1
|
Skates E, Delattre H, Schofield Z, Asally M, Soyer OS. Thioflavin T indicates mitochondrial membrane potential in mammalian cells. BIOPHYSICAL REPORTS 2023; 3:100134. [PMID: 38026684 PMCID: PMC10679866 DOI: 10.1016/j.bpr.2023.100134] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/14/2023] [Accepted: 10/25/2023] [Indexed: 12/01/2023]
Abstract
The fluorescent benzothiazole dye thioflavin T (ThT) is widely used as a marker for protein aggregates, most commonly in the context of neurodegenerative disease research and diagnosis. Recently, this same dye was shown to indicate membrane potential in bacteria due to its cationic nature. This finding prompted a question whether ThT fluorescence is linked to the membrane potential in mammalian cells, which would be important for appropriate utilization of ThT in research and diagnosis. Here, we show that ThT localizes into the mitochondria of HeLa cells in a membrane-potential-dependent manner. Specifically, ThT colocalized in cells with the mitochondrial membrane potential indicator tetramethylrhodamine methyl ester (TMRM) and gave similar temporal responses as TMRM to treatment with a protonophore, carbonyl cyanide-4-(trifluoromethoxy) phenylhydrazone (FCCP). Additionally, we found that presence of ThT together with exposure to blue light (λ = 405 nm), but neither factor alone, caused depolarization of mitochondrial membrane potential. This additive effect of the concentration and blue light was recapitulated by a mathematical model implementing the potential-dependent distribution of ThT and its effect on mitochondrial membrane potential through photosensitization. These results show that ThT can act as a mitochondrial membrane potential indicator in mammalian cells, when used at low concentrations and with low blue light exposure. However, it causes dissipation of the mitochondrial membrane potential depending additively on its concentrations and blue light exposure. This conclusion motivates a re-evaluation of ThT's use at micromolar range in live-cell analyses and indicates that this dye can enable future studies on the potential connections between mitochondrial membrane potential dynamics and protein aggregation.
Collapse
Affiliation(s)
- Emily Skates
- Bio-Electrical Engineering Innovation Hub, University of Warwick, Coventry, United Kingdom
- School of Life Sciences, University of Warwick, Coventry, United Kingdom
- Warwick Integrative Synthetic Biology Centre (WISB), University of Warwick, Coventry, United Kingdom
- Midlands Integrative Doctoral Training Program; University of Warwick, Coventry, United Kingdom
| | - Hadrien Delattre
- School of Life Sciences, University of Warwick, Coventry, United Kingdom
| | - Zoe Schofield
- Bio-Electrical Engineering Innovation Hub, University of Warwick, Coventry, United Kingdom
- School of Life Sciences, University of Warwick, Coventry, United Kingdom
- Warwick Integrative Synthetic Biology Centre (WISB), University of Warwick, Coventry, United Kingdom
| | - Munehiro Asally
- Bio-Electrical Engineering Innovation Hub, University of Warwick, Coventry, United Kingdom
- School of Life Sciences, University of Warwick, Coventry, United Kingdom
- Warwick Integrative Synthetic Biology Centre (WISB), University of Warwick, Coventry, United Kingdom
| | - Orkun S. Soyer
- Bio-Electrical Engineering Innovation Hub, University of Warwick, Coventry, United Kingdom
- School of Life Sciences, University of Warwick, Coventry, United Kingdom
- Warwick Integrative Synthetic Biology Centre (WISB), University of Warwick, Coventry, United Kingdom
| |
Collapse
|
2
|
Han ZQ, Wen LN. Application of G-quadruplex targets in gastrointestinal cancers: Advancements, challenges and prospects. World J Gastrointest Oncol 2023; 15:1149-1173. [PMID: 37546556 PMCID: PMC10401460 DOI: 10.4251/wjgo.v15.i7.1149] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/11/2023] [Revised: 04/11/2023] [Accepted: 05/08/2023] [Indexed: 07/12/2023] Open
Abstract
Genomic instability and inflammation are considered to be two enabling characteristics that support cancer development and progression. G-quadruplex structure is a key element that contributes to genomic instability and inflammation. G-quadruplexes were once regarded as simply an obstacle that can block the transcription of oncogenes. A ligand targeting G-quadruplexes was found to have anticancer activity, making G-quadruplexes potential anticancer targets. However, further investigation has revealed that G-quadruplexes are widely distributed throughout the human genome and have many functions, such as regulating DNA replication, DNA repair, transcription, translation, epigenetics, and inflammatory response. G-quadruplexes play double regulatory roles in transcription and translation. In this review, we focus on G-quadruplexes as novel targets for the treatment of gastrointestinal cancers. We summarize the application basis of G-quadruplexes in gastrointestinal cancers, including their distribution sites, structural characteristics, and physiological functions. We describe the current status of applications for the treatment of esophageal cancer, pancreatic cancer, hepatocellular carcinoma, gastric cancer, colorectal cancer, and gastrointestinal stromal tumors, as well as the associated challenges. Finally, we review the prospective clinical applications of G-quadruplex targets, providing references for targeted treatment strategies in gastrointestinal cancers.
Collapse
Affiliation(s)
- Zong-Qiang Han
- Department of Laboratory Medicine, Beijing Xiaotangshan Hospital, Beijing 102211, China
| | - Li-Na Wen
- Department of Clinical Nutrition, Beijing Shijitan Hospital, Capital Medical University, Beijing 100038, China
| |
Collapse
|
3
|
He C, Peng J, Li Z, Yang Q, Zhang Y, Luo X, Liu Z, Feng G, Fang J. Engineering a Red Fluorescent Protein Chromophore for Visualization of RNA G-Quadruplexes. Biochemistry 2023. [PMID: 37376793 DOI: 10.1021/acs.biochem.3c00149] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/29/2023]
Abstract
Synthetic red fluorescent protein (RFP) chromophores have emerged as valuable tools for biological imaging and therapeutic applications, but their application in the visualization of endogenous RNA G-quadruplexes (G4s) in living cells has been rarely reported so far. Here, by integrating the group of the excellent G4 dye ThT, we modulate RFP chromophores to create a novel fluorescent probe DEBIT with red emission. DEBIT selectively recognizes the G4 structure with the advantage of strong binding affinity, high selectivity, and excellent photostability. Using DEBIT as a fluorescent indicator, the real-time monitoring of RNA G4 in biological systems can be achieved. In summary, our work expands the application of synthetic RFP chromophores and provides an essential dye category to the classical G4 probes.
Collapse
Affiliation(s)
- Chang He
- School of Bioscience and Biotechnology, Hunan Agricultural University, Changsha 410128, China
| | - Jiasheng Peng
- School of Bioscience and Biotechnology, Hunan Agricultural University, Changsha 410128, China
| | - Zheng Li
- School of Bioscience and Biotechnology, Hunan Agricultural University, Changsha 410128, China
| | - Qinghui Yang
- School of Bioscience and Biotechnology, Hunan Agricultural University, Changsha 410128, China
| | - Ying Zhang
- School of Bioscience and Biotechnology, Hunan Agricultural University, Changsha 410128, China
| | - Xingyu Luo
- School of Chemistry and Chemical Engineering, Guangxi University, Nanning 530004, P. R. China
| | - Zekai Liu
- School of Bioscience and Biotechnology, Hunan Agricultural University, Changsha 410128, China
| | - Guangfu Feng
- School of Bioscience and Biotechnology, Hunan Agricultural University, Changsha 410128, China
| | - Jun Fang
- School of Bioscience and Biotechnology, Hunan Agricultural University, Changsha 410128, China
| |
Collapse
|
4
|
Goshisht MK, Tripathi N, Patra GK, Chaskar M. Organelle-targeting ratiometric fluorescent probes: design principles, detection mechanisms, bio-applications, and challenges. Chem Sci 2023; 14:5842-5871. [PMID: 37293660 PMCID: PMC10246671 DOI: 10.1039/d3sc01036h] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2023] [Accepted: 04/27/2023] [Indexed: 06/10/2023] Open
Abstract
Biological species, including reactive oxygen species (ROS), reactive sulfur species (RSS), reactive nitrogen species (RNS), F-, Pd2+, Cu2+, Hg2+, and others, are crucial for the healthy functioning of cells in living organisms. However, their aberrant concentration can result in various serious diseases. Therefore, it is essential to monitor biological species in cellular organelles such as the cell membrane, mitochondria, lysosome, endoplasmic reticulum, Golgi apparatus, and nucleus. Among various fluorescent probes for species detection within the organelles, ratiometric fluorescent probes have drawn special attention as a potential way to get beyond the drawbacks of intensity-based probes. This method depends on measuring the intensity change of two emission bands (caused by an analyte), which produces an efficient internal referencing that increases the detection's sensitivity. This review article discusses the literature publications (from 2015 to 2022) on organelle-targeting ratiometric fluorescent probes, the general strategies, the detecting mechanisms, the broad scope, and the challenges currently faced by fluorescent probes.
Collapse
Affiliation(s)
- Manoj Kumar Goshisht
- Department of Chemistry, Natural and Applied Sciences, University of Wisconsin-Green Bay 2420 Nicolet Drive Green Bay WI 54311-7001 USA
- Department of Chemistry, Government Naveen College Tokapal Bastar Chhattisgarh 494442 India
| | - Neetu Tripathi
- Department of Chemistry, Guru Nanak Dev University Amritsar Punjab 143005 India
| | - Goutam Kumar Patra
- Department of Chemistry, Faculty of Physical Sciences Guru Ghasidas Vishwavidyalaya Bilaspur Chhattisgarh 495009 India
| | - Manohar Chaskar
- Department of Technology, Savitribai Phule Pune University Ganeshkhind Pune 411007 India
| |
Collapse
|
5
|
Pavlova I, Iudin M, Surdina A, Severov V, Varizhuk A. G-Quadruplexes in Nuclear Biomolecular Condensates. Genes (Basel) 2023; 14:genes14051076. [PMID: 37239436 DOI: 10.3390/genes14051076] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2023] [Revised: 05/10/2023] [Accepted: 05/11/2023] [Indexed: 05/28/2023] Open
Abstract
G-quadruplexes (G4s) have long been implicated in the regulation of chromatin packaging and gene expression. These processes require or are accelerated by the separation of related proteins into liquid condensates on DNA/RNA matrices. While cytoplasmic G4s are acknowledged scaffolds of potentially pathogenic condensates, the possible contribution of G4s to phase transitions in the nucleus has only recently come to light. In this review, we summarize the growing evidence for the G4-dependent assembly of biomolecular condensates at telomeres and transcription initiation sites, as well as nucleoli, speckles, and paraspeckles. The limitations of the underlying assays and the remaining open questions are outlined. We also discuss the molecular basis for the apparent permissive role of G4s in the in vitro condensate assembly based on the interactome data. To highlight the prospects and risks of G4-targeting therapies with respect to the phase transitions, we also touch upon the reported effects of G4-stabilizing small molecules on nuclear biomolecular condensates.
