1
|
Kawai M, Oda H, Mimura H, Osaki T, Takeuchi S. Open-source and low-cost miniature microscope for on-site fluorescence detection. HARDWAREX 2024; 19:e00545. [PMID: 39006472 PMCID: PMC11239704 DOI: 10.1016/j.ohx.2024.e00545] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/21/2024] [Revised: 05/30/2024] [Accepted: 06/10/2024] [Indexed: 07/16/2024]
Abstract
The development of a compact and affordable fluorescence microscope can be a formidable challenge for growing needs in on-site testing and detection of fluorescent labeled biological systems, especially for those who specialize in biology rather than in engineering. In response to such a situation, we present an open-source miniature fluorescence microscope using Raspberry Pi. Our fluorescence microscope, with dimensions of 19.2 × 13.6 × 8.2 cm3 (including the display, computer, light-blocking case, and other operational requirements), not only offers cost-effectiveness (costing less than $500) but is also highly customizable to meet specific application needs. The 12.3-megapixel Raspberry Pi HQ Camera captures high-resolution imagery, while the equipped wide-angle lens provides a field of view measuring 21 × 15 mm2. The integrated wireless LAN in the Raspberry Pi, along with software-controllable high-powered fluorescence LEDs, holds potential for a wide range of applications. This open-source fluorescence microscope offers biohybrid sensor developers a versatile tool to streamline unfamiliar mechanical design tasks and open new opportunities for on-site fluorescence detections.
Collapse
Affiliation(s)
- Michio Kawai
- Department of Mechano-Informatics, Graduate School of Information Science and Technology, The University of Tokyo, Tokyo, Japan
| | - Haruka Oda
- Department of Mechano-Informatics, Graduate School of Information Science and Technology, The University of Tokyo, Tokyo, Japan
| | - Hisatoshi Mimura
- Artificial Cell Membrane Systems Group, Kanagawa Institute of Industrial Science and Technology, Kanagawa, Japan
| | - Toshihisa Osaki
- Artificial Cell Membrane Systems Group, Kanagawa Institute of Industrial Science and Technology, Kanagawa, Japan
| | - Shoji Takeuchi
- Department of Mechano-Informatics, Graduate School of Information Science and Technology, The University of Tokyo, Tokyo, Japan
- Institute of Industrial Science (IIS), The University of Tokyo, Tokyo, Japan
- Artificial Cell Membrane Systems Group, Kanagawa Institute of Industrial Science and Technology, Kanagawa, Japan
| |
Collapse
|
2
|
Ding LG, Ji X, Liu YY, Shi M, Li JD, Liu F, Zhang YY, Yu J, Wu JQ. Covalent Organic Framework-Based Theranostic Platforms for Restricting H1N1 Influenza Virus Infection. Int J Nanomedicine 2024; 19:7399-7414. [PMID: 39071500 PMCID: PMC11278156 DOI: 10.2147/ijn.s461866] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2024] [Accepted: 07/13/2024] [Indexed: 07/30/2024] Open
Abstract
Background Influenza A (H1N1) virus is a highly contagious respiratory disease that causes severe illness and death. Vaccines and antiviral drugs are limited by viral variation and drug resistance, so developing efficient integrated theranostic options appears significant in anti-influenza virus infection. Methods In this study, we designed and fabricated covalent organic framework (COF) based theranostic platforms (T705@DATA-COF-Pro), which was composed of an RNA polymerase inhibitor (favipiravir, T705), the carboxyl-enriched COF (DATA-COF) nano-carrier and Cy3-labeled single DNA (ssDNA) probe. Results The multi-porosity COF core provided an excellent micro-environment and smooth delivery for T705. The ssDNA probe coating bound to the nucleic acids of H1N1 selectively, thus controlling drug release and allowing fluorescence imaging. The combination of COF and probe triggered the synergism, promoting drug further therapeutic outcomes. With the aid of T705@DATA-COF-Pro platforms, the H1N1-infected mouse models lightly achieved diagnosis and significantly prolonged survival. Conclusion This research underscores the distinctive benefits and immense potential of COF materials in nano-preparations for virus infection, offering novel avenues for the detection and treatment of H1N1 virus infection.
Collapse
Affiliation(s)
- Luo-Gang Ding
- Shandong Key Laboratory of Disease Control and Breeding, Institute of Animal Science and Veterinary Medicine, Shandong Academy of Agricultural Sciences, Jinan, 250100, People’s Republic of China
| | - Xiang Ji
- Key Laboratory of Shandong Microbial Engineering, College of Bioengineering, Qilu University of Technology (Shandong Academy of Sciences), Jinan, 250353, People’s Republic of China
| | - Yue-Yue Liu
- Institute of Poultry Science, Shandong Academy of Agricultural Science, Jinan, 250100, People’s Republic of China
| | - Min Shi
- Shandong Key Laboratory of Disease Control and Breeding, Institute of Animal Science and Veterinary Medicine, Shandong Academy of Agricultural Sciences, Jinan, 250100, People’s Republic of China
| | - Jian-Da Li
- Shandong Key Laboratory of Disease Control and Breeding, Institute of Animal Science and Veterinary Medicine, Shandong Academy of Agricultural Sciences, Jinan, 250100, People’s Republic of China
| | - Fei Liu
- Shandong Key Laboratory of Disease Control and Breeding, Institute of Animal Science and Veterinary Medicine, Shandong Academy of Agricultural Sciences, Jinan, 250100, People’s Republic of China
| | - Yu-Yu Zhang
- Shandong Key Laboratory of Disease Control and Breeding, Institute of Animal Science and Veterinary Medicine, Shandong Academy of Agricultural Sciences, Jinan, 250100, People’s Republic of China
| | - Jiang Yu
- Shandong Key Laboratory of Disease Control and Breeding, Institute of Animal Science and Veterinary Medicine, Shandong Academy of Agricultural Sciences, Jinan, 250100, People’s Republic of China
| | - Jia-Qiang Wu
- Shandong Key Laboratory of Disease Control and Breeding, Institute of Animal Science and Veterinary Medicine, Shandong Academy of Agricultural Sciences, Jinan, 250100, People’s Republic of China
| |
Collapse
|
3
|
Matić J, Piotrowski P, Vrban L, Kobetić R, Vianello R, Jurić I, Fabijanić I, Pernar Kovač M, Brozovic A, Piantanida I, Schmuck C, Radić Stojković M. Distinctive Nucleic Acid Recognition by Lysine-Embedded Phenanthridine Peptides. Int J Mol Sci 2024; 25:4866. [PMID: 38732083 PMCID: PMC11084427 DOI: 10.3390/ijms25094866] [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] [Received: 03/28/2024] [Revised: 04/25/2024] [Accepted: 04/27/2024] [Indexed: 05/13/2024] Open
Abstract
Three new phenanthridine peptide derivatives (19, 22, and 23) were synthesized to explore their potential as spectrophotometric probes for DNA and RNA. UV/Vis and circular dichroism (CD) spectra, mass spectroscopy, and computational analysis confirmed the presence of intramolecular interactions in all three compounds. Computational analysis revealed that compounds alternate between bent and open conformations, highlighting the latter's crucial influence on successful polynucleotide recognition. Substituting one glycine with lysine in two regioisomers (22, 23) resulted in stronger binding interactions with DNA and RNA than for a compound containing two glycines (19), thus emphasizing the importance of lysine. The regioisomer with lysine closer to the phenanthridine ring (23) exhibited a dual and selective fluorimetric response with non-alternating AT and ATT polynucleotides and induction of triplex formation from the AT duplex. The best binding constant (K) with a value of 2.5 × 107 M-1 was obtained for the interaction with AT and ATT polynucleotides. Furthermore, apart from distinguishing between different types of ds-DNA and ds-RNA, the same compound could recognize GC-rich DNA through distinct induced CD signals.
Collapse
Affiliation(s)
- Josipa Matić
- Laboratory for Biomolecular Interactions and Spectroscopy, Division of Organic Chemistry and Biochemistry, Ruđer Bošković Institute, Bijenička Cesta 54, 10000 Zagreb, Croatia; (J.M.); (R.K.); (I.J.); (I.F.); (I.P.)
| | - Patryciusz Piotrowski
- Institute for Organic Chemistry, University of Duisburg-Essen, Universitätsstrasse 7, 45141 Essen, Germany; (P.P.)
| | - Lucija Vrban
- Laboratory for the Computational Design and Synthesis of Functional Materials, Division of Organic Chemistry and Biochemistry, Ruđer Bošković Institute, Bijenička Cesta 54, 10000 Zagreb, Croatia; (L.V.); (R.V.)
| | - Renata Kobetić
- Laboratory for Biomolecular Interactions and Spectroscopy, Division of Organic Chemistry and Biochemistry, Ruđer Bošković Institute, Bijenička Cesta 54, 10000 Zagreb, Croatia; (J.M.); (R.K.); (I.J.); (I.F.); (I.P.)
| | - Robert Vianello
- Laboratory for the Computational Design and Synthesis of Functional Materials, Division of Organic Chemistry and Biochemistry, Ruđer Bošković Institute, Bijenička Cesta 54, 10000 Zagreb, Croatia; (L.V.); (R.V.)
| | - Ivona Jurić
- Laboratory for Biomolecular Interactions and Spectroscopy, Division of Organic Chemistry and Biochemistry, Ruđer Bošković Institute, Bijenička Cesta 54, 10000 Zagreb, Croatia; (J.M.); (R.K.); (I.J.); (I.F.); (I.P.)
| | - Ivana Fabijanić
- Laboratory for Biomolecular Interactions and Spectroscopy, Division of Organic Chemistry and Biochemistry, Ruđer Bošković Institute, Bijenička Cesta 54, 10000 Zagreb, Croatia; (J.M.); (R.K.); (I.J.); (I.F.); (I.P.)
| | - Margareta Pernar Kovač
- Division of Molecular Biology, Ruđer Bošković Institute, Bijenička Cesta 54, 10000 Zagreb, Croatia; (M.P.K.); (A.B.)
| | - Anamaria Brozovic
- Division of Molecular Biology, Ruđer Bošković Institute, Bijenička Cesta 54, 10000 Zagreb, Croatia; (M.P.K.); (A.B.)
| | - Ivo Piantanida
- Laboratory for Biomolecular Interactions and Spectroscopy, Division of Organic Chemistry and Biochemistry, Ruđer Bošković Institute, Bijenička Cesta 54, 10000 Zagreb, Croatia; (J.M.); (R.K.); (I.J.); (I.F.); (I.P.)
| | - Carsten Schmuck
- Institute for Organic Chemistry, University of Duisburg-Essen, Universitätsstrasse 7, 45141 Essen, Germany; (P.P.)
| | - Marijana Radić Stojković
- Laboratory for Biomolecular Interactions and Spectroscopy, Division of Organic Chemistry and Biochemistry, Ruđer Bošković Institute, Bijenička Cesta 54, 10000 Zagreb, Croatia; (J.M.); (R.K.); (I.J.); (I.F.); (I.P.)
| |
Collapse
|
4
|
Heath NG, Segal DJ. CRISPR-Based Split Luciferase as a Biosensor for Unique DNA Sequences In Situ. Methods Mol Biol 2024; 2784:285-299. [PMID: 38502493 DOI: 10.1007/978-1-0716-3766-1_19] [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: 03/21/2024]
Abstract
To date, CRISPR-based DNA targeting approaches have typically used fusion proteins between full fluorescent reporters and catalytically inactive Cas9 (dCas9) for imaging rather than detection of endogenous genomic DNA sequences. A promising alternative strategy for DNA targeting is the direct biosensing of user-defined sequences at single copy with single-cell resolution. Our recently described DNA biosensing approach using a dual fusion protein biosensor comprised of two independently optimized fragments of NanoLuc luciferase (NLuc) directionally fused to dCas9 paired with user-defined single-guide RNAs (sgRNAs) could allow users to sensitively detect unique copies of a target sequence in individual living cells using common laboratory equipment such as a microscope or a luminescence-equipped microplate reader. Here we describe a protocol for using such a DNA biosensor noninvasively in situ.
Collapse
Affiliation(s)
- Nicholas G Heath
- Genome Center and Department of Biochemistry and Molecular Medicine, University of California, Davis, Davis, CA, USA
- Integrative Genetics and Genomics, University of California, Davis, Davis, CA, USA
- Innovative Genomics Institute, University of California, Berkeley, CA, USA
| | - David J Segal
- Genome Center and Department of Biochemistry and Molecular Medicine, University of California, Davis, Davis, CA, USA.
