a light absorber for n-Si/PEDOT:PSS hybrid solar cells. The light is effectively trapped within the nanotubes and the device reveals a Jsc of 29.9 mA · cm(-2) and a power conversion efficiency of 10.03%, which is an enhancement of 13.4% compared to the cell having the best-known Si architecture of nanocones as a light absorber to date.
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Affiliation(s)
- Huisu Jeong
- School of Materials Science and Engineering, Gwangju Institute of Science and Technology (GIST), Gwangju, 500-712, Republic of Korea
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40
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Kim J, Kim CS, Sohn E, Lee YM, Jo K, Shin SD, Kim JS. Aminoguanidine protects against apoptosis of retinal ganglion cells in Zucker diabetic fatty rats. Eur Rev Med Pharmacol Sci 2014; 18:1573-1578. [PMID: 24943965] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 06/03/2023]
Abstract
AIM The inhibition of advanced glycation end products (AGEs) and the receptor for AGEs (RAGE) mediated downstream signaling pathways have been suggested to have retinoprotective actions in diabetic retinopathy. Herein, we examined the protective effects of aminoguanidine (AG), an AGEs inhibitor, on diabetes-induced injury of retinal ganglion cells in the Zucker diabetic fatty (ZDF) rats. MATERIALS AND METHODS Seven-week-old male ZDF rats were treated with AG (50 mg/kg body weight) once a day orally for 13 weeks. Serum and vitreous concentration of AGEs were examined. Expressions of AGEs and its receptor (RAGE) were assessed by immunohistochemistry. Southwestern histochemistry was used to detect activated nuclear factor (NF)-κB. RESULTS At the end of the study, vitreal levels of AGEs were significantly reduced in ZDF rats treated with AG. Similary, immunohistochemical analysis showed that AG significantly reduced the positive areas for AGEs and RAGE. Furthermore, AG strongly inhibited the loss of retinal ganglion cells by apoptosis. AG also suppressed the activation of to NF-κB. CONCLUSIONS Our results suggest that AG has retinoprotective properties through not only direct inhibition of AGEs formation but also downregulation of NF-κB.
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Affiliation(s)
- J Kim
- Korean Medicine Based Herbal Drug Development Group, Herbal Medicine Research Division, Korea Institute of Oriental Medicine, Daejeon, South Korea.
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Kounovsky-Shafer KL, Hernández-Ortiz JP, Jo K, Odijk T, de Pablo JJ, Schwartz DC. Presentation of large DNA molecules for analysis as nanoconfined dumbbells. Macromolecules 2013; 46:8356-8368. [PMID: 24683272 PMCID: PMC3964590 DOI: 10.1021/ma400926h] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
The analysis of very large DNA molecules intrinsically supports long-range, phased sequence information, but requires new approaches for their effective presentation as part of any genome analysis platform. Using a multi-pronged approach that marshaled molecular confinement, ionic environment, and DNA elastic properties-but tressed by molecular simulations-we have developed an efficient and scalable approach for presentation of large DNA molecules within nanoscale slits. Our approach relies on the formation of DNA dumbbells, where large segments of the molecules remain outside the nanoslits used to confine them. The low ionic environment, synergizing other features of our approach, enables DNA molecules to adopt a fully stretched conformation, comparable to the contour length, thereby facilitating analysis by optical microscopy. Accordingly, a molecular model is proposed to describe the conformation and dynamics of the DNA molecules within the nanoslits; a Langevin description of the polymer dynamics is adopted in which hydrodynamic effects are included through a Green's function formalism. Our simulations reveal that a delicate balance between electrostatic and hydrodynamic interactions is responsible for the observed molecular conformations. We demonstrate and further confirm that the "Odijk regime" does indeed start when the confinement dimensions size are of the same order of magnitude as the persistence length of the molecule. We also summarize current theories concerning dumbbell dynamics.
