1
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Lacen A, Symasek A, Gunter A, Lee HT. Slow G-Quadruplex Conformation Rearrangement and Accessibility Change Induced by Potassium in Human Telomeric Single-Stranded DNA. J Phys Chem B 2024; 128:5950-5965. [PMID: 38875355 PMCID: PMC11216195 DOI: 10.1021/acs.jpcb.4c00719] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2024] [Revised: 05/24/2024] [Accepted: 06/03/2024] [Indexed: 06/16/2024]
Abstract
The guanine-rich telomeric repeats can form G-quadruplexes (G4s) that alter the accessibility of the single-stranded telomeric overhang. In this study, we investigated the effects of Na+ and K+ on G4 folding and accessibility through cation introduction and exchange. We combined differential scanning calorimetry (DSC), circular dichroism (CD), and single molecule Förster resonance energy transfer (smFRET) to monitor the stability, conformational dynamics, and complementary strand binding accessibility of G4 formed by single-stranded telomeric DNA. Our data showed that G4 formed through heating and slow cooling in K+ solution exhibited fewer conformational dynamics than G4 formed in Na+ solution, which is consistent with the higher thermal stability of G4 in K+. Monitoring cation exchange with real time smFRET at room temperature shows that Na+ and K+ can replace each other in G4. When encountering high K+ at room or body temperature, G4 undergoes a slow conformational rearrangement process which is mostly complete by 2 h. The slow conformational rearrangement ends with a stable G4 that is unable to be unfolded by a complementary strand. This study provides new insights into the accessibility of G4 forming sequences at different time points after introduction to a high K+ environment in cells, which may affect how the nascent telomeric overhang interacts with proteins and telomerase.
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Affiliation(s)
- Arianna
N. Lacen
- Department of Chemistry, University
of Alabama at Birmingham, 901 14th Street South, Birmingham, Alabama 35294, United
States
| | - Andrew Symasek
- Department of Chemistry, University
of Alabama at Birmingham, 901 14th Street South, Birmingham, Alabama 35294, United
States
| | - Alan Gunter
- Department of Chemistry, University
of Alabama at Birmingham, 901 14th Street South, Birmingham, Alabama 35294, United
States
| | - Hui-Ting Lee
- Department of Chemistry, University
of Alabama at Birmingham, 901 14th Street South, Birmingham, Alabama 35294, United
States
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2
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Libera V, Fasolato C, Ripanti F, Catalini S, Bertini L, Petrillo C, Schirò G, D'Amico F, Rossi B, Paciaroni A, Comez L. Molecular mechanisms behind BRACO19 and human telomeric G-quadruplex interaction. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2024; 322:124684. [PMID: 38981290 DOI: 10.1016/j.saa.2024.124684] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/18/2024] [Revised: 06/12/2024] [Accepted: 06/18/2024] [Indexed: 07/11/2024]
Abstract
Human telomeres (HTs) can form DNA G-quadruplex (G4), an attractive target for anticancer and antiviral drugs. HT-G4s exhibit inherent structural polymorphism, posing challenges for understanding their specific recognition by ligands. Here, we aim to explore the impact of different topologies within a small segment of the HT (Tel22) on its interaction with BRACO19, a rationally designed G4 ligand with high quadruplex affinity, already employed in in-vivo treatments. Our multi-technique approach is based on the combined use of a set of contactless spectroscopic tools. Circular dichroism and UV resonance Raman spectroscopy probe ligand-induced conformational changes in the G4 sequence, while UV-visible absorption, coupled with steady-state fluorescence spectroscopy, provides further insights into the electronic features of the complex, exploiting the photoresponsive properties of BRACO19. Overall, we find that modifying the topology of the unbound Tel22 through cations (K+ or Na+), serves as a critical determinant for ligand interactions and binding modes, thus influencing the HT-G4's assembly capabilities. Furthermore, we show how fluorescence serves as a valuable probe for recognizing cation-driven multimeric structures, which may be present in living organisms, giving rise to pathological forms.
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Affiliation(s)
- Valeria Libera
- Department of Physics and Geology, University of Perugia, via Alessandro Pascoli, 06123, Perugia, Italy.
| | - Claudia Fasolato
- Institute for Complex System, National Research Council (ISC-CNR), Piazzale Aldo Moro, 5, 00185, Roma, Italy
| | - Francesca Ripanti
- Department of Physics and Geology, University of Perugia, via Alessandro Pascoli, 06123, Perugia, Italy
| | - Sara Catalini
- Department of Physics and Geology, University of Perugia, via Alessandro Pascoli, 06123, Perugia, Italy; European Laboratory for Non-Linear Spectroscopy (LENS), via Nello Carrara 1, 50019, Sesto Fiorentino (FI), Italy; National Research Council-National Institute of Optics (CNR-INO), Largo Fermi 6, 50125, Florence, Italy
| | - Luca Bertini
- Department of Physics and Geology, University of Perugia, via Alessandro Pascoli, 06123, Perugia, Italy
| | - Caterina Petrillo
- Department of Physics and Geology, University of Perugia, via Alessandro Pascoli, 06123, Perugia, Italy
| | - Giorgio Schirò
- Univ. Grenoble Alpes, CEA, CNRS, Institut de Biologie Structurale, F-38044, Grenoble, France
| | - Francesco D'Amico
- Elettra - Sincrotrone Trieste S.C.p.A, s.s. 14 km 163, 500 in Area Science Park, 34149, Trieste, Italy
| | - Barbara Rossi
- Elettra - Sincrotrone Trieste S.C.p.A, s.s. 14 km 163, 500 in Area Science Park, 34149, Trieste, Italy
| | - Alessandro Paciaroni
- Department of Physics and Geology, University of Perugia, via Alessandro Pascoli, 06123, Perugia, Italy
| | - Lucia Comez
- CNR-IOM - Istituto Officina dei Materiali, Via Alessandro Pascoli, 06123, Perugia, Italy.
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3
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Zhao LL, Gu YX, Dong JH, Li XT, Pan HY, Xue CY, Liu Y, Zhou YL, Zhang XX. New G-Triplex DNA Dramatically Activates the Fluorescence of Thioflavin T and Acts as a Turn-On Fluorescent Sensor for Uracil-DNA Glycosylase Activity Detection. Anal Chem 2024; 96:8458-8466. [PMID: 38710075 DOI: 10.1021/acs.analchem.4c00164] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/08/2024]
Abstract
G-triplexes are G-rich oligonucleotides composed of three G-tracts and have absorbed much attention due to their potential biological functions and attractive performance in biosensing. Through the optimization of loop compositions, DNA lengths, and 5'-flanking bases of G-rich sequences, a new stable G-triplex sequence with 14 bases (G3-F15) was discovered to dramatically activate the fluorescence of Thioflavin T (ThT), a water-soluble fluorogenic dye. The fluorescence enhancement of ThT after binding with G3-F15 reached 3200 times, which was the strongest one by far among all of the G-rich sequences. The conformations of G3-F15 and G3-F15/ThT were studied by circular dichroism. The thermal stability measurements indicated that G3-F15 was a highly stable G-triplex structure. The conformations of G3-F15 and G3-F15/ThT in the presence of different metal cations were studied thoroughly by fluorescent spectroscopy, circular dichroism, and nuclear magnetic resonance. Furthermore, using the G3-F15/ThT complex as a fluorescent probe, a robust and simple turn-on fluorescent sensor for uracil-DNA glycosylase activity was developed. This study proposes a new systematic strategy to explore new functional G-rich sequences and their ligands, which will promote their applications in diagnosis, therapy, and biosensing.
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Affiliation(s)
- Ling-Li Zhao
- Beijing National Laboratory for Molecular Sciences (BNLMS), MOE Key Laboratory of Bioorganic Chemistry and Molecular Engineering, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China
- Department of Chemistry, Zhejiang University, Hangzhou 310027, China
| | - Yi-Xuan Gu
- Beijing National Laboratory for Molecular Sciences (BNLMS), MOE Key Laboratory of Bioorganic Chemistry and Molecular Engineering, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China
| | - Jia-Hui Dong
- Beijing National Laboratory for Molecular Sciences (BNLMS), MOE Key Laboratory of Bioorganic Chemistry and Molecular Engineering, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China
| | - Xiao-Tong Li
- Beijing National Laboratory for Molecular Sciences (BNLMS), MOE Key Laboratory of Bioorganic Chemistry and Molecular Engineering, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China
| | - Hui-Yu Pan
- Beijing National Laboratory for Molecular Sciences (BNLMS), MOE Key Laboratory of Bioorganic Chemistry and Molecular Engineering, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China
| | - Chen-Yu Xue
- Key Laboratory of Forensic Toxicology, Ministry of Public Security, Beijing 100191, China
| | - Ying Liu
- Beijing National Laboratory for Molecular Sciences (BNLMS), MOE Key Laboratory of Bioorganic Chemistry and Molecular Engineering, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China
| | - Ying-Lin Zhou
- Beijing National Laboratory for Molecular Sciences (BNLMS), MOE Key Laboratory of Bioorganic Chemistry and Molecular Engineering, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China
| | - Xin-Xiang Zhang
- Beijing National Laboratory for Molecular Sciences (BNLMS), MOE Key Laboratory of Bioorganic Chemistry and Molecular Engineering, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China
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4
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Cervenak M, Molnár OR, Horváth P, Smeller L. Stabilization of G-Quadruplex Structures of the SARS-CoV-2 Genome by TMPyP4, BRACO19, and PhenDC3. Int J Mol Sci 2024; 25:2482. [PMID: 38473730 DOI: 10.3390/ijms25052482] [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: 12/19/2023] [Revised: 02/14/2024] [Accepted: 02/16/2024] [Indexed: 03/14/2024] Open
Abstract
The G-quadruplex is one of the non-canonical structures formed by nucleic acids, which can be formed by guanine-rich sequences. They became the focus of much research when they were found in several oncogene promoter regions and also in the telomeres. Later on, they were discovered in viruses as well. Various ligands have been developed in order to stabilize DNA G-quadruplexes, which were believed to have an anti-cancer or antiviral effect. We investigated three of these ligands, and whether they can also affect the stability of the G-quadruplex-forming sequences of the RNA genome of SARS-CoV-2. All three investigated oligonucleotides showed the G-quadruplex form. We characterized their stability and measured their thermodynamic parameters using the Förster resonance energy transfer method. The addition of the ligands caused an increase in the unfolding temperature, but this effect was smaller compared to that found earlier in the case of G-quadruplexes of the hepatitis B virus, which has a DNA genome.
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Affiliation(s)
- Miklós Cervenak
- Department of Biophysics and Radiation Biology, Semmelweis University, 1094 Budapest, Hungary
| | - Orsolya Réka Molnár
- Department of Biophysics and Radiation Biology, Semmelweis University, 1094 Budapest, Hungary
| | - Péter Horváth
- Department of Pharmaceutical Chemistry, Semmelweis University, 1092 Budapest, Hungary
| | - László Smeller
- Department of Biophysics and Radiation Biology, Semmelweis University, 1094 Budapest, Hungary
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5
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Lorenzatti A, Piga EJ, Gismondi M, Binolfi A, Margarit E, Calcaterra N, Armas P. Genetic variations in G-quadruplex forming sequences affect the transcription of human disease-related genes. Nucleic Acids Res 2023; 51:12124-12139. [PMID: 37930868 PMCID: PMC10711447 DOI: 10.1093/nar/gkad948] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2022] [Revised: 09/22/2023] [Accepted: 10/12/2023] [Indexed: 11/08/2023] Open
Abstract
Guanine-rich DNA strands can fold into non-canonical four-stranded secondary structures named G-quadruplexes (G4s). G4s folded in proximal promoter regions (PPR) are associated either with positive or negative transcriptional regulation. Given that single nucleotide variants (SNVs) affecting G4 folding (G4-Vars) may alter gene transcription, and that SNVs are associated with the human diseases' onset, we undertook a novel comprehensive study of the G4-Vars genome-wide (G4-variome) to find disease-associated G4-Vars located into PPRs. We developed a bioinformatics strategy to find disease-related SNVs located into PPRs simultaneously overlapping with putative G4-forming sequences (PQSs). We studied five G4-Vars disturbing in vitro the folding and stability of the G4s located into PPRs, which had been formerly associated with sporadic Alzheimer's disease (GRIN2B), a severe familiar coagulopathy (F7), atopic dermatitis (CSF2), myocardial infarction (SIRT1) and deafness (LHFPL5). Results obtained in cultured cells for these five G4-Vars suggest that the changes in the G4s affect the transcription, potentially contributing to the development of the mentioned diseases. Collectively, data reinforce the general idea that G4-Vars may impact on the different susceptibilities to human genetic diseases' onset, and could be novel targets for diagnosis and drug design in precision medicine.