- Integrative Genetics and Genomics, University of California, Davis, Davis, CA, USA.
- Innovative Genomics Institute, University of California, Berkeley, CA, USA.
| |
Collapse
|
5
|
Shen C, Huang Z, Chen X, Wang Z, Zhou J, Wang Z, Liu D, Li C, Zhao T, Zhang Y, Xu S, Zhou W, Peng W. Rapid ultra-sensitive nucleic acid detection using plasmonic fiber-optic spectral combs and gold nanoparticle-tagged targets. Biosens Bioelectron 2023; 242:115719. [PMID: 37797532 DOI: 10.1016/j.bios.2023.115719] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2023] [Revised: 08/24/2023] [Accepted: 09/28/2023] [Indexed: 10/07/2023]
Abstract
Nucleic acid (NA) is a widely-used biomarker for viruses. Accurate quantification of NA can provide a reliable basis for point-of-care diagnosis and treatment. Here, we propose a tilted fiber Bragg grating (TFBG)-based plasmonic fiber-optic spectral comb for fast response and ultralow limit NA detection. The TFBG is coated with a gold film which enables excitation of surface plasmon resonance (SPR), and single-stranded probe NAs with known base sequences are assembled on the gold film. To enhance sensitivity of refractive index (RI) for sensing a chosen combination of probe and target NAs around the TFBG surface, gold nanoparticles (AuNPs) are bonded to the target NA molecules as "RI-labels". The NA combination-induced aggregation of AuNPs induces significant spectral responses in the TFBG that would be below the detection threshold for the NAs in the absence of the AuNPs. The proposed TFBG-SPR NA sensor shows a fast response time of 30 s and an ultra-wide NA detection range from 1 × 10-18 mol/L to 1 × 10-7 mol/L. In the NA concentration range of 1 × 10-12 mol/L (1 pM) to 105 pM, an ultra-high sensitivity of 1.534 dB/lg(pM) is obtained. The sensor achieves an ultra-low limit of detection down to 1.0 × 10-18 mol/L (1 aM), which is more than an order of magnitude lower than the previous reports. The proposed sensor not only shows potentials in practical applications of NA detection, but also provides a new way for TFBG-SPR biochemical sensors to achieve higher RI sensitivity.
Collapse
Affiliation(s)
- Changyu Shen
- College of Optical and Electronic Technology, China Jiliang University, Hangzhou, Zhejiang, 310018, China.
| | - Zhenlin Huang
- College of Optical and Electronic Technology, China Jiliang University, Hangzhou, Zhejiang, 310018, China
| | - Xiaoman Chen
- College of Optical and Electronic Technology, China Jiliang University, Hangzhou, Zhejiang, 310018, China
| | - Zhihao Wang
- College of Optical and Electronic Technology, China Jiliang University, Hangzhou, Zhejiang, 310018, China
| | - Jun Zhou
- College of Optical and Electronic Technology, China Jiliang University, Hangzhou, Zhejiang, 310018, China
| | - Zhaokun Wang
- College of Optical and Electronic Technology, China Jiliang University, Hangzhou, Zhejiang, 310018, China
| | - Dejun Liu
- Key Laboratory of Optoelectronic Devices and Systems of Ministry of Education/Guangdong Province, College of Physics and Optoelectronic Engineering, Shenzhen University, Shenzhen, 518060, China
| | - Chenxia Li
- College of Optical and Electronic Technology, China Jiliang University, Hangzhou, Zhejiang, 310018, China
| | - Tianqi Zhao
- College of Optical and Electronic Technology, China Jiliang University, Hangzhou, Zhejiang, 310018, China
| | - Yang Zhang
- School of Physics, Dalian University of Technology, Dalian, Liaoning, 116024, China
| | - Shiqing Xu
- College of Optical and Electronic Technology, China Jiliang University, Hangzhou, Zhejiang, 310018, China
| | - Wenjun Zhou
- College of Optical and Electronic Technology, China Jiliang University, Hangzhou, Zhejiang, 310018, China
| | - Wei Peng
- School of Physics, Dalian University of Technology, Dalian, Liaoning, 116024, China
| |
Collapse
|
6
|
Chen K, Wang Y. CRISPR/Cas systems for in situ imaging of intracellular nucleic acids: Concepts and applications. Biotechnol Bioeng 2023; 120:3446-3464. [PMID: 37641170 DOI: 10.1002/bit.28543] [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] [Received: 05/20/2023] [Revised: 07/13/2023] [Accepted: 08/15/2023] [Indexed: 08/31/2023]
Abstract
Accurate and precise localization of intracellular nucleic acids is crucial for regulating genetic information transcription and diagnosing diseases. Although intracellular nucleic acid imaging methods are available for various cell types, their widespread utilization is impeded by the intricate nature of the process and its exorbitant cost. Recently, numerous intracellular nucleic acid labeling techniques based on clustered regularly interspaced short palindromic repeats (CRISPR) have been established due to their modularity, flexibility, and specificity. In this work, we present various CRISPR methods that are currently employed for visualizing intracellular genomic sequences and RNA, based on their detection principles and application scenarios. Furthermore, we discuss the advantages and drawbacks of the existing CRISPR imaging methods, as well as future research directions. We anticipate that with continued refinement, more advanced CRISPR-based imaging techniques can be developed to better elucidate the localization and dynamics of intracellular nucleic acids, thereby providing a powerful tool for molecular biology research and clinical molecular pathology diagnosis.
Collapse
Affiliation(s)
- Kun Chen
- Department of Clinical Laboratory, Peking University Cancer Hospital & Institute, Key laboratory of Carcinogenesis and Translational Research (Ministry of Education/Beijing), Beijing, China
| | - Yufei Wang
- Department of Clinical Diagnosis, Laboratory of Beijing Tiantan Hospital, Capital Medical University, NMPA Key Laboratory for Quality Control of In Vitro Diagnostics, Beijing Engineering Research Center of Immunological Reagents Clinical Research, Beijing, China
| |
Collapse
|
7
|
Pradhan S, Apaydin S, Bucevičius J, Gerasimaitė R, Kostiuk G, Lukinavičius G. Sequence-specific DNA labelling for fluorescence microscopy. Biosens Bioelectron 2023; 230:115256. [PMID: 36989663 DOI: 10.1016/j.bios.2023.115256] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2022] [Revised: 03/04/2023] [Accepted: 03/21/2023] [Indexed: 03/29/2023]
Abstract
The preservation of nucleus structure during microscopy imaging is a top priority for understanding chromatin organization, genome dynamics, and gene expression regulation. In this review, we summarize the sequence-specific DNA labelling methods that can be used for imaging in fixed and/or living cells without harsh treatment and DNA denaturation: (i) hairpin polyamides, (ii) triplex-forming oligonucleotides, (iii) dCas9 proteins, (iv) transcription activator-like effectors (TALEs) and (v) DNA methyltransferases (MTases). All these techniques are capable of identifying repetitive DNA loci and robust probes are available for telomeres and centromeres, but visualizing single-copy sequences is still challenging. In our futuristic vision, we see gradual replacement of the historically important fluorescence in situ hybridization (FISH) by less invasive and non-destructive methods compatible with live cell imaging. Combined with super-resolution fluorescence microscopy, these methods will open the possibility to look into unperturbed structure and dynamics of chromatin in living cells, tissues and whole organisms.
Collapse
|
8
|
Schlosser J, Ihmels H. Ligands for Abasic Site-containing DNA and their Use as Fluorescent Probes. Curr Org Synth 2023; 20:96-113. [PMID: 35170411 DOI: 10.2174/1570179419666220216091422] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2021] [Revised: 12/16/2021] [Accepted: 12/16/2021] [Indexed: 12/16/2022]
Abstract
Apurinic and apyrimidinic sites, also referred to as abasic or AP sites, are residues of duplex DNA in which one DNA base is removed from a Watson-Crick base pair. They are formed during the enzymatic repair of DNA and offer binding sites for a variety of guest molecules. Specifically, the AP site may bind an appropriate ligand as a substitute for the missing nucleic base, thus stabilizing the abasic site-containing DNA (AP-DNA). Notably, ligands that bind selectively to abasic sites may be employed for analytical and therapeutical purposes. As a result, there is a search for structural features that establish a strong and selective association of a given ligand with the abasic position in DNA. Against this background, this review provides an overview of the different classes of ligands for abasic site-containing DNA (AP-DNA). This review covers covalently binding substrates, namely amine and oxyamine derivatives, as well as ligands that bind to AP-DNA by noncovalent association, as represented by small heterocyclic aromatic compounds, metal-organic complexes, macrocyclic cyclophanes, and intercalator-nucleobase conjugates. As the systematic development of fluorescent probes for AP-DNA has been somewhat neglected so far, this review article contains a survey of the available reports on the fluorimetric response of the ligand upon binding to the AP-DNA. Based on these data, this compilation shall present a perspective for future developments of fluorescent probes for AP-DNA.
Collapse
Affiliation(s)
- Julika Schlosser
- Department of Chemistry and Biology, University of Siegen, Center of Micro- and Nanochemistry and (Bio)Technology (Cμ), Adolf-Reichwein-Str. 2, 57068 Siegen, Germany
| | - Heiko Ihmels
- Department of Chemistry and Biology, University of Siegen, Center of Micro- and Nanochemistry and (Bio)Technology (Cμ), Adolf-Reichwein-Str. 2, 57068 Siegen, Germany
| |
Collapse
|
9
|
Zhang H, Wang Z, Liu Y, Xie P. Exploring the direct effects of microcystin-LR on DNA via using cross-technical means. ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY 2022; 241:113841. [PMID: 36068764 DOI: 10.1016/j.ecoenv.2022.113841] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/08/2022] [Revised: 06/13/2022] [Accepted: 06/30/2022] [Indexed: 06/15/2023]
Abstract
Microcystin-leucine arginine (MC-LR) is the most toxic and abundant microcystin produced by cyanobacteria. Previous studies have demonstrated that MC-LR can lead to DNA damage by increasing intracellular reactive oxygen species content to induce oxidative stress. However, the direct effect of MC-LR on DNA has not been fully described. In this study, the direct effect of MC-LR on DNA was explored by using spectral analysis and molecular biology technology. First, the fluorescent probe Bptp-R2 was developed to monitor different types of DNA and explore the direct interaction between DNA and MC-LR. The significant differences in the fluorescence of probe-plasmid DNA and probe-ds DNA at various MC-LR concentrations (0, 5, 10, 20, and 30 μmol/L) and MC-LR exposure times (0, 6, 12, and 24 h) showed that the direct interaction between DNA and MC-LR was significant (P ≤ 0.01). Gel electrophoresis demonstrated that the direct interaction between DNA and MC-LR cannot cause DNA strand breaks or change DNA configuration. Then, PCR experiments revealed that the direct interaction between DNA and MC-LR cannot affect DNA replication in a PCR system (P ≤ 0.01). This study discovered that the effects of MC-LR on DNA originate mainly from the secondary effects of MC-LR rather than from the direct interaction between DNA and MC-LR.
Collapse
Affiliation(s)
- Huixia Zhang
- Institute for Ecological Research and Pollution Control of Plateau Lakes; School of Ecology and Environmental Sciences, Yunnan University, Kunming 650500, P.R. China
| | - Zhaomin Wang
- School of Chemistry and Chemical Engineering, University of Jinan, Shandong 250022, P.R. China
| | - Yong Liu
- Institute for Ecological Research and Pollution Control of Plateau Lakes; School of Ecology and Environmental Sciences, Yunnan University, Kunming 650500, P.R. China.
| | - Ping Xie
- Institute for Ecological Research and Pollution Control of Plateau Lakes; School of Ecology and Environmental Sciences, Yunnan University, Kunming 650500, P.R. China; Donghu Experimental Station of Lake Ecosystems, State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, P.R. China.
| |
Collapse
|
10
|
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.
