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Greitens C, Leroux JC, Burger M. The intracellular visualization of exogenous DNA in fluorescence microscopy. Drug Deliv Transl Res 2024; 14:2242-2261. [PMID: 38526634 PMCID: PMC11208204 DOI: 10.1007/s13346-024-01563-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/28/2024] [Indexed: 03/27/2024]
Abstract
In the development of non-viral gene delivery vectors, it is essential to reliably localize and quantify transfected DNA inside the cell. To track DNA, fluorescence microscopy methods are commonly applied. These mostly rely on fluorescently labeled DNA, DNA binding proteins fused to a fluorescent protein, or fluorescence in situ hybridization (FISH). In addition, co-stainings are often used to determine the colocalization of the DNA in specific cellular compartments, such as the endolysosomes or the nucleus. We provide an overview of these DNA tracking methods, advice on how they should be combined, and indicate which co-stainings or additional methods are required to draw precise conclusions from a DNA tracking experiment. Some emphasis is given to the localization of exogenous DNA inside the nucleus, which is the last step of DNA delivery. We argue that suitable tools which allow for the nuclear detection of faint signals are still missing, hampering the rational development of more efficient non-viral transfection systems.
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Affiliation(s)
- Christina Greitens
- Institute of Pharmaceutical Sciences, Department of Chemistry and Applied Biosciences, ETH Zurich, 8093, Zurich, Switzerland
| | - Jean-Christophe Leroux
- Institute of Pharmaceutical Sciences, Department of Chemistry and Applied Biosciences, ETH Zurich, 8093, Zurich, Switzerland.
| | - Michael Burger
- Institute of Pharmaceutical Sciences, Department of Chemistry and Applied Biosciences, ETH Zurich, 8093, Zurich, Switzerland.
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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] [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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Jin X, Kim YT, Jo K. DNA Visualization Using Fluorescent Proteins. Methods Mol Biol 2023; 2564:223-246. [PMID: 36107345 DOI: 10.1007/978-1-0716-2667-2_11] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
DNA binding fluorescent proteins are a powerful tool for single-molecule visualization. In this chapter, we discuss a protocol for the synthesis of DNA binding fluorescent proteins and visualization of single DNA molecules. This chapter includes stepwise methods for molecular cloning, reversible staining, two-color staining, sequence-specific staining, and microscopic visualization of single DNA molecules in a microfluidic device. This content will be useful for DNA characterization using DNA binding fluorescent proteins and its visualization at the single-molecule level.
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Affiliation(s)
- Xuelin Jin
- College of Agriculture, Yanbian University, Yanji, Jilin Province, China.
| | - Y Tehee Kim
- Department of Chemistry and Program of Integrated Biotechnology, Sogang University, Seoul, Korea
| | - Kyubong Jo
- Department of Chemistry and Program of Integrated Biotechnology, Sogang University, Seoul, Korea.
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Kim 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] [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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Kim YT, Oh H, Seo MJ, Lee DH, Shin J, Bong S, Heo S, Hapsari ND, Jo K. 21 Fluorescent Protein-Based DNA Staining Dyes. Molecules 2022; 27:5248. [PMID: 36014487 PMCID: PMC9412447 DOI: 10.3390/molecules27165248] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2022] [Revised: 08/10/2022] [Accepted: 08/12/2022] [Indexed: 11/22/2022] Open
Abstract
Fluorescent protein-DNA-binding peptides or proteins (FP-DBP) are a powerful means to stain and visualize large DNA molecules on a fluorescence microscope. Here, we constructed 21 kinds of FP-DBPs using various colors of fluorescent proteins and two DNA-binding motifs. From the database of fluorescent proteins (FPbase.org), we chose bright FPs, such as RRvT, tdTomato, mNeonGreen, mClover3, YPet, and mScarlet, which are four to eight times brighter than original wild-type GFP. Additionally, we chose other FPs, such as mOrange2, Emerald, mTurquoise2, mStrawberry, and mCherry, for variations in emitting wavelengths. For DNA-binding motifs, we used HMG (high mobility group) as an 11-mer peptide or a 36 kDa tTALE (truncated transcription activator-like effector). Using 21 FP-DBPs, we attempted to stain DNA molecules and then analyzed fluorescence intensities. Most FP-DBPs successfully visualized DNA molecules. Even with the same DNA-binding motif, the order of FP and DBP affected DNA staining in terms of brightness and DNA stretching. The DNA staining pattern by FP-DBPs was also affected by the FP types. The data from 21 FP-DBPs provided a guideline to develop novel DNA-binding fluorescent proteins.