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Affiliation(s)
- Agustín Lorenzatti
- Instituto de Biología Molecular y Celular de Rosario (IBR), Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET) - Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario (UNR), Ocampo y Esmeralda, Rosario S2000EZP, Santa Fe, Argentina
| | - Ernesto J Piga
- Instituto de Biología Molecular y Celular de Rosario (IBR), Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET) - Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario (UNR), Ocampo y Esmeralda, Rosario S2000EZP, Santa Fe, Argentina
| | - Mauro Gismondi
- Centro de Estudios Fotosintéticos y Bioquímicos (CEFOBI), Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET) - Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario (UNR), Suipacha 531, Rosario, Santa Fe, Argentina
| | - Andrés Binolfi
- Instituto de Biología Molecular y Celular de Rosario (IBR), Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET) - Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario (UNR), Ocampo y Esmeralda, Rosario S2000EZP, Santa Fe, Argentina
- Plataforma Argentina de Biología Estructural y Metabolómica (PLABEM), Ocampo y Esmeralda, Rosario S200EZP, Santa Fe, Argentina
| | - Ezequiel Margarit
- Centro de Estudios Fotosintéticos y Bioquímicos (CEFOBI), Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET) - Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario (UNR), Suipacha 531, Rosario, Santa Fe, Argentina
| | - Nora B Calcaterra
- Instituto de Biología Molecular y Celular de Rosario (IBR), Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET) - Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario (UNR), Ocampo y Esmeralda, Rosario S2000EZP, Santa Fe, Argentina
| | - Pablo Armas
- Instituto de Biología Molecular y Celular de Rosario (IBR), Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET) - Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario (UNR), Ocampo y Esmeralda, Rosario S2000EZP, Santa Fe, Argentina
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6
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Pandey A, Roy S, Srivatsan SG. Probing the Competition between Duplex, G-Quadruplex and i-Motif Structures of the Oncogenic c-Myc DNA Promoter Region. Chem Asian J 2023; 18:e202300510. [PMID: 37541298 DOI: 10.1002/asia.202300510] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2023] [Revised: 07/09/2023] [Indexed: 08/06/2023]
Abstract
Development of probe systems that provide unique spectral signatures for duplex, G-quadruplex (GQ) and i-motif (iM) structures is very important to understand the relative propensity of a G-rich-C-rich promoter region to form these structures. Here, we devise a platform using a combination of two environment-sensitive nucleoside analogs namely, 5-fluorobenzofuran-modified 2'-deoxyuridine (FBF-dU) and 5-fluoro-2'-deoxyuridine (F-dU) to study the structures adopted by a promoter region of the c-Myc oncogene. FBF-dU serves as a dual-purpose probe containing a fluorescent and 19 F NMR label. When incorporated into the C-rich sequence, it reports the formation of different iMs via changes in its fluorescence properties and 19 F signal. F-dU incorporated into the G-rich ON reports the formation of a GQ structure whose 19 F signal is clearly different from the signals obtained for iMs. Rewardingly, the labeled ONs when mixed with respective complementary strands allows us to determine the relative population of different structures formed by the c-Myc promoter by the virtue of the probe's ability to produce distinct and resolved 19 F signatures for different structures. Our results indicate that at physiological pH and temperature the c-Myc promoter forms duplex, random coil and GQ structures, and does not form an iM. Whereas at acidic pH, the mixture largely forms iM and GQ structures. Taken together, our system will complement existing tools and provide unprecedented insights on the population equilibrium and dynamics of nucleic acid structures under different conditions.
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Affiliation(s)
- Akanksha Pandey
- Department of Chemistry, Indian Institute of Science Education and Research (IISER), Pune, Dr. Homi Bhabha Road, Pune, 411008, India
| | - Sarupa Roy
- Department of Chemistry, Indian Institute of Science Education and Research (IISER), Pune, Dr. Homi Bhabha Road, Pune, 411008, India
| | - Seergazhi G Srivatsan
- Department of Chemistry, Indian Institute of Science Education and Research (IISER), Pune, Dr. Homi Bhabha Road, Pune, 411008, India
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7
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Gao P, Yao F, Pang J, Yin K, Zhu X. m 6A methylation in cellular senescence of age-associated diseases. Acta Biochim Biophys Sin (Shanghai) 2023; 55:1168-1183. [PMID: 37394885 PMCID: PMC10449638 DOI: 10.3724/abbs.2023107] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2023] [Accepted: 04/14/2023] [Indexed: 07/04/2023] Open
Abstract
Cellular senescence is a state of irreversible cellular growth arrest that occurs in response to various stresses. In addition to exiting the cell cycle, senescent cells undergo many phenotypic alterations, including metabolic reprogramming, chromatin rearrangement, and senescence-associated secretory phenotype (SASP) development. Furthermore, senescent cells can affect most physiological and pathological processes, such as physiological development; tissue homeostasis; tumour regression; and age-associated disease progression, including diabetes, atherosclerosis, Alzheimer's disease, and hypertension. Although corresponding anti-senescence therapies are actively being explored for the treatment of age-associated diseases, the specific regulatory mechanisms of senescence remain unclear. N 6-methyladenosine (m 6A), a chemical modification commonly distributed in eukaryotic RNA, plays an important role in biological processes such as translation, shearing, and RNA transcription. Numerous studies have shown that m 6A plays an important regulatory role in cellular senescence and aging-related disease. In this review, we systematically summarize the role of m 6A modifications in cellular senescence with regard to oxidative stress, DNA damage, telomere alterations, and SASP development. Additionally, diabetes, atherosclerosis, and Alzheimer's disease regulation via m 6A-mediated cellular senescence is discussed. We further discuss the challenges and prospects of m 6A in cellular senescence and age-associated diseases with the aim of providing rational strategies for the treatment of these age-associated diseases.
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Affiliation(s)
- Pan Gao
- Guangxi Key Laboratory of Diabetic Systems MedicineGuilin Medical UniversityGuilin541100China
| | - Feng Yao
- Guangxi Key Laboratory of Diabetic Systems MedicineGuilin Medical UniversityGuilin541100China
| | - Jin Pang
- Guangxi Key Laboratory of Diabetic Systems MedicineGuilin Medical UniversityGuilin541100China
| | - Kai Yin
- The Fifth Affiliated Hospital of Southern Medical UniversityGuangzhou510900China
| | - Xiao Zhu
- Guangxi Key Laboratory of Diabetic Systems MedicineGuilin Medical UniversityGuilin541100China
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8
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Khatik SY, Sudhakar S, Mishra S, Kalia J, Pradeepkumar PI, Srivatsan SG. Probing juxtaposed G-quadruplex and hairpin motifs using a responsive nucleoside probe: a unique scaffold for chemotherapy. Chem Sci 2023; 14:5627-5637. [PMID: 37265741 PMCID: PMC10231310 DOI: 10.1039/d3sc00519d] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2023] [Accepted: 04/30/2023] [Indexed: 06/03/2023] Open
Abstract
Paucity of efficient probes and small molecule ligands that can distinguish different G-quadruplex (GQ) topologies poses challenges not only in understanding their basic structure but also in targeting an individual GQ form from others. Alternatively, G-rich sequences that harbour unique chimeric structural motifs (e.g., GQ-duplex or GQ-hairpin junctions) are perceived as new therapeutic hotspots. In this context, the epidermal growth factor receptor (EGFR) gene, implicated in many cancers, contains a 30 nucleotide G-rich segment in the promoter region, which adopts in vitro two unique architectures each composed of a GQ topology (parallel and hybrid-type) juxtaposed with a hairpin domain. Here, we report the use of a novel dual-app probe, C5-trifluoromethyl benzofuran-modified 2'-deoxyuridine (TFBF-dU), in the systematic analysis of EGFR GQs and their interaction with small molecules by fluorescence and 19F NMR techniques. Notably, distinct fluorescence and 19F NMR signals exhibited by the probe enabled the quantification of the relative population of random, parallel and hybrid-type GQ structures under different conditions, which could not be obtained by conventional CD and 1H NMR techniques. Using the fluorescence component, we quantified ligand binding properties of GQs, whereas the 19F label enabled the assessment of ligand-induced changes in GQ dynamics. Studies also revealed that mutations in the hairpin domain affected GQ formation and stability, which was further functionally verified in polymerase stop assay. We anticipate that these findings and useful properties of the nucleoside probe could be utilized in designing and evaluating binders that jointly target both GQ and hairpin domains for enhanced selectivity and druggability.
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Affiliation(s)
- Saddam Y Khatik
- Department of Chemistry, Indian Institute of Science Education and Research (IISER) Pune, Dr Homi Bhabha Road Pune 411008 India
| | - Sruthi Sudhakar
- Department of Chemistry, Indian Institute of Technology Bombay Mumbai 400076 India
| | - Satyajit Mishra
- Department of Biological Sciences, Indian Institute of Science Education and Research (IISER) Bhopal Bhopal Bypass Road, Bhauri Bhopal 462066 India
| | - Jeet Kalia
- Department of Biological Sciences, Indian Institute of Science Education and Research (IISER) Bhopal Bhopal Bypass Road, Bhauri Bhopal 462066 India
- Department of Chemistry, Indian Institute of Science Education and Research (IISER) Bhopal Bhopal Bypass Road, Bhauri Bhopal 462066 India
| | - P I Pradeepkumar
- Department of Chemistry, Indian Institute of Technology Bombay Mumbai 400076 India
| | - Seergazhi G Srivatsan
- Department of Chemistry, Indian Institute of Science Education and Research (IISER) Pune, Dr Homi Bhabha Road Pune 411008 India
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9
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Libera V, Ripanti F, Petrillo C, Sacchetti F, Ramos-Soriano J, Galan MC, Schirò G, Paciaroni A, Comez L. Stability of Human Telomeric G-Quadruplexes Complexed with Photosensitive Ligands and Irradiated with Visible Light. Int J Mol Sci 2023; 24:ijms24109090. [PMID: 37240437 DOI: 10.3390/ijms24109090] [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: 04/26/2023] [Revised: 05/16/2023] [Accepted: 05/19/2023] [Indexed: 05/28/2023] Open
Abstract
Guanine-rich DNA sequences can fold into non-canonical nucleic acid structures called G-quadruplexes (G4s). These nanostructures have strong implications in many fields, from medical science to bottom-up nanotechnologies. As a result, ligands interacting with G4s have attracted great attention as candidates in medical therapies, molecular probe applications, and biosensing. In recent years, the use of G4-ligand complexes as photopharmacological targets has shown significant promise for developing novel therapeutic strategies and nanodevices. Here, we studied the possibility of manipulating the secondary structure of a human telomeric G4 sequence through the interaction with two photosensitive ligands, DTE and TMPyP4, whose response to visible light is different. The effect of these two ligands on G4 thermal unfolding was also considered, revealing the occurrence of peculiar multi-step melting pathways and the different attitudes of the two molecules on the quadruplex stabilization.
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Affiliation(s)
- Valeria Libera
- Department of Physics and Geology, University of Perugia, Via Alessandro Pascoli, 06123 Perugia, Italy
- Istituto Officina dei Materiali-IOM, National Research Council-CNR, Via Alessandro Pascoli, 06123 Perugia, Italy
| | - Francesca Ripanti
- Department of Physics and Geology, University of Perugia, Via Alessandro Pascoli, 06123 Perugia, Italy
| | - Caterina Petrillo
- Department of Physics and Geology, University of Perugia, Via Alessandro Pascoli, 06123 Perugia, Italy
| | - Francesco Sacchetti
- Department of Physics and Geology, University of Perugia, Via Alessandro Pascoli, 06123 Perugia, Italy
| | - Javier Ramos-Soriano
- School of Chemistry, University of Bristol, Cantock's Close, Bristol BS8 1TS, UK
| | - Maria Carmen Galan
- School of Chemistry, University of Bristol, Cantock's Close, Bristol BS8 1TS, UK
| | - Giorgio Schirò
- CNRS, CEA, IBS, c/o University Grenoble Alpes, 38400 Grenoble, France
| | - Alessandro Paciaroni
- Department of Physics and Geology, University of Perugia, Via Alessandro Pascoli, 06123 Perugia, Italy
| | - Lucia Comez
- Istituto Officina dei Materiali-IOM, National Research Council-CNR, Via Alessandro Pascoli, 06123 Perugia, Italy
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10
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Song YQ, Li GD, Niu D, Chen F, Jing S, Wai Wong VK, Wang W, Leung CH. A robust luminescent assay for screening alkyladenine DNA glycosylase inhibitors to overcome DNA repair and temozolomide drug resistance. J Pharm Anal 2023; 13:514-522. [PMID: 37305785 PMCID: PMC10257196 DOI: 10.1016/j.jpha.2023.04.010] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2023] [Revised: 03/22/2023] [Accepted: 04/15/2023] [Indexed: 06/13/2023] Open
Abstract
Temozolomide (TMZ) is an anticancer agent used to treat glioblastoma, typically following radiation therapy and/or surgical resection. However, despite its effectiveness, at least 50% of patients do not respond to TMZ, which is associated with repair and/or tolerance of TMZ-induced DNA lesions. Studies have demonstrated that alkyladenine DNA glycosylase (AAG), an enzyme that triggers the base excision repair (BER) pathway by excising TMZ-induced N3-methyladenine (3meA) and N7-methylguanine lesions, is overexpressed in glioblastoma tissues compared to normal tissues. Therefore, it is essential to develop a rapid and efficient screening method for AAG inhibitors to overcome TMZ resistance in glioblastomas. Herein, we report a robust time-resolved photoluminescence platform for identifying AAG inhibitors with improved sensitivity compared to conventional steady-state spectroscopic methods. As a proof-of-concept, this assay was used to screen 1440 food and drug administration-approved drugs against AAG, resulting in the repurposing of sunitinib as a potential AAG inhibitor. Sunitinib restored glioblastoma (GBM) cancer cell sensitivity to TMZ, inhibited GBM cell proliferation and stem cell characteristics, and induced GBM cell cycle arrest. Overall, this strategy offers a new method for the rapid identification of small-molecule inhibitors of BER enzyme activities that can prevent false negatives due to a fluorescent background.