Collapse
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
| |
Collapse
|
11
|
Heath NG, O’Geen H, Halmai NB, Corn JE, Segal DJ. Imaging Unique DNA Sequences in Individual Cells Using a CRISPR-Cas9-Based, Split Luciferase Biosensor. Front Genome Ed 2022; 4:867390. [PMID: 35403097 PMCID: PMC8990833 DOI: 10.3389/fgeed.2022.867390] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2022] [Accepted: 03/09/2022] [Indexed: 11/13/2022] Open
Abstract
An extensive arsenal of biosensing tools has been developed based on the clustered regularly interspaced short palindromic repeat (CRISPR) platform, including those that detect specific DNA sequences both in vitro and in live cells. To date, DNA imaging approaches have traditionally used full fluorescent reporter-based fusion probes. Such “always-on” probes differentiate poorly between bound and unbound probe and are unable to sensitively detect unique copies of a target sequence in individual cells. Herein we describe a DNA biosensor that provides a sensitive readout for such low-copy DNA sequences through proximity-mediated reassembly of two independently optimized fragments of NanoLuc luciferase (NLuc), a small, bright luminescent reporter. Applying this “turn-on” probe in live cells, we demonstrate an application not easily achieved by fluorescent reporter-based probes, detection of individual endogenous genomic loci using standard epifluorescence microscopy. This approach could enable detection of gene edits during ex vivo editing procedures and should be a useful platform for many other live cell DNA biosensing applications.
Collapse
Affiliation(s)
- Nicholas G. Heath
- Genome Center and Department of Biochemistry and Molecular Medicine, University of California, Davis, Davis, CA, United States
- Integrative Genetics and Genomics, University of California, Davis, Davis, CA, United States
- Innovative Genomics Institute, University of California, Berkeley, Berkeley, CA, United States
| | - Henriette O’Geen
- Genome Center and Department of Biochemistry and Molecular Medicine, University of California, Davis, Davis, CA, United States
- Innovative Genomics Institute, University of California, Berkeley, Berkeley, CA, United States
| | - Nicole B. Halmai
- Genome Center and Department of Biochemistry and Molecular Medicine, University of California, Davis, Davis, CA, United States
- Innovative Genomics Institute, University of California, Berkeley, Berkeley, CA, United States
| | - Jacob E. Corn
- Innovative Genomics Institute, University of California, Berkeley, Berkeley, CA, United States
- Department of Biology, ETH, Zürich, Switzerland
| | - David J. Segal
- Genome Center and Department of Biochemistry and Molecular Medicine, University of California, Davis, Davis, CA, United States
- Integrative Genetics and Genomics, University of California, Davis, Davis, CA, United States
- Innovative Genomics Institute, University of California, Berkeley, Berkeley, CA, United States
- *Correspondence: David J. Segal,
| |
Collapse
|
12
|
Photoactive homomolecular bis(n)-Lophine dyads: Multicomponent synthesis, photophysical properties, theoretical investigation, docking and interaction studies with biomacromolecules. J Mol Liq 2022. [DOI: 10.1016/j.molliq.2021.118084] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
|
13
|
Zhou H, Li Y, Gan Y, Wang R. Total RNA Synthesis and its Covalent Labeling Innovation. Top Curr Chem (Cham) 2022; 380:16. [PMID: 35218412 DOI: 10.1007/s41061-022-00371-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2021] [Accepted: 01/24/2022] [Indexed: 12/16/2022]
Abstract
RNA plays critical roles in a wide range of physiological processes. For example, it is well known that RNA plays an important role in regulating gene expression, cell proliferation, and differentiation, and many other chemical and biological processes. However, the research community still suffers from limited approaches that can be applied to readily visualize a specific RNA-of-interest (ROI). Several methods can be used to track RNAs; these rely mainly on biological properties, namely, hybridization, aptamer, reporter protein, and protein binding. With respect to covalent approaches, very few cases have been reported. Happily, several new methods for efficient labeling studies of ROIs have been demonstrated successfully in recent years. Additionally, methods employed for the detection of ROIs by RNA modifying enzymes have also proved feasible. Several approaches, namely, phosphoramidite chemistry, in vitro transcription reactions, co-transcription reactions, chemical post-modification, RNA modifying enzymes, ligation, and other methods targeted at RNA labeling have been revealed in the past decades. To illustrate the most recent achievements, this review aims to summarize the most recent research in the field of synthesis of RNAs-of-interest bearing a variety of unnatural nucleosides, the subsequent RNA labeling research via biocompatible ligation, and beyond.
Collapse
Affiliation(s)
- Hongling Zhou
- School of Pharmacy, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, China
| | - Yuanyuan Li
- School of Pharmacy, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, China
| | - Youfang Gan
- School of Pharmacy, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, China
| | - Rui Wang
- School of Pharmacy, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, China. .,Hubei Key Laboratory of Natural Medicinal Chemistry and Resource Evaluation, Huazhong University of Science and Technology, Wuhan, 430030, China. .,Key Laboratory of Natural Product and Resource, Shanghai Institute of Organic Chemistry, Shanghai, 230030, China.
| |
Collapse
|
14
|
Janssen AFJ, Breusegem SY, Larrieu D. Current Methods and Pipelines for Image-Based Quantitation of Nuclear Shape and Nuclear Envelope Abnormalities. Cells 2022; 11:347. [PMID: 35159153 PMCID: PMC8834579 DOI: 10.3390/cells11030347] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2021] [Revised: 01/17/2022] [Accepted: 01/18/2022] [Indexed: 02/02/2023] Open
Abstract
Any given cell type has an associated "normal" nuclear morphology, which is important to maintain proper cellular functioning and safeguard genomic integrity. Deviations from this can be indicative of diseases such as cancer or premature aging syndrome. To accurately assess nuclear abnormalities, it is important to use quantitative measures of nuclear morphology. Here, we give an overview of several nuclear abnormalities, including micronuclei, nuclear envelope invaginations, blebs and ruptures, and review the current methods used for image-based quantification of these abnormalities. We discuss several parameters that can be used to quantify nuclear shape and compare their outputs using example images. In addition, we present new pipelines for quantitative analysis of nuclear blebs and invaginations. Quantitative analyses of nuclear aberrations and shape will be important in a wide range of applications, from assessments of cancer cell anomalies to studies of nucleus deformability under mechanical or other types of stress.
Collapse
Affiliation(s)
| | | | - Delphine Larrieu
- Department of Clinical Biochemistry, Addenbrookes Biomedical Campus, Cambridge Institute for Medical Research, University of Cambridge, Cambridge CB2 0XY, UK; (A.F.J.J.); (S.Y.B.)
| |
Collapse
|
15
|
Saarnio VK, Alaranta JM, Lahtinen TM. Systematic study of SYBR green chromophore reveals major improvement with one heteroatom difference. J Mater Chem B 2021; 9:3484-3488. [PMID: 33909740 DOI: 10.1039/d1tb00312g] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Five nucleic acid binding cyanine dyes were synthesized and their photophysical properties were evaluated. Changing a single heteroatom in the chromophore causes major differences both in brightness and photostability between the dyes. With such alteration, the brightness of the chromophore increased two-fold compared to the one found in SYBR Green I.
Collapse
Affiliation(s)
- Ville K Saarnio
- Department of Chemistry, Nanoscience Center, University of Jyväskylä, Jyväskylä FI-40500, Finland.
| | - Johanna M Alaranta
- Department of Chemistry, Nanoscience Center, University of Jyväskylä, Jyväskylä FI-40500, Finland.
| | - Tanja M Lahtinen
- Department of Chemistry, Nanoscience Center, University of Jyväskylä, Jyväskylä FI-40500, Finland.
| |
Collapse
|
16
|
Dziuba D, Didier P, Ciaco S, Barth A, Seidel CAM, Mély Y. Fundamental photophysics of isomorphic and expanded fluorescent nucleoside analogues. Chem Soc Rev 2021; 50:7062-7107. [PMID: 33956014 DOI: 10.1039/d1cs00194a] [Citation(s) in RCA: 29] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Fluorescent nucleoside analogues (FNAs) are structurally diverse mimics of the natural essentially non-fluorescent nucleosides which have found numerous applications in probing the structure and dynamics of nucleic acids as well as their interactions with various biomolecules. In order to minimize disturbance in the labelled nucleic acid sequences, the FNA chromophoric groups should resemble the natural nucleobases in size and hydrogen-bonding patterns. Isomorphic and expanded FNAs are the two groups that best meet the criteria of non-perturbing fluorescent labels for DNA and RNA. Significant progress has been made over the past decades in understanding the fundamental photophysics that governs the spectroscopic and environmentally sensitive properties of these FNAs. Herein, we review recent advances in the spectroscopic and computational studies of selected isomorphic and expanded FNAs. We also show how this information can be used as a rational basis to design new FNAs, select appropriate sequences for optimal spectroscopic response and interpret fluorescence data in FNA applications.
Collapse
Affiliation(s)
- Dmytro Dziuba
- Laboratoire de Bioimagerie et Pathologies, UMR 7021, Université de Strasbourg, 74 route du Rhin, 67401 Illkirch, France.
| | - Pascal Didier
- Laboratoire de Bioimagerie et Pathologies, UMR 7021, Université de Strasbourg, 74 route du Rhin, 67401 Illkirch, France.
| | - Stefano Ciaco
- Laboratoire de Bioimagerie et Pathologies, UMR 7021, Université de Strasbourg, 74 route du Rhin, 67401 Illkirch, France. and Department of Biotechnology, Chemistry and Pharmacy, University of Siena, via Aldo Moro 2, 53100 Siena, Italy
| | - Anders Barth
- Institut für Physikalische Chemie, Lehrstuhl für Molekulare Physikalische Chemie, Heinrich-Heine-Universität, 40225 Düsseldorf, Germany
| | - Claus A M Seidel
- Institut für Physikalische Chemie, Lehrstuhl für Molekulare Physikalische Chemie, Heinrich-Heine-Universität, 40225 Düsseldorf, Germany
| | - Yves Mély
- Laboratoire de Bioimagerie et Pathologies, UMR 7021, Université de Strasbourg, 74 route du Rhin, 67401 Illkirch, France.
| |
Collapse
|
17
|
Suss O, Motiei L, Margulies D. Broad Applications of Thiazole Orange in Fluorescent Sensing of Biomolecules and Ions. Molecules 2021; 26:2828. [PMID: 34068759 PMCID: PMC8126248 DOI: 10.3390/molecules26092828] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2021] [Revised: 04/26/2021] [Accepted: 04/27/2021] [Indexed: 12/13/2022] Open
Abstract
Fluorescent sensing of biomolecules has served as a revolutionary tool for studying and better understanding various biological systems. Therefore, it has become increasingly important to identify fluorescent building blocks that can be easily converted into sensing probes, which can detect specific targets with increasing sensitivity and accuracy. Over the past 30 years, thiazole orange (TO) has garnered great attention due to its low fluorescence background signal and remarkable 'turn-on' fluorescence response, being controlled only by its intramolecular torsional movement. These features have led to the development of numerous molecular probes that apply TO in order to sense a variety of biomolecules and metal ions. Here, we highlight the tremendous progress made in the field of TO-based sensors and demonstrate the different strategies that have enabled TO to evolve into a versatile dye for monitoring a collection of biomolecules.
Collapse
Affiliation(s)
| | | | - David Margulies
- Department of Chemical and Structural Biology, Weizmann Institute of Science, Rehovot 7610001, Israel; (O.S.); (L.M.)
| |
Collapse
|
18
|
Semikolenova OA, Golyshev VM, Kim BH, Venyaminova AG, Novopashina DS. New Two-Component Pyrene Probes Based on Oligo(2'-O-Methylribonucleotides) for microRNA Detection. RUSSIAN JOURNAL OF BIOORGANIC CHEMISTRY 2021. [DOI: 10.1134/s1068162021020230] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
|
19
|
Liu LY, Zhao Y, Zhang N, Wang KN, Tian M, Pan Q, Lin W. Ratiometric Fluorescence Imaging for the Distribution of Nucleic Acid Content in Living Cells and Human Tissue Sections. Anal Chem 2021; 93:1612-1619. [PMID: 33381958 DOI: 10.1021/acs.analchem.0c04064] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The misregulation of nucleic acids behavior leads to cell dysfunction and induces serious diseases. A ratiometric fluorescence probe is a powerful tool to study the dynamic behavior and function relationships of nucleic acids. However, currently, no such effective probe has been reported for in situ, real-time tracking of nucleic acids in living cells and tissue sections. Herein, the unique probe named QPP-AS was rationally designed for ratiometric fluorescence response to nucleic acids through skillful regulation of the intramolecular charge-transfer capabilities of the electron acceptor and donor. Encouraged by the advantages of the selective nucleic acid response, ideal biocompatibility, and high signal-to-noise ratio, QPP-AS has been applied for in situ, real-time ratiometric fluorescence imaging of nucleic acids in living cells for the first time. Furthermore, we have demonstrated that QPP-AS is capable of visualizing the dynamic behavior of nucleic acids during different cellular processes (e.g., cell division and apoptosis) by ratiometric fluorescence imaging. More significantly, QPP-AS has been successfully used for ratiometric fluorescence imaging of nucleic acids in human tissue sections, which provides not only the cell contour, nuclear morphology, and nuclear-plasma ratio but also the nucleic acid content information and may greatly improve accuracy in clinicopathological diagnosis.