Collapse
Affiliation(s)
- Iuliia Pavlova
- Lopukhin Federal Research and Clinical Center of Physical-Chemical Medicine, 119435 Moscow, Russia
- Moscow Institute of Physics and Technology, 141701 Dolgoprudny, Russia
| | - Mikhail Iudin
- Lopukhin Federal Research and Clinical Center of Physical-Chemical Medicine, 119435 Moscow, Russia
- Moscow Institute of Physics and Technology, 141701 Dolgoprudny, Russia
| | - Anastasiya Surdina
- Lopukhin Federal Research and Clinical Center of Physical-Chemical Medicine, 119435 Moscow, Russia
| | - Vjacheslav Severov
- Lopukhin Federal Research and Clinical Center of Physical-Chemical Medicine, 119435 Moscow, Russia
| | - Anna Varizhuk
- Lopukhin Federal Research and Clinical Center of Physical-Chemical Medicine, 119435 Moscow, Russia
- Moscow Institute of Physics and Technology, 141701 Dolgoprudny, Russia
| |
Collapse
|
6
|
Kitamura A, Tornmalm J, Demirbay B, Piguet J, Kinjo M, Widengren J. Trans-cis isomerization kinetics of cyanine dyes reports on the folding states of exogeneous RNA G-quadruplexes in live cells. Nucleic Acids Res 2023; 51:e27. [PMID: 36651281 PMCID: PMC10018373 DOI: 10.1093/nar/gkac1255] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2021] [Revised: 11/23/2022] [Accepted: 12/19/2022] [Indexed: 01/19/2023] Open
Abstract
Guanine (G)-rich nucleic acids are prone to assemble into four-stranded structures, so-called G-quadruplexes. Abnormal GGGGCC repeat elongations, and in particular their folding states, are associated with amyotrophic lateral sclerosis and frontotemporal dementia. Due to methodological constraints however, most studies of G quadruplex structures are restricted to in vitro conditions. Evidence of how GGGGCC repeats form into G-quadruplexes in vivo is sparse. We devised a readout strategy, exploiting the sensitivity of trans-cis isomerization of cyanine dyes to local viscosity and sterical constraints. Thereby, folding states of cyanine-labeled RNA, and in particular G-quadruplexes, can be identified in a sensitive manner. The isomerization kinetics, monitored via fluorescence blinking generated upon transitions between a fluorescent trans isomer and a non-fluorescent cis isomer, was first characterized for RNA with GGGGCC repeats in aqueous solution using fluorescence correlation spectroscopy and transient state (TRAST) monitoring. With TRAST, monitoring the isomerization kinetics from how the average fluorescence intensity varies with laser excitation modulation characteristics, we could then detect folding states of fluorescently tagged RNA introduced into live cells.
Collapse
Affiliation(s)
| | | | - Baris Demirbay
- Experimental Biomolecular Physics, Department of Applied Physics, Royal Institute of Technology (KTH), Stockholm, Sweden
| | - Joachim Piguet
- Experimental Biomolecular Physics, Department of Applied Physics, Royal Institute of Technology (KTH), Stockholm, Sweden
| | - Masataka Kinjo
- Laboratory of Molecular Cell Dynamics, Faculty of Advanced Life Science, Hokkaido University, Sapporo, Japan
| | | |
Collapse
|
7
|
Wu S, Jiang L, Lei L, Fu C, Huang J, Hu Y, Dong Y, Chen J, Zeng Q. Crosstalk between G-quadruplex and ROS. Cell Death Dis 2023; 14:37. [PMID: 36653351 PMCID: PMC9849334 DOI: 10.1038/s41419-023-05562-0] [Citation(s) in RCA: 14] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2022] [Revised: 12/25/2022] [Accepted: 01/05/2023] [Indexed: 01/19/2023]
Abstract
The excessive production of reactive oxygen species (ROS) can lead to single nucleic acid base damage, DNA strand breakage, inter- and intra-strand cross-linking of nucleic acids, and protein-DNA cross-linking involved in the pathogenesis of cancer, neurodegenerative diseases, and aging. G-quadruplex (G4) is a stacked nucleic acid structure that is ubiquitous across regulatory regions of multiple genes. Abnormal formation and destruction of G4s due to multiple factors, including cations, helicases, transcription factors (TFs), G4-binding proteins, and epigenetic modifications, affect gene replication, transcription, translation, and epigenetic regulation. Due to the lower redox potential of G-rich sequences and unique structural characteristics, G4s are highly susceptible to oxidative damage. Additionally, the formation, stability, and biological regulatory role of G4s are affected by ROS. G4s are involved in regulating gene transcription, translation, and telomere length maintenance, and are therefore key players in age-related degeneration. Furthermore, G4s also mediate the antioxidant process by forming stress granules and activating Nrf2, which is suggestive of their involvement in developing ROS-related diseases. In this review, we have summarized the crosstalk between ROS and G4s, and the possible regulatory mechanisms through which G4s play roles in aging and age-related diseases.
Collapse
Affiliation(s)
- Songjiang Wu
- Department of Dermatology, Third Xiangya Hospital, Central South University, 138 Tongzipo Road, 410013, Changsha, Hunan, PR China
| | - Ling Jiang
- Department of Dermatology, Third Xiangya Hospital, Central South University, 138 Tongzipo Road, 410013, Changsha, Hunan, PR China
| | - Li Lei
- Department of Dermatology, Third Xiangya Hospital, Central South University, 138 Tongzipo Road, 410013, Changsha, Hunan, PR China
| | - Chuhan Fu
- Department of Dermatology, Third Xiangya Hospital, Central South University, 138 Tongzipo Road, 410013, Changsha, Hunan, PR China
| | - Jinhua Huang
- Department of Dermatology, Third Xiangya Hospital, Central South University, 138 Tongzipo Road, 410013, Changsha, Hunan, PR China
| | - Yibo Hu
- Department of Dermatology, Third Xiangya Hospital, Central South University, 138 Tongzipo Road, 410013, Changsha, Hunan, PR China
| | - Yumeng Dong
- Department of Dermatology, Third Xiangya Hospital, Central South University, 138 Tongzipo Road, 410013, Changsha, Hunan, PR China
| | - Jing Chen
- Department of Dermatology, Third Xiangya Hospital, Central South University, 138 Tongzipo Road, 410013, Changsha, Hunan, PR China.
| | - Qinghai Zeng
- Department of Dermatology, Third Xiangya Hospital, Central South University, 138 Tongzipo Road, 410013, Changsha, Hunan, PR China.
| |
Collapse
|
8
|
Fabijanić I, Kurutos A, Tomašić Paić A, Tadić V, Kamounah FS, Horvat L, Brozovic A, Crnolatac I, Radić Stojković M. Selenium-Substituted Monomethine Cyanine Dyes as Selective G-Quadruplex Spectroscopic Probes with Theranostic Potential. Biomolecules 2023; 13:biom13010128. [PMID: 36671513 PMCID: PMC9856044 DOI: 10.3390/biom13010128] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2022] [Revised: 12/31/2022] [Accepted: 01/05/2023] [Indexed: 01/11/2023] Open
Abstract
The binding interactions of six ligands, neutral and monocationic asymmetric monomethine cyanine dyes comprising benzoselenazolyl moiety with duplex DNA and RNA and G-quadruplex structures were evaluated using fluorescence, UV/Vis (thermal melting) and circular dichroism (CD) spectroscopy. The main objective was to assess the impact of different substituents (methyl vs. sulfopropyl vs. thiopropyl/thioethyl) on the nitrogen atom of the benzothiazolyl chromophore on various nucleic acid structures. The monomethine cyanine dyes with methyl substituents showed a 100-fold selectivity for G-quadruplex versus duplex DNA. Study results indicate that cyanines bind with G-quadruplex via end π-π stacking interactions and possible additional interactions with nucleobases/phosphate backbone of grooves or loop bases. Cyanine with thioethyl substituent distinguishes duplex DNA and RNA and G-quadruplex structures by distinctly varying ICD signals. Furthermore, cell viability assay reveals the submicromolar activity of cyanines with methyl substituents against all tested human cancer cell lines. Confocal microscopy analysis shows preferential accumulation of cyanines with sulfopropyl and thioethyl substituents in mitochondria and indicates localization of cyanines with methyl in nucleus, particularly nucleolus. This confirms the potential of examined cyanines as theranostic agents, possessing both fluorescent properties and cell viability inhibitory effect.
Collapse
Affiliation(s)
- Ivana Fabijanić
- Division of Organic Chemistry and Biochemistry, Ruđer Bošković Institute, Bijenička Cesta 54, 10000 Zagreb, Croatia
| | - Atanas Kurutos
- Institute of Organic Chemistry with Centre of Phytochemistry, Bulgarian Academy of Sciences, Acad. G. Bonchev Str., Bl. 9, 1113 Sofia, Bulgaria
| | - Ana Tomašić Paić
- Division of Organic Chemistry and Biochemistry, Ruđer Bošković Institute, Bijenička Cesta 54, 10000 Zagreb, Croatia
| | - Vanja Tadić
- Division of Molecular Biology, Ruđer Bošković Institute, Bijenička Cesta 54, 10000 Zagreb, Croatia
| | - Fadhil S. Kamounah
- Department of Chemistry, University of Copenhagen, Universitetsparken 5, DK-2100 Copenhagen, Denmark
| | - Lucija Horvat
- Division of Molecular Biology, Ruđer Bošković Institute, Bijenička Cesta 54, 10000 Zagreb, Croatia
| | - Anamaria Brozovic
- Division of Molecular Biology, Ruđer Bošković Institute, Bijenička Cesta 54, 10000 Zagreb, Croatia
| | - Ivo Crnolatac
- Division of Organic Chemistry and Biochemistry, Ruđer Bošković Institute, Bijenička Cesta 54, 10000 Zagreb, Croatia
| | - Marijana Radić Stojković
- Division of Organic Chemistry and Biochemistry, Ruđer Bošković Institute, Bijenička Cesta 54, 10000 Zagreb, Croatia
- Correspondence: ; Tel.: +385-14571220; Fax: +385-14680195
| |
Collapse
|
9
|
Advances in
G
‐quadruplexes‐based fluorescent imaging. Biopolymers 2022; 113:e23528. [DOI: 10.1002/bip.23528] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2022] [Revised: 11/16/2022] [Accepted: 11/16/2022] [Indexed: 12/03/2022]
|
10
|
Dubrovin EV, Barinov NA, Klinov DV. Visualization of G-Quadruplexes, i-Motifs and Their Associates. Acta Naturae 2022; 14:4-18. [DOI: 10.32607/actanaturae.11705] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2022] [Accepted: 07/13/2022] [Indexed: 11/20/2022] Open
Abstract
The non-canonical structures formed by G- or C-rich DNA regions, such as quadruplexes and i-motifs, as well as their associates, have recently been attracting increasing attention both because of the arguments in favor of their existence in vivo and their potential application in nanobiotechnology. When studying the structure and properties of non-canonical forms of DNA, as well as when controlling the artificially created architectures based on them, visualization plays an important role. This review analyzes the methods used to visualize quadruplexes, i-motifs, and their associates with high spatial resolution: fluorescence microscopy, transmission electron microscopy (TEM), and atomic force microscopy (AFM). The key approaches to preparing specimens for the visualization of this type of structures are presented. Examples of visualization of non-canonical DNA structures having various morphologies, such as G-wires, G-loops, as well as individual quadruplexes, i-motifs and their associates, are considered. The potential for using AFM for visualizing non-canonical DNA structures is demonstrated.