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Affiliation(s)
- Ying-Qi Song
- State Key Laboratory of Quality Research in Chinese Medicine, Institute of Chinese Medical Sciences, University of Macau, Macao, 999078, China
| | - Guo-Dong Li
- State Key Laboratory of Quality Research in Chinese Medicine, Institute of Chinese Medical Sciences, University of Macau, Macao, 999078, China
| | - Dou Niu
- State Key Laboratory of Quality Research in Chinese Medicine, Institute of Chinese Medical Sciences, University of Macau, Macao, 999078, China
| | - Feng Chen
- State Key Laboratory of Quality Research in Chinese Medicine, Institute of Chinese Medical Sciences, University of Macau, Macao, 999078, China
| | - Shaozhen Jing
- Institute of Medical Research, Northwestern Polytechnical University, Xi'an, 710072, China
| | - Vincent Kam Wai Wong
- Dr. Neher's Biophysics Laboratory for Innovative Drug Discovery, State Key Laboratory of Quality Research in Chinese Medicine, Macau University of Science and Technology, Macao, 999078, China
| | - Wanhe Wang
- Institute of Medical Research, Northwestern Polytechnical University, Xi'an, 710072, China
| | - Chung-Hang Leung
- State Key Laboratory of Quality Research in Chinese Medicine, Institute of Chinese Medical Sciences, University of Macau, Macao, 999078, China
- Department of Biomedical Sciences, Faculty of Health Sciences, University of Macau, Macao, 999078, China
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11
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Oprzeska-Zingrebe EA, Smiatek J. Basket-type G-quadruplex with two tetrads in the presence of TMAO and urea: A molecular dynamics study. J Mol Struct 2023. [DOI: 10.1016/j.molstruc.2022.134375] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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12
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Salem AA, El Haty IA, Ghattas MA. GW-2974 and SCH-442416 modulators of tyrosine kinase and adenosine receptors can also stabilize human telomeric G-quadruplex DNA. PLoS One 2022; 17:e0277963. [PMID: 36476719 PMCID: PMC9728906 DOI: 10.1371/journal.pone.0277963] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2022] [Accepted: 11/08/2022] [Indexed: 12/13/2022] Open
Abstract
GW-2974 is a potent tyrosine kinase receptor inhibitor while SCH-442416 is a potent adenosine receptors' antagonist with high selectivity towards human adenosine A2A receptor over other adenosine receptors. The two compounds were reported to possess anti-cancer properties. This study aimed to investigate whether stabilization of human telomeric G-quadruplex DNA by GW-2974- and SCH-442416 is a plausible fundamental mechanism underlying their anti-cancer effects. Human telomeric G-quadruplex DNA with sequence AG3(TTAGGG)3 was used. The study used ultraviolet-visible (UV-Vis), fluorescence, fluorescence quenching, circular dichroism (CD), melting temperatures (Tm) and molecular docking techniques to evaluate interactions. The results showed that GW-2974 and SCH-442416 interacted with G-quadruplex DNA through intercalation binding into two types of dependent binding sites. Binding affinities of 1.3 × 108-1.72 × 106 M-1 and 1.55 × 107-3.74 × 105 M-1 were obtained for GW-2974 and SCH-442416, respectively. An average number of binding sites between 1 and 2 was obtained. Additionally, the melting temperature curves indicated that complexation of both compounds to G-quadruplex DNA provided more stability (ΔTm = 9.9°C and 9.6°C, respectively) compared to non-complexed G-quadruplex DNA. Increasing the molar ratios over 1:1 (drug:G-quadruplex) showed less stabilization effect on DNA. Furthermore, GW-2974 and SCH-442516 have proven ≥ 4.0 folds better selective towards G-quadruplex over double-stranded ct-DNA. In silico molecular docking and dynamics revealed favorable exothermic binding for the two compounds into two sites of parallel and hybrid G-quadruplex DNA structures. The results supported the hypothesis that GW-2974 and SCH-442416 firmly stabilize human telomeric G-quadruplex DNA in additions to modulating tyrosine kinase and adenosine receptors. Consequently, stabilizing G-quadruplex DNA could be a mechanism underlying their anti-cancer activity.
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Affiliation(s)
- Alaa A. Salem
- Department of Chemistry, College of science, United Arab Emirates University, Al Ain, United Arab Emirates
- * E-mail:
| | - Ismail A. El Haty
- Department of Chemistry, College of science, United Arab Emirates University, Al Ain, United Arab Emirates
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13
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Falanga AP, Terracciano M, Oliviero G, Roviello GN, Borbone N. Exploring the Relationship between G-Quadruplex Nucleic Acids and Plants: From Plant G-Quadruplex Function to Phytochemical G4 Ligands with Pharmaceutic Potential. Pharmaceutics 2022; 14:2377. [PMID: 36365194 PMCID: PMC9698481 DOI: 10.3390/pharmaceutics14112377] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2022] [Revised: 10/19/2022] [Accepted: 11/01/2022] [Indexed: 10/31/2023] Open
Abstract
G-quadruplex (G4) oligonucleotides are higher-order DNA and RNA secondary structures of enormous relevance due to their implication in several biological processes and pathological states in different organisms. Strategies aiming at modulating human G4 structures and their interrelated functions are first-line approaches in modern research aiming at finding new potential anticancer treatments or G4-based aptamers for various biomedical and biotechnological applications. Plants offer a cornucopia of phytocompounds that, in many cases, are effective in binding and modulating the thermal stability of G4s and, on the other hand, contain almost unexplored G4 motifs in their genome that could inspire new biotechnological strategies. Herein, we describe some G4 structures found in plants, summarizing the existing knowledge of their functions and biological role. Moreover, we review some of the most promising G4 ligands isolated from vegetal sources and report on the known relationships between such phytochemicals and G4-mediated biological processes that make them potential leads in the pharmaceutical sector.
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Affiliation(s)
- Andrea P. Falanga
- Department of Pharmacy, University of Naples Federico II, Via Domenico Montesano 49, 80131 Naples, Italy
| | - Monica Terracciano
- Department of Pharmacy, University of Naples Federico II, Via Domenico Montesano 49, 80131 Naples, Italy
| | - Giorgia Oliviero
- Department of Molecular Medicine and Medical Biotechnologies, Via Sergio Pansini 5, 80131 Naples, Italy
| | - Giovanni N. Roviello
- Institute of Biostructures and Bioimaging, Italian National Council for Research (IBB-CNR), Area di Ricerca site and Headquarters, Via Pietro Castellino 111, 80131 Naples, Italy
| | - Nicola Borbone
- Department of Pharmacy, University of Naples Federico II, Via Domenico Montesano 49, 80131 Naples, Italy
- Institute of Applied Sciences and Intelligent Systems, Italian National Council of Research (ISASI-CNR), Via Pietro Castellino 111, 80131 Napoli, Italy
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14
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Simisi Clovis N, Alam P, Kumar Chand A, Sardana D, Firoz Khan M, Sen S. Molecular Crowders Modulate Ligand Binding Affinity to G-Quadruplex DNA by Decelerating Ligand Association. J Photochem Photobiol A Chem 2022. [DOI: 10.1016/j.jphotochem.2022.114432] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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15
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Olejko L, Dutta A, Shahsavar K, Bald I. Influence of Different Salts on the G-Quadruplex Structure Formed from the Reversed Human Telomeric DNA Sequence. Int J Mol Sci 2022; 23:ijms232012206. [PMID: 36293060 PMCID: PMC9602856 DOI: 10.3390/ijms232012206] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2022] [Revised: 10/07/2022] [Accepted: 10/09/2022] [Indexed: 11/16/2022] Open
Abstract
G-rich telomeric DNA plays a major role in the stabilization of chromosomes and can fold into a plethora of different G-quadruplex structures in the presence of mono- and divalent cations. The reversed human telomeric DNA sequence (5′-(GGG ATT)4; RevHumTel) was previously shown to have interesting properties that can be exploited for chemical sensing and as a chemical switch in DNA nanotechnology. Here, we analyze the specific G-quadruplex structures formed by RevHumTel in the presence of K+, Na+, Mg2+ and Ca2+ cations using circular dichroism spectroscopy (CDS) and Förster resonance energy transfer (FRET) based on fluorescence lifetimes. CDS is able to reveal strand and loop orientations, whereas FRET gives information about the distances between the 5′-end and the 3′-end, and also, the number of G-quadruplex species formed. Based on this combined information we derived specific G-quadruplex structures formed from RevHumTel, i.e., a chair-type and a hybrid-type G-quadruplex structure formed in presence of K+, whereas Na+ induces the formation of up to three different G-quadruplexes (a basket-type, a propeller-type and a hybrid-type structure). In the presence of Mg2+ and Ca2+ two different parallel G-quadruplexes are formed (one of which is a propeller-type structure). This study will support the fundamental understanding of the G-quadruplex formation in different environments and a rational design of G-quadruplex-based applications in sensing and nanotechnology.
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16
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Economos NG, Thapar U, Balasubramanian N, Karras GI, Glazer PM. An ELISA-based platform for rapid identification of structure-dependent nucleic acid-protein interactions detects novel DNA triplex interactors. J Biol Chem 2022; 298:102398. [PMID: 35988651 PMCID: PMC9493393 DOI: 10.1016/j.jbc.2022.102398] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2022] [Revised: 08/11/2022] [Accepted: 08/13/2022] [Indexed: 11/21/2022] Open
Abstract
Unusual nucleic acid structures play vital roles as intermediates in many cellular processes and, in the case of peptide nucleic acid (PNA)–mediated triplexes, are leveraged as tools for therapeutic gene editing. However, due to their transient nature, an understanding of the factors that interact with and process dynamic nucleic acid structures remains limited. Here, we developed snapELISA (structure-specific nucleic acid-binding protein ELISA), a rapid high-throughput platform to interrogate and compare up to 2688 parallel nucleic acid structure–protein interactions in vitro. We applied this system to both triplex-forming oligonucleotide–induced DNA triplexes and DNA-bound PNA heterotriplexes to describe the identification of previously known and novel interactors for both structures. For PNA heterotriplex recognition analyses, snapELISA identified factors implicated in nucleotide excision repair (XPA, XPC), single-strand annealing repair (RAD52), and recombination intermediate structure binding (TOP3A, BLM, MUS81). We went on to validate selected factor localization to genome-targeted PNA structures within clinically relevant loci in human cells. Surprisingly, these results demonstrated XRCC5 localization to PNA triplex-forming sites in the genome, suggesting the presence of a double-strand break intermediate. These results describe a powerful comparative approach for identifying structure-specific nucleic acid interactions and expand our understanding of the mechanisms of triplex structure recognition and repair.
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Affiliation(s)
- Nicholas G Economos
- Department of Therapeutic Radiology, Yale University School of Medicine, New Haven, CT; Department of Genetics, Yale University School of Medicine, New Haven, CT
| | - Upasna Thapar
- Department of Genetics, The University of Texas MD Anderson Cancer Center, Houston, TX
| | - Nanda Balasubramanian
- Department of Therapeutic Radiology, Yale University School of Medicine, New Haven, CT
| | - Georgios I Karras
- Department of Genetics, The University of Texas MD Anderson Cancer Center, Houston, TX; Genetics and Epigenetics Graduate Program, The University of Texas MD Anderson Cancer Center UTHealth Houston Graduate School of Biomedical Sciences, Houston, TX.
| | - Peter M Glazer
- Department of Therapeutic Radiology, Yale University School of Medicine, New Haven, CT; Department of Genetics, Yale University School of Medicine, New Haven, CT.
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17
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Khatik SY, Srivatsan SG. Environment-Sensitive Nucleoside Probe Unravels the Complex Structural Dynamics of i-Motif DNAs. Bioconjug Chem 2022; 33:1515-1526. [PMID: 35819865 DOI: 10.1021/acs.bioconjchem.2c00237] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Although evidence for the existence and biological role of i-motif (iM) DNA structures in cells is emerging, probing their structural polymorphism and identifying physiologically active conformations using currently available tools remain a major challenge. Here, we describe the development of an innovative device to investigate the conformation equilibrium of different iMs formed by C-rich telomeric repeat and oncogenic B-raf promoter sequences using a new conformation-sensitive dual-purpose nucleoside probe. The nucleoside is composed of a trifluoromethyl-benzofuran-2-yl moiety at the C5 position of 2'-deoxyuridine, which functions as a responsive fluorescent and 19F NMR probe. While the fluorescent component is useful in monitoring and estimating the folding process, the 19F label provides spectral signatures for various iMs, thereby enabling a systematic analysis of their complex population equilibrium under different conditions (e.g., pH, temperature, metal ions, and cell lysate). Distinct 19F signals exhibited by the iMs formed by the human telomeric repeat helped in calculating their relative population. A battery of fluorescence and 19F NMR studies using native and mutated B-raf oligonucleotides gave valuable insights into the iM structure landscape and its dependence on environmental conditions and also helped in predicting the structure of the major iM conformation. Overall, our findings indicate that the probe is highly suitable for studying complex nucleic acid systems.