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Affiliation(s)
- Kristy L. Kounovsky-Shafer
- Laboratory for Molecular and Computational Genomics, Department of Chemistry, Laboratory of Genetics, and UW-Biotechnology Center, University of Wisconsin-Madison, Madison, WI 53706-1580
| | - Juan P. Hernández-Ortiz
- Departamento de Materiales, Universidad Nacional de Colombia, Sede Medellín, Kra 80 # 65-223
| | - Kyubong Jo
- Bloque M3-050, Medellín Colombia, Department of Chemistry, Sogang University, Seoul, Korea
| | - Theo Odijk
- Lorentz Institute for Theoretical Physics, University of Leiden, The Netherlands
| | - Juan J. de Pablo
- Institute for Molecular Engineering, University of Chicago, Chicago, IL 60637
| | - David C. Schwartz
- Laboratory for Molecular and Computational Genomics, Department of Chemistry, Laboratory of Genetics, and UW-Biotechnology Center, University of Wisconsin-Madison, Madison, WI 53706-1580
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42
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Jin S, Jo K. Long-term prognostic factors for microvascular decompression for trigeminal neuralgia. J Neurol Sci 2013. [DOI: 10.1016/j.jns.2013.07.1879] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
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43
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Smith DW, Han MR, Park JS, Kim KR, Yeom T, Lee JY, Kim DJ, Bingman CA, Kim HJ, Jo K, Han BW, Phillips GN. Crystal structure of the protein from Arabidopsis thaliana gene At5g06450, a putative DnaQ-like exonuclease domain-containing protein with homohexameric assembly. Proteins 2013; 81:1669-1675. [PMID: 23616405 DOI: 10.1002/prot.24315] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2013] [Revised: 03/09/2013] [Accepted: 03/17/2013] [Indexed: 01/17/2023]
Abstract
Arabidopsis thaliana gene At5g06450 encodes a putative DnaQ-like 3'-5' exonuclease domain-containing protein (AtDECP). The DnaQ-like 3'-5' exonuclease domain is often found as a proofreading domain of DNA polymerases. The overall structure of AtDECP adopts an RNase H fold that consists of a mixed β-sheet flanked by α-helices. Interestingly, AtDECP forms a homohexameric assembly with a central six fold symmetry, generating a central cavity. The ring-shaped structure and comparison with WRN-exo, the best structural homologue of AtDECP, suggest a possible mechanism for implementing its exonuclease activity using positively charged patch on the N-terminal side of the homohexameric assembly. The homohexameric structure of AtDECP provides unique information about the interaction between the DnaQ-like 3'-5' exonuclease and its substrate nucleic acids.
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Affiliation(s)
- David W Smith
- Center for Eukaryotic Structural Genomics, Department of Biochemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706, USA
| | - Mi Ra Han
- Research Institute of Pharmaceutical Sciences, College of Pharmacy, Seoul National University, Seoul 151-742, Korea
| | - Joon Sung Park
- Research Institute of Pharmaceutical Sciences, College of Pharmacy, Seoul National University, Seoul 151-742, Korea
| | - Kyung Rok Kim
- Research Institute of Pharmaceutical Sciences, College of Pharmacy, Seoul National University, Seoul 151-742, Korea
| | - Taeho Yeom
- Department of Chemistry, Sogang University, Seoul 121-742, Korea
| | - Ji Yeon Lee
- Research Institute of Pharmaceutical Sciences, College of Pharmacy, Seoul National University, Seoul 151-742, Korea
| | - Do Jin Kim
- Research Institute of Pharmaceutical Sciences, College of Pharmacy, Seoul National University, Seoul 151-742, Korea
| | - Craig A Bingman
- Center for Eukaryotic Structural Genomics, Department of Biochemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706, USA
| | - Hyun-Jung Kim
- College of Pharmacy, Chung-Ang University, Seoul 156-756, Korea
| | - Kyubong Jo
- Department of Chemistry, Sogang University, Seoul 121-742, Korea
| | - Byung Woo Han
- Research Institute of Pharmaceutical Sciences, College of Pharmacy, Seoul National University, Seoul 151-742, Korea
| | - George N Phillips
- Center for Eukaryotic Structural Genomics, Department of Biochemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706, USA.,Department of Biochemistry and Cell Biology, Rice University, Houston, TX 77251, USA
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45
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Cho S, Shin J, Park S, Jeong C, Jo K, Shin D, Lim Y. SU-E-T-112: Dose Distribution Verification of Proton Beam Using Light Output On Scintillation Plate. Med Phys 2013. [DOI: 10.1118/1.4814547] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022] Open
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46
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47
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Abstract
We have performed canonical ensemble Monte Carlo simulations of a primitive DNA model to study the conformation of 2.56 ~ 21.8 μm long DNA molecules confined in nanochannels at various ionic concentrations with the comparison of our previous experimental findings. In the model, the DNA molecule is represented as a chain of charged hard spheres connected by fixed bond length and the nanochannels as planar hard walls. System potentials consist of explicit electrostatic potential along with short-ranged hard-sphere and angle potentials. Our primitive model system provides valuable insight into the DNA conformation, which cannot be easily obtained from experiments or theories. First, the visualization and statistical analysis of DNA molecules in various channel dimensions and ionic strengths verified the formation of locally coiled structures such as backfolding or hairpin and their significance even in highly stretched states. Although the folding events mostly occur within the region of ~0.5 μm from both chain ends, significant portion of the events still take place in the middle region. Second, our study also showed that two controlling factors such as channel dimension and ionic strength widely used in stretching DNA molecules have different influence on the local DNA structure. Ionic strength changes local correlation between neighboring monomers by controlling the strength of electrostatic interaction (and thus the persistence length of DNA), which leads to more coiled local conformation. On the other hand, channel dimension controls the overall stretch by applying the geometric constraint to the non-local DNA conformation instead of directly affecting local correlation. Third, the molecular weight dependence of DNA stretch was observed especially in low stretch regime, which is mainly due to the fact that low stretch modes observed in short DNA molecules are not readily accessible to much longer DNA molecules, resulting in the increase in the stretch of longer DNA molecules.
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Affiliation(s)
- Rakwoo Chang
- Department of Chemistry, Kwangwoon University, Seoul 139-701, South Korea.