Collapse
|
11
|
Lu X, Wu X, Kuang S, Lei C, Nie Z. Visualization of Deep Tissue G-quadruplexes with a Novel Large Stokes-Shifted Red Fluorescent Benzothiazole Derivative. Anal Chem 2022; 94:10283-10290. [PMID: 35776781 DOI: 10.1021/acs.analchem.2c02049] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
G-quadruplex (G4) is a noncanonical nucleic acid secondary structure that has implications for various physiological and pathological processes and is thus essential to exploring new approaches to G4 detection in live cells. However, the deficiency of molecular imaging tools makes it challenging to visualize the G4 in ex vivo tissue samples. In this study, we established a G4 probe design strategy and presented a red fluorescent benzothiazole derivative, ThT-NA, to detect and image G4 structures in living cells and tissue samples. By enhancing the electron-donating group of thioflavin T (ThT) and optimizing molecular structure, ThT-NA shows excellent photophysical properties, including red emission (610 nm), a large Stokes shift (>100 nm), high sensitivity selectivity toward G4s (1600-fold fluorescence turn-on ratio) and robust two-photon fluorescence emission. Therefore, these features enable ThT-NA to reveal the endogenous RNA G4 distribution in living cells and differentiate the cell cycle by monitoring the changes of RNA G4 folding. Significantly, to the best of our knowledge, ThT-NA is the first benzothiazole-derived G4 probe that has been developed for imaging G4s in ex vivo cancer tissue samples by two-photon microscopy techniques.
Collapse
Affiliation(s)
- Xu Lu
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan Provincial Key Laboratory of Biomacromolecular Chemical Biology, Hunan University, Changsha 410082, People's Republic of China
| | - Xianhua Wu
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan Provincial Key Laboratory of Biomacromolecular Chemical Biology, Hunan University, Changsha 410082, People's Republic of China
| | - Shi Kuang
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan Provincial Key Laboratory of Biomacromolecular Chemical Biology, Hunan University, Changsha 410082, People's Republic of China
| | - Chunyang Lei
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan Provincial Key Laboratory of Biomacromolecular Chemical Biology, Hunan University, Changsha 410082, People's Republic of China
| | - Zhou Nie
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan Provincial Key Laboratory of Biomacromolecular Chemical Biology, Hunan University, Changsha 410082, People's Republic of China
| |
Collapse
|
12
|
Kang Y, Wei C. Highly selective turn-on red fluorescence probes for visualization of the G-quadruplexes DNA in living cells. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2022; 267:120518. [PMID: 34700155 DOI: 10.1016/j.saa.2021.120518] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/15/2021] [Revised: 10/12/2021] [Accepted: 10/14/2021] [Indexed: 06/13/2023]
Abstract
Studies on small molecule fluorescent probes for detecting G-quadruplexes DNA have bring about an extensive attention in recent years. In this paper, we designed and synthesized three benzothiazole derivatives named 2a-2c under moderate reaction conditions and investigated their interactions with DNA (single-stranded, duplex, i-motif and G-quadruplex) and distribution in living cell. Three compounds present a large Stokes shift (∼90 nm) and a weak red fluorescence emission, and they exhibit a good selectivity and sensitive turn-on fluorescence response for the promoter G-quadruplex DNA (bcl-2, c-myc and c-kit 2) and mitochondria G-quadruplex (KSS). The affinity of 2a and 2b with N-alkyl side chain group to DNA is stronger than that of 2c with an anion group, therefore, they also increase the stability of the G-quadruplex structure. 2b induces the conformational change of both bcl-2 and KSS G-quadruplexes, while all compounds induce the folding of bcl-2 from the coiled structure to the hybrid G-qrudruplex. Three compounds interact with the G-quadruplex DNA mainly by end-stacking mode. Furthermore, MTT assays and confocal fluorescence images show that these compounds can enter the living HepG2 cells with low cytotoxicity. 2a-2c are mainly located in the mitochondrion and interacted with mitochondria G-quadruplex DNA, while only weak fluorescence can be found in cell nucleus. In a word, 2a-2c can be implied in image of G-quadruplex DNA in living cells.
Collapse
Affiliation(s)
- Yongqiang Kang
- Institute of Molecular Science, Shanxi University, Taiyuan 030006, PR China
| | - Chunying Wei
- Institute of Molecular Science, Shanxi University, Taiyuan 030006, PR China.
| |
Collapse
|
13
|
Green AT, Pickard AJ, Li R, MacKerell AD, Bierbach U, Cho SS. Computational and Experimental Characterization of rDNA and rRNA G-Quadruplexes. J Phys Chem B 2022; 126:609-619. [PMID: 35026949 DOI: 10.1021/acs.jpcb.1c08340] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
DNA G-quadruplexes in human telomeres and gene promoters are being extensively studied for their role in controlling the growth of cancer cells. G-quadruplexes have been unambiguously shown to exist both in vitro and in vivo, including in the guanine (G)-rich DNA genes encoding pre-ribosomal RNA (pre-rRNA), which is transcribed in the cell's nucleolus. Recent studies strongly suggest that these DNA sequences ("rDNA"), and the transcribed rRNA, are a potential anticancer target through the inhibition of RNA polymerase I (Pol I) in ribosome biogenesis, but the structures of ribosomal G-quadruplexes at atomic resolution are unknown and very little biophysical characterization has been performed on them to date. In the present study, circular dichroism (CD) spectroscopy is used to show that two putative rDNA G-quadruplex sequences, NUC 19P and NUC 23P and their counterpart rRNAs, predominantly adopt parallel topologies, reminiscent of the analogous telomeric quadruplex structures. Based on this information, we modeled parallel topology atomistic structures of the putative ribosomal G-quadruplexes. We then validated and refined the modeled ribosomal G-quadruplex structures using all-atom molecular dynamics (MD) simulations with the CHARMM36 force field in the presence and absence of stabilizing K+. Motivated by preliminary MD simulations of the telomeric parallel G-quadruplex (TEL 24P) in which the K+ ion is expelled, we used updated CHARMM36 force field K+ parameters that were optimized, targeting the data from quantum mechanical calculations and the polarizable Drude model force field. In subsequent MD simulations with optimized CHARMM36 parameters, the K+ ions are predominantly in the G-quadruplex channel and the rDNA G-quadruplexes have more well-defined, predominantly parallel-topology structures as compared to rRNA. In addition, NUC 19P is more structured than NUC 23P, which contains extended loops. Results from this study set the structural foundation for understanding G-quadruplex functions and the design of novel chemotherapeutics against these nucleolar targets and can be readily extended to other DNA and RNA G-quadruplexes.
Collapse
Affiliation(s)
- Adam T Green
- Department of Physics, Wake Forest University, Winston-Salem, North Carolina 27109, United States
| | - Amanda J Pickard
- Department of Chemistry, Wake Forest University, Wake Downtown Campus, Winston-Salem, North Carolina 27101, United States
| | - Rongzhong Li
- Department of Physics, Wake Forest University, Winston-Salem, North Carolina 27109, United States.,Department of Computer Science, Wake Forest University, Winston-Salem, North Carolina 27109, United States
| | - Alexander D MacKerell
- Department of Pharmaceutical Sciences, School of Pharmacy, University of Maryland, Baltimore, Maryland 21201, United States
| | - Ulrich Bierbach
- Department of Chemistry, Wake Forest University, Wake Downtown Campus, Winston-Salem, North Carolina 27101, United States
| | - Samuel S Cho
- Department of Physics, Wake Forest University, Winston-Salem, North Carolina 27109, United States.,Department of Computer Science, Wake Forest University, Winston-Salem, North Carolina 27109, United States
| |
Collapse
|
14
|
Noh B, Blasco-Conesa MP, Lai YJ, Ganesh BP, Urayama A, Moreno-Gonzalez I, Marrelli SP, McCullough LD, Moruno-Manchon JF. G-quadruplexes Stabilization Upregulates CCN1 and Accelerates Aging in Cultured Cerebral Endothelial Cells. FRONTIERS IN AGING 2022; 2:797562. [PMID: 35822045 PMCID: PMC9261356 DOI: 10.3389/fragi.2021.797562] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/18/2021] [Accepted: 12/07/2021] [Indexed: 11/27/2022]
Abstract
Senescence in the cerebral endothelium has been proposed as a mechanism that can drive dysfunction of the cerebral vasculature, which precedes vascular dementia. Cysteine-rich angiogenic inducer 61 (Cyr61/CCN1) is a matricellular protein secreted by cerebral endothelial cells (CEC). CCN1 induces senescence in fibroblasts. However, whether CCN1 contributes to senescence in CEC and how this is regulated requires further study. Aging has been associated with the formation of four-stranded Guanine-quadruplexes (G4s) in G-rich motifs of DNA and RNA. Stabilization of the G4 structures regulates transcription and translation either by upregulation or downregulation depending on the gene target. Previously, we showed that aged mice treated with a G4-stabilizing compound had enhanced senescence-associated (SA) phenotypes in their brains, and these mice exhibited enhanced cognitive deficits. A sequence in the 3'-UTR of the human CCN1 mRNA has the ability to fold into G4s in vitro. We hypothesize that G4 stabilization regulates CCN1 in cultured primary CEC and induces endothelial senescence. We used cerebral microvessel fractions and cultured primary CEC from young (4-months old, m/o) and aged (18-m/o) mice to determine CCN1 levels. SA phenotypes were determined by high-resolution fluorescence microscopy in cultured primary CEC, and we used Thioflavin T to recognize RNA-G4s for fluorescence spectra. We found that cultured CEC from aged mice exhibited enhanced levels of SA phenotypes, and higher levels of CCN1 and G4 stabilization. In cultured CEC, CCN1 induced SA phenotypes, such as SA β-galactosidase activity, and double-strand DNA damage. Furthermore, CCN1 levels were upregulated by a G4 ligand, and a G-rich motif in the 3'-UTR of the Ccn1 mRNA was folded into a G4. In conclusion, we demonstrate that CCN1 can induce senescence in cultured primary CEC, and we provide evidence that G4 stabilization is a novel mechanism regulating the SASP component CCN1.