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Affiliation(s)
- Saddam Y Khatik
- Department of Chemistry, Indian Institute of Science Education and Research (IISER), Pune, Dr. Homi Bhabha Road, Pune 411008, India
| | - Seergazhi G Srivatsan
- Department of Chemistry, Indian Institute of Science Education and Research (IISER), Pune, Dr. Homi Bhabha Road, Pune 411008, India
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18
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Paul T, Opresko PL, Ha T, Myong S. Vectorial folding of telomere overhang promotes higher accessibility. Nucleic Acids Res 2022; 50:6271-6283. [PMID: 35687089 PMCID: PMC9226509 DOI: 10.1093/nar/gkac401] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2022] [Revised: 04/20/2022] [Accepted: 06/08/2022] [Indexed: 11/13/2022] Open
Abstract
Human telomere overhang composed of tandem repeats of TTAGGG folds into G-quadruplex (G4). Unlike in an experimental setting in the test tube in which the entire length is allowed to fold at once, inside the cell, the overhang is expected to fold as it is synthesized directionally (5' to 3') and released segmentally by a specialized enzyme, the telomerase. To mimic such vectorial G4 folding process, we employed a superhelicase, Rep-X which can unwind DNA to release the TTAGGG repeats in 5' to 3' direction. We demonstrate that the folded conformation achieved by the refolding of full sequence is significantly different from that of the vectorial folding for two to eight TTAGGG repeats. Strikingly, the vectorially folded state leads to a remarkably higher accessibility to complementary C-rich strand and the telomere binding protein POT1, reflecting a less stably folded state resulting from the vectorial folding. Importantly, our study points to an inherent difference between the co-polymerizing and post-polymerized folding of telomere overhang that can impact telomere architecture and downstream processes.
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Affiliation(s)
- Tapas Paul
- Department of Biophysics, Johns Hopkins University, Baltimore, MD21218, USA
| | - Patricia L Opresko
- Department of Environmental and Occupational Health, University of Pittsburgh Graduate School of Public Health, and UPMC Hillman Cancer Center, Pittsburgh, PA15213, USA
| | - Taekjip Ha
- Department of Biophysics, Johns Hopkins University, Baltimore, MD21218, USA.,Physics Frontier Center (Center for Physics of Living Cells), University of Illinois, 1110 W. Green St., Urbana, IL 61801, USA.,Howard Hughes Medical Institute, Johns Hopkins University, Baltimore, MD, USA
| | - Sua Myong
- Department of Biophysics, Johns Hopkins University, Baltimore, MD21218, USA.,Physics Frontier Center (Center for Physics of Living Cells), University of Illinois, 1110 W. Green St., Urbana, IL 61801, USA
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19
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Libera V, Bianchi F, Rossi B, D’Amico F, Masciovecchio C, Petrillo C, Sacchetti F, Paciaroni A, Comez L. Solvent Vibrations as a Proxy of the Telomere G-Quadruplex Rearrangements across Thermal Unfolding. Int J Mol Sci 2022; 23:ijms23095123. [PMID: 35563512 PMCID: PMC9100830 DOI: 10.3390/ijms23095123] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2022] [Revised: 04/26/2022] [Accepted: 04/29/2022] [Indexed: 11/16/2022] Open
Abstract
G-quadruplexes (G4s) are noncanonical forms of DNA involved in many key genome functions. Here, we exploited UV Resonance Raman scattering to simultaneously explore the vibrational behavior of a human telomeric G4 (Tel22) and its aqueous solvent as the biomolecule underwent thermal melting. We found that the OH stretching band, related to the local hydrogen-bonded network of a water molecule, was in strict relation with the vibrational features of the G4 structure as a function of temperature. In particular, the modifications to the tetrahedral ordering of the water network were strongly coupled to the DNA rearrangements, showing changes in temperature that mirrored the multi-step melting process of Tel22. The comparison between circular dichroism and Raman results supported this view. The present findings provide novel insights into the impact of the molecular environment on G4 conformation. Improving current knowledge on the solvent structural properties will also contribute to a better understanding of the role played by water arrangement in the complexation of G4s with ligands.
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Affiliation(s)
- Valeria Libera
- Dipartimento di Fisica e Geologia, Università degli Studi di Perugia, 06123 Perugia, Italy; (V.L.); (F.B.); (C.P.); (F.S.)
- IOM-CNR c/o Department of Physics and Geology, Università degli Studi di Perugia, 06123 Perugia, Italy
| | - Federico Bianchi
- Dipartimento di Fisica e Geologia, Università degli Studi di Perugia, 06123 Perugia, Italy; (V.L.); (F.B.); (C.P.); (F.S.)
| | - Barbara Rossi
- Elettra Sincrotrone Trieste, S.S. 14 Km 163.5, 34012 Trieste, Italy; (B.R.); (F.D.); (C.M.)
| | - Francesco D’Amico
- Elettra Sincrotrone Trieste, S.S. 14 Km 163.5, 34012 Trieste, Italy; (B.R.); (F.D.); (C.M.)
| | - Claudio Masciovecchio
- Elettra Sincrotrone Trieste, S.S. 14 Km 163.5, 34012 Trieste, Italy; (B.R.); (F.D.); (C.M.)
| | - Caterina Petrillo
- Dipartimento di Fisica e Geologia, Università degli Studi di Perugia, 06123 Perugia, Italy; (V.L.); (F.B.); (C.P.); (F.S.)
| | - Francesco Sacchetti
- Dipartimento di Fisica e Geologia, Università degli Studi di Perugia, 06123 Perugia, Italy; (V.L.); (F.B.); (C.P.); (F.S.)
| | - Alessandro Paciaroni
- Dipartimento di Fisica e Geologia, Università degli Studi di Perugia, 06123 Perugia, Italy; (V.L.); (F.B.); (C.P.); (F.S.)
- Correspondence: (A.P.); (L.C.)
| | - Lucia Comez
- IOM-CNR c/o Department of Physics and Geology, Università degli Studi di Perugia, 06123 Perugia, Italy
- Correspondence: (A.P.); (L.C.)
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20
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Yadav K, Sardana D, Shweta H, Clovis NS, Sen S. Molecular Picture of the Effect of Cosolvent Crowding on Ligand Binding and Dispersed Solvation Dynamics in G-Quadruplex DNA. J Phys Chem B 2022; 126:1668-1681. [PMID: 35170968 DOI: 10.1021/acs.jpcb.1c09349] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Understanding molecular interactions and dynamics of proteins and DNA in a cell-like crowded environment is crucial for predicting their functions within the cell. Noncanonical G-quadruplex DNA (GqDNA) structures adopt various topologies that were shown to be strongly affected by molecular crowding. However, it is unknown how such crowding affects the solvation dynamics in GqDNA. Here, we study the effect of cosolvent (acetonitrile) crowding on ligand (DAPI) solvation dynamics within human telomeric antiparallel GqDNA through direct comparison of time-resolved fluorescence Stokes shift (TRFSS) experiments and molecular dynamics (MD) simulations results. We show that ligand binding affinity to GqDNA is drastically affected by acetonitrile (ACN). Solvation dynamics probed by DAPI in GqDNA groove show dispersed dynamics from ∼100 fs to 10 ns in the absence and presence of 20% and 40% (v/v) ACN. The nature of dynamics remain similar in buffer and 20% ACN, although in 40% ACN, distinct dynamics is observed in <100 ps. MD simulations performed on GqDNA/DAPI complex reveal preferential solvation of ligand by ACN, particularly in 40% ACN. Simulated solvation time-correlation functions calculated from MD trajectories compare very well to the overall solvation dynamics of DAPI in GqDNA, observed in experiments. Linear response decomposition of simulated solvation correlation functions unfolds the origin of dispersed dynamics, showing that the slower dynamics is dominated by DNA-motion in the presence of ACN (and also by the ACN dynamics at higher concentration). However, water-DNA coupled motion controls the slow dynamics in the absence of ACN. Our data, thus, unravel a detailed molecular picture showing that though ACN crowding affect ligand binding affinity to GqDNA significantly, the overall dispersed solvation dynamics in GqDNA remain similar in the absence and the presence of 20% ACN, albeit with a small effect on the dynamics in the presence of 40% ACN due to preferential solvation of ligand by ACN.
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Affiliation(s)
- Kavita Yadav
- Spectroscopy Laboratory, School of Physical Sciences, Jawaharlal Nehru University, New Delhi 110067, India
| | - Deepika Sardana
- Spectroscopy Laboratory, School of Physical Sciences, Jawaharlal Nehru University, New Delhi 110067, India
| | - Him Shweta
- Spectroscopy Laboratory, School of Physical Sciences, Jawaharlal Nehru University, New Delhi 110067, India
| | - Ndege Simisi Clovis
- Spectroscopy Laboratory, School of Physical Sciences, Jawaharlal Nehru University, New Delhi 110067, India
| | - Sobhan Sen
- Spectroscopy Laboratory, School of Physical Sciences, Jawaharlal Nehru University, New Delhi 110067, India
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21
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Debbarma S, Acharya PC. Targeting G-Quadruplex Dna For Cancer Chemotherapy. Curr Drug Discov Technol 2022; 19:e140222201110. [PMID: 35156574 DOI: 10.2174/1570163819666220214115408] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2021] [Revised: 09/24/2021] [Accepted: 12/03/2021] [Indexed: 11/22/2022]
Abstract
The self-association of DNA formed by Hoogsteen hydrogen bonding comprises several layers of four guanine or G-tetrads or G4s. The distinct feature of G4s, such as the G-tetrads and loops, qualify structure-selective recognition by small molecules and various ligands and can act as potential anticancer therapeutic molecules. The G4 selective-ligands, can influence gene expression by targeting a nucleic acid structure rather than sequence. Telomere G4 can be targeted for cancer treatment by small molecules inhibiting the telomerase activity whereas c-MYC is capable of controlling transcription, can be targeted to influence transcription. The k-RAS is one of the most frequently encountered oncogenic driver mutations in pancreatic, colorectal, and lung cancers. The k-RAS oncogene plays important role in acquiring and increasing the drug resistance and can also be directly targeted by small molecules to combat k-RAS mutant tumors. Modular G4 ligands with different functional groups, side chains and rotatable bonds as well as conformation affect the binding affinity/selectivity in cancer chemotherapeutic interventions. These modular G4 ligands act by targeting the diversity of G4 loops and groves and assists to develop more drug-like compounds with selectivity. In this review, we present the recent research on synthetic G4 DNA-interacting ligands as an approach toward the discovery of target specific anticancer chemotherapeutic agents.
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Affiliation(s)
- Sumanta Debbarma
- Department of Pharmacy, Tripura University, Suryamaninagar-799022, India
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22
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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.