Collapse
Affiliation(s)
- Liu-Yi Liu
- Shunde Hospital of Southern Medical University (The First People's Hospital of Shunde), Foshan, Guangdong 528308, P.R. China.,MOE Key Laboratory of Bioinorganic and Synthetic Chemistry, School of Chemistry, Sun Yat-sen University, Guangzhou 510275, P.R. China
| | - Yuping Zhao
- Institute of Optical Materials and Chemical Biology, School of Chemistry and Chemical Engineering, Guangxi University, Nanning, Guangxi 530004, P.R. China.,Institute of Fluorescent Probes for Biological Imaging, School of Chemistry and Chemical Engineering, School of Materials Science and Engineering, University of Jinan, Jinan, Shandong 250022, P.R. China
| | - Nan Zhang
- Department of Physiology, Zhongshan School of Medicine, Sun Yat-Sen University, 74 Zhongshan Road 2, Guangzhou 510080, P.R. China
| | - Kang-Nan Wang
- Shunde Hospital of Southern Medical University (The First People's Hospital of Shunde), Foshan, Guangdong 528308, P.R. China.,MOE Key Laboratory of Bioinorganic and Synthetic Chemistry, School of Chemistry, Sun Yat-sen University, Guangzhou 510275, P.R. China
| | - Minggang Tian
- Institute of Fluorescent Probes for Biological Imaging, School of Chemistry and Chemical Engineering, School of Materials Science and Engineering, University of Jinan, Jinan, Shandong 250022, P.R. China
| | - Qiling Pan
- Shunde Hospital of Southern Medical University (The First People's Hospital of Shunde), Foshan, Guangdong 528308, P.R. China
| | - Weiying Lin
- Institute of Optical Materials and Chemical Biology, School of Chemistry and Chemical Engineering, Guangxi University, Nanning, Guangxi 530004, P.R. China.,Institute of Fluorescent Probes for Biological Imaging, School of Chemistry and Chemical Engineering, School of Materials Science and Engineering, University of Jinan, Jinan, Shandong 250022, P.R. China
| |
Collapse
|
20
|
Novopashina DS, Semikolenova OA, Venyaminova AG. 5'-Monopyrene and 5'-Bispyrene 2'-O-methyl RNA Probes for Detection of RNA Mismatches. Methods Mol Biol 2020; 2063:45-56. [PMID: 31667762 DOI: 10.1007/978-1-0716-0138-9_5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
Progress in synthesis of novel fluorescent oligonucleotides has provided effective instruments for nucleic acid detection. Pyrene conjugated oligonucleotides have demonstrated their effectiveness as fluorescent hybridization probes. Here we describe the synthesis, isolation, and analysis of 5'-monopyrene and 5'-bispyrene conjugates of oligo(2'-O-methylribonucleotides) and their application as probes for fluorescent detection of mismatches in RNA targets.
Collapse
Affiliation(s)
- D S Novopashina
- Institute of Chemical Biology and Fundamental Medicine SB RAS, Novosibirsk, Russia. .,Novosibirsk State University, Novosibirsk, Russia.
| | | | - A G Venyaminova
- Institute of Chemical Biology and Fundamental Medicine SB RAS, Novosibirsk, Russia
| |
Collapse
|
21
|
Gouda AS, Przypis Ł, Walczak K, Jørgensen PT, Wengel J. Carbazole modified oligonucleotides: synthesis, hybridization studies and fluorescence properties. Org Biomol Chem 2020; 18:6935-6948. [PMID: 32936176 DOI: 10.1039/d0ob01553a] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
Synthesis of the novel thiophenyl carbazole phosphoramidite DNA building block 5 was accomplished in four steps using a Suzuki-Miyaura cross-coupling reaction from the core carbazole and it was seamlessly accommodated into a 9-mer DNA-based oligonucleotide by incorporation at the flanking 5'-end in combination with a central insertion of an LNA-T nucleotide. The carbazole-containing oligonucleotide was combined in different duplex hybrids, which were characterized by thermal denaturation, circular dichroism and fluorescence studies. The carbazole monomer modulates the duplex stability in various ways. Thus, monomer Z increased the thermal stability of the 9-mer towards the complementary 9-mer/15-mer DNA duplex by 4.2 °C. Furthermore, indications of its intercalation into the duplex were obtained by modeling studies and robust decreases in fluorescence emission intensities upon duplex formation. In contrast, no clear intercalating tendency was corroborated for monomer Z within the DNA/RNA hybrid duplex as indicated by moderate quenching of the fluorescence and similar duplex thermal stabilities relative to the corresponding control duplex. The recognition efficiencies of the carbazole modified oligonucleotide toward single nucleotide mismatches were studied with two 15-mer model targets (DNA and RNA). For both systems, mismatches positioned at the juxtaposition of the carbazole monomer showed pronounced deceases in thermal denaturation temperature. Steady-state fluorescence emission studies of all mismatched duplexes with incorporation of Z monomer typically displayed efficient fluorescence quenching.
Collapse
Affiliation(s)
- Alaa S Gouda
- Biomolecular Nanoscale Engineering Center, Department of Physics, Chemistry and Pharmacy, University of Southern Denmark, Campusvej 55, 5230 Odense M, Denmark.
| | | | | | | | | |
Collapse
|
22
|
Ahoulou EO, Drinkard KK, Basnet K, St. Lorenz A, Taratula O, Henary M, Grant KB. DNA Photocleavage in the Near-Infrared Wavelength Range by 2-Quinolinium Dicarbocyanine Dyes. Molecules 2020; 25:molecules25122926. [PMID: 32630496 PMCID: PMC7355653 DOI: 10.3390/molecules25122926] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2020] [Revised: 06/19/2020] [Accepted: 06/22/2020] [Indexed: 12/21/2022] Open
Abstract
Here, we report the syntheses of two pentamethine cyanine dyes containing quinolinium rings and substituted with either hydrogen (3) or bromine (4) at the meso carbon. The electron withdrawing bromine atom stabilizes dye 4 in aqueous buffer, allowing complex formation to occur between the dye and double-helical DNA. UV–visible, CD, and fluorescence spectra recorded at low DNA concentrations suggest that dye 4 initially binds to the DNA as a high-order aggregate. As the ratio of DNA to dye is increased, the aggregate is converted to monomeric and other low-order dye forms that interact with DNA in a non-intercalative fashion. The brominated dye 4 is relatively unreactive in the dark, but, under 707–759 nm illumination, generates hydroxyl radicals that cleave DNA in high yield (pH 7.0, 22 °C). Dye 4 is also taken up by ES2 ovarian carcinoma cells, where it is non-toxic under dark conditions. Upon irradiation of the ES2 cells at 694 nm, the brominated cyanine reduces cell viability from 100 ± 10% to 14 ± 1%. Our results suggest that 2-quinolinium-based carbocyanine dyes equipped with stabilizing electron withdrawing groups may have the potential to serve as sensitizing agents in long-wavelength phototherapeutic applications.
Collapse
Affiliation(s)
- Effibe O. Ahoulou
- Department of Chemistry, Georgia State University, Atlanta, GA 30303, USA; (E.O.A.); (K.K.D.); (K.B.)
| | - Kaitlyn K. Drinkard
- Department of Chemistry, Georgia State University, Atlanta, GA 30303, USA; (E.O.A.); (K.K.D.); (K.B.)
| | - Kanchan Basnet
- Department of Chemistry, Georgia State University, Atlanta, GA 30303, USA; (E.O.A.); (K.K.D.); (K.B.)
| | - Anna St. Lorenz
- Department of Pharmaceutical Sciences, College of Pharmacy, Oregon State University, Portland, OR 97201, USA; (A.S.L.); (O.T.)
| | - Oleh Taratula
- Department of Pharmaceutical Sciences, College of Pharmacy, Oregon State University, Portland, OR 97201, USA; (A.S.L.); (O.T.)
| | - Maged Henary
- Department of Chemistry, Georgia State University, Atlanta, GA 30303, USA; (E.O.A.); (K.K.D.); (K.B.)
- Center for Diagnostics and Therapeutics, Georgia State University, Atlanta, GA 30303, USA
- Correspondence: (M.H.); (K.B.G.); Tel.: +1-404-413-5566 (M.H.); +1-404-413-5522 (K.B.G.)
| | - Kathryn B. Grant
- Department of Chemistry, Georgia State University, Atlanta, GA 30303, USA; (E.O.A.); (K.K.D.); (K.B.)
- Correspondence: (M.H.); (K.B.G.); Tel.: +1-404-413-5566 (M.H.); +1-404-413-5522 (K.B.G.)
| |
Collapse
|
23
|
Saneyoshi H, Yamamoto Y, Ohta T, Akai S, Ono A. Thiol-responsive pro-fluorophore labeling: Synthesis of a pro-fluorescent labeled oligonucleotide for monitoring cellular uptake. Bioorg Med Chem Lett 2020; 30:127222. [PMID: 32386978 DOI: 10.1016/j.bmcl.2020.127222] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2020] [Revised: 04/21/2020] [Accepted: 04/25/2020] [Indexed: 10/24/2022]
Abstract
Pro-fluorescent labeled oligonucleotides are potential alternative tools to classical fluorescently labeled oligonucleotides for monitoring cellular uptake. Here, we report the design and synthesis of a thiol-responsive pro-fluorophore labeled oligonucleotide, and its fluorescence responsivity to glutathione in the test tube and live cells.
Collapse
Affiliation(s)
- Hisao Saneyoshi
- Department of Material and Life Chemistry, Faculty of Engineering, Kanagawa University, 3-27-1 Rokkakubashi, Kanagawa-ku, Yokohama 221-8686, Japan; Department of Chemistry, Shiga University of Medical Science, Seta Tsukinowa-cho, Otsu, Shiga 520-2192, Japan.
| | - Yuta Yamamoto
- Department of Material and Life Chemistry, Faculty of Engineering, Kanagawa University, 3-27-1 Rokkakubashi, Kanagawa-ku, Yokohama 221-8686, Japan
| | - Takayuki Ohta
- Department of Material and Life Chemistry, Faculty of Engineering, Kanagawa University, 3-27-1 Rokkakubashi, Kanagawa-ku, Yokohama 221-8686, Japan
| | - Shoji Akai
- Laboratory of Synthetic Organic Chemistry, Kagawa Nutrition University, 3-9-21 Chiyoda, Sakado, Saitama 350-0288, Japan
| | - Akira Ono
- Department of Material and Life Chemistry, Faculty of Engineering, Kanagawa University, 3-27-1 Rokkakubashi, Kanagawa-ku, Yokohama 221-8686, Japan.
| |
Collapse
|
24
|
Sato H, Das S, Singer RH, Vera M. Imaging of DNA and RNA in Living Eukaryotic Cells to Reveal Spatiotemporal Dynamics of Gene Expression. Annu Rev Biochem 2020; 89:159-187. [PMID: 32176523 DOI: 10.1146/annurev-biochem-011520-104955] [Citation(s) in RCA: 32] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
This review focuses on imaging DNA and single RNA molecules in living cells to define eukaryotic functional organization and dynamic processes. The latest advances in technologies to visualize individual DNA loci and RNAs in real time are discussed. Single-molecule fluorescence microscopy provides the spatial and temporal resolution to reveal mechanisms regulating fundamental cell functions. Novel insights into the regulation of nuclear architecture, transcription, posttranscriptional RNA processing, and RNA localization provided by multicolor fluorescence microscopy are reviewed. A perspective on the future use of live imaging technologies and overcoming their current limitations is provided.