Collapse
Affiliation(s)
- Brian Noh
- Department of Neurology, McGovern Medical School at the University of Texas Health Science Center at Houston, Houston, TX, United States
| | - Maria P. Blasco-Conesa
- Department of Neurology, McGovern Medical School at the University of Texas Health Science Center at Houston, Houston, TX, United States
| | - Yun-Ju Lai
- Department of Neurology, McGovern Medical School at the University of Texas Health Science Center at Houston, Houston, TX, United States
- Solomont School of Nursing, Zuckerberg College of Health Sciences, University of Massachusetts Lowell, Lowell, MA, United States
| | - Bhanu Priya Ganesh
- Department of Neurology, McGovern Medical School at the University of Texas Health Science Center at Houston, Houston, TX, United States
| | - Akihiko Urayama
- Department of Neurology, McGovern Medical School at the University of Texas Health Science Center at Houston, Houston, TX, United States
| | - Ines Moreno-Gonzalez
- Department of Neurology, McGovern Medical School at the University of Texas Health Science Center at Houston, Houston, TX, United States
- Department of Cell Biology, Faculty of Sciences, Instituto de Investigacion Biomedica de Malaga-IBIMA, Malaga University, Malaga, Spain
- Networking Biomedical Research Networking Center on Neurodegenerative Diseases (CIBERNED), Madrid, Spain
| | - Sean P. Marrelli
- Department of Neurology, McGovern Medical School at the University of Texas Health Science Center at Houston, Houston, TX, United States
| | - Louise D. McCullough
- Department of Neurology, McGovern Medical School at the University of Texas Health Science Center at Houston, Houston, TX, United States
| | - Jose Felix Moruno-Manchon
- Department of Neurology, McGovern Medical School at the University of Texas Health Science Center at Houston, Houston, TX, United States
| |
Collapse
|
15
|
Sanchez-Martin V, Schneider DA, Ortiz-Gonzalez M, Soriano-Lerma A, Linde-Rodriguez A, Perez-Carrasco V, Gutierrez-Fernandez J, Cuadros M, González C, Soriano M, Garcia-Salcedo JA. Targeting ribosomal G-quadruplexes with naphthalene-diimides as RNA polymerase I inhibitors for colorectal cancer treatment. Cell Chem Biol 2021; 28:1590-1601.e4. [PMID: 34166611 DOI: 10.1016/j.chembiol.2021.05.021] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2021] [Revised: 04/05/2021] [Accepted: 05/27/2021] [Indexed: 12/11/2022]
Abstract
Guanine quadruplexes (G4s) are non-canonical nucleic acid structures commonly found in regulatory genomic regions. G4 targeting has emerged as a therapeutic approach in cancer. We have screened naphthalene-diimides (NDIs), a class of G4 ligands, in a cellular model of colorectal cancer (CRC). Here, we identify the leading compound T5 with a potent and selective inhibition of cell growth by high-affinity binding to G4s in ribosomal DNA, impairing RNA polymerase I (Pol I) elongation. Consequently, T5 induces a rapid inhibition of Pol I transcription, nucleolus disruption, proteasome-dependent Pol I catalytic subunit A degradation and autophagy. Moreover, we attribute the higher selectivity of carbohydrate-conjugated T5 for tumoral cells to its preferential uptake through the overexpressed glucose transporter 1. Finally, we succinctly demonstrate that T5 could be explored as a therapeutic agent in a patient cohort with CRC. Therefore, we report a mode of action for these NDIs involving ribosomal G4 targeting.
Collapse
Affiliation(s)
- Victoria Sanchez-Martin
- GENYO. Centre for Genomics and Oncological Research: Pfizer/University of Granada/Andalusian Regional Government, Granada 18016, Spain; Microbiology Unit, Biosanitary Research Institute IBS.Granada, University Hospital Virgen de las Nieves, Granada 18014, Spain; Department of Biochemistry, Molecular Biology III and Immunology, University of Granada, Granada 18016, Spain
| | - David A Schneider
- Department of Biochemistry and Molecular Genetics, University of Alabama at Birmingham, Birmingham, AL 35294, USA
| | - Matilde Ortiz-Gonzalez
- GENYO. Centre for Genomics and Oncological Research: Pfizer/University of Granada/Andalusian Regional Government, Granada 18016, Spain; Centre for Intensive Mediterranean Agrosystems and Agri-food Biotechnology (CIAIMBITAL), University of Almeria, Almeria 04001, Spain
| | - Ana Soriano-Lerma
- GENYO. Centre for Genomics and Oncological Research: Pfizer/University of Granada/Andalusian Regional Government, Granada 18016, Spain; Department of Physiology, University of Granada, Granada 18011, Spain
| | - Angel Linde-Rodriguez
- GENYO. Centre for Genomics and Oncological Research: Pfizer/University of Granada/Andalusian Regional Government, Granada 18016, Spain; Microbiology Unit, Biosanitary Research Institute IBS.Granada, University Hospital Virgen de las Nieves, Granada 18014, Spain
| | - Virginia Perez-Carrasco
- GENYO. Centre for Genomics and Oncological Research: Pfizer/University of Granada/Andalusian Regional Government, Granada 18016, Spain; Microbiology Unit, Biosanitary Research Institute IBS.Granada, University Hospital Virgen de las Nieves, Granada 18014, Spain
| | - Jose Gutierrez-Fernandez
- Microbiology Unit, Biosanitary Research Institute IBS.Granada, University Hospital Virgen de las Nieves, Granada 18014, Spain; Department of Microbiology, University of Granada, Granada 18011, Spain
| | - Marta Cuadros
- GENYO. Centre for Genomics and Oncological Research: Pfizer/University of Granada/Andalusian Regional Government, Granada 18016, Spain; Department of Biochemistry, Molecular Biology III and Immunology, University of Granada, Granada 18016, Spain
| | - Carlos González
- Instituto de Química Física "Rocasolano", CSIC, Madrid 28006, Spain
| | - Miguel Soriano
- GENYO. Centre for Genomics and Oncological Research: Pfizer/University of Granada/Andalusian Regional Government, Granada 18016, Spain; Centre for Intensive Mediterranean Agrosystems and Agri-food Biotechnology (CIAIMBITAL), University of Almeria, Almeria 04001, Spain
| | - Jose A Garcia-Salcedo
- GENYO. Centre for Genomics and Oncological Research: Pfizer/University of Granada/Andalusian Regional Government, Granada 18016, Spain; Microbiology Unit, Biosanitary Research Institute IBS.Granada, University Hospital Virgen de las Nieves, Granada 18014, Spain.
| |
Collapse
|
16
|
DNA Binding Mode Analysis of a Core-Extended Naphthalene Diimide as a Conformation-Sensitive Fluorescent Probe of G-Quadruplex Structures. Int J Mol Sci 2021; 22:ijms221910624. [PMID: 34638964 PMCID: PMC8508963 DOI: 10.3390/ijms221910624] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2021] [Revised: 09/24/2021] [Accepted: 09/27/2021] [Indexed: 12/27/2022] Open
Abstract
G-quadruplex existence was proved in cells by using both antibodies and small molecule fluorescent probes. However, the G-quadruplex probes designed thus far are structure- but not conformation-specific. Recently, a core-extended naphthalene diimide (cex-NDI) was designed and found to provide fluorescent signals of markedly different intensities when bound to G-quadruplexes of different conformations or duplexes. Aiming at evaluating how the fluorescence behaviour of this compound is associated with specific binding modes to the different DNA targets, cex-NDI was here studied in its interaction with hybrid G-quadruplex, parallel G-quadruplex, and B-DNA duplex models by biophysical techniques, molecular docking, and biological assays. cex-NDI showed different binding modes associated with different amounts of stacking interactions with the three DNA targets. The preferential binding sites were the groove, outer quartet, or intercalative site of the hybrid G-quadruplex, parallel G-quadruplex, and B-DNA duplex, respectively. Interestingly, our data show that the fluorescence intensity of DNA-bound cex-NDI correlates with the amount of stacking interactions formed by the ligand with each DNA target, thus providing the rationale behind the conformation-sensitive properties of cex-NDI and supporting its use as a fluorescent probe of G-quadruplex structures. Notably, biological assays proved that cex-NDI mainly localizes in the G-quadruplex-rich nuclei of cancer cells.
Collapse
|
17
|
Deiana M, Mosser M, Le Bahers T, Dumont E, Dudek M, Denis-Quanquin S, Sabouri N, Andraud C, Matczyszyn K, Monnereau C, Guy L. Light-induced in situ chemical activation of a fluorescent probe for monitoring intracellular G-quadruplex structures. NANOSCALE 2021; 13:13795-13808. [PMID: 34477654 DOI: 10.1039/d1nr02855c] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/22/2023]
Abstract
Light-activated functional materials capable of remote control over duplex and G-quadruplex (G4) nucleic acids formation at the cellular level are still very rare. Herein, we report on the photoinduced macrocyclisation of a helicenoid quinoline derivative of binaphthol that selectively provides easy access to an unprecedented class of extended heteroaromatic structures with remarkable photophysical and DNA/RNA binding properties. Thus, while the native bisquinoline precursor shows no DNA binding activity, the new in situ photochemically generated probe features high association constants to DNA and RNA G4s. The latter inhibits DNA synthesis by selectively stabilizing G4 structures associated with oncogenic promoters and telomere repeat units. Finally, the light sensitive compound is capable of in cellulo photoconversion, localizes primarily in the G4-rich sites of cancer cells, competes with a well-known G4 binder and shows a clear nuclear co-localization with the quadruplex specific antibody BG4. This work provides a benchmark for the future design and development of a brand-new generation of light-activated target-selective G4-binders.
Collapse
Affiliation(s)
- Marco Deiana
- Department of Medical Biochemistry and Biophysics, Umeå University, 90187 Umeå, Sweden.
| | | | | | | | | | | | | | | | | | | | | |
Collapse
|
18
|
Desai N, Shah V, Datta B. Assessing G4-Binding Ligands In Vitro and in Cellulo Using Dimeric Carbocyanine Dye Displacement Assay. Molecules 2021; 26:molecules26051400. [PMID: 33807659 PMCID: PMC7961521 DOI: 10.3390/molecules26051400] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2021] [Revised: 01/31/2021] [Accepted: 02/24/2021] [Indexed: 12/05/2022] Open
Abstract
G-quadruplexes (G4) are the most actively studied non-canonical secondary structures formed by contiguous repeats of guanines in DNA or RNA strands. Small molecule mediated targeting of G-quadruplexes has emerged as an attractive tool for visualization and stabilization of these structures inside the cell. Limited number of DNA and RNA G4-selective assays have been reported for primary ligand screening. A combination of fluorescence spectroscopy, AFM, CD, PAGE, and confocal microscopy have been used to assess a dimeric carbocyanine dye B6,5 for screening G4-binding ligands in vitro and in cellulo. The dye B6,5 interacts with physiologically relevant DNA and RNA G4 structures, resulting in fluorescence enhancement of the molecule as an in vitro readout for G4 selectivity. Interaction of the dye with G4 is accompanied by quadruplex stabilization that extends its use in primary screening of G4 specific ligands. The molecule is cell permeable and enables visualization of quadruplex dominated cellular regions of nucleoli using confocal microscopy. The dye is displaced by quarfloxin in live cells. The dye B6,5 shows remarkable duplex to quadruplex selectivity in vitro along with ligand-like stabilization of DNA G4 structures. Cell permeability and response to RNA G4 structures project the dye with interesting theranostic potential. Our results validate that B6,5 can serve the dual purpose of visualization of DNA and RNA G4 structures and screening of G4 specific ligands, and adds to the limited number of probes with such potential.
Collapse
Affiliation(s)
- Nakshi Desai
- Department of Biological Engineering, Indian Institute of Technology, Gandhinagar 382355, India; (N.D.); (V.S.)
| | - Viraj Shah
- Department of Biological Engineering, Indian Institute of Technology, Gandhinagar 382355, India; (N.D.); (V.S.)
| | - Bhaskar Datta
- Department of Biological Engineering, Indian Institute of Technology, Gandhinagar 382355, India; (N.D.); (V.S.)