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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
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23
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Paul T, Myong S. Helicase mediated vectorial folding of telomere G-quadruplex. Methods Enzymol 2022; 672:283-297. [DOI: 10.1016/bs.mie.2022.03.065] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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24
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Wang Z, Deng J, Umer M, Anwar N, Wang Y, Dong X, Xu H, He Y, Gao C. RHPS4 shifted the conformation ensemble equilibrium of Tel24 by preferentially stabilizing the (3 + 1) hybrid-2 conformation. RSC Adv 2022; 12:26011-26015. [PMID: 36199604 PMCID: PMC9469490 DOI: 10.1039/d2ra03959a] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2022] [Accepted: 09/04/2022] [Indexed: 11/21/2022] Open
Abstract
Telomeric G-quadruplexes have been a promising target for developing antitumor drugs with fewer side effects. The intracellular environment is usually in a state of molecular crowding. Studying the interaction mechanism among ligands and telomeric G-quadruplexes under crowded conditions is important for designing drugs that target telomeric G-quadruplexes. In the present study, the telomeric G-quadruplex Tel24 (TTAGGG)4 was found to fold into a conformational ensemble of parallel and (3 + 1) hybrid-2 conformations in solution with molecular crowding conditions created by PEG200. G-quadruplex-ligand 3,11-difluoro-6,8,13-trimethyl-8H-quino[4,3,2-kl] acridinium methosulfate (RHPS4) preferentially stabilized the (3 + 1) hybrid-2 conformation and shifted the conformational ensemble equilibrium of Tel24 towards the hybrid conformation. We also found that the (3 + 1) hybrid-2 conformation of Tel24 was more likely to form as compared to the parallel conformation in the conformational ensemble of Tel24. Overall, this study provides new insights into the conformation of telomere G-quadruplexes and their interactions with ligands in a physiological environment. Tel24 G-quadruplex can form a conformational ensemble consisting of parallel and (3 + 1) hybrid-2 conformations. RHPS4 preferentially stabilized the hybrid-2 conformation and shifted the conformational ensemble equilibrium.![]()
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Affiliation(s)
- Zhangqian Wang
- National R&D Center for Se-rich Agricultural Products Processing, Hubei Engineering Research Center for Deep Processing of Green Se-rich Agricultural Products, School of Modern Industry for Selenium Science and Engineering, Wuhan Polytechnic University, Wuhan 430023, China
- State Key Laboratory of Biocatalysis and Enzyme Engineering, School of Life Sciences, Hubei University, Wuhan 430062, China
| | - Jieya Deng
- National R&D Center for Se-rich Agricultural Products Processing, Hubei Engineering Research Center for Deep Processing of Green Se-rich Agricultural Products, School of Modern Industry for Selenium Science and Engineering, Wuhan Polytechnic University, Wuhan 430023, China
| | - Muhammad Umer
- Institute for Forest Resources and Environment of Guizhou and Forestry College, Research Center of Forest Ecology, Guizhou University, Guiyang, 550025, China
| | - Naureen Anwar
- Department of Zoology, University of Narowal, Narowal, Punjab, 51600, Pakistan
| | - Yidang Wang
- National R&D Center for Se-rich Agricultural Products Processing, Hubei Engineering Research Center for Deep Processing of Green Se-rich Agricultural Products, School of Modern Industry for Selenium Science and Engineering, Wuhan Polytechnic University, Wuhan 430023, China
| | - XingXing Dong
- National R&D Center for Se-rich Agricultural Products Processing, Hubei Engineering Research Center for Deep Processing of Green Se-rich Agricultural Products, School of Modern Industry for Selenium Science and Engineering, Wuhan Polytechnic University, Wuhan 430023, China
| | - Hua Xu
- National R&D Center for Se-rich Agricultural Products Processing, Hubei Engineering Research Center for Deep Processing of Green Se-rich Agricultural Products, School of Modern Industry for Selenium Science and Engineering, Wuhan Polytechnic University, Wuhan 430023, China
| | - Yi He
- National R&D Center for Se-rich Agricultural Products Processing, Hubei Engineering Research Center for Deep Processing of Green Se-rich Agricultural Products, School of Modern Industry for Selenium Science and Engineering, Wuhan Polytechnic University, Wuhan 430023, China
| | - Chao Gao
- National R&D Center for Se-rich Agricultural Products Processing, Hubei Engineering Research Center for Deep Processing of Green Se-rich Agricultural Products, School of Modern Industry for Selenium Science and Engineering, Wuhan Polytechnic University, Wuhan 430023, China
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25
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Molnár OR, Végh A, Somkuti J, Smeller L. Characterization of a G-quadruplex from hepatitis B virus and its stabilization by binding TMPyP4, BRACO19 and PhenDC3. Sci Rep 2021; 11:23243. [PMID: 34853392 PMCID: PMC8636512 DOI: 10.1038/s41598-021-02689-y] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2021] [Accepted: 11/12/2021] [Indexed: 12/22/2022] Open
Abstract
Specific guanine rich nucleic acid sequences can form non-canonical structures, like the four stranded G-quadruplex (GQ). We studied the GQ-forming sequence (named HepB) found in the genome of the hepatitis B virus. Fluorescence-, infrared- and CD-spectroscopy were used. HepB shows a hybrid form in presence of K+, but Na+, Li+, and Rb+ induce parallel structure. Higher concentrations of metal ions increase the unfolding temperature, which was explained by a short thermodynamic calculation. Temperature stability of the GQ structure was determined for all these ions. Na+ has stronger stabilizing effect on HepB than K+, which is highly unusual. The transition temperatures were 56.6, 53.8, 58.5 and 54.4 °C for Na+, K+, Li+, and Rb+ respectively. Binding constants for Na+ and K+ were 10.2 mM and 7.1 mM respectively. Study of three ligands designed in cancer research for GQ targeting (TMPyP4, BRACO19 and PhenDC3) showed unequivocally their binding to HepB. Binding was proven by the increased stability of the bound form. The stabilization was higher than 20 °C for TMPyP4 and PhenDC3, while it was considerably lower for BRACO19. These results might have medical importance in the fight against the hepatitis B virus.
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Affiliation(s)
- Orsolya Réka Molnár
- Department of Biophysics and Radiation Biology, Semmelweis University, Budapest, 1094, Hungary
| | - András Végh
- Department of Biophysics and Radiation Biology, Semmelweis University, Budapest, 1094, Hungary.,Department of Ophthalmology, Semmelweis University, Budapest, 1085, Hungary
| | - Judit Somkuti
- Department of Biophysics and Radiation Biology, Semmelweis University, Budapest, 1094, Hungary
| | - László Smeller
- Department of Biophysics and Radiation Biology, Semmelweis University, Budapest, 1094, Hungary.
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26
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Liu YC, Yang DY, Sheu SY. Insights into the free energy landscape and salt-controlled mechanism of the conformational conversions between human telomeric G-quadruplex structures. Int J Biol Macromol 2021; 191:230-242. [PMID: 34536474 DOI: 10.1016/j.ijbiomac.2021.09.057] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2021] [Revised: 08/23/2021] [Accepted: 09/10/2021] [Indexed: 12/16/2022]
Abstract
G-quadruplexes have become attractive drug targets in cancer therapy. However, due to the polymorphism of G-quadruplex structures, it is difficult to experimentally verify the relevant structures of multiple intermediates and transition states in dynamic equilibrium. Hence, understanding the mechanism by which structural conversions of G-quadruplexes occur is still challenging. We conducted targeted molecular dynamics simulation with umbrella sampling to investigate how salt affects the conformational conversion of human telomeric G-quadruplex. Our results explore a unique view into the structures and energy barrier of the intermediates and transition states in the interconversion process. The pathway of G-quadruplex conformational interconversion was mapped out by a free energy landscape, consisting of branched parallel pathways with multiple energy basins. We propose a salt-controlled mechanism that as the salt concentration increases, the conformational conversion mechanism switches from multi-pathway folding to sequential folding pathways. The hybrid-I and hybrid-II structures are intermediates in the basket-propeller transformation. In high-salt solutions, the conformational conversion upon K+ binding is more feasible than upon Na+ binding. The free energy barrier for conformational conversions ranges from 1.6 to 4.6 kcal/mol. Our work will be beneficial in developing anticancer agents.
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Affiliation(s)
- Yu-Cheng Liu
- Institute of Biomedical Informatics, National Yang Ming Chiao Tung University, Taipei 112, Taiwan
| | - Dah-Yen Yang
- Institute of Atomic and Molecular Sciences, Academia Sinica, Taipei 106, Taiwan.
| | - Sheh-Yi Sheu
- Institute of Biomedical Informatics, National Yang Ming Chiao Tung University, Taipei 112, Taiwan; Department of Life Sciences and Institute of Genome Sciences, National Yang Ming Chiao Tung University, Taipei 112, Taiwan.
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27
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Somkuti J, Molnár OR, Grád A, Smeller L. Pressure Perturbation Studies of Noncanonical Viral Nucleic Acid Structures. BIOLOGY 2021; 10:1173. [PMID: 34827166 PMCID: PMC8615049 DOI: 10.3390/biology10111173] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/29/2021] [Revised: 11/08/2021] [Accepted: 11/08/2021] [Indexed: 12/16/2022]
Abstract
G-quadruplexes are noncanonical structures formed by guanine-rich sequences of the genome. They are found in crucial loci of the human genome, they take part in the regulation of important processes like cell proliferation and cell death. Much less is known about the subjects of this work, the viral G-quadruplexes. We have chosen three potentially G-quadruplex-forming sequences of hepatitis B. We measured the stability and the thermodynamic parameters of these quadruplexes. We also investigated the potential stabilization of these G-quadruplexes by binding a special ligand that was originally developed for cancer therapy. Fluorescence and infrared spectroscopic measurements were performed over wide temperature and pressure ranges. Our experiments indicate the small unfolding volume change of all three oligos. We found a difference between the unfolding of the 2-quartet and the 3-quartet G-quadruplexes. All three G-quadruplexes were stabilized by TMPyP4, which is a cationic porphyrin developed for stabilizing the human telomere.
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Affiliation(s)
| | | | | | - László Smeller
- Department of Biophysics and Radiation Biology, Semmelweis University, 1094 Budapest, Hungary; (J.S.); (O.R.M.); (A.G.)
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28
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Pal S, Fatma K, Ravichandiran V, Dash J. Triazolyl Dibenzo[ a,c]phenazines Stabilize Telomeric G-quadruplex and Inhibit Telomerase. ASIAN J ORG CHEM 2021; 10:2921-2926. [PMID: 37823002 PMCID: PMC7614908 DOI: 10.1002/ajoc.202100468] [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: 07/27/2021] [Indexed: 11/10/2022]
Abstract
We herein report the synthesis and biophysical evaluation of triazolyl dibenzo[a,c]phenazine derivatives as a novel class of G-quadruplex ligands. The aromatic core facilitates π-π interaction and the flexible, protonatable side chains interact with the phosphate backbone of DNA via electrostatic interactions. Förster resonance energy transfer (FRET) melting assay and isothermal titration calorimetry (ITC) studies suggest that these ligands show binding preference for the hTELO G-quadruplex over G-quadruplexes found in the promoter region of various oncogenes and duplex DNA. The in vitro telomeric repeat amplification protocol (Q-TRAP) assay reveals that these ligands reduce telomerase activity in cancer cells.
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Affiliation(s)
- Sarmistha Pal
- School of Chemical Sciences, Indian Association for the Cultivation of Science, Jadavpur, Kolkata-700032, India
- Department of Medicinal Chemistry, NIPER-KOLKATA, Chunilal Bhawan (Adjacent to BCPL), 168, Maniktala Main Road P.O. Bengal Chemicals, P.S. Phoolbagan, Kolkata – 700054, West Bengal
| | - Khushnood Fatma
- School of Chemical Sciences, Indian Association for the Cultivation of Science, Jadavpur, Kolkata-700032, India
| | - Velayutham Ravichandiran
- Department of Medicinal Chemistry, NIPER-KOLKATA, Chunilal Bhawan (Adjacent to BCPL), 168, Maniktala Main Road P.O. Bengal Chemicals, P.S. Phoolbagan, Kolkata – 700054, West Bengal
| | - Jyotirmayee Dash
- School of Chemical Sciences, Indian Association for the Cultivation of Science, Jadavpur, Kolkata-700032, India
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29
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Cavalcante SG, Pereira BJA, Lerario AM, Sola PR, Oba-Shinjo SM, Marie SKN. The chromatin remodeler complex ATRX-DAXX-H3.3 and telomere length in meningiomas. Clin Neurol Neurosurg 2021; 210:106962. [PMID: 34624827 DOI: 10.1016/j.clineuro.2021.106962] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2021] [Revised: 09/06/2021] [Accepted: 09/27/2021] [Indexed: 02/08/2023]
Abstract
ATRX-DAXX-H3.3 chromatin remodeler complex is a well known epigenetic factor responsible for the heterochromatin maintenance and control. ATRX is an important nucleosome controller, especially in tandem repeat regions, and DAXX is a multi-function protein with particular role in histone H3.3 deposition due to its chaperone characteristic. Abnormalities in this complex have been associated with telomere dysfunction and consequently with activation of alternative lengthening of telomeres mechanism, genomic instability, and tumor progression in different types of cancer. However, the characterization of this complex is still incomplete in meningioma. We analyzed ATRX, DAXX and H3.3 expressions and the telomere length in a cohort of meningioma of different malignant grades. We observed ATRX upregulation at gene and protein levels in grade II/III meningiomas. A low variability of telomere length was observed in meningiomas across different ages and malignant grades, in contrast to the shortening of telomere length with aging in normal controls.
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Affiliation(s)
- Stella G Cavalcante
- Laboratory of Molecular and Cellular Biology, LIM 15, Department of Neurology, Faculdade de Medicina FMUSP, Universidade de Sao Paulo, Av. Dr. Arnaldo, 455 - 4º floor, room 4110, Pacaembu, São Paulo, SP, Brazil.
| | - Benedito J A Pereira
- Laboratory of Molecular and Cellular Biology, LIM 15, Department of Neurology, Faculdade de Medicina FMUSP, Universidade de Sao Paulo, Av. Dr. Arnaldo, 455 - 4º floor, room 4110, Pacaembu, São Paulo, SP, Brazil.
| | - Antonio M Lerario
- Department of Internal Medicine, Division of Metabolism, Endocrinology and Diabetes, University of Michigan, Brehm Tower, Suite 5100, SPC 5714, 1000 Wall Street, Ann Arbor, MI 48109, USA.
| | - Paula R Sola
- Laboratory of Molecular and Cellular Biology, LIM 15, Department of Neurology, Faculdade de Medicina FMUSP, Universidade de Sao Paulo, Av. Dr. Arnaldo, 455 - 4º floor, room 4110, Pacaembu, São Paulo, SP, Brazil.
| | - Sueli M Oba-Shinjo
- Laboratory of Molecular and Cellular Biology, LIM 15, Department of Neurology, Faculdade de Medicina FMUSP, Universidade de Sao Paulo, Av. Dr. Arnaldo, 455 - 4º floor, room 4110, Pacaembu, São Paulo, SP, Brazil.
| | - Suely K N Marie
- Laboratory of Molecular and Cellular Biology, LIM 15, Department of Neurology, Faculdade de Medicina FMUSP, Universidade de Sao Paulo, Av. Dr. Arnaldo, 455 - 4º floor, room 4110, Pacaembu, São Paulo, SP, Brazil.