Collapse
Affiliation(s)
- Hanae Sato
- Department of Anatomy and Structural Biology, Albert Einstein College of Medicine, Bronx, New York 10461, USA; , ,
| | - Sulagna Das
- Department of Anatomy and Structural Biology, Albert Einstein College of Medicine, Bronx, New York 10461, USA; , ,
| | - Robert H Singer
- Department of Anatomy and Structural Biology, Albert Einstein College of Medicine, Bronx, New York 10461, USA; , , .,Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, Virginia 20147, USA
| | - Maria Vera
- Department of Anatomy and Structural Biology, Albert Einstein College of Medicine, Bronx, New York 10461, USA; , , .,Department of Biochemistry, McGill University, Montreal, Quebec H3G 1Y6, Canada;
| |
Collapse
|
25
|
Emehiser RG, Hall E, Guenther DC, Karmakar S, Hrdlicka PJ. Head-to-head comparison of LNA, MPγPNA, INA and Invader probes targeting mixed-sequence double-stranded DNA. Org Biomol Chem 2020; 18:56-65. [PMID: 31681928 DOI: 10.1039/c9ob02111f] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Four probe chemistries are characterized and compared with respect to thermal denaturation temperatures (Tms), thermodynamic parameters associated with duplex formation, and recognition of mixed-sequence double-stranded (ds) DNA targets: (i) oligodeoxyribonucleotides (ONs) modified with Locked Nucleic Acid (LNA) monomers, (ii) MPγPNAs, i.e., single-stranded peptide nucleic acid (PNA) probes that are functionalized at the γ-position with (R)-diethylene glycol (mini-PEG, MP) moieties, (iii) Invader probes, i.e., DNA duplexes modified with +1 interstrand zipper arrangements of 2'-O-(pyren-1-yl)methyl-RNA monomers, and (iv) intercalating nucleic acids (INAs), i.e., DNA duplexes with opposing insertions of 1-O-(1-pyrenylmethyl)glycerol bulges. Invader and INA probes, which are designed to violate the nearest-neighbor exclusion principle, denature readily, whereas the individual probe strands display exceptionally high affinity towards complementary DNA (cDNA) as indicated by increases in Tms of up to 8 °C per modification. Optimized Invader and INA probes enable efficient and highly specific recognition of mixed-sequence dsDNA targets with self-complementary regions (C50 = 30-50 nM), whereas recognition is less efficient with LNA-modified ONs and fully modified MPγPNAs due to lower cDNA affinity (LNA) and a proclivity for dimerization (LNA and MPγPNA). A Cy3-labeled Invader probe is shown to stain telomeric DNA of individual chromosomes in metaphasic spreads under non-denaturing conditions with excellent specificity.
Collapse
|
26
|
Largy E, Gabelica V. Native Hydrogen/Deuterium Exchange Mass Spectrometry of Structured DNA Oligonucleotides. Anal Chem 2020; 92:4402-4410. [PMID: 32039580 DOI: 10.1021/acs.analchem.9b05298] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Although solution hydrogen-deuterium exchange mass spectrometry (HDX/MS) is well-established for the analysis of the structure and dynamics of proteins, it is currently not exploited for nucleic acids. Here we used DNA G-quadruplex structures as model systems to demonstrate that DNA oligonucleotides are amenable to in-solution HDX/MS in native conditions. In trimethylammonium acetate solutions and in soft source conditions, the protonated phosphate groups are fully back-exchanged in the source, while the exchanged nucleobases remain labeled without detectable back-exchange. As a result, the exchange rates depend strongly on the secondary structure (hydrogen bonding status) of the oligonucleotides, but neither on their charge state nor on the presence of nonspecific adducts. We show that native mass spectrometry methods can measure these exchange rates on the second to the day time scale with high precision. Such combination of HDX with native MS opens promising avenues for the analysis of the structural and biophysical properties of oligonucleotides and their complexes.
Collapse
Affiliation(s)
- Eric Largy
- University of Bordeaux, INSERM and CNRS, Laboratoires Acides Nucléiques: Régulations Naturelle et Artificielle (ARNA, U1212, UMR5320), IECB, 2 rue Robert Escarpit, 33600 Pessac, France
| | - Valérie Gabelica
- University of Bordeaux, INSERM and CNRS, Laboratoires Acides Nucléiques: Régulations Naturelle et Artificielle (ARNA, U1212, UMR5320), IECB, 2 rue Robert Escarpit, 33600 Pessac, France
| |
Collapse
|
27
|
Pandith A, Seo YJ. Label-free sensing platform for miRNA-146a based on chromo-fluorogenic pyrophosphate recognition. J Inorg Biochem 2020; 203:110867. [DOI: 10.1016/j.jinorgbio.2019.110867] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2019] [Revised: 09/19/2019] [Accepted: 09/24/2019] [Indexed: 12/11/2022]
|
28
|
Sigaeva A, Ong Y, Damle VG, Morita A, van der Laan KJ, Schirhagl R. Optical Detection of Intracellular Quantities Using Nanoscale Technologies. Acc Chem Res 2019; 52:1739-1749. [PMID: 31187980 PMCID: PMC6639779 DOI: 10.1021/acs.accounts.9b00102] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2019] [Indexed: 12/11/2022]
Abstract
Optical probes that can be used to measure certain quantities with subcellular resolution give us access to a new level of information at which physics, chemistry, life sciences, and medicine become strongly intertwined. The emergence of these new technologies is owed to great advances in the physical sciences. However, evaluating and improving these methods to new standards requires a joint effort with life sciences and clinical practice. In this Account, we give an overview of the probes that have been developed for measuring a few highly relevant parameters at the subcellular scale: temperature, pH, oxygen, free radicals, inorganic ions, genetic material, and biomarkers. Luminescent probes are available in many varieties, which can be used for measuring temperature, pH, and oxygen. Since they are influenced by virtually any metabolic process in the healthy or diseased cell, these quantities are extremely useful to understand intracellular processes. Probes for them can roughly be divided into molecular dyes with a parameter dependent fluorescence or phosphorescence and nanoparticle platforms. Nanoparticle probes can provide enhanced photostability, measurement quality, and potential for multiple functionalities. Embedding into coatings can improve biocompatibility or prevent nonspecific interactions between the probe and the cellular environment. These qualities need to be matched however with good uptake properties, colloidal properties and eventually intracellular targeting to optimize their practical applicability. Inorganic ions constitute a broad class of compounds or elements, some of which play specific roles in signaling, while others are toxic. Their detection is often difficult due to the cross-talk with similar ions, as well as other parameters. The detection of free radicals, DNA, and biomarkers at extremely low levels has significant potential for biomedical applications. Their presence is linked more directly to physiological and clinical manifestations. Since existing methods for free radical detection are generally poor in sensitivity and spatiotemporal resolution, new reliable methods that are generally applicable can contribute greatly to advancing this topic in biology. Optical methods that detect DNA or RNA and protein biomarkers exist for intracellular applications, but are mostly relevant for the development of rapid point-of-care sample testing. To elucidate the inner workings of cells, focused multidisciplinary research is required to define the validity and limitations of a nanoparticle probe, in both physical and biological terms. Multifunctional platforms and those that are easily made compatible with conventional research equipment have an edge over other techniques in growing the body of research evidencing their versatility.
Collapse
Affiliation(s)
- Alina Sigaeva
- Groningen
University, University Medical
Center Groningen, Antonius
Deusinglaan 1, 9713 AV Groningen, The Netherlands
| | - Yori Ong
- Groningen
University, University Medical
Center Groningen, Antonius
Deusinglaan 1, 9713 AV Groningen, The Netherlands
| | - Viraj G. Damle
- Groningen
University, University Medical
Center Groningen, Antonius
Deusinglaan 1, 9713 AV Groningen, The Netherlands
| | - Aryan Morita
- Groningen
University, University Medical
Center Groningen, Antonius
Deusinglaan 1, 9713 AV Groningen, The Netherlands
- Dept.
Dental Biomedical Sciences, Faculty of Dentistry, Universitas Gadjah Mada, Yogyakarta 55281, Indonesia
| | - Kiran J. van der Laan
- Groningen
University, University Medical
Center Groningen, Antonius
Deusinglaan 1, 9713 AV Groningen, The Netherlands
| | - Romana Schirhagl
- Groningen
University, University Medical
Center Groningen, Antonius
Deusinglaan 1, 9713 AV Groningen, The Netherlands
| |
Collapse
|
29
|
Sundah NR, Ho NRY, Lim GS, Natalia A, Ding X, Liu Y, Seet JE, Chan CW, Loh TP, Shao H. Barcoded DNA nanostructures for the multiplexed profiling of subcellular protein distribution. Nat Biomed Eng 2019; 3:684-694. [PMID: 31285580 DOI: 10.1038/s41551-019-0417-0] [Citation(s) in RCA: 44] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2018] [Accepted: 05/14/2019] [Indexed: 11/09/2022]
Abstract
Massively parallel DNA sequencing is established, yet high-throughput protein profiling remains challenging. Here, we report a barcoding approach that leverages the combinatorial sequence content and the configurational programmability of DNA nanostructures for high-throughput multiplexed profiling of the subcellular expression and distribution of proteins in whole cells. The barcodes are formed by in situ hybridization of tetrahedral DNA nanostructures and short DNA sequences conjugated with protein-targeting antibodies, and by nanostructure-assisted ligation (either enzymatic or chemical) of the nanostructures and exogenous DNA sequences bound to nanoparticles of different sizes (which cause these localization sequences to differentially distribute across subcellular compartments). Compared with linear DNA barcoding, the nanostructured barcodes enhance the signal by more than 100-fold. By implementing the barcoding approach on a microfluidic device for the analysis of rare patient samples, we show that molecular subtypes of breast cancer can be accurately classified and that subcellular spatial markers of disease aggressiveness can be identified.
Collapse
Affiliation(s)
- Noah R Sundah
- Department of Biomedical Engineering, Faculty of Engineering, National University of Singapore, Singapore, Singapore.,Institute for Health Innovation and Technology, National University of Singapore, Singapore, Singapore
| | - Nicholas R Y Ho
- Institute for Health Innovation and Technology, National University of Singapore, Singapore, Singapore.,Institute of Molecular and Cell Biology, Agency for Science, Technology and Research, Singapore, Singapore
| | - Geok Soon Lim
- Institute for Health Innovation and Technology, National University of Singapore, Singapore, Singapore.,Institute of Molecular and Cell Biology, Agency for Science, Technology and Research, Singapore, Singapore
| | - Auginia Natalia
- Institute for Health Innovation and Technology, National University of Singapore, Singapore, Singapore
| | - Xianguang Ding
- Institute for Health Innovation and Technology, National University of Singapore, Singapore, Singapore
| | - Yu Liu
- Department of Biomedical Engineering, Faculty of Engineering, National University of Singapore, Singapore, Singapore.,Institute for Health Innovation and Technology, National University of Singapore, Singapore, Singapore
| | - Ju Ee Seet
- Department of Pathology, National University Hospital, Singapore, Singapore
| | - Ching Wan Chan
- Department of Surgery, National University Hospital, Singapore, Singapore.,Department of Surgery, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
| | - Tze Ping Loh
- Institute for Health Innovation and Technology, National University of Singapore, Singapore, Singapore.,Department of Laboratory Medicine, National University Hospital, Singapore, Singapore
| | - Huilin Shao
- Department of Biomedical Engineering, Faculty of Engineering, National University of Singapore, Singapore, Singapore. .,Institute for Health Innovation and Technology, National University of Singapore, Singapore, Singapore. .,Institute of Molecular and Cell Biology, Agency for Science, Technology and Research, Singapore, Singapore. .,Department of Surgery, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore.
| |
Collapse
|
30
|
Birk UJ. Super-Resolution Microscopy of Chromatin. Genes (Basel) 2019; 10:E493. [PMID: 31261775 PMCID: PMC6678334 DOI: 10.3390/genes10070493] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2019] [Revised: 06/17/2019] [Accepted: 06/26/2019] [Indexed: 01/05/2023] Open
Abstract
Since the advent of super-resolution microscopy, countless approaches and studies have been published contributing significantly to our understanding of cellular processes. With the aid of chromatin-specific fluorescence labeling techniques, we are gaining increasing insight into gene regulation and chromatin organization. Combined with super-resolution imaging and data analysis, these labeling techniques enable direct assessment not only of chromatin interactions but also of the function of specific chromatin conformational states.
Collapse
Affiliation(s)
- Udo J Birk
- University of Applied Sciences HTW Chur, Pulvermühlestrasse 57, 7004 Chur, Switzerland.