- Department of Chemistry, Indian Institute of Technology, Gandhinagar, Gandhinagar 382355, India
- Correspondence: ; Tel.: +91-79-2395-2427; Fax: +91-79-2397-2622
| |
Collapse
|
19
|
Choi NE, Lee JY, Park EC, Lee JH, Lee J. Recent Advances in Organelle-Targeted Fluorescent Probes. Molecules 2021; 26:E217. [PMID: 33406634 PMCID: PMC7795030 DOI: 10.3390/molecules26010217] [Citation(s) in RCA: 38] [Impact Index Per Article: 12.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2020] [Revised: 11/19/2020] [Accepted: 11/21/2020] [Indexed: 12/27/2022] Open
Abstract
Recent advances in fluorescence imaging techniques and super-resolution microscopy have extended the applications of fluorescent probes in studying various cellular processes at the molecular level. Specifically, organelle-targeted probes have been commonly used to detect cellular metabolites and transient chemical messengers with high precision and have become invaluable tools to study biochemical pathways. Moreover, several recent studies reported various labeling strategies and novel chemical scaffolds to enhance target specificity and responsiveness. In this review, we will survey the most recent reports of organelle-targeted fluorescent probes and assess their general strategies and structural features on the basis of their target organelles. We will discuss the advantages of the currently used probes and the potential challenges in their application as well as future directions.
Collapse
Affiliation(s)
| | | | | | | | - Jiyoun Lee
- Department of Next-Generation Applied Science, and Global Medical Science, Sungshin University, Seoul 01133, Korea; (N.-E.C.); (J.-Y.L.); (E.-C.P.); (J.-H.L.)
| |
Collapse
|
20
|
Zheng KW, Zhang JY, He YD, Gong JY, Wen CJ, Chen JN, Hao YH, Zhao Y, Tan Z. Detection of genomic G-quadruplexes in living cells using a small artificial protein. Nucleic Acids Res 2020; 48:11706-11720. [PMID: 33045726 PMCID: PMC7672459 DOI: 10.1093/nar/gkaa841] [Citation(s) in RCA: 82] [Impact Index Per Article: 20.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2020] [Revised: 09/16/2020] [Accepted: 09/19/2020] [Indexed: 01/08/2023] Open
Abstract
G-quadruplex (G4) structures formed by guanine-rich nucleic acids are implicated in essential physiological and pathological processes and serve as important drug targets. The genome-wide detection of G4s in living cells is important for exploring the functional role of G4s but has not yet been achieved due to the lack of a suitable G4 probe. Here we report an artificial 6.7 kDa G4 probe (G4P) protein that binds G4s with high affinity and specificity. We used it to capture G4s in living human, mouse, and chicken cells with the ChIP-Seq technique, yielding genome-wide landscape as well as details on the positions, frequencies, and sequence identities of G4 formation in these cells. Our results indicate that transcription is accompanied by a robust formation of G4s in genes. In human cells, we detected up to >123 000 G4P peaks, of which >1/3 had a fold increase of ≥5 and were present in >60% promoters and ∼70% genes. Being much smaller than a scFv antibody (27 kDa) or even a nanobody (12-15 kDa), we expect that the G4P may find diverse applications in biology, medicine, and molecular devices as a G4 affinity agent.
Collapse
Affiliation(s)
- Ke-wei Zheng
- State Key Laboratory of Membrane Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, P.R. China
- School of Pharmaceutical Sciences (Shenzhen), Sun Yat-Sen University, Guangzhou 510275, P.R. China
| | - Jia-yu Zhang
- State Key Laboratory of Membrane Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, P.R. China
- CAS Key Laboratory for Biomedical Effects of Nanomaterials and Nanosafety, Multidisciplinary Research Division, Institute of High Energy Physics, Chinese Academy of Sciences, Beijing 100049, P.R. China
| | - Yi-de He
- State Key Laboratory of Membrane Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, P.R. China
- School of Life Sciences, Sun Yat-Sen University, Guangzhou 510006, P.R. China
| | - Jia-yuan Gong
- State Key Laboratory of Membrane Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, P.R. China
| | - Cui-jiao Wen
- State Key Laboratory of Membrane Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, P.R. China
| | - Juan-nan Chen
- School of Pharmaceutical Sciences (Shenzhen), Sun Yat-Sen University, Guangzhou 510275, P.R. China
| | - Yu-hua Hao
- State Key Laboratory of Membrane Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, P.R. China
| | - Yong Zhao
- School of Life Sciences, Sun Yat-Sen University, Guangzhou 510006, P.R. China
| | - Zheng Tan
- State Key Laboratory of Membrane Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, P.R. China
- Center for Healthy Aging, Changzhi Medical College, Changzhi 046000, Shanxi, P.R. China
| |
Collapse
|
21
|
Yasuda M, Ma Y, Okabe S, Wakabayashi Y, Su D, Chang YT, Seimiya H, Tera M, Nagasawa K. Target identification of a macrocyclic hexaoxazole G-quadruplex ligand using post-target-binding visualization. Chem Commun (Camb) 2020; 56:12905-12908. [PMID: 33030187 DOI: 10.1039/d0cc04957c] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Macrocyclic hexaoxazoles (6OTDs) are G-quadruplex (G4) ligands, and some derivatives, such as L2H2-6OTD (1a) bearing two aminobutyl side chains, show cytotoxicity towards cancer cells. To identify the cellular target of 1a, we employed a post-target-binding strategy utilizing click reaction (Huisgen cyclization) between the azide-conjugated ligand L2H2-6OTD-Az (1b) and the cell-permeable dye CO-1 bearing a strained alkyne moiety and the BODIPY fluorophore under Cu-free conditions. We confirmed that introduction of the small azide group did not alter the physical or biological properties, including anti-cancer activity, of 1a, and we also demonstrated bias-free localization of CO-1. The post-binding visualization strategy suggested that L2H2-6OTD (1a) colocalized with RNA G4 in living cells.
Collapse
Affiliation(s)
- Mizuho Yasuda
- Department of Biotechnology and Life Science, Tokyo University of Agriculture and Technology, 2-24-16 Naka-cho, Koganei, Tokyo 184-8588, Japan.
| | | | | | | | | | | | | | | | | |
Collapse
|
22
|
Suseela YV, Satha P, Murugan NA, Govindaraju T. Recognition of G-quadruplex topology through hybrid binding with implications in cancer theranostics. Theranostics 2020; 10:10394-10414. [PMID: 32929356 PMCID: PMC7482797 DOI: 10.7150/thno.48675] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2020] [Accepted: 07/09/2020] [Indexed: 12/19/2022] Open
Abstract
The selective recognition and imaging of oncogene specific G-quadruplex (GQ) structures holds great promise in the development of diagnostic therapy (theranostics) for cancer and has been challenging due to their structural dynamics and diversity. We report selective recognition of GQ by a small molecule through unique hybrid loop stacking and groove binding mode with turn on far-red fluorescence response and anticancer activity demonstrating the potential implications for GQ-targeted cancer theranostics. Methods: Biophysical investigation reveal the turn on far-red emission property of TGP18 for selective recognition of GQ. In cellulo studies including DNA damage and oxidative stress evaluation guided us to perform in vitro (3D spheroid) and in vivo (xenograft mice model) anti-cancer activity, and tumor tissue imaging to assess the theranostic potential of TGP18. Results: Neocuproine-based far-red turn on fluorescence probe TGP18 shows GQ-to-duplex selectivity and specifically recognizes BCL-2 GQ with high affinity through a unique hybrid binding mode involving loop-stacking and groove interactions. Our study reveals that the selective recognition originating from the distinct loop structure of GQ that alters the overall probe interaction and binding affinity. TGP18 binding to anti-apoptotic BCL-2 GQ ablates the pro-survival function and elicit anti-cancer activity by inducing apoptosis in cancer cells. We deciphered that inhibition of BCL-2 transcription synergized with signaling cascade of nucleolar stress, DNA damage and oxidative stress in triggering apoptosis signaling pathway. Conclusion: Intervention of GQ mediated lethality by TGP18 has translated into anti-cancer activity in both in vitro 3D spheroid culture and in vivo xenograft models of lung and breast cancer with superior efficacy for the former. In vivo therapeutic efficacy supplemented with tumor 3D spheroid and tissue imaging potential define the role of TGP18 in GQ-targeted cancer theranostics.
Collapse
|
23
|
Tian Z, Peng P, Wang H, Zheng J, Shi L, Li T. Aptamer-Braked Multi-hairpin Cascade Circuits for Logic-Controlled Label-Free In Situ Bioimaging. Anal Chem 2020; 92:10357-10364. [PMID: 32600028 DOI: 10.1021/acs.analchem.0c00583] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
As a common hairpin-based amplification strategy, catalytic-hairpin assembly (CHA) has been widely used to construct various DNA circuits for biosensing and imaging. However, the hairpin substrates can potentially react without catalysts and result in circuit leakage, which may be quite severe in a CHA reaction consisting of three or four hairpins due to the formation of stable three-/four-way junction product. To circumvent this problem, here we introduce a well-designed ATP aptamer as a DNA brake into a four-hairpin cascade circuit, where the triggering toehold is blocked by the aptamer brake and thus the circuit leakage decreases dramatically. Such an aptamer-braked DNA circuit is then employed to build an AND logic gate in response to multiple external stimuli in acidic cell membrane microenvironments. Induced by a bimolecular i-motif that binds thioflavin T (ThT), the dimerization of a four-way junction in situ assembled on the cell surface is accomplished, enabling the logic-controlled cell membrane imaging in a label-free manner. Our design would be applicable to other hairpin-based amplification strategies and may find more applications in the construction of multiresponsive DNA cascade circuits in complex living systems.
Collapse
Affiliation(s)
- Zhijin Tian
- Department of Chemistry, University of Science & Technology of China, Hefei, Anhui 230026, China
| | - Pai Peng
- Department of Chemistry, University of Science & Technology of China, Hefei, Anhui 230026, China
| | - Huihui Wang
- Department of Chemistry, University of Science & Technology of China, Hefei, Anhui 230026, China
| | - Jiao Zheng
- Department of Chemistry, University of Science & Technology of China, Hefei, Anhui 230026, China
| | - Lili Shi
- Department of Chemistry, University of Science & Technology of China, Hefei, Anhui 230026, China
| | - Tao Li
- Department of Chemistry, University of Science & Technology of China, Hefei, Anhui 230026, China
| |
Collapse
|
24
|
In-Gel Probing Polymorphic Structures of G-Quadruplexes Derived from c-Myc Promoter. CHINESE JOURNAL OF ANALYTICAL CHEMISTRY 2020. [DOI: 10.1016/s1872-2040(20)60002-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
|
25
|
Sulatsky MI, Sulatskaya AI, Stepanenko OV, Povarova OI, Kuznetsova IM, Turoverov KK. Denaturant effect on amyloid fibrils: Declasterization, depolymerization, denaturation and reassembly. Int J Biol Macromol 2020; 150:681-694. [PMID: 32057863 DOI: 10.1016/j.ijbiomac.2020.01.290] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2019] [Revised: 01/28/2020] [Accepted: 01/29/2020] [Indexed: 01/07/2023]
Abstract
Accumulation of amyloid fibrils in organism accompanies many serious diseases, such as Alzheimer's and Parkinson's diseases, diabetes, prion diseases, etc. It is generally accepted that amyloids are highly resistant to degradation, which complicates their elimination in vivo and is one of the reasons for their pathogenicity. However, using a wide range of physicochemical approaches and specially elaborated method for the tested samples preparation by equilibrium microdialysis technique, it is proved that the stability of amyloids is greatly exaggerated. It turned out that amyloid fibrils formed from at least two amyloidogenic proteins, one of which is a model object for fibrils studying and the second is the cause of hemodialysis amyloidosis in an acute renal failure, are less stable than monomeric proteins. A mechanism of the degradation/reassembly of amyloid fibrils was proposed. It was shown that amyloid «seed» is a factor affecting not only the rate of the fibrils formation, but also their structure. Obtained results are a step towards identifying effects that can lead to degradation of amyloids and their clearance without adverse influence on the functionally active state of the protein or to change the structure and, as a result, the pathogenicity of these protein aggregates.