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30
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Abstract
Invention of DNA origami has transformed the fabrication and application of biological nanomaterials. In this review, we discuss DNA origami nanoassemblies according to their four fundamental mechanical properties in response to external forces: elasticity, pliability, plasticity and stability. While elasticity and pliability refer to reversible changes in structures and associated properties, plasticity shows irreversible variation in topologies. The irreversible property is also inherent in the disintegration of DNA nanoassemblies, which is manifested by its mechanical stability. Disparate DNA origami devices in the past decade have exploited the mechanical regimes of pliability, elasticity, and plasticity, among which plasticity has shown its dominating potential in biomechanical and physiochemical applications. On the other hand, the mechanical stability of the DNA origami has been used to understand the mechanics of the assembly and disassembly of DNA nano-devices. At the end of this review, we discuss the challenges and future development of DNA origami nanoassemblies, again, from these fundamental mechanical perspectives.
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Affiliation(s)
- Jiahao Ji
- Department of Chemistry and Biochemistry, Kent State University, Kent, OH, 44240, USA.
| | - Deepak Karna
- Department of Chemistry and Biochemistry, Kent State University, Kent, OH, 44240, USA.
| | - Hanbin Mao
- Department of Chemistry and Biochemistry, Kent State University, Kent, OH, 44240, USA.
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31
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He Q, Liu Y, Li K, Wu Y, Wang T, Tan Y, Jiang T, Liu X, Liu Z. Deoxyribonucleic acid anchored on cell membranes for biomedical application. Biomater Sci 2021; 9:6691-6717. [PMID: 34494042 DOI: 10.1039/d1bm01057c] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Engineering cellular membranes with functional molecules provides an attractive strategy to manipulate cellular behaviors and functionalities. Currently, synthetic deoxyribonucleic acid (DNA) has emerged as a promising molecular tool to engineer cellular membranes for biomedical applications due to its molecular recognition and programmable properties. In this review, we summarized the recent advances in anchoring DNA on the cellular membranes and their applications. The strategies for anchoring DNA on cell membranes were summarized. Then their applications, such as immune response activation, receptor oligomerization regulation, membrane structure mimicking, cell-surface biosensing, and construction of cell clusters, were listed. The DNA-enabled intelligent systems which were able to sense stimuli such as DNA strands, light, and metal ions were highlighted. Finally, insights regarding the remaining challenges and possible future directions were provided.
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Affiliation(s)
- Qunye He
- Department of Pharmaceutics, Xiangya School of Pharmaceutical Sciences, Central South University, Changsha, 410013, Hunan Province, P. R. China.
| | - Yanfei Liu
- Department of Pharmaceutical Engineering, College of Chemistry and Chemical Engineering, Central South University, Changsha, 410083, Hunan Province, P. R. China
| | - Ke Li
- Department of Pharmaceutics, Xiangya School of Pharmaceutical Sciences, Central South University, Changsha, 410013, Hunan Province, P. R. China.
| | - Yuwei Wu
- Department of Pharmaceutics, Xiangya School of Pharmaceutical Sciences, Central South University, Changsha, 410013, Hunan Province, P. R. China.
| | - Ting Wang
- Department of Pharmaceutics, Xiangya School of Pharmaceutical Sciences, Central South University, Changsha, 410013, Hunan Province, P. R. China.
| | - Yifu Tan
- Department of Pharmaceutical Engineering, College of Chemistry and Chemical Engineering, Central South University, Changsha, 410083, Hunan Province, P. R. China
| | - Ting Jiang
- Department of Pharmaceutical Engineering, College of Chemistry and Chemical Engineering, Central South University, Changsha, 410083, Hunan Province, P. R. China
| | - Xiaoqin Liu
- Department of Pharmaceutical Engineering, College of Chemistry and Chemical Engineering, Central South University, Changsha, 410083, Hunan Province, P. R. China
| | - Zhenbao Liu
- Department of Pharmaceutics, Xiangya School of Pharmaceutical Sciences, Central South University, Changsha, 410013, Hunan Province, P. R. China. .,Molecular Imaging Research Center of Central South University, Changsha 410008, Hunan, P. R. China
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32
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Fu W, Jing H, Xu X, Xu S, Wang T, Hu W, Li H, Zhang N. Two coexisting pseudo-mirror heteromolecular telomeric G-quadruplexes in opposite loop progressions differentially recognized by a low equivalent of Thioflavin T. Nucleic Acids Res 2021; 49:10717-10734. [PMID: 34500466 PMCID: PMC8501994 DOI: 10.1093/nar/gkab755] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2021] [Revised: 07/24/2021] [Accepted: 08/31/2021] [Indexed: 11/13/2022] Open
Abstract
The final 3′-terminal residue of the telomeric DNA G-overhang is inherently less precise. Here, we describe how alteration of the last 3′-terminal base affects the mutual recognition between two different G-rich oligomers of human telomeric DNA in the formation of heteromolecular G-quadruplexes (hetero-GQs). Associations between three- and single-repeat fragments of human telomeric DNA, target d(GGGTTAGGGTTAGGG) and probe d(TAGGGT), in Na+ solution yield two coexisting forms of (3 + 1) hybrid hetero-GQs: the kinetically favourable LLP-form (left loop progression) and the thermodynamically controlled RLP-form (right loop progression). However, only the adoption of a single LLP-form has been previously reported between the same probe d(TAGGGT) and a target variant d(GGGTTAGGGTTAGGGT) having one extra 3′-end thymine. Moreover, the flanking base alterations of short G-rich probe variants also significantly affect the loop progressions of hetero-GQs. Although seemingly two pseudo-mirror counter partners, the RLP-form exhibits a preference over the LLP-form to be recognized by a low equivalent of fluorescence dye thioflavin T (ThT). To a greater extent, ThT preferentially binds to RLP hetero-GQ than with the corresponding telomeric DNA duplex context or several other representative unimolecular GQs.
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Affiliation(s)
- Wenqiang Fu
- High Magnetic Field Laboratory, Chinese Academy of Sciences, Hefei 230031, China.,University of Science and Technology of China, Hefei 230026, China
| | - Haitao Jing
- High Magnetic Field Laboratory, Chinese Academy of Sciences, Hefei 230031, China.,University of Science and Technology of China, Hefei 230026, China
| | - Xiaojuan Xu
- High Magnetic Field Laboratory, Chinese Academy of Sciences, Hefei 230031, China.,University of Science and Technology of China, Hefei 230026, China
| | - Suping Xu
- High Magnetic Field Laboratory, Chinese Academy of Sciences, Hefei 230031, China
| | - Tao Wang
- High Magnetic Field Laboratory, Chinese Academy of Sciences, Hefei 230031, China
| | - Wenxuan Hu
- High Magnetic Field Laboratory, Chinese Academy of Sciences, Hefei 230031, China.,University of Science and Technology of China, Hefei 230026, China
| | - Huihui Li
- High Magnetic Field Laboratory, Chinese Academy of Sciences, Hefei 230031, China.,University of Science and Technology of China, Hefei 230026, China
| | - Na Zhang
- High Magnetic Field Laboratory, Chinese Academy of Sciences, Hefei 230031, China.,Key Laboratory of High Magnetic Field and Ion Beam Physical Biology, Hefei Institutes of Physical Science, Chinese Academy of Sciences, Hefei 230031, China.,Key Laboratory of Anhui Province for High Field Magnetic Resonance Imaging, Hefei 230031, China.,High Magnetic Field Laboratory of Anhui Province, Hefei 230031, China
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33
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Comparison of Telomere Length in Young and Master Endurance Runners and Sprinters. J Aging Phys Act 2021; 30:510-516. [PMID: 34564066 DOI: 10.1123/japa.2021-0236] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2021] [Revised: 08/10/2021] [Accepted: 08/21/2021] [Indexed: 11/18/2022]
Abstract
It is unclear how running modality influences telomere length (TL). This single laboratory visit study compared the TL of master sprinters and endurance runners with their young counterparts. The correlation between leukocyte and buccal cell TL in athletes was also explored. Participants consisted of 11 young controls, 11 young sprinters, 12 young endurance runners, 12 middle-aged controls, 11 master sprinters, and 12 master endurance runners. Blood and buccal samples were collected and randomized for analysis of TL by quantitative polymerase chain reaction. Young endurance runners displayed longer telomeres than master athletes (p < .05); however, these differences were not significant when controlled for covariates (p > .05). A positive correlation existed between leukocyte and buccal cell TL in athletes (r = .567, p < .001). In conclusion, young endurance runners possess longer telomeres than master endurance runners and sprinters, a consequence of lower body mass index and visceral fat.
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34
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Hagihara M. Inhibition of protein synthesis through RNA-based tandem G-quadruplex formation. Chem Commun (Camb) 2021; 57:8063-8066. [PMID: 34296230 DOI: 10.1039/d1cc02995a] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
We demonstrate that an RNA template containing eight GGG repeat sequences exhibits a unique tandem G-quadruplex structure in which two individual G-quadruplexes are aligned in close proximity. Because of their unexpected stability, tandem G-quadruplexes formed in the coding region of mRNA strands effectively inhibited in vitro protein synthesis.
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Affiliation(s)
- Masaki Hagihara
- Graduate School of Science and Technology, Hirosaki University, Hirosaki 036-8561, Japan.
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35
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Conformer Analysis of a Biological G-Quadruplex Element in the Human c-MYC Promoter by Native Polyacrylamide Gel Electrophoresis. JOURNAL OF ANALYSIS AND TESTING 2021. [DOI: 10.1007/s41664-021-00181-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
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36
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Mustafa G, Shiekh S, Gc K, Abeysirigunawardena S, Balci H. Interrogating accessibility of telomeric sequences with FRET-PAINT: evidence for length-dependent telomere compaction. Nucleic Acids Res 2021; 49:3371-3380. [PMID: 33693934 PMCID: PMC8034622 DOI: 10.1093/nar/gkab067] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2020] [Revised: 01/23/2021] [Accepted: 03/08/2021] [Indexed: 12/25/2022] Open
Abstract
Single-stranded telomeric overhangs are ∼200 nucleotides long and can form tandem G-quadruplex (GQ) structures, which reduce their accessibility to nucleases and proteins that activate DNA damage response. Whether these tandem GQs further stack to form compact superstructures, which may provide better protection for longer telomeres, is not known. We report single-molecule measurements where the accessibility of 24-144 nucleotide long human telomeric DNA molecules is interrogated by a short PNA molecule that is complementary to a single GGGTTA repeat, as implemented in the FRET-PAINT method. Binding of the PNA strand to available GGGTTA sequences results in discrete FRET bursts which were analyzed in terms of their dwell times, binding frequencies, and topographic distributions. The binding frequencies were greater for binding to intermediate regions of telomeric DNA compared to 3'- or 5'-ends, suggesting these regions are more accessible. Significantly, the binding frequency per telomeric repeat monotonically decreased with increasing telomere length. These results are consistent with telomeres forming more compact structures at longer lengths, reducing accessibility of these critical genomic sites.
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Affiliation(s)
- Golam Mustafa
- Department of Physics, Kent State University, Kent, OH 44242, USA
| | - Sajad Shiekh
- Department of Physics, Kent State University, Kent, OH 44242, USA
| | - Keshav Gc
- Department of Chemistry and Biochemistry, Kent State University, Kent, OH 44242, USA
| | | | - Hamza Balci
- Department of Physics, Kent State University, Kent, OH 44242, USA
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37
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Sadhukhan R, Ghosh U. PARP1 modulates telomere sister chromatid exchange and telomere length homeostasis by regulating telomere localization of SLX4 in U2OS cells. Life Sci 2021; 277:119556. [PMID: 33945829 DOI: 10.1016/j.lfs.2021.119556] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2021] [Revised: 04/12/2021] [Accepted: 04/20/2021] [Indexed: 11/16/2022]
Abstract
OBJECTIVE Poly(ADP-ribose) polymerase1 (PARP1) interacts and poly(ADP-ribosyl)ates telomere repeat binding factor 2 (TRF2), which acts as a platform to recruit a large number of proteins at the telomere. Since the discovery of TRF2-SLX4 interaction, SLX4 is becoming the key player in telomere length (TL) maintenance and repair by telomere sister chromatid exchange (T-SCE). Defective TL maintenance pathway results in a spectrum of diseases called telomeropathies like dyskeratosis congenita, aplastic anemia, fanconi anemia, cancer. We aimed to study the role of SLX4 and PARP1 on each other's telomere localization, T-SCE, and TL maintenance in human telomerase-negative osteosarcoma U2OS cells to understand some of the molecular mechanisms of telomere homeostasis. MATERIALS AND METHODS We checked the role of SLX4 and PARP1 on each other's telomere localization by telomere immunofluorescence. We have cloned full-length wild-type and catalytically inactive mutant PARP1 to understand the role of poly(ADP-ribosyl)ation reaction by PARP1 in telomere length homeostasis. TL of U2OS cells was measured by Q-FISH. T-SCE was measured by Telomere-FISH. KEY FINDINGS We observed that SLX4 has no role in the telomere localization of PARP1. However, reduced localization of SLX4 at undamaged and damaged telomere upon PARP1 depletion was reversed by overexpression of exogenous wild-type PARP1 but not by overexpression of catalytically inactive mutant PARP1. PARP1 depletion synergized SLX4 depletion-mediated reduction of T-SCE. Furthermore, SLX4 depletion elongated TL, and combined insufficiency of SLX4 with PARP1 further elongated TL. CONCLUSION So, PARP1 controls SLX4 recruitment at telomere by poly(ADP-ribosyl)ation reaction, thereby regulating SLX4-mediated T-SCE and TL homeostasis.