- Institut für Physik, Universität Mainz, 55122 Mainz, Germany.
| |
Collapse
|
31
|
Bayindir S, Toprak M. A novel pyrene-based selective colorimetric and ratiometric turn-on sensing for copper. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2019; 213:6-11. [PMID: 30669074 DOI: 10.1016/j.saa.2019.01.053] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/10/2018] [Revised: 11/20/2018] [Accepted: 01/15/2019] [Indexed: 05/13/2023]
Abstract
Detection of copper attracts important in most environmental and biological systems. In this study, a simple probe BisPyTSC containing bis-pyrene core was synthesized, and cation binding and sensing properties were studied using colorimetric and fluorometric detection. The research indicated that the specific ligand affinity for Cu2+ ions results in drastic color and spectral changes. According to the data obtained, while the peak intensity increases at 376 nm, the peak intensity decreased at 280 nm in the absorption spectrum of BisPyTSC and an increase in fluorescence intensity of BisPyTSC was observed in the presence of Cu2+ ions. The binding ratio of BisPyTSC to Cu2+ was found to be 1:1 according to Job's plot experiments. The binding constant was calculated using the Benesi-Hildebrand equation and found to be 3.26 × 104 M-1. Based on these concentration dependent fluorescence changes, the limit of detection (LOD) value was calculated to be 14.5 μM for Cu2+, which is the range of copper that should be in the blood (11.8-23.6 μM). As a result of all these studies, we can understand that BisPyTSC is a good selective candidate turn-on sensor that can be used for Cu2+ detection.
Collapse
Affiliation(s)
- Sinan Bayindir
- Department of Chemistry, Faculty of Sciences and Arts, Bingol University, Bingol, Turkey.
| | - Mahmut Toprak
- Department of Chemistry, Faculty of Sciences and Arts, Bingol University, Bingol, Turkey
| |
Collapse
|
32
|
Oh YJ, Koehler M, Lee Y, Mishra S, Park JW, Hinterdorfer P. Ultra-Sensitive and Label-Free Probing of Binding Affinity Using Recognition Imaging. NANO LETTERS 2019; 19:612-617. [PMID: 30560669 DOI: 10.1021/acs.nanolett.8b04883] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Abstract
Reliable quantification of binding affinity is important in biotechnology and pharmacology and increasingly coupled with a demand for ultrasensitivity, nanoscale resolution, and minute sample amounts. Standard techniques are not able to meet these criteria. This study provides a new platform based on atomic force microscopy (AFM)-derived recognition imaging to determine affinity by visualizing single molecular bindings on nanosize dendrons. Using DNA hybridization as a demonstrator, an AFM sensor adorned with a cognate binding strand senses and localizes target DNAs at nanometer resolution. To overcome the limitations of speed and resolution, the AFM cantilever is sinusoidally oscillated close to resonance conditions at small amplitudes. The equilibrium dissociation constant of capturing DNA duplexes was obtained, yielding 2.4 × 10-10 M. Our label-free single-molecular biochemical analysis approach evidences the utility of recognition imaging and analysis in quantifying biomolecular interactions of just a few hundred molecules.
Collapse
Affiliation(s)
- Yoo Jin Oh
- Institute of Biophysics , Johannes Kepler University Linz , Gruberstrasse 40 , A-4020 Linz , Austria
| | - Melanie Koehler
- Institute of Biophysics , Johannes Kepler University Linz , Gruberstrasse 40 , A-4020 Linz , Austria
| | - Yoonhee Lee
- Department of Chemistry , Pohang University of Science and Technology , 77 Cheongam-Ro , Nam-Gu, Pohang 37673 , Republic of Korea
| | - Sourav Mishra
- Department of Chemistry , Pohang University of Science and Technology , 77 Cheongam-Ro , Nam-Gu, Pohang 37673 , Republic of Korea
| | - Joon Won Park
- Department of Chemistry , Pohang University of Science and Technology , 77 Cheongam-Ro , Nam-Gu, Pohang 37673 , Republic of Korea
| | - Peter Hinterdorfer
- Institute of Biophysics , Johannes Kepler University Linz , Gruberstrasse 40 , A-4020 Linz , Austria
| |
Collapse
|
33
|
Lyalina TA, Goncharova EA, Prokofeva NY, Voroshilina ES, Kolpashchikov DM. A DNA minimachine for selective and sensitive detection of DNA. Analyst 2019; 144:416-420. [DOI: 10.1039/c8an02274g] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Synthetic molecular machines have been explored to manipulate matter at the molecular level.
Collapse
Affiliation(s)
- Tatiana A. Lyalina
- ITMO University
- Laboratory of Solution Chemistry of Advanced Materials and Technologies
- St. Petersburg
- Russian Federation
| | - Ekaterina A. Goncharova
- ITMO University
- Laboratory of Solution Chemistry of Advanced Materials and Technologies
- St. Petersburg
- Russian Federation
| | - Nadezhda Y. Prokofeva
- ITMO University
- Laboratory of Solution Chemistry of Advanced Materials and Technologies
- St. Petersburg
- Russian Federation
| | - Ekaterina S. Voroshilina
- Ural State Medical University
- Department of Microbiology
- Virology and immunology
- Ekaterinburg
- Russian Federation
| | - Dmitry M. Kolpashchikov
- ITMO University
- Laboratory of Solution Chemistry of Advanced Materials and Technologies
- St. Petersburg
- Russian Federation
- Chemistry Department
| |
Collapse
|
34
|
Zhang H, Ba S, Mahajan D, Lee JY, Ye R, Shao F, Lu L, Li T. Versatile Types of DNA-Based Nanobiosensors for Specific Detection of Cancer Biomarker FEN1 in Living Cells and Cell-Free Systems. NANO LETTERS 2018; 18:7383-7388. [PMID: 30336066 DOI: 10.1021/acs.nanolett.8b03724] [Citation(s) in RCA: 41] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
Flap structure-specific endonuclease 1 (FEN1) is overexpressed in various types of human cancer cells and has been recognized as a promising biomarker for cancer diagnosis in the recent years. In order to specifically detect the abundance and activity of this cancer-overexpressed enzyme, different types of DNA-based nanodevices were created during our investigations. It is shown in our studies that these newly designed biosensors are highly sensitive and specific for FEN1 in living cells as well as in cell-free systems. It is expected that these nanoprobes could be useful for monitoring FEN1 activity in human cancer cells, and also for cell-based screening of FEN1 inhibitors as new anticancer drugs.
Collapse
Affiliation(s)
- Hao Zhang
- Division of Chemistry and Biological Chemistry, School of Physical and Mathematical Sciences , Nanyang Technological University , Singapore 637371
| | - Sai Ba
- Division of Chemistry and Biological Chemistry, School of Physical and Mathematical Sciences , Nanyang Technological University , Singapore 637371
| | - Divyanshu Mahajan
- School of Biological Sciences , Nanyang Technological University , Singapore 637551
| | - Jasmine Yiqin Lee
- Division of Chemistry and Biological Chemistry, School of Physical and Mathematical Sciences , Nanyang Technological University , Singapore 637371
| | - Ruijuan Ye
- Division of Chemistry and Biological Chemistry, School of Physical and Mathematical Sciences , Nanyang Technological University , Singapore 637371
| | - Fangwei Shao
- Division of Chemistry and Biological Chemistry, School of Physical and Mathematical Sciences , Nanyang Technological University , Singapore 637371
| | - Lei Lu
- School of Biological Sciences , Nanyang Technological University , Singapore 637551
| | - Tianhu Li
- Division of Chemistry and Biological Chemistry, School of Physical and Mathematical Sciences , Nanyang Technological University , Singapore 637371
| |
Collapse
|
35
|
Mitrea DM, Chandra B, Ferrolino MC, Gibbs EB, Tolbert M, White MR, Kriwacki RW. Methods for Physical Characterization of Phase-Separated Bodies and Membrane-less Organelles. J Mol Biol 2018; 430:4773-4805. [PMID: 30017918 PMCID: PMC6503534 DOI: 10.1016/j.jmb.2018.07.006] [Citation(s) in RCA: 98] [Impact Index Per Article: 16.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2018] [Revised: 07/04/2018] [Accepted: 07/09/2018] [Indexed: 12/17/2022]
Abstract
Membrane-less organelles are cellular structures which arise through the phenomenon of phase separation. This process enables compartmentalization of specific sets of macromolecules (e.g., proteins, nucleic acids), thereby regulating cellular processes by increasing local concentration, and modulating the structure and dynamics of their constituents. Understanding the connection between structure, material properties and function of membrane-less organelles requires inter-disciplinary approaches, which address length and timescales that span several orders of magnitude (e.g., Ångstroms to micrometer, picoseconds to hours). In this review, we discuss the wide variety of methods that have been applied to characterize the morphology, rheology, structure and dynamics of membrane-less organelles and their components, in vitro and in live cells.
Collapse
Affiliation(s)
- Diana M Mitrea
- Department of Structural Biology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA.
| | - Bappaditya Chandra
- Department of Structural Biology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Mylene C Ferrolino
- Department of Structural Biology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Eric B Gibbs
- Department of Structural Biology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Michele Tolbert
- Department of Structural Biology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Michael R White
- Department of Structural Biology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Richard W Kriwacki
- Department of Structural Biology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA; Department of Microbiology, Immunology and Biochemistry, University of Tennessee Health Sciences Center, Memphis, TN 38163, USA.
| |
Collapse
|
36
|
Seio K, Kanamori T, Masaki Y. Synthesis of Fluorescent Nucleic Acids bearing Nucleobases Modified with Heteroaryl Group and Fluorophores. J SYN ORG CHEM JPN 2018. [DOI: 10.5059/yukigoseikyokaishi.76.792] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
- Kohji Seio
- Department of Life Science and Technology, Tokyo Institute of Technology
| | | | | |
Collapse
|
37
|
Nozeret K, Loll F, Cardoso GM, Escudé C, Boutorine AS. Interaction of fluorescently labeled pyrrole-imidazole polyamide probes with fixed and living murine and human cells. Biochimie 2018; 149:122-134. [DOI: 10.1016/j.biochi.2018.03.008] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2017] [Accepted: 03/14/2018] [Indexed: 12/26/2022]
|
38
|
Karadeema RJ, Stancescu M, Steidl TP, Bertot SC, Kolpashchikov DM. The owl sensor: a 'fragile' DNA nanostructure for the analysis of single nucleotide variations. NANOSCALE 2018; 10:10116-10122. [PMID: 29781024 DOI: 10.1039/c8nr01107a] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
Analysis of single nucleotide variations (SNVs) in DNA and RNA sequences is instrumental in healthcare for the detection of genetic and infectious diseases and drug-resistant pathogens. Here we took advantage of the developments in DNA nanotechnology to design a hybridization sensor, named the 'owl sensor', which produces a fluorescence signal only when it complexes with fully complementary DNA or RNA analytes. The novelty of the owl sensor operation is that the selectivity of analyte recognition is, at least in part, determined by the structural rigidity and stability of the entire DNA nanostructure rather than exclusively by the stability of the analyte-probe duplex, as is the case for conventional hybridization probes. Using two DNA and two RNA analytes we demonstrated that owl sensors differentiate SNVs in a wide temperature range of 5 °C-32 °C, a performance unachievable by conventional hybridization probes including the molecular beacon probe. The owl sensor reliably detects cognate analytes even in the presence of 100 times excess of single base mismatched sequences. The approach, therefore, promises to add to the toolbox for the diagnosis of SNVs at ambient temperatures.