Collapse
Affiliation(s)
- M I Sulatsky
- Institute of Cytology Russian Academy of Science, St. Petersburg, Tikhoretsky ave. 4, 194064, Russia
| | - A I Sulatskaya
- Institute of Cytology Russian Academy of Science, St. Petersburg, Tikhoretsky ave. 4, 194064, Russia
| | - Olga V Stepanenko
- Institute of Cytology Russian Academy of Science, St. Petersburg, Tikhoretsky ave. 4, 194064, Russia
| | - O I Povarova
- Institute of Cytology Russian Academy of Science, St. Petersburg, Tikhoretsky ave. 4, 194064, Russia
| | - I M Kuznetsova
- Institute of Cytology Russian Academy of Science, St. Petersburg, Tikhoretsky ave. 4, 194064, Russia
| | - K K Turoverov
- Institute of Cytology Russian Academy of Science, St. Petersburg, Tikhoretsky ave. 4, 194064, Russia; Peter the Great St.-Petersburg Polytechnic University, St. Petersburg, Polytechnicheskaya 29, 195251, Russia.
| |
Collapse
|
26
|
Deiana M, Chand K, Jamroskovic J, Obi I, Chorell E, Sabouri N. A Light‐up Logic Platform for Selective Recognition of Parallel G‐Quadruplex Structures via Disaggregation‐Induced Emission. Angew Chem Int Ed Engl 2020; 59:896-902. [DOI: 10.1002/anie.201912027] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2019] [Revised: 10/23/2019] [Indexed: 12/23/2022]
Affiliation(s)
- Marco Deiana
- Department of Medical Biochemistry and BiophysicsUmeå University 90187 Umeå Sweden
| | - Karam Chand
- Department of ChemistryUmeå University 90187 Umeå Sweden
| | - Jan Jamroskovic
- Department of Medical Biochemistry and BiophysicsUmeå University 90187 Umeå Sweden
| | - Ikenna Obi
- Department of Medical Biochemistry and BiophysicsUmeå University 90187 Umeå Sweden
| | - Erik Chorell
- Department of ChemistryUmeå University 90187 Umeå Sweden
| | - Nasim Sabouri
- Department of Medical Biochemistry and BiophysicsUmeå University 90187 Umeå Sweden
| |
Collapse
|
27
|
|
28
|
Meeting report: Seventh International Meeting on Quadruplex Nucleic Acids (Changchun, P.R. China, September 6–9, 2019). Biochimie 2020; 168:100-109. [DOI: 10.1016/j.biochi.2019.10.019] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2019] [Accepted: 10/31/2019] [Indexed: 12/24/2022]
|
29
|
Mestre-Fos S, Penev PI, Richards JC, Dean WL, Gray RD, Chaires JB, Williams LD. Profusion of G-quadruplexes on both subunits of metazoan ribosomes. PLoS One 2019; 14:e0226177. [PMID: 31834895 PMCID: PMC6910669 DOI: 10.1371/journal.pone.0226177] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2019] [Accepted: 11/03/2019] [Indexed: 01/17/2023] Open
Abstract
Mammalian and bird ribosomes are nearly twice the mass of prokaryotic ribosomes in part because of their extraordinarily long rRNA tentacles. Human rRNA tentacles are not fully observable in current three-dimensional structures and their conformations remain to be fully resolved. In previous work we identified sequences that favor G-quadruplexes in silico and in vitro in rRNA tentacles of the human large ribosomal subunit. We demonstrated by experiment that these sequences form G-quadruplexes in vitro. Here, using a more recent motif definition, we report additional G-quadruplex sequences on surfaces of both subunits of the human ribosome. The revised sequence definition reveals expansive arrays of potential G-quadruplex sequences on LSU tentacles. In addition, we demonstrate by a variety of experimental methods that fragments of the small subunit rRNA form G-quadruplexes in vitro. Prior to this report rRNA sequences that form G-quadruplexes were confined to the large ribosomal subunit. Our combined results indicate that the surface of the assembled human ribosome contains numerous sequences capable of forming G-quadruplexes on both ribosomal subunits. The data suggest conversion between duplexes and G-quadruplexes in response to association with proteins, ions, or other RNAs. In some systems it seems likely that the integrated population of RNA G-quadruplexes may be dominated by rRNA, which is the most abundant cellular RNA.
Collapse
Affiliation(s)
- Santi Mestre-Fos
- Center for the Origin of Life, Georgia Institute of Technology, Atlanta, Georgia, United States of America
- School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, Georgia, United States of America
| | - Petar I. Penev
- Center for the Origin of Life, Georgia Institute of Technology, Atlanta, Georgia, United States of America
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, Georgia, United States of America
| | - John Colin Richards
- Center for the Origin of Life, Georgia Institute of Technology, Atlanta, Georgia, United States of America
- School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, Georgia, United States of America
| | - William L. Dean
- James Graham Brown Cancer Center, University of Louisville, Louisville, Kentucky, United States of America
| | - Robert D. Gray
- James Graham Brown Cancer Center, University of Louisville, Louisville, Kentucky, United States of America
| | - Jonathan B. Chaires
- James Graham Brown Cancer Center, University of Louisville, Louisville, Kentucky, United States of America
| | - Loren Dean Williams
- Center for the Origin of Life, Georgia Institute of Technology, Atlanta, Georgia, United States of America
- School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, Georgia, United States of America
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, Georgia, United States of America
- * E-mail:
| |
Collapse
|
30
|
Deiana M, Chand K, Jamroskovic J, Obi I, Chorell E, Sabouri N. A Light‐up Logic Platform for Selective Recognition of Parallel G‐Quadruplex Structures via Disaggregation‐Induced Emission. Angew Chem Int Ed Engl 2019. [DOI: 10.1002/ange.201912027] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Affiliation(s)
- Marco Deiana
- Department of Medical Biochemistry and BiophysicsUmeå University 90187 Umeå Sweden
| | - Karam Chand
- Department of ChemistryUmeå University 90187 Umeå Sweden
| | - Jan Jamroskovic
- Department of Medical Biochemistry and BiophysicsUmeå University 90187 Umeå Sweden
| | - Ikenna Obi
- Department of Medical Biochemistry and BiophysicsUmeå University 90187 Umeå Sweden
| | - Erik Chorell
- Department of ChemistryUmeå University 90187 Umeå Sweden
| | - Nasim Sabouri
- Department of Medical Biochemistry and BiophysicsUmeå University 90187 Umeå Sweden
| |
Collapse
|
31
|
Bacolla A, Ye Z, Ahmed Z, Tainer JA. Cancer mutational burden is shaped by G4 DNA, replication stress and mitochondrial dysfunction. PROGRESS IN BIOPHYSICS AND MOLECULAR BIOLOGY 2019; 147:47-61. [PMID: 30880007 PMCID: PMC6745008 DOI: 10.1016/j.pbiomolbio.2019.03.004] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/23/2018] [Revised: 03/08/2019] [Accepted: 03/12/2019] [Indexed: 02/01/2023]
Abstract
A hallmark of cancer is genomic instability, which can enable cancer cells to evade therapeutic strategies. Here we employed a computational approach to uncover mechanisms underlying cancer mutational burden by focusing upon relationships between 1) translocation breakpoints and the thousands of G4 DNA-forming sequences within retrotransposons impacting transcription and exemplifying probable non-B DNA structures and 2) transcriptome profiling and cancer mutations. We determined the location and number of G4 DNA-forming sequences in the Genome Reference Consortium Human Build 38 and found a total of 358,605 covering ∼13.4 million bases. By analyzing >97,000 unique translocation breakpoints from the Catalogue Of Somatic Mutations In Cancer (COSMIC), we found that breakpoints are overrepresented at G4 DNA-forming sequences within hominid-specific SVA retrotransposons, and generally occur in tumors with mutations in tumor suppressor genes, such as TP53. Furthermore, correlation analyses between mRNA levels and exome mutational loads from The Cancer Genome Atlas (TCGA) encompassing >450,000 gene-mutation regressions revealed strong positive and negative associations, which depended upon tissue of origin. The strongest positive correlations originated from genes not listed as cancer genes in COSMIC; yet, these show strong predictive power for survival in most tumor types by Kaplan-Meier estimation. Thus, correlation analyses of DNA structure and gene expression with mutation loads complement and extend more traditional approaches to elucidate processes shaping genomic instability in cancer. The combined results point to G4 DNA, activation of cell cycle/DNA repair pathways, and mitochondrial dysfunction as three major factors driving the accumulation of somatic mutations in cancer cells.
Collapse
Affiliation(s)
- Albino Bacolla
- Departments of Cancer Biology and of Molecular and Cellular Oncology, The University of Texas M.D. Anderson Cancer Center, 6767 Bertner Avenue, Houston, TX, 77030, USA.
| | - Zu Ye
- Departments of Cancer Biology and of Molecular and Cellular Oncology, The University of Texas M.D. Anderson Cancer Center, 6767 Bertner Avenue, Houston, TX, 77030, USA.
| | - Zamal Ahmed
- Departments of Cancer Biology and of Molecular and Cellular Oncology, The University of Texas M.D. Anderson Cancer Center, 6767 Bertner Avenue, Houston, TX, 77030, USA.
| | - John A Tainer
- Departments of Cancer Biology and of Molecular and Cellular Oncology, The University of Texas M.D. Anderson Cancer Center, 6767 Bertner Avenue, Houston, TX, 77030, USA.
| |
Collapse
|
32
|
Pandith A, Siddappa RG, Seo YJ. Recent developments in novel blue/green/red/NIR small fluorescent probes for in cellulo tracking of RNA/DNA G-quadruplexes. JOURNAL OF PHOTOCHEMISTRY AND PHOTOBIOLOGY C-PHOTOCHEMISTRY REVIEWS 2019. [DOI: 10.1016/j.jphotochemrev.2019.08.001] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
|
33
|
Zhang S, Sun H, Wang L, Liu Y, Chen H, Li Q, Guan A, Liu M, Tang Y. Real-time monitoring of DNA G-quadruplexes in living cells with a small-molecule fluorescent probe. Nucleic Acids Res 2019; 46:7522-7532. [PMID: 30085206 PMCID: PMC6125622 DOI: 10.1093/nar/gky665] [Citation(s) in RCA: 84] [Impact Index Per Article: 16.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2018] [Accepted: 07/13/2018] [Indexed: 12/14/2022] Open
Abstract
G-quadruplex DNA has been viewed as a prospective anti-cancer target owing to its potential biological relevance. Real-time monitoring of DNA G-quadruplex structures in living cells can provide valuable insights into the relationship between G-quadruplex formation and its cellular consequences. However, the probes capable of detecting DNA G-quadruplexes in living cells are still very limited. Herein, we reported a new fluorescent probe, IMT, for real-time visualization of DNA G-quadruplex structures in living cells. Using IMT as a fluorescent indicator, the quantity changes of DNA G-quadruplex at different points in time during continuous cellular progression responding to Aphidicolin and Hydroxyurea treatment have been directly visualized. Our data demonstrate that IMT will be a valuable tool for exploring DNA G-quadruplexes in live cells. Further application of IMT in fluorescence imaging may reveal more information on the roles of DNA G-quadruplexes in biological systems.