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Affiliation(s)
- Ratan Sadhukhan
- Department of Biochemistry & Biophysics, University of Kalyani, Kalyani 741235, India
| | - Utpal Ghosh
- Department of Biochemistry & Biophysics, University of Kalyani, Kalyani 741235, India.
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Cave JW, Willis DE. G-quadruplex regulation of neural gene expression. FEBS J 2021; 289:3284-3303. [PMID: 33905176 DOI: 10.1111/febs.15900] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2020] [Revised: 03/24/2021] [Accepted: 04/23/2021] [Indexed: 12/11/2022]
Abstract
G-quadruplexes are four-stranded helical nucleic acid structures characterized by stacked tetrads of guanosine bases. These structures are widespread throughout mammalian genomic DNA and RNA transcriptomes, and prevalent across all tissues. The role of G-quadruplexes in cancer is well-established, but there has been a growing exploration of these structures in the development and homeostasis of normal tissue. In this review, we focus on the roles of G-quadruplexes in directing gene expression in the nervous system, including the regulation of gene transcription, mRNA processing, and trafficking, as well as protein translation. The role of G-quadruplexes and their molecular interactions in the pathology of neurological diseases is also examined. Outside of cancer, there has been only limited exploration of G-quadruplexes as potential intervention targets to treat disease or injury. We discuss studies that have used small-molecule ligands to manipulate G-quadruplex stability in order to treat disease or direct neural stem/progenitor cell proliferation and differentiation into therapeutically relevant cell types. Understanding the many roles that G-quadruplexes have in the nervous system not only provides critical insight into fundamental molecular mechanisms that control neurological function, but also provides opportunities to identify novel therapeutic targets to treat injury and disease.
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Affiliation(s)
- John W Cave
- InVitro Cell Research LLC, Englewood, NJ, USA
| | - Dianna E Willis
- Burke Neurological Institute, White Plains, NY, USA.,Feil Family Brain & Mind Research Institute, Weill Cornell Medicine, New York, NY, USA
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Podder A, Lee HJ, Kim BH. Fluorescent Nucleic Acid Systems for Biosensors. BULLETIN OF THE CHEMICAL SOCIETY OF JAPAN 2021. [DOI: 10.1246/bcsj.20200351] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Affiliation(s)
- Arup Podder
- Department of Chemistry, Division of Advanced Materials Science, Pohang University of Science and Technology (POSTECH), Pohang 37673, Korea
| | - Ha Jung Lee
- Department of Chemistry, Division of Advanced Materials Science, Pohang University of Science and Technology (POSTECH), Pohang 37673, Korea
| | - Byeang Hyean Kim
- Department of Chemistry, Division of Advanced Materials Science, Pohang University of Science and Technology (POSTECH), Pohang 37673, Korea
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Ghosh A, Largy E, Gabelica V. DNA G-quadruplexes for native mass spectrometry in potassium: a database of validated structures in electrospray-compatible conditions. Nucleic Acids Res 2021; 49:2333-2345. [PMID: 33555347 PMCID: PMC7913678 DOI: 10.1093/nar/gkab039] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2020] [Revised: 12/22/2020] [Accepted: 01/19/2021] [Indexed: 02/07/2023] Open
Abstract
G-quadruplex DNA structures have become attractive drug targets, and native mass spectrometry can provide detailed characterization of drug binding stoichiometry and affinity, potentially at high throughput. However, the G-quadruplex DNA polymorphism poses problems for interpreting ligand screening assays. In order to establish standardized MS-based screening assays, we studied 28 sequences with documented NMR structures in (usually ∼100 mM) potassium, and report here their circular dichroism (CD), melting temperature (Tm), NMR spectra and electrospray mass spectra in 1 mM KCl/100 mM trimethylammonium acetate. Based on these results, we make a short-list of sequences that adopt the same structure in the MS assay as reported by NMR, and provide recommendations on using them for MS-based assays. We also built an R-based open-source application to build and consult a database, wherein further sequences can be incorporated in the future. The application handles automatically most of the data processing, and allows generating custom figures and reports. The database is included in the g4dbr package (https://github.com/EricLarG4/g4dbr) and can be explored online (https://ericlarg4.github.io/G4_database.html).
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Affiliation(s)
- Anirban Ghosh
- Univ. Bordeaux, CNRS, INSERM, ARNA, UMR 5320, U1212, IECB, F-33000 Bordeaux, France
| | - Eric Largy
- Univ. Bordeaux, CNRS, INSERM, ARNA, UMR 5320, U1212, IECB, F-33000 Bordeaux, France
| | - Valérie Gabelica
- Univ. Bordeaux, CNRS, INSERM, ARNA, UMR 5320, U1212, IECB, F-33000 Bordeaux, France
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41
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Thermal Stability Changes in Telomeric G-Quadruplex Structures Due to N6-Methyladenine Modification. EPIGENOMES 2021; 5:epigenomes5010005. [PMID: 34968256 PMCID: PMC8594671 DOI: 10.3390/epigenomes5010005] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2021] [Revised: 01/26/2021] [Accepted: 01/27/2021] [Indexed: 11/17/2022] Open
Abstract
N6-methyladenine modification (m6dA) has recently been identified in eukaryote genomic DNA. The methylation destabilizes the duplex structure when the adenine forms a Watson-Crick base pair, whereas the methylation on a terminal unpaired adenine stabilizes the duplex structure by increasing the stacking interaction. In this study, the effects of m6dA modification on the thermal stability of four distinct telomeric G-quadruplex (G4) structures were investigated. The m6dA-modified telomeric oligonucleotide d[AGGG(TTAGGG)3] that forms a basket-type G4 in Na+, d[(TTAGGG)4TT] that forms a hybrid-type G4 in K+ (Form-2), d[AAAGGG(TTAGGG)3AA] that forms a hybrid-type G4 in K+ (Form-1), and d[GGG(TTAGGG)3T] that forms a basket-type G4 with two G-tetrads in K+ (Form-3) were analyzed. Circular dichroism melting analysis demonstrated that (1) A7- and A19-methylation destabilized the basket-type G4 structure that formed in Na+, whereas A13-methylation stabilized the structure; (2) A15-methylation stabilized the Form-2 G4 structure; (3) A15- and A21-methylations stabilized the Form-1 G4 structure; and (4) A12-methylation stabilized the Form-3 G4 structure. These results suggest that m6dA modifications may affect the thermal stability of human telomeric G4 structures in regulating the biological functions.
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Nishio M, Tsukakoshi K, Ikebukuro K. G-quadruplex: Flexible conformational changes by cations, pH, crowding and its applications to biosensing. Biosens Bioelectron 2021; 178:113030. [PMID: 33524709 DOI: 10.1016/j.bios.2021.113030] [Citation(s) in RCA: 55] [Impact Index Per Article: 18.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2020] [Revised: 01/07/2021] [Accepted: 01/20/2021] [Indexed: 12/20/2022]
Abstract
G-quadruplex (G4) is a non-canonical structure that is formed in G-rich sequences of nucleic acids. G4s play important roles in vivo, such as telomere maintenance, transcription, and DNA replication. There are three typical topologies of G4: parallel, anti-parallel, and hybrid. In general, metal cations, such as potassium and sodium, stabilize G4s through coordination in the G-quartet. While G4s have some functions in vivo, there are many reports of developed applications that use G4s. As various conformations of G4s could form from one sequence depending on varying conditions, many researchers have developed G4-based sensors. Furthermore, G4 is a great scaffold of aptamers since many aptamers folded into G4s have also been reported. However, there are some challenges about its practical use due to the difference between practical sample conditions and experimental ones. G4 conformations are dramatically altered by the surrounding conditions, such as metal cations, pH, and crowding. Many studies have been conducted to characterize G4 conformations under various conditions, not only to use G4s in practical applications but also to reveal its function in vivo. In this review, we summarize recent studies that have investigated the effects of surrounding conditions (e.g., metal cations, pH, and crowding) on G4 conformations and the application of G4s mainly in biosensor fields, and in others.
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Affiliation(s)
- Maui Nishio
- Department of Biotechnology and Life Science, Tokyo University of Agriculture and Technology, 2-24-16 Naka-cho, Koganei, Tokyo, 184-8588, Japan
| | - Kaori Tsukakoshi
- Department of Biotechnology and Life Science, Tokyo University of Agriculture and Technology, 2-24-16 Naka-cho, Koganei, Tokyo, 184-8588, Japan
| | - Kazunori Ikebukuro
- Department of Biotechnology and Life Science, Tokyo University of Agriculture and Technology, 2-24-16 Naka-cho, Koganei, Tokyo, 184-8588, Japan.
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Sun Y, Lu Y, Bian M, Yang Z, Ma X, Liu W. Pt(II) and Au(III) complexes containing Schiff-base ligands: A promising source for antitumor treatment. Eur J Med Chem 2020; 211:113098. [PMID: 33348237 DOI: 10.1016/j.ejmech.2020.113098] [Citation(s) in RCA: 39] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2020] [Revised: 11/24/2020] [Accepted: 12/08/2020] [Indexed: 12/11/2022]
Abstract
The effective application of cisplatin in the clinic as an antitumor treatment has stimulated widespread interest in inorganic metal drugs. In particular, complexes containing the transition metals platinum and gold have attracted considerable attention due to their antitumor effects. The Pt(II) and Au(III) Schiff-base complexes are potential antitumor agents because of their remarkable biological activities and good stability, lipophilicity, and electroluminescent properties. These complexes act via various antitumor mechanisms that are unlike those of the classic platinum drugs, providing a feasible solution for improving the serious side effects caused by metal chemotherapy. In this review, promising antitumor agents based on Pt(II) and Au(III) complexes containing Schiff-base ligands, and their biological targets, including G-quadruplex DNA and thioredoxin reductase, are comprehensively summarized.
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Affiliation(s)
- Ying Sun
- Jiangsu Collaborative Innovation Center of Chinese Medicinal Resources Industrialization, School of Pharmacy, School of Medicine & Holistic Integrative Medicine, Nanjing University of Chinese Medicine, Nanjing, 210023, China
| | - Yunlong Lu
- Jiangsu Collaborative Innovation Center of Chinese Medicinal Resources Industrialization, School of Pharmacy, School of Medicine & Holistic Integrative Medicine, Nanjing University of Chinese Medicine, Nanjing, 210023, China
| | - Mianli Bian
- Jiangsu Collaborative Innovation Center of Chinese Medicinal Resources Industrialization, School of Pharmacy, School of Medicine & Holistic Integrative Medicine, Nanjing University of Chinese Medicine, Nanjing, 210023, China
| | - Zhibin Yang
- Jiangsu Collaborative Innovation Center of Chinese Medicinal Resources Industrialization, School of Pharmacy, School of Medicine & Holistic Integrative Medicine, Nanjing University of Chinese Medicine, Nanjing, 210023, China
| | - Xiaoyan Ma
- Jiangsu Collaborative Innovation Center of Chinese Medicinal Resources Industrialization, School of Pharmacy, School of Medicine & Holistic Integrative Medicine, Nanjing University of Chinese Medicine, Nanjing, 210023, China
| | - Wukun Liu
- Jiangsu Collaborative Innovation Center of Chinese Medicinal Resources Industrialization, School of Pharmacy, School of Medicine & Holistic Integrative Medicine, Nanjing University of Chinese Medicine, Nanjing, 210023, China; State Key Laboratory of Natural Medicines, China Pharmaceutical University, Nanjing, 210009, China; State Key Laboratory of Coordination Chemistry, Nanjing University, Nanjing, 210023, China.
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44
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Turcotte MA, Garant JM, Cossette-Roberge H, Perreault JP. Guanine Nucleotide-Binding Protein-Like 1 (GNL1) binds RNA G-quadruplex structures in genes associated with Parkinson's disease. RNA Biol 2020; 18:1339-1353. [PMID: 33305682 PMCID: PMC8354592 DOI: 10.1080/15476286.2020.1847866] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
RNAs are highly regulated at the post-transcriptional level in neurodegenerative diseases and just a few mutations can significantly affect the fate of neuronal cells. To date, the impact of G-quadruplex (G4) regulation in neurodegenerative diseases like Parkinson’s disease (PD) has not been analysed. In this study, in silico potential G4s located in deregulated genes related to the nervous system were initially identified and were found to be significantly enriched. Several G4 sequences found in the 5ʹ untranslated regions (5ʹUTR) of mRNAs associated with Parkinson’s disease were demonstrated to in fact fold in vitro by biochemical assays. Subcloning of the full-length 5ʹUTRs of these candidates upstream of a luciferase reporter system led to the demonstration that the G4s of both Parkin RBR E3 Ubiquitin Protein Ligase (PRKN) and Vacuolar Protein Sorting-Associated Protein 35 (VPS35) significantly repressed the translation of both genes in SH-SY5Y cells. Subsequently, a strategy of using label-free RNA affinity purification assays with either of these two G4 sequences as bait isolated the Guanine Nucleotide-Binding Protein-Like 1 (GNL1). The latter was shown to have a higher affinity for the G4 sequences than for their mutated version. This study sheds light on new RNA G-quadruplexes located in genes dysregulated in Parkinson disease and a new G4-binding protein, GNL1.