Collapse
Affiliation(s)
- Rebekah J Karadeema
- Chemistry Department, University of Central Florida, Orlando, FL 32816, USA.
| | | | | | | | | |
Collapse
|
39
|
Ghosh K, Perlíková P, Havlíček V, Yang C, Pohl R, Tloušťová E, Hodek J, Gurská S, Džubák P, Hajdúch M, Hocek M. Isomeric Naphtho-Fused 7-Deazapurine Nucleosides and Nucleotides: Synthesis, Biological Activity, Photophysical Properties and Enzymatic Incorporation to Nucleic Acids. European J Org Chem 2018. [DOI: 10.1002/ejoc.201800165] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Affiliation(s)
- Ketaki Ghosh
- Institute of Organic Chemistry and Biochemistry; Czech Academy of Sciences; Flemingovo nam. 2 CZ-16610 Prague 6 Czech Republic
| | - Pavla Perlíková
- Institute of Organic Chemistry and Biochemistry; Czech Academy of Sciences; Flemingovo nam. 2 CZ-16610 Prague 6 Czech Republic
| | - Vojtěch Havlíček
- Institute of Organic Chemistry and Biochemistry; Czech Academy of Sciences; Flemingovo nam. 2 CZ-16610 Prague 6 Czech Republic
- Department of Organic Chemistry; Faculty of Science; Charles University in Prague; Hlavova 8 CZ-12843 Prague 2 Czech Republic
| | - Chao Yang
- Institute of Organic Chemistry and Biochemistry; Czech Academy of Sciences; Flemingovo nam. 2 CZ-16610 Prague 6 Czech Republic
- Department of Organic Chemistry; Faculty of Science; Charles University in Prague; Hlavova 8 CZ-12843 Prague 2 Czech Republic
| | - Radek Pohl
- Institute of Organic Chemistry and Biochemistry; Czech Academy of Sciences; Flemingovo nam. 2 CZ-16610 Prague 6 Czech Republic
| | - Eva Tloušťová
- Institute of Organic Chemistry and Biochemistry; Czech Academy of Sciences; Flemingovo nam. 2 CZ-16610 Prague 6 Czech Republic
| | - Jan Hodek
- Institute of Organic Chemistry and Biochemistry; Czech Academy of Sciences; Flemingovo nam. 2 CZ-16610 Prague 6 Czech Republic
| | - Soňa Gurská
- Institute of Molecular and Translational Medicine; Palacky University and University Hospital in Olomouc; Faculty of Medicine and Dentistry; Hněvotínská 5 CZ-775 15 Olomouc Czech Republic
| | - Petr Džubák
- Institute of Molecular and Translational Medicine; Palacky University and University Hospital in Olomouc; Faculty of Medicine and Dentistry; Hněvotínská 5 CZ-775 15 Olomouc Czech Republic
| | - Marián Hajdúch
- Institute of Molecular and Translational Medicine; Palacky University and University Hospital in Olomouc; Faculty of Medicine and Dentistry; Hněvotínská 5 CZ-775 15 Olomouc Czech Republic
| | - Michal Hocek
- Institute of Organic Chemistry and Biochemistry; Czech Academy of Sciences; Flemingovo nam. 2 CZ-16610 Prague 6 Czech Republic
- Department of Organic Chemistry; Faculty of Science; Charles University in Prague; Hlavova 8 CZ-12843 Prague 2 Czech Republic
| |
Collapse
|
40
|
Wiraja C, Yeo DC, Tham KC, Chew SWT, Lim X, Xu C. Real-Time Imaging of Dynamic Cell Reprogramming with Nanosensors. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2018; 14:e1703440. [PMID: 29611333 DOI: 10.1002/smll.201703440] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/02/2017] [Revised: 02/22/2018] [Indexed: 06/08/2023]
Abstract
Cellular reprogramming, the process by which somatic cells regain pluripotency, is relevant in many disease modeling, therapeutic, and drug discovery applications. Molecular evaluation of reprogramming (e.g., polymerase chain reaction, immunostaining) is typically disruptive, and only provides snapshots of phenotypic traits. Gene reporter constructs facilitate live-cell evaluation but is labor intensive and may risk insertional mutagenesis during viral transfection. Herein, the utilization of a non-integrative nanosensor is demonstrated to visualize key reprogramming events in situ within live cells. Principally based on sustained intracellular release of encapsulated molecular probes, nanosensors successfully monitored mesenchymal-epithelial transition, pluripotency acquisition, and transdifferentiation events. Tracking the dynamic expression of four pivotal biomarkers (i.e., THY1, E-CADHERIN, OCT4, and GATA4 mRNA), nanosensor signal showed great agreement with polymerase chain reaction and gene reporter imaging (R2 > 0.9). Overall, such facile, versatile nanosensor enables real-time monitoring of low-frequency reprogramming events, thereby useful for high-throughput assessment, optimization, and biomarker-specific cell enrichment.
Collapse
Affiliation(s)
- Christian Wiraja
- School of Chemical and Biomedical Engineering, Nanyang Technological University, 62 Nanyang Drive, Singapore, 637459, Singapore
| | - David C Yeo
- School of Chemical and Biomedical Engineering, Nanyang Technological University, 62 Nanyang Drive, Singapore, 637459, Singapore
| | - Khek-Chian Tham
- Institute of Medical Biology, Agency for Science, Technology and Research (A*STAR), Immunos, Singapore, 138648, Singapore
| | - Sharon W T Chew
- School of Chemical and Biomedical Engineering, Nanyang Technological University, 62 Nanyang Drive, Singapore, 637459, Singapore
- NTU Institute for Health Technologies, Interdisciplinary Graduate School, Nanyang Technological University, 50 Nanyang Avenue, Singapore, 639798, Singapore
| | - Xinhong Lim
- Institute of Medical Biology, Agency for Science, Technology and Research (A*STAR), Immunos, Singapore, 138648, Singapore
- Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore, 639798, Singapore
- Program in Cancer and Stem Cell Biology, Duke-NUS Graduate Medical School, Singapore, 169857, Singapore
| | - Chenjie Xu
- School of Chemical and Biomedical Engineering, Nanyang Technological University, 62 Nanyang Drive, Singapore, 637459, Singapore
- NTU-Northwestern Institute for Nanomedicine, Nanyang Technological University, 50 Nanyang Avenue, Singapore, 639798, Singapore
| |
Collapse
|
41
|
Vilela P, Heuer-Jungemann A, El-Sagheer A, Brown T, Muskens OL, Smyth NR, Kanaras AG. Sensing of Vimentin mRNA in 2D and 3D Models of Wounded Skin Using DNA-Coated Gold Nanoparticles. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2018; 14:e1703489. [PMID: 29464860 DOI: 10.1002/smll.201703489] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/06/2017] [Revised: 01/11/2018] [Indexed: 06/08/2023]
Abstract
Wound healing is a highly complex biological process, which is accompanied by changes in cell phenotype, variations in protein expression, and the production of active biomolecules. Currently, the detection of proteins in cells is done by immunostaining where the proteins in fixed cells are detected by labeled antibodies. However, immunostaining cannot provide information about dynamic processes in living cells, within the whole tissue. Here, an easy method is presented to detect the transition of epithelial to mesenchymal cells during wound healing. The method employs DNA-coated gold nanoparticle fluorescent nanoprobes to sense the production of Vimentin mRNA expressed in mesenchymal cells. Fluorescence microscopy is used to achieve temporal detection of Vimentin mRNA in wounds. 3D light-sheet microscopy is utilized to observe the dynamic expression of Vimentin mRNA spatially around the wounded site in skin tissue. The use of DNA-gold nanoprobes to detect mRNA expression during wound healing opens up new possibilities for the study of real-time mechanisms in complex biological processes.
Collapse
Affiliation(s)
- Patrick Vilela
- Physics and Astronomy, Faculty of Physical Sciences and Engineering, University of Southampton, Southampton, SO17 1BJ, UK
| | - Amelie Heuer-Jungemann
- Physics and Astronomy, Faculty of Physical Sciences and Engineering, University of Southampton, Southampton, SO17 1BJ, UK
| | - Afaf El-Sagheer
- Chemistry Research Laboratory, Department of Chemistry, University of Oxford, 12 Mansfield Road, Oxford, OX1 3TA, UK
- Chemistry Branch, Department of Science and Mathematics, Faculty of Petroleum and Mining Engineering, Suez University, Suez, 43721, Egypt
| | - Tom Brown
- Chemistry Research Laboratory, Department of Chemistry, University of Oxford, 12 Mansfield Road, Oxford, OX1 3TA, UK
| | - Otto L Muskens
- Physics and Astronomy, Faculty of Physical Sciences and Engineering, University of Southampton, Southampton, SO17 1BJ, UK
- Institute for Life Sciences, University of Southampton, Southampton, SO17 1BJ, UK
| | - Neil R Smyth
- Biological Sciences, Faculty of Natural and Environmental Sciences, University of Southampton, Southampton, SO17 1BJ, UK
| | - Antonios G Kanaras
- Physics and Astronomy, Faculty of Physical Sciences and Engineering, University of Southampton, Southampton, SO17 1BJ, UK
- Institute for Life Sciences, University of Southampton, Southampton, SO17 1BJ, UK
| |
Collapse
|
42
|
Suseela YV, Narayanaswamy N, Pratihar S, Govindaraju T. Far-red fluorescent probes for canonical and non-canonical nucleic acid structures: current progress and future implications. Chem Soc Rev 2018; 47:1098-1131. [DOI: 10.1039/c7cs00774d] [Citation(s) in RCA: 126] [Impact Index Per Article: 21.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Our review presents the recent progress on far-red fluorescent probes of canonical and non-canonical nucleic acid (NA) structures, critically discusses the design principles, applications, limitations and outline the future prospects of developing newer probes with target-specificity for different NA structures.
Collapse
Affiliation(s)
- Y. V. Suseela
- Bioorganic Chemistry Laboratory
- New Chemistry Unit
- Jawaharlal Nehru Centre for Advanced Scientific Research
- Bengaluru 560064
- India
| | - Nagarjun Narayanaswamy
- Bioorganic Chemistry Laboratory
- New Chemistry Unit
- Jawaharlal Nehru Centre for Advanced Scientific Research
- Bengaluru 560064
- India
| | - Sumon Pratihar
- Bioorganic Chemistry Laboratory
- New Chemistry Unit
- Jawaharlal Nehru Centre for Advanced Scientific Research
- Bengaluru 560064
- India
| | - Thimmaiah Govindaraju
- Bioorganic Chemistry Laboratory
- New Chemistry Unit
- Jawaharlal Nehru Centre for Advanced Scientific Research
- Bengaluru 560064
- India
| |
Collapse
|
43
|
Krasheninina OA, Novopashina DS, Apartsin EK, Venyaminova AG. Recent Advances in Nucleic Acid Targeting Probes and Supramolecular Constructs Based on Pyrene-Modified Oligonucleotides. Molecules 2017; 22:E2108. [PMID: 29189716 PMCID: PMC6150046 DOI: 10.3390/molecules22122108] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2017] [Revised: 11/28/2017] [Accepted: 11/28/2017] [Indexed: 12/17/2022] Open
Abstract
In this review, we summarize the recent advances in the use of pyrene-modified oligonucleotides as a platform for functional nucleic acid-based constructs. Pyrene is of special interest for the development of nucleic acid-based tools due to its unique fluorescent properties (sensitivity of fluorescence to the microenvironment, ability to form excimers and exciplexes, long fluorescence lifetime, high quantum yield), ability to intercalate into the nucleic acid duplex, to act as a π-π-stacking (including anchoring) moiety, and others. These properties of pyrene have been used to construct novel sensitive fluorescent probes for the sequence-specific detection of nucleic acids and the discrimination of single nucleotide polymorphisms (SNPs), aptamer-based biosensors, agents for binding of double-stranded DNAs, and building blocks for supramolecular complexes. Special attention is paid to the influence of the design of pyrene-modified oligonucleotides on their properties, i.e., the structure-function relationships. The perspectives for the applications of pyrene-modified oligonucleotides in biomolecular studies, diagnostics, and nanotechnology are discussed.
Collapse
Affiliation(s)
- Olga A Krasheninina
- Institute of Chemical Biology and Fundamental Medicine SB RAS, Acad. Lavrentiev Ave. 8, Novosibirsk 630090, Russia.
| | - Darya S Novopashina
- Institute of Chemical Biology and Fundamental Medicine SB RAS, Acad. Lavrentiev Ave. 8, Novosibirsk 630090, Russia.
| | - Evgeny K Apartsin
- Institute of Chemical Biology and Fundamental Medicine SB RAS, Acad. Lavrentiev Ave. 8, Novosibirsk 630090, Russia.
| | - Alya G Venyaminova
- Institute of Chemical Biology and Fundamental Medicine SB RAS, Acad. Lavrentiev Ave. 8, Novosibirsk 630090, Russia.
| |
Collapse
|
44
|
Comparative Study of Novel Fluorescent Cyanine Nucleotides: Hybridization Analysis of Labeled PCR Products Using a Biochip. J Fluoresc 2017; 27:2001-2016. [PMID: 28752470 DOI: 10.1007/s10895-017-2139-6] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2016] [Accepted: 07/18/2017] [Indexed: 01/08/2023]
Abstract
This study investigated the synthesis and substrate properties of Cy5-labeled dUTP derivatives with different substituents, linkers between the dye unit and pyrimidine heterocycle and fluorophore charges. Fluorescently labeled nucleoside triphosphates were studied as substrates using multiplex PCR with Taq and Vent (exo-) DNA polymerases, the typical representatives of the A and B polymerase families. The efficiency of nucleotide incorporation during PCR was assessed with a multi-parameter hybridization analysis using a diagnostic DNA microarray. The hybridization analysis indirectly estimates the incorporation efficiency of dye-labeled nucleotides in multiplex PCR. Our results demonstrated higher efficiencies of substrates with electrically neutral dyes than electropositive and electronegative Cy5 residues.