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48
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Yeom T, Kim Y, Jo K. Reversible DNA Immobilization on the Neutravidin Coated Surfaces. Biophys J 2012. [DOI: 10.1016/j.bpj.2011.11.2657] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
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49
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Kim D, Lee MS, Jo K, Lee KE, Hwang JK. Therapeutic potential of panduratin A, LKB1-dependent AMP-activated protein kinase stimulator, with activation of PPARα/δ for the treatment of obesity. Diabetes Obes Metab 2011; 13:584-93. [PMID: 21320266 DOI: 10.1111/j.1463-1326.2011.01379.x] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Abstract
AIM AMP-activated protein kinase (AMPK) activators have shown potential as therapeutic agents for metabolic disorders. This study was conducted to evaluate therapeutic potential of panduratin (PAN) A, a natural AMPK stimulator, with activation of PPARα/δ for the treatment of obesity. METHODS We used the novel AMPK activator PAN A, a natural compound isolated from Boesenbergia pandurata rhizomes, to investigate the regulation of LKB1-dependent AMPK-PPARα/δ signalling by western blot, reporter gene assay and small interfering RNA knockdown analysis. In addition, the antiobesity effects of PAN A were evaluated in C57BL/6J mice with high-fat diet (HFD)-induced obesity. RESULTS PAN A stimulated AMPK signalling, induced nuclear translocation of the AMPKα2 subunit and activated PPARα/δ; LKB1, a kinase that lies upstream of AMPK, mediated these effects. PAN A stimulated the direct binding of the AMPKα2 subunit to PPARα/δ, but PPARδ activation required direct interaction with PPARγ coactivator 1α (PGC-1α). Further, PAN A (50 mg/kg/day) reduced weight gain, fat mass, fatty liver and improved serum lipid profiles in obese mice. Additionally, PAN A reduced ectopic fat accumulation and increased the proportion of slow-twitch myofibres and mitochondria content in skeletal muscle, thereby increasing running endurance. CONCLUSIONS PAN A, an LKB1-dependent AMPK stimulator, activated PPARα/δ and attenuated HFD-induced obesity and dysregulation of lipid metabolism. Our findings suggest that PAN A is a potent AMPK activator and show a novel molecular mechanism for the treatment of metabolic disorders.
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Affiliation(s)
- D Kim
- Department of Biotechnology, College of Life Science and Biotechnology, Yonsei University, Seongsanno, Seodaemun-gu, Seoul, Korea
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Kim Y, Kim KS, Kounovsky KL, Chang R, Jung GY, de Pablo JJ, Jo K, Schwartz DC. Nanochannel confinement: DNA stretch approaching full contour length. Lab Chip 2011; 11:1721-9. [PMID: 21431167 PMCID: PMC3222331 DOI: 10.1039/c0lc00680g] [Citation(s) in RCA: 55] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Abstract
Fully stretched DNA molecules are becoming a fundamental component of new systems for comprehensive genome analysis. Among a number of approaches for elongating DNA molecules, nanofluidic molecular confinement has received enormous attentions from physical and biological communities for the last several years. Here we demonstrate a well-optimized condition that a DNA molecule can stretch almost to its full contour length: the average stretch is 19.1 µm ± 1.1 µm for YOYO-1 stained λ DNA (21.8 µm contour length) in 250 nm × 400 nm channel, which is the longest stretch value ever reported in any nanochannels or nanoslits. In addition, based on Odijk's polymer physics theory, we interpret our experimental findings as a function of channel dimensions and ionic strengths. Furthermore, we develop a Monte Carlo simulation approach using a primitive model for the rigorous understanding of DNA confinement effects. Collectively, we present a more complete understanding of nanochannel confined DNA stretching via the comparisons to computer simulation results and Odijk's polymer physics theory.
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Affiliation(s)
- Yoori Kim
- Department of Chemistry and Interdisciplinary Program of Integrated Biotechnology, Sogang University, Seoul, 121-742, Republic of Korea, Tel: +82 2 705 8881
| | - Ki Seok Kim
- Department of Material Science and Engineering, Gwangju Institute of Science and Technology (GIST), Gwangju, 500-712, Republic of Korea
| | - Kristy L. Kounovsky
- Laboratory for Molecular and Computational Genomics, Department of Chemistry, Laboratory of Genetics, University of Wisconsin-Madison, Madison, Wisconsin, 53706 Tel: +1 608 265-0546
| | - Rakwoo Chang
- Department of Chemistry, Kwangwoon University, Seoul 139-701, Republic of Korea
| | - Gun Young Jung
- Department of Material Science and Engineering, Gwangju Institute of Science and Technology (GIST), Gwangju, 500-712, Republic of Korea
| | - Juan J. de Pablo
- Department of Chemical and Biological Engineering, University of Wisconsin-Madison, 1415 Engineering Drive, Madison, WI 53706
| | - Kyubong Jo
- Department of Chemistry and Interdisciplinary Program of Integrated Biotechnology, Sogang University, Seoul, 121-742, Republic of Korea, Tel: +82 2 705 8881
| | - David C. Schwartz
- Laboratory for Molecular and Computational Genomics, Department of Chemistry, Laboratory of Genetics, University of Wisconsin-Madison, Madison, Wisconsin, 53706 Tel: +1 608 265-0546
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