Collapse
Affiliation(s)
- Suge Zhang
- Beijing National Laboratory for Molecular Sciences, State Key Laboratory for Structural Chemistry of Unstable and Stable Species, CAS Research/Education Center for Excellence in Molecular Sciences, Institute of Chemistry Chinese Academy of Sciences, Beijing 100190, P.R. China.,University of Chinese Academy of Sciences, Beijing 100049, P.R. China
| | - Hongxia Sun
- Beijing National Laboratory for Molecular Sciences, State Key Laboratory for Structural Chemistry of Unstable and Stable Species, CAS Research/Education Center for Excellence in Molecular Sciences, Institute of Chemistry Chinese Academy of Sciences, Beijing 100190, P.R. China
| | - Lixia Wang
- Beijing National Laboratory for Molecular Sciences, State Key Laboratory for Structural Chemistry of Unstable and Stable Species, CAS Research/Education Center for Excellence in Molecular Sciences, Institute of Chemistry Chinese Academy of Sciences, Beijing 100190, P.R. China
| | - Yan Liu
- Beijing National Laboratory for Molecular Sciences, State Key Laboratory for Structural Chemistry of Unstable and Stable Species, CAS Research/Education Center for Excellence in Molecular Sciences, Institute of Chemistry Chinese Academy of Sciences, Beijing 100190, P.R. China
| | - Hongbo Chen
- Beijing National Laboratory for Molecular Sciences, State Key Laboratory for Structural Chemistry of Unstable and Stable Species, CAS Research/Education Center for Excellence in Molecular Sciences, Institute of Chemistry Chinese Academy of Sciences, Beijing 100190, P.R. China.,University of Chinese Academy of Sciences, Beijing 100049, P.R. China
| | - Qian Li
- Beijing National Laboratory for Molecular Sciences, State Key Laboratory for Structural Chemistry of Unstable and Stable Species, CAS Research/Education Center for Excellence in Molecular Sciences, Institute of Chemistry Chinese Academy of Sciences, Beijing 100190, P.R. China
| | - Aijiao Guan
- Beijing National Laboratory for Molecular Sciences, State Key Laboratory for Structural Chemistry of Unstable and Stable Species, CAS Research/Education Center for Excellence in Molecular Sciences, Institute of Chemistry Chinese Academy of Sciences, Beijing 100190, P.R. China
| | - Meirong Liu
- Center for Physiochemical Analysis & Measurement, Institute of Chemistry Chinese Academy of Sciences, Beijing 100190, P.R. China
| | - Yalin Tang
- Beijing National Laboratory for Molecular Sciences, State Key Laboratory for Structural Chemistry of Unstable and Stable Species, CAS Research/Education Center for Excellence in Molecular Sciences, Institute of Chemistry Chinese Academy of Sciences, Beijing 100190, P.R. China.,University of Chinese Academy of Sciences, Beijing 100049, P.R. China
| |
Collapse
|
34
|
Umar MI, Ji D, Chan CY, Kwok CK. G-Quadruplex-Based Fluorescent Turn-On Ligands and Aptamers: From Development to Applications. Molecules 2019; 24:E2416. [PMID: 31262059 PMCID: PMC6650947 DOI: 10.3390/molecules24132416] [Citation(s) in RCA: 50] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2019] [Revised: 06/17/2019] [Accepted: 06/24/2019] [Indexed: 02/08/2023] Open
Abstract
Guanine (G)-quadruplexes (G4s) are unique nucleic acid structures that are formed by stacked G-tetrads in G-rich DNA or RNA sequences. G4s have been reported to play significant roles in various cellular events in both macro- and micro-organisms. The identification and characterization of G4s can help to understand their different biological roles and potential applications in diagnosis and therapy. In addition to biophysical and biochemical methods to interrogate G4 formation, G4 fluorescent turn-on ligands can be used to target and visualize G4 formation both in vitro and in cells. Here, we review several representative classes of G4 fluorescent turn-on ligands in terms of their interaction mechanism and application perspectives. Interestingly, G4 structures are commonly identified in DNA and RNA aptamers against targets that include proteins and small molecules, which can be utilized as G4 tools for diverse applications. We therefore also summarize the recent development of G4-containing aptamers and highlight their applications in biosensing, bioimaging, and therapy. Moreover, we discuss the current challenges and future perspectives of G4 fluorescent turn-on ligands and G4-containing aptamers.
Collapse
Affiliation(s)
- Mubarak I Umar
- Department of Chemistry, City University of Hong Kong, Kowloon Tong, Hong Kong SAR, China
| | - Danyang Ji
- Department of Chemistry, City University of Hong Kong, Kowloon Tong, Hong Kong SAR, China
| | - Chun-Yin Chan
- Department of Chemistry, City University of Hong Kong, Kowloon Tong, Hong Kong SAR, China
| | - Chun Kit Kwok
- Department of Chemistry, City University of Hong Kong, Kowloon Tong, Hong Kong SAR, China.
| |
Collapse
|
35
|
Lee D, Kim SM, Kim HY, Kim Y. Fluorescence Chemicals To Detect Insoluble and Soluble Amyloid-β Aggregates. ACS Chem Neurosci 2019; 10:2647-2657. [PMID: 31009195 DOI: 10.1021/acschemneuro.9b00199] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Misfolded amyloid-β (Aβ) is the key biomarker of Alzheimer's disease (AD), and discoveries of fluorescence chemicals visualizing such Aβ aggregates in the brain have made major contributions in postmortem and antemortem diagnosis of the disorder. Insoluble senile plaques of Aβ in brain tissues are commonly stained with thioflavin and congo red dyes and observed through microscopy, while those in living patient brains are detected via radioisotope-labeled fluorescence chemicals for positron emission tomography. Clinical evidence strongly supports the view that plaques are well-associated with the onset but not with the progression of AD. Plaques could accumulate while cognitive functions of at-risk individuals are still intact, and thus, another biomarker is needed to monitor neurodegeneration. Soluble Aβ oligomers are considered to have strong correlation with neuronal loss and brain atrophy as they are the most neurotoxic forms of misfolded Aβ. However, oligomer-targeting probes encounter several major difficulties in development. There is a significant structural distinction between two Aβ species-plaques are β-sheet-rich while oligomers are unordered-and it is still difficult to isolate and stabilize the oligomeric forms of Aβ. Due to these challenges, soluble oligomer-detecting imaging probes are relatively rare compared to the plaque-targeting chemical probes. This Review describes biochemical and optical characteristics of up-to-date fluorescence chemicals targeting insoluble plaques and soluble oligomers of Aβ. We also highlight the contributions of Aβ fluorescence chemicals to the clinical diagnosis of AD and technical challenges in searching for enhanced imaging probes.
Collapse
|
36
|
Domarco O, Kieler C, Pirker C, Dinhof C, Englinger B, Reisecker JM, Timelthaler G, García MD, Peinador C, Keppler BK, Berger W, Terenzi A. Subcellular Duplex DNA and G-Quadruplex Interaction Profiling of a Hexagonal Pt II Metallacycle. Angew Chem Int Ed Engl 2019; 58:8007-8012. [PMID: 31002438 PMCID: PMC6563712 DOI: 10.1002/anie.201900934] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2019] [Revised: 04/17/2019] [Indexed: 12/21/2022]
Abstract
Metal-driven self-assembly afforded a multitude of fascinating supramolecular coordination complexes (SCCs) with applications as catalysts, host-guest, and stimuli-responsive systems. However, the interest in the biological applications of SCCs is only starting to emerge and thorough characterization of their behavior in biological milieus is still lacking. Herein, we report on the synthesis and detailed in-cell tracking of a Pt2 L2 metallacycle. We show that our hexagonal supramolecule accumulates in cancer cell nuclei, exerting a distinctive blue fluorescence staining of chromatin resistant to UV photobleaching selectively in nucleolar G4-rich regions. SCC co-localizes with epitopes of the quadruplex-specific antibody BG4 and replaces other well-known G4 stabilizers. Moreover, the photophysical changes accompanying the metallacycle binding to G4s in solution (fluorescence quenching, absorption enhancement) also take place intracellularly, allowing its subcellular interaction tracking.