Collapse
|
45
|
Astakhova K, Golovin AV, Prokhorenko IA, Ustinov AV, Stepanova IA, Zatsepin TS, Korshun VA. Design of 2′-phenylethynylpyrene excimer forming DNA/RNA probes for homogeneous SNP detection: The attachment manner matters. Tetrahedron 2017. [DOI: 10.1016/j.tet.2017.04.045] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
|
46
|
Xia Y, Zhang R, Wang Z, Tian J, Chen X. Recent advances in high-performance fluorescent and bioluminescent RNA imaging probes. Chem Soc Rev 2017; 46:2824-2843. [PMID: 28345687 PMCID: PMC5472208 DOI: 10.1039/c6cs00675b] [Citation(s) in RCA: 100] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
RNA plays an important role in life processes. Imaging of messenger RNAs (mRNAs) and micro-RNAs (miRNAs) not only allows us to learn the formation and transcription of mRNAs and the biogenesis of miRNAs involved in various life processes, but also helps in detecting cancer. High-performance RNA imaging probes greatly expand our view of life processes and enhance the cancer detection accuracy. In this review, we summarize the state-of-the-art high-performance RNA imaging probes, including exogenous probes that can image RNA sequences with special modification and endogeneous probes that can directly image endogenous RNAs without special treatment. For each probe, we review its structure and imaging principle in detail. Finally, we summarize the application of mRNA and miRNA imaging probes in studying life processes as well as in detecting cancer. By correlating the structures and principles of various probes with their practical uses, we compare different RNA imaging probes and offer guidance for better utilization of the current imaging probes and the future design of higher-performance RNA imaging probes.
Collapse
Affiliation(s)
- Yuqiong Xia
- Engineering Research Center of Molecular-imaging and Neuro-imaging of Ministry of Education, School of Life Science and Technology, Xidian University, Xi'an, Shaanxi 710126, China.
| | | | | | | | | |
Collapse
|
47
|
Li ZH, Liu R, Tan ZL, He L, Lu ZL, Gong B. Aromatization of 9,10-Dihydroacridine Derivatives: Discovering a Highly Selective and Rapid-Responding Fluorescent Probe for Peroxynitrite. ACS Sens 2017; 2:501-505. [PMID: 28723194 DOI: 10.1021/acssensors.7b00139] [Citation(s) in RCA: 43] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
As part of an effort to develop generally applicable strategies for creating probes suitable for detecting important molecular and ionic species, the oxidative aromatization of nonfluorescent 9,10-dihydroacridine derivatives triggered by peroxynitrite (ONOO-) led to the identification of compound 2H, 9-phenyl-9,10-dihydroacridine-4-carboxylic acid, as a rapid-responding fluorescent probe capable of detecting ONOO- with an extraordinary selectivity. Adding a little more than 1 equiv of ONOO- to a solution of 2H resulted in over 100-fold fluorescence enhancement. In sharp contrast, treating 2H with excessive amounts of other oxidants that often interfere with the detection of ONOO- failed to lead to noticeable fluorescence increase. The reaction of ONOO- with 2H shows a similar efficiency in the pH range of 2-8. Low cytotoxicity was observed for 2H and its aromatized product. Bioimaging experiments revealed the promising potential of 2H as a new fluorescent probe for the selective detection of intracellular ONOO-.
Collapse
Affiliation(s)
- Zhi-heng Li
- College
of Chemistry, Beijing Normal University, Beijing 100875, China
| | - Rui Liu
- College
of Chemistry, Beijing Normal University, Beijing 100875, China
| | - Zheng-li Tan
- College
of Chemistry, Beijing Normal University, Beijing 100875, China
| | - Lan He
- National Institute for Food and Drug Control, Beijing 100050, China
| | - Zhong-lin Lu
- College
of Chemistry, Beijing Normal University, Beijing 100875, China
| | - Bing Gong
- College
of Chemistry, Beijing Normal University, Beijing 100875, China
- Department
of Chemistry, University at Buffalo, The State University of New York, Buffalo, New York 14260, United States
| |
Collapse
|
48
|
Tyagi A, Chu KL, Abidi IH, Cagang AA, Zhang Q, Leung NLC, Zhao E, Tang BZ, Luo Z. Single-probe multistate detection of DNA via aggregation-induced emission on a graphene oxide platform. Acta Biomater 2017; 50:334-343. [PMID: 27940196 DOI: 10.1016/j.actbio.2016.12.003] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2016] [Revised: 11/23/2016] [Accepted: 12/05/2016] [Indexed: 01/27/2023]
Abstract
Graphene and graphene oxides (GO), or their reduced forms, have been introduced in a variety of biosensing platforms and have exhibited enhanced performance levels in these forms. We herein report a DNA sensing platform consisting of aggregation-induced emission (AIE) molecules and complementary DNA (comDNA) adsorbed on GO. We experimentally turned the AIE molecule on and off by adjusting its distance, which correlates with DNA structures as shown in our computational results, from the GO sheet, which quenches depending on its distance from the graphene plane. The changes in florescence are reproducible, which demonstrates the probe's ability to identify the binding state of the DNA. Our molecular dynamics simulation results reveal strong π-π interactions between single-strand DNA (ssDNA) and GO, which enable the ssDNA molecule to move closer to the graphene oxide. This reduces the center of mass and binding free energies in the simulation. When hybridized with comDNA, the increased distance, evidenced by the reduced interaction, eliminates the quenching effect and turns on the AIE molecule. Our protocol use of the AIE molecule as a probe thus avoids the complicated steps involved in covalent functionalization and allows the rapid and label-free detection of DNA molecules. STATEMENT OF SIGNIFICANCE A simple, rapid method of fluorescent measurement of DNA hybridization in the presence of graphene (oxide) is presented. Conventional fluorescent dyes offer high performance in biosensors. However, labeling procedures are synthetically demanding in time and resources making it less cost-effective. Molecules with aggregation-induced-emission (AIE) property have advantages over traditional fluorescent molecules because of their intrinsic preference for detection as a turn-on probe and their single-molecule detection ability. Previous work has shown AIE dyes act as excellent "label-free" bioprobes with high sensitivity but with limited selectivity. Graphene oxide (GO) with its unique optical properties and affinity to different kinds of biomolecules can be used as an auxiliary to enhance selectivity of AIE dyes. In this work, we report a label-free strategy to detect DNA of particular sequence by water-soluble AIE probes with the aid of GO, supported by the computational explanations for this phenomenon.
Collapse
Affiliation(s)
- Abhishek Tyagi
- Department of Chemical and Biomolecular Engineering and The Hong Kong Branch of Chinese National Engineering Research Center for Tissue Restoration & Reconstruction, The Hong Kong University of Science & Technology, Clear Water Bay, Kowloon, Hong Kong
| | - Kin Leung Chu
- Department of Chemical and Biomolecular Engineering and The Hong Kong Branch of Chinese National Engineering Research Center for Tissue Restoration & Reconstruction, The Hong Kong University of Science & Technology, Clear Water Bay, Kowloon, Hong Kong
| | - Irfan Haider Abidi
- Department of Chemical and Biomolecular Engineering and The Hong Kong Branch of Chinese National Engineering Research Center for Tissue Restoration & Reconstruction, The Hong Kong University of Science & Technology, Clear Water Bay, Kowloon, Hong Kong
| | - Aldrine Abenoja Cagang
- Department of Chemical and Biomolecular Engineering and The Hong Kong Branch of Chinese National Engineering Research Center for Tissue Restoration & Reconstruction, The Hong Kong University of Science & Technology, Clear Water Bay, Kowloon, Hong Kong
| | - Qicheng Zhang
- Department of Chemical and Biomolecular Engineering and The Hong Kong Branch of Chinese National Engineering Research Center for Tissue Restoration & Reconstruction, The Hong Kong University of Science & Technology, Clear Water Bay, Kowloon, Hong Kong
| | - Nelson L C Leung
- Department of Chemistry and Division of Biomedical Engineering, The Hong Kong University of Science & Technology, Clear Water Bay, Kowloon, Hong Kong
| | - Engui Zhao
- Department of Chemistry and Division of Biomedical Engineering, The Hong Kong University of Science & Technology, Clear Water Bay, Kowloon, Hong Kong
| | - Ben Zhong Tang
- Department of Chemistry and Division of Biomedical Engineering, The Hong Kong University of Science & Technology, Clear Water Bay, Kowloon, Hong Kong
| | - Zhengtang Luo
- Department of Chemical and Biomolecular Engineering and The Hong Kong Branch of Chinese National Engineering Research Center for Tissue Restoration & Reconstruction, The Hong Kong University of Science & Technology, Clear Water Bay, Kowloon, Hong Kong.
| |
Collapse
|
49
|
Krasheninina OA, Lomzov AA, Fishman VS, Novopashina DS, Venyaminova AG. Rational design and studies of excimer forming novel dual probes to target RNA. Bioorg Med Chem 2017; 25:2244-2250. [PMID: 28279557 DOI: 10.1016/j.bmc.2017.02.042] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2016] [Revised: 01/31/2017] [Accepted: 02/22/2017] [Indexed: 11/18/2022]
Abstract
In this paper, we report structure-based rational design and physico-chemical and biological studies of novel pyrene excimer forming dual probes for visualization of intracellular RNAs. Herein, the probes based on 2'-O-methyl RNA with linkers of different structure and length between pyrene moiety and ribose are studied with respect to their hybridization and spectral properties. We found optimal linkers that provide more intense excimer emission (at ∼480nm) of RNA-bound probes; particularly, the length of the linker arm of the 3'-component of dual probes plays a key role in formation of pyrene excimer. Calculated molecular dynamics trajectories and probability distributions of pyrene-pyrene dimer formation upon hybridization of the dual probes with RNA target are in agreement with the obtained fluorescence spectroscopy data for the corresponding duplexes. Our study demonstrates the excellent binding properties of new dual probes to structured RNA and their feasibility for the visualization of intracellular RNA targets.
Collapse
Affiliation(s)
- O A Krasheninina
- Institute of Chemical Biology and Fundamental Medicine SB RAS, 8 Lavrentiev Ave., Novosibirsk 630090, Russia; Novosibirsk State University, 2 Pirogov str., Novosibirsk 630090, Russia.
| | - A A Lomzov
- Institute of Chemical Biology and Fundamental Medicine SB RAS, 8 Lavrentiev Ave., Novosibirsk 630090, Russia; Novosibirsk State University, 2 Pirogov str., Novosibirsk 630090, Russia
| | - V S Fishman
- Institute of Cytology and Genetics SB RAS, 10 Lavrentiev Ave., Novosibirsk 630090, Russia
| | - D S Novopashina
- Institute of Chemical Biology and Fundamental Medicine SB RAS, 8 Lavrentiev Ave., Novosibirsk 630090, Russia; Novosibirsk State University, 2 Pirogov str., Novosibirsk 630090, Russia
| | - A G Venyaminova
- Institute of Chemical Biology and Fundamental Medicine SB RAS, 8 Lavrentiev Ave., Novosibirsk 630090, Russia
| |
Collapse
|
50
|
Kumar P, Sharma PK, Nielsen P. Synthesis, hybridization and fluorescence properties of a 2'-C-pyrene-triazole modified arabino-uridine nucleotide. Bioorg Med Chem 2017; 25:2084-2090. [PMID: 28242171 DOI: 10.1016/j.bmc.2017.02.011] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2016] [Accepted: 02/07/2017] [Indexed: 01/12/2023]
Abstract
A new pyrene-modified nucleotide monomer is introduced, wherein pyrene is attached to the 2'-position of arabino-uridine through a triazolemethyl linker. When the monomer is introduced into oligonucleotides, very stable DNA duplexes and three way junctions are obtained. An oligonucleotide featuring two modifications in the center shows four-fold increase in the intensity of the pyrene excimer signal on hybridization with an RNA target but not with a DNA target. The new nucleotide monomer has potential in DNA invader probes as well as in RNA targeting and detection.
Collapse
Affiliation(s)
- Pawan Kumar
- Nucleic Acid Center, Department of Physics, Chemistry and Pharmacy, University of Southern Denmark, 5230 Odense M, Denmark
| | - Pawan K Sharma
- Department of Chemistry, Kurukshetra University, Kurukshetra 136 119, India
| | - Poul Nielsen
- Nucleic Acid Center, Department of Physics, Chemistry and Pharmacy, University of Southern Denmark, 5230 Odense M, Denmark.
| |
Collapse
|