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Affiliation(s)
- Marc-Antoine Turcotte
- Department of Biochemistry, Pavillon de Recherche Appliquée Sur le Cancer, Université de Sherbrooke, Sherbrooke, Québec, Canada
| | - Jean-Michel Garant
- Department of Biochemistry, Pavillon de Recherche Appliquée Sur le Cancer, Université de Sherbrooke, Sherbrooke, Québec, Canada
| | - Hélène Cossette-Roberge
- Department of Biochemistry, Pavillon de Recherche Appliquée Sur le Cancer, Université de Sherbrooke, Sherbrooke, Québec, Canada
| | - Jean-Pierre Perreault
- Department of Biochemistry, Pavillon de Recherche Appliquée Sur le Cancer, Université de Sherbrooke, Sherbrooke, Québec, Canada
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45
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Berlyoung AS, Armitage BA. Assembly and Characterization of RNA/DNA Hetero-G-Quadruplexes. Biochemistry 2020; 59:4072-4080. [PMID: 33048532 DOI: 10.1021/acs.biochem.0c00657] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Transient association of guanine-rich RNA and DNA in the form of hetero-G-quadruplexes (RDQs) has emerged as an important mechanism for regulating genome transcription and replication but relatively little is known about the structure and biophysical properties of RDQs compared with DNA and RNA homo-G-quadruplexes. Herein, we report the assembly and characterization of three RDQs based on sequence motifs found in human telomeres and mitochondrial nucleic acids. Stable RDQs were assembled using a duplex scaffold, which prevented segregation of the DNA and RNA strands into separate homo-GQs. Each of the RDQs exhibited UV melting temperatures above 50 °C in 100 mM KCl and predominantly parallel morphologies, evidently driven by the RNA component. The fluorogenic dye thioflavin T binds to each RDQ with low micromolar KD values, similar to its binding to RNA and DNA homo-GQs. These results establish a method for assembling RDQs that should be amenable to screening compounds and libraries to identify selective RDQ-binding small molecules, oligonucleotides, and proteins.
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Affiliation(s)
- April S Berlyoung
- Department of Chemistry and Center for Nucleic Acids Science and Technology, Carnegie Mellon University, 4400 Fifth Avenue, Pittsburgh, Pennsylvania 15213, United States
| | - Bruce A Armitage
- Department of Chemistry and Center for Nucleic Acids Science and Technology, Carnegie Mellon University, 4400 Fifth Avenue, Pittsburgh, Pennsylvania 15213, United States
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46
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Lee SH, Patel PC, Phan PH. Are the self-employed more stressed? New evidence on an old question. JOURNAL OF SMALL BUSINESS MANAGEMENT 2020. [DOI: 10.1080/00472778.2020.1796467] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Affiliation(s)
- Soo Hoon Lee
- Strome College of Business, Old Dominion University, USA
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Zhao J, Yang Z, Zhai Q, Wei D. Specific recognition of telomeric multimeric G-quadruplexes by a simple-structure quinoline derivative. Anal Chim Acta 2020; 1132:93-100. [PMID: 32980115 DOI: 10.1016/j.aca.2020.07.017] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2019] [Revised: 07/02/2020] [Accepted: 07/07/2020] [Indexed: 11/17/2022]
Abstract
The development of highly sensitive fluorescence probes for telomeric multimeric G-quadruplexes has attracted extensive attention. However, few probes reported have exhibited selectivity for telomeric multimeric G-quadruplexes. Thus, it is challenging to design fluorescence probes with high specificity and selectivity for telomeric multimeric G-quadruplexes. This study employed a commercially available quinoline derivative BEPQ-1 as an effective switch-on sensor for telomeric multimeric G-quadruplexes. The fluorescence intensity enhanced more than 20 folds upon the addition of telomeric multimeric G-quadruplexes. This probe exhibited good selectivity and sensitivity for telomeric multimeric G-quadruplexes. And the detection limit of BEPQ-1 for the telomeric multimeric G-quadruplex TTA45 was calculated to be 0.11 μM. The distinctive feature of BEPQ-1 is the simple structure and small size. In the light of binding mode, BEPQ-1 could even simultaneously bind to the end two G-quartets of the two adjacent G-quadruplex units in telomeric multimeric G-quadruplex by π-π stacking. To our knowledge, this is the first simple-structure fluorescence probe for telomeric multimeric G-quadruplex. This finding might provide a strategy to design specific probes for telomeric multimeric G-quadruplexes and contribute to understand the structures and functions of G-quadruplexes in the telomere region.
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Affiliation(s)
- Jingfang Zhao
- Department of Chemistry, College of Science, Huazhong Agricultural University, Wuhan, 430070, PR China
| | - Ziyan Yang
- Department of Chemistry, College of Science, Huazhong Agricultural University, Wuhan, 430070, PR China
| | - Qianqian Zhai
- Department of Chemistry, College of Science, Huazhong Agricultural University, Wuhan, 430070, PR China.
| | - Dengguo Wei
- College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, 430070, PR China; State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, 430070, PR China.
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48
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Lopera A, Aguilar JA, Belda R, Verdejo B, Steed JW, García-España E. Hybrid GMP-polyamine hydrogels as new biocompatible materials for drug encapsulation. SOFT MATTER 2020; 16:6514-6522. [PMID: 32597453 DOI: 10.1039/d0sm00704h] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Here we present the preparation and characterization of new biocompatible materials for drug encapsulation. These new gels are based on positively charged [1+1] 1H-pyrazole-based azamacrocycles which minimise the electrostatic repulsions between the negatively charged GMP molecules. Rheological measurements confirm the electroneutral hydrogel structure as the most stable for all the GMP-polyamine systems. Nuclear magnetic resonance (NMR) was employed to investigate the kinetics of the hydrogel formation and cryo-scanning electron microscopy (cryo-SEM) was used to obtain information about the hydrogel morphology, which exhibited a non-homogeneous structure with a high degree of cross-linking. It is possible to introduce isoniazid, which is the most employed antibiotic for tuberculosis treatment, into the hydrogels without disrupting the hydrogel structure at appropriate concentrations for oral administration.
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Affiliation(s)
- Alberto Lopera
- Departamento de Química Inorgánica, Instituto de Ciencia Molecular, Universidad de Valencia, Calle Catedrático José Beltrán 2, 46980 Paterna, Valencia, Spain.
| | - Juan A Aguilar
- Department of Chemistry, Durham University, South Road, DH1 3LE Durham, UK.
| | - Raquel Belda
- Department of Chemistry, Durham University, South Road, DH1 3LE Durham, UK.
| | - Begoña Verdejo
- Departamento de Química Inorgánica, Instituto de Ciencia Molecular, Universidad de Valencia, Calle Catedrático José Beltrán 2, 46980 Paterna, Valencia, Spain.
| | - Jonathan W Steed
- Department of Chemistry, Durham University, South Road, DH1 3LE Durham, UK.
| | - Enrique García-España
- Departamento de Química Inorgánica, Instituto de Ciencia Molecular, Universidad de Valencia, Calle Catedrático José Beltrán 2, 46980 Paterna, Valencia, Spain.
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Hu Y, Wang Y, Yan J, Wen N, Xiong H, Cai S, He Q, Peng D, Liu Z, Liu Y. Dynamic DNA Assemblies in Biomedical Applications. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2020; 7:2000557. [PMID: 32714763 PMCID: PMC7375253 DOI: 10.1002/advs.202000557] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/15/2020] [Revised: 04/07/2020] [Indexed: 05/13/2023]
Abstract
Deoxyribonucleic acid (DNA) has been widely used to construct homogeneous structures with increasing complexity for biological and biomedical applications due to their powerful functionalities. Especially, dynamic DNA assemblies (DDAs) have demonstrated the ability to simulate molecular motions and fluctuations in bionic systems. DDAs, including DNA robots, DNA probes, DNA nanochannels, DNA templates, etc., can perform structural transformations or predictable behaviors in response to corresponding stimuli and show potential in the fields of single molecule sensing, drug delivery, molecular assembly, etc. A wave of exploration of the principles in designing and usage of DDAs has occurred, however, knowledge on these concepts is still limited. Although some previous reviews have been reported, systematic and detailed reviews are rare. To achieve a better understanding of the mechanisms in DDAs, herein, the recent progress on the fundamental principles regarding DDAs and their applications are summarized. The relative assembly principles and computer-aided software for their designing are introduced. The advantages and disadvantages of each software are discussed. The motional mechanisms of the DDAs are classified into exogenous and endogenous stimuli-triggered responses. The special dynamic behaviors of DDAs in biomedical applications are also summarized. Moreover, the current challenges and future directions of DDAs are proposed.
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Affiliation(s)
- Yaqin Hu
- Department of Pharmaceutical EngineeringCollege of Chemistry and Chemical EngineeringCentral South UniversityChangshaHunan410083P. R. China
| | - Ying Wang
- Department of Pharmaceutical EngineeringCollege of Chemistry and Chemical EngineeringCentral South UniversityChangshaHunan410083P. R. China
| | - Jianhua Yan
- Xiangya School of Pharmaceutical SciencesCentral South UniversityChangshaHunan410013P. R. China
| | - Nachuan Wen
- Department of Pharmaceutical EngineeringCollege of Chemistry and Chemical EngineeringCentral South UniversityChangshaHunan410083P. R. China
| | - Hongjie Xiong
- Xiangya School of Pharmaceutical SciencesCentral South UniversityChangshaHunan410013P. R. China
| | - Shundong Cai
- Xiangya School of Pharmaceutical SciencesCentral South UniversityChangshaHunan410013P. R. China
| | - Qunye He
- Xiangya School of Pharmaceutical SciencesCentral South UniversityChangshaHunan410013P. R. China
| | - Dongming Peng
- Department of Medicinal ChemistrySchool of PharmacyHunan University of Chinese MedicineChangshaHunan410013P. R. China
| | - Zhenbao Liu
- Xiangya School of Pharmaceutical SciencesCentral South UniversityChangshaHunan410013P. R. China
- Molecular Imaging Research Center of Central South UniversityChangshaHunan410013P. R. China
| | - Yanfei Liu
- Department of Pharmaceutical EngineeringCollege of Chemistry and Chemical EngineeringCentral South UniversityChangshaHunan410083P. R. China
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Nickels M, Mastana S, Hunter D, Denniff M, Codd V, Akam E. The effect of a 12-week resistance training intervention on leukocyte telomere length. Heliyon 2020; 6:e04151. [PMID: 32551387 PMCID: PMC7292922 DOI: 10.1016/j.heliyon.2020.e04151] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2020] [Revised: 04/29/2020] [Accepted: 06/02/2020] [Indexed: 01/06/2023] Open
Abstract
Telomere dynamics are an active biological process and positive lifestyle factors such as exercise are proposed to potentiate their length. The aim of this study was to investigate the effect of a low-resistance, high-repetition resistance training intervention on leukocyte telomere length (LTL) and associated health parameters. 23 sedentary middle-aged adults volunteered for this study (16 female/7 male; age = 51.5 ± 4.9 years) and performed two one-hour sessions of Les Mills BODYPUMP™ per week for 12 weeks. Outcome measures were taken at baseline, after the training intervention and at 12-month follow-up. LTL remained unchanged following the training intervention (pre 0.819 ± 0.121 vs post 0.812 ± 0.114, p = 0.420), despite a borderline significant increase in hTERT expression (p = 0.050). Circulating levels of tumour necrosis factor alpha were reduced after the intervention (p = 0.001). At 12-month follow-up, subjects who returned to a sedentary lifestyle (n = 10) displayed shorter telomeres compared to their pre (p = 0.036) values. In conclusion, no changes were observed in LTL following the 12-week training intervention, despite improvements in molecular parameters associated with telomere dynamics. It appears continued long-term exercise (>12 months) is necessary to preserve LTL in previously sedentary individuals.
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Affiliation(s)
- Matt Nickels
- School of Sport, Exercise and Health Sciences, Loughborough University, Loughborough, Leicestershire, LE11 3TU, United Kingdom
| | - Sarabjit Mastana
- School of Sport, Exercise and Health Sciences, Loughborough University, Loughborough, Leicestershire, LE11 3TU, United Kingdom
| | - David Hunter
- School of Sport, Exercise and Health Sciences, Loughborough University, Loughborough, Leicestershire, LE11 3TU, United Kingdom
| | - Matthew Denniff
- Department of Cardiovascular Sciences, University of Leicester, Leicester, United Kingdom.,NIHR Leicester Cardiovascular Biomedical Research Unit, Glenfield Hospital, Leicester, LE3 9QP, United Kingdom
| | - Veryan Codd
- Department of Cardiovascular Sciences, University of Leicester, Leicester, United Kingdom.,NIHR Leicester Cardiovascular Biomedical Research Unit, Glenfield Hospital, Leicester, LE3 9QP, United Kingdom
| | - Elizabeth Akam
- School of Sport, Exercise and Health Sciences, Loughborough University, Loughborough, Leicestershire, LE11 3TU, United Kingdom
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