Collapse
Affiliation(s)
- Olaya Domarco
- Universidade da CoruñaDepartamento de Química y Centro de Investigacións Científicas AvanzadasE-15071 ACoruñaSpain
| | - Claudia Kieler
- Medical University of ViennaDepartment of Medicine IInstitute of Cancer Research and Comprehensive Cancer CenterBorschkegasse 8aA-1090ViennaAustria
| | - Christine Pirker
- Medical University of ViennaDepartment of Medicine IInstitute of Cancer Research and Comprehensive Cancer CenterBorschkegasse 8aA-1090ViennaAustria
| | - Carina Dinhof
- Medical University of ViennaDepartment of Medicine IInstitute of Cancer Research and Comprehensive Cancer CenterBorschkegasse 8aA-1090ViennaAustria
| | - Bernhard Englinger
- Medical University of ViennaDepartment of Medicine IInstitute of Cancer Research and Comprehensive Cancer CenterBorschkegasse 8aA-1090ViennaAustria
| | - Johannes M. Reisecker
- Medical University of ViennaDepartment of Medicine IInstitute of Cancer Research and Comprehensive Cancer CenterBorschkegasse 8aA-1090ViennaAustria
| | - Gerald Timelthaler
- Medical University of ViennaDepartment of Medicine IInstitute of Cancer Research and Comprehensive Cancer CenterBorschkegasse 8aA-1090ViennaAustria
| | - Marcos D. García
- Universidade da CoruñaDepartamento de Química y Centro de Investigacións Científicas AvanzadasE-15071 ACoruñaSpain
| | - Carlos Peinador
- Universidade da CoruñaDepartamento de Química y Centro de Investigacións Científicas AvanzadasE-15071 ACoruñaSpain
| | - Bernhard K. Keppler
- University of ViennaInstitute of Inorganic ChemistryWaehringerstrasse 42A-1090ViennaAustria
| | - Walter Berger
- Medical University of ViennaDepartment of Medicine IInstitute of Cancer Research and Comprehensive Cancer CenterBorschkegasse 8aA-1090ViennaAustria
| | - Alessio Terenzi
- University of ViennaInstitute of Inorganic ChemistryWaehringerstrasse 42A-1090ViennaAustria
- Present address: Donostia International Physics CenterPaseo Manuel de Lardizabal 420018DonostiaSpain
| |
Collapse
|
37
|
Domarco O, Kieler C, Pirker C, Dinhof C, Englinger B, Reisecker JM, Timelthaler G, García MD, Peinador C, Keppler BK, Berger W, Terenzi A. Subcellular Duplex DNA and G‐Quadruplex Interaction Profiling of a Hexagonal Pt
II
Metallacycle. Angew Chem Int Ed Engl 2019. [DOI: 10.1002/ange.201900934] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Affiliation(s)
- Olaya Domarco
- Universidade da Coruña Departamento de Química y Centro de Investigacións Científicas Avanzadas E-15071 A Coruña Spain
| | - Claudia Kieler
- Medical University of Vienna Department of Medicine I Institute of Cancer Research and Comprehensive Cancer Center Borschkegasse 8a A-1090 Vienna Austria
| | - Christine Pirker
- Medical University of Vienna Department of Medicine I Institute of Cancer Research and Comprehensive Cancer Center Borschkegasse 8a A-1090 Vienna Austria
| | - Carina Dinhof
- Medical University of Vienna Department of Medicine I Institute of Cancer Research and Comprehensive Cancer Center Borschkegasse 8a A-1090 Vienna Austria
| | - Bernhard Englinger
- Medical University of Vienna Department of Medicine I Institute of Cancer Research and Comprehensive Cancer Center Borschkegasse 8a A-1090 Vienna Austria
| | - Johannes M. Reisecker
- Medical University of Vienna Department of Medicine I Institute of Cancer Research and Comprehensive Cancer Center Borschkegasse 8a A-1090 Vienna Austria
| | - Gerald Timelthaler
- Medical University of Vienna Department of Medicine I Institute of Cancer Research and Comprehensive Cancer Center Borschkegasse 8a A-1090 Vienna Austria
| | - Marcos D. García
- Universidade da Coruña Departamento de Química y Centro de Investigacións Científicas Avanzadas E-15071 A Coruña Spain
| | - Carlos Peinador
- Universidade da Coruña Departamento de Química y Centro de Investigacións Científicas Avanzadas E-15071 A Coruña Spain
| | - Bernhard K. Keppler
- University of Vienna Institute of Inorganic Chemistry Waehringerstrasse 42 A-1090 Vienna Austria
| | - Walter Berger
- Medical University of Vienna Department of Medicine I Institute of Cancer Research and Comprehensive Cancer Center Borschkegasse 8a A-1090 Vienna Austria
| | - Alessio Terenzi
- University of Vienna Institute of Inorganic Chemistry Waehringerstrasse 42 A-1090 Vienna Austria
- Present address: Donostia International Physics Center Paseo Manuel de Lardizabal 4 20018 Donostia Spain
| |
Collapse
|
38
|
Turaev AV, Tsvetkov VB, Tankevich MV, Smirnov IP, Aralov AV, Pozmogova GE, Varizhuk AM. Benzothiazole-based cyanines as fluorescent "light-up" probes for duplex and quadruplex DNA. Biochimie 2019; 162:216-228. [PMID: 31022429 DOI: 10.1016/j.biochi.2019.04.018] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2018] [Accepted: 04/18/2019] [Indexed: 11/30/2022]
Abstract
Analogs of benzothiazole orange (BO) with one, two or three methylbenzothiazolylmethylidene substituents in the 1-methylpyridinium ring were obtained from the respective picolinium, lutidinium or collidinium salts. Fluorescence parameters of the known and new dyes in complexes with various DNA structures, including G-quadruplexes (G4s) and i-motifs (IMs), were analyzed. All dyes efficiently distinguished G4s and ss-DNA. The bi- and tri-substituted derivatives had basically similar distributions of relative fluorescence intensities. The mono-substituted derivatives exhibited enhanced sensitivity to parallel G4s. All dyes were particularly sensitive to a G4 structure with an additional duplex module (the thrombin-binding aptamer TBA31), presumably due to a distinctive binding mode (interaction with the junction between the two modules). In particular, BO showed a strong (160-fold) enhancement in fluorescence quantum yield in complex with TBA31 compared to the free dye. The fluorescence quantum yields of the 2,4-bisubstituted derivative in complex with well-characterized G4s from oncogene promoters were in the range of 0.04-0.28, i.e. comparable to those of ThT. The mono/bi-substituted derivatives should be considered as possible light-up probes for G4 formation.
Collapse
Affiliation(s)
- Anton V Turaev
- Biophysics Department, Research and Clinical Center for Physical Chemical Medicine, Malaya Pirogovskaya Str. 1a, Moscow, 119435, Russia; Moscow Institute of Physics and Technology, Institutsky Lane 9, Dolgoprudny, 141700, Russia
| | - Vladimir B Tsvetkov
- Biophysics Department, Research and Clinical Center for Physical Chemical Medicine, Malaya Pirogovskaya Str. 1a, Moscow, 119435, Russia; Department of Molecular Virology, FSBI Research Institute of Influenza, Ministry of Health of Russian Federation, Prof. Popov Str. 15/17, Saint-Petersburg, 197376, Russia; Computational Oncology Group, I.M. Sechenov First Moscow State Medical University, Bolshaya Pirogovskaya Str. 19/1, Moscow, 119146, Russia
| | - Maria V Tankevich
- Biophysics Department, Research and Clinical Center for Physical Chemical Medicine, Malaya Pirogovskaya Str. 1a, Moscow, 119435, Russia
| | - Igor P Smirnov
- Biophysics Department, Research and Clinical Center for Physical Chemical Medicine, Malaya Pirogovskaya Str. 1a, Moscow, 119435, Russia
| | - Andrey V Aralov
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Miklukho-Maklaya Str. 16/10, Moscow, 117997, Russia.
| | - Galina E Pozmogova
- Biophysics Department, Research and Clinical Center for Physical Chemical Medicine, Malaya Pirogovskaya Str. 1a, Moscow, 119435, Russia; Institute of Bioengineering, Research Center of Biotechnology of the Russian Academy of Sciences, Leninsky Prospect, 33, Build. 2, Moscow, 119071, Russia.
| | - Anna M Varizhuk
- Biophysics Department, Research and Clinical Center for Physical Chemical Medicine, Malaya Pirogovskaya Str. 1a, Moscow, 119435, Russia; Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Vavilov Str. 32, Moscow, 119991, Russia
| |
Collapse
|
39
|
Verma S, Ghuge SA, Ravichandiran V, Ranjan N. Spectroscopic studies of Thioflavin-T binding to c-Myc G-quadruplex DNA. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2019; 212:388-395. [PMID: 30703662 DOI: 10.1016/j.saa.2018.12.044] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/19/2018] [Revised: 11/16/2018] [Accepted: 12/22/2018] [Indexed: 05/29/2023]
Abstract
G-quadruplexes are well-known DNA secondary structures which can be formed both within the DNA and the RNA sequences of the human genome. While many functions of G-quadruplex during cell regulatory events are still unknown, a number of reports have established their role in finding new cancer therapies. In this report, we provide a detailed account of Thioflavin T (ThT) interacting with a promoter gene (c-Myc) which has relevance in several types of human cancers. Using a variety of spectroscopic techniques, we have shown that the binding of ThT is selective to c-Myc G-quadruplex only, having poor interactions with the duplex DNA sequences. UV-Visible titration experiments show that binding involves stacking interactions which were further corroborated by CD experiments. Fluorescence studies showed that the binding of ThT to c-Myc G-quadruplex results in a large increase in the fluorescence emission spectrum of c-Myc G-quadruplex while the same to duplex DNAs was much poor. Binding of ThT to c-Myc G-quadruplex results in thermal stabilization of the quadruplex DNA by up to 7.4 °C and Job plot experiments demonstrated the presence of 1:1 and 2:1 ligand to quadruplex complexes. Finally, the docking study suggested that ThT stacks with the guanine bases in one of the grooves which is in agreement with the CD studies. These results are expected to provide leads into the design of new ThT analogs and derivatives for enhancing the stability and selectivity of new G-quadruplex targeting ligands.
Collapse
Affiliation(s)
- Smita Verma
- National Institute of Pharmaceutical Education and Research, ITI Compound, Raebareli 229010, India; National Institute of Pharmaceutical Education and Research, Kolkata, Maniktala Main Road, Kolkata 700054, India
| | - Sandip A Ghuge
- TERI-Deakin Nanobiotechnology Research Center, Sustainable Agriculture Division, The Energy and Resources Institute, New Delhi 110003, India
| | - V Ravichandiran
- National Institute of Pharmaceutical Education and Research, Kolkata, Maniktala Main Road, Kolkata 700054, India
| | - Nihar Ranjan
- National Institute of Pharmaceutical Education and Research, ITI Compound, Raebareli 229010, India.
| |
Collapse
|
40
|
G-Quadruplexes in Human Ribosomal RNA. J Mol Biol 2019; 431:1940-1955. [PMID: 30885721 DOI: 10.1016/j.jmb.2019.03.010] [Citation(s) in RCA: 35] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2018] [Revised: 03/07/2019] [Accepted: 03/08/2019] [Indexed: 11/20/2022]
Abstract
rRNA is the single most abundant polymer in most cells. Mammalian rRNAs are nearly twice as large as those of prokaryotes. Differences in rRNA size are due to expansion segments, which contain extended tentacles in metazoans. Here we show that the terminus of an rRNA tentacle of Homo sapiens contains 10 tandem G-tracts that form highly stable G-quadruplexes in vitro. We characterized rRNA of the H. sapiens large ribosomal subunit by computation, circular dichroism, UV melting, fluorescent probes, nuclease accessibility, electrophoretic mobility shifts, and blotting. We investigated Expansion Segment 7 (ES7), oligomers derived from ES7, intact 28S rRNA, 80S ribosomes, and polysomes. We used mass spectrometry to identify proteins that bind to rRNA G-quadruplexes in cell lysates. These proteins include helicases (DDX3, CNBP, DDX21, DDX17) and heterogeneous nuclear ribonucleoproteins. Finally, by multiple sequence alignments, we observe that G-quadruplex-forming sequences are a general feature of LSU rRNA of Chordata but not, as far as we can tell, of other species. Chordata ribosomes present polymorphic tentacles with the potential to switch between inter- and intramolecular G-quadruplexes. To our knowledge, G-quadruplexes have not been reported previously in ribosomes.
Collapse
|
41
|
Sulatskaya AI, Sulatsky MI, Antifeeva IA, Kuznetsova IM, Turoverov KK. Structural Analogue of Thioflavin T, DMASEBT, as a Tool for Amyloid Fibrils Study. Anal Chem 2019; 91:3131-3140. [DOI: 10.1021/acs.analchem.8b05737] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Affiliation(s)
- A. I. Sulatskaya
- Laboratory of Structural Dynamics, Stability and Folding of Proteins, Institute of Cytology of the Russian Academy of Sciences, St. Petersburg 194064, Russia
| | - M. I. Sulatsky
- Laboratory of Cell Morphology, Institute of Cytology of the Russian Academy of Sciences, St. Petersburg 194064, Russia
| | - Iu. A. Antifeeva
- Laboratory of Structural Dynamics, Stability and Folding of Proteins, Institute of Cytology of the Russian Academy of Sciences, St. Petersburg 194064, Russia
| | - I. M. Kuznetsova
- Laboratory of Structural Dynamics, Stability and Folding of Proteins, Institute of Cytology of the Russian Academy of Sciences, St. Petersburg 194064, Russia
| | - K. K. Turoverov
- Laboratory of Structural Dynamics, Stability and Folding of Proteins, Institute of Cytology of the Russian Academy of Sciences, St. Petersburg 194064, Russia
- Peter the Great St. Petersburg Polytechnic University (SPbPU), St. Petersburg 195251, Russia
| |
Collapse
|