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Affiliation(s)
- Yurie Tehee Kim
- Department of Chemistry, Sogang University, 35 Baekbeom-ro, Mapogu, Seoul 04107, Korea
| | - Hyesoo Oh
- Department of Chemistry, Sogang University, 35 Baekbeom-ro, Mapogu, Seoul 04107, Korea
| | - Myung Jun Seo
- Department of Chemistry, Sogang University, 35 Baekbeom-ro, Mapogu, Seoul 04107, Korea
| | - Dong Hyeun Lee
- Department of Chemistry, Sogang University, 35 Baekbeom-ro, Mapogu, Seoul 04107, Korea
| | - Jieun Shin
- Department of Chemistry, Sogang University, 35 Baekbeom-ro, Mapogu, Seoul 04107, Korea
| | - Serang Bong
- Department of Chemistry, Sogang University, 35 Baekbeom-ro, Mapogu, Seoul 04107, Korea
| | - Sujeong Heo
- Department of Chemistry, Sogang University, 35 Baekbeom-ro, Mapogu, Seoul 04107, Korea
| | - Natalia Diyah Hapsari
- Department of Chemistry, Sogang University, 35 Baekbeom-ro, Mapogu, Seoul 04107, Korea
- Chemistry Education Program, Department of Mathematics and Science Education, Sanata Dharma University, Yogyakarta 55282, Indonesia
| | - Kyubong Jo
- Department of Chemistry, Sogang University, 35 Baekbeom-ro, Mapogu, Seoul 04107, Korea
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Dong X, Huang Y, Jiang D. Fluorescent Polymerase Chain Reaction Nanokit for the Detection of DNA Sequence in Single Living Cells. Anal Chem 2022; 94:10304-10307. [PMID: 35833720 DOI: 10.1021/acs.analchem.2c02470] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Here, a fluorescent polymerase chain reaction (PCR) nanokit is established to detect the specific DNA sequence in a single living cell. Different from well-developed protocols to load cell-permeable probes into single cell for recognition, the DNA sequence in a cellular nucleus is sorted into a nanopipette in our strategy. The target DNA sequence is reacted with the PCR kit components in the nanopipette to complete a PCR amplification reaction. SYBR Green prefilled in the nanopipette is intercalated into double-stranded DNA to induce fluorescence emission for real-time detection down to a single copy. An obvious increase in the fluorescence is observed that validates the detection of the target DNA sequence in single living cells. The established real-time fluorescent PCR nanokit could adapt the PCR kit for single cell analysis and thus offers an alternatively general and highly sensitive strategy for the detection of specific DNA sequences in single living cells.
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Affiliation(s)
- Xinran Dong
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210092, China
| | - Yuchen Huang
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210092, China
| | - Dechen Jiang
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210092, China
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Capturing and Understanding the Dynamics and Heterogeneity of Gene Expression in the Living Cell. Int J Mol Sci 2020; 21:ijms21218278. [PMID: 33167354 PMCID: PMC7663833 DOI: 10.3390/ijms21218278] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2020] [Revised: 10/29/2020] [Accepted: 11/03/2020] [Indexed: 11/21/2022] Open
Abstract
The regulation of gene expression is a fundamental process enabling cells to respond to internal and external stimuli or to execute developmental programs. Changes in gene expression are highly dynamic and depend on many intrinsic and extrinsic factors. In this review, we highlight the dynamic nature of transient gene expression changes to better understand cell physiology and development in general. We will start by comparing recent in vivo procedures to capture gene expression in real time. Intrinsic factors modulating gene expression dynamics will then be discussed, focusing on chromatin modifications. Furthermore, we will dissect how cell physiology or age impacts on dynamic gene regulation and especially discuss molecular insights into acquired transcriptional memory. Finally, this review will give an update on the mechanisms of heterogeneous gene expression among genetically identical individual cells. We will mainly focus on state-of-the-art developments in the yeast model but also cover higher eukaryotic systems.
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Toksöz YS, Özyiğit İE, Bilen Ç, Arsu N, Karakuş E. Development of a fluorometric measurement system used in biological samples upon the determination of iron (II) metal ion. Prep Biochem Biotechnol 2020; 51:361-374. [PMID: 32935651 DOI: 10.1080/10826068.2020.1818257] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
Abstract
2-thioxanthone thioacetic acid (TXSCH2COOH, T), which has a fluorometric character, was used for new fluorometric system upon Fe(II) analysis in biological samples as the main target. T-BSA binary complex was firstly consisted with non-covalent interactions between T and BSA at the equilibrium concentration as 1.77 × 10-4.M. T-BSA binary complex emission was increased at the ratio of 24.40% due to stabilization property of BSA (pH:7), compared with T emission intensity. Fluorescence emission spectroscopy was used for the all measurements because of an economic, a sensitive and a practical method compared with other spectroscopic analysis. T-BSA-Fe(II) triple complex was also obtained by adding Fe(II) ion to T-BSA binary complex solution. Its characterization was performed to be investigated with optimum excitation wavelength, buffer concentration, pH and temperature as 297 nm, 10-3 M Tris HCl (10-2M NaCI), pH:7.2 at 25 °C, respectively. The results of Fe(II) analysis in serum showed a certain response in fluorometric T-BSA-Fe(II) triple complex measurement system as 50.42 ± 5.8 µg/dL. The analyses of our fluorometric triple complex system were compared with the reference electrochemiluminescence method and similar results were obtained. Fluorometric measurements of T-BSA-Fe(II) triple complex, its characterization and Fe(II) analysis in this system have not been investigated in literature gives originality to our study.
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Affiliation(s)
- Yavuz Selim Toksöz
- Department of Chemistry, Yildiz Technical University, Esenler, Istanbul, Turkey
| | | | - Çiğdem Bilen
- Department of Chemistry, Yildiz Technical University, Esenler, Istanbul, Turkey
| | - Nergis Arsu
- Department of Chemistry, Yildiz Technical University, Esenler, Istanbul, Turkey
| | - Emine Karakuş
- Department of Chemistry, Yildiz Technical University, Esenler, Istanbul, Turkey
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