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Tao YH, Schulke S, Schwaab G, Nealon GL, Pezzotti S, Hodgetts SI, Harvey AR, Havenith M, Wallace VP. Hydration water drives the self-assembly of guanosine monophosphate. Biophys J 2024; 123:931-939. [PMID: 38454599 PMCID: PMC11052693 DOI: 10.1016/j.bpj.2024.03.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2023] [Revised: 03/04/2024] [Accepted: 03/04/2024] [Indexed: 03/09/2024] Open
Abstract
Guanosine monophosphate (GMP) is a nucleotide that can self-assemble in aqueous solution under certain conditions. An understanding of the process at the molecular level is an essential step to comprehend the involvement of DNA substructures in transcription and replication, as well as their relationship to genetic diseases such as cancer. We present the temperature-dependent terahertz (1.5-12 THz, 50-400 cm-1) absorptivity spectra of aqueous Na2 GMP solution in comparison with the aqueous solutions of other RNA nucleotides. Distinct absorption features were observed in the spectrum of GMP, which we attribute to the intramolecular modes of the self-assemblies (i.e., G-complexes) that, at 1 M, start to form at 313 K and below. Changes in broad-band features of the terahertz spectrum were also observed, which we associate with the release of hydration water in the temperature-dependent formation of guanine quadruplexes. Using a state-of-the-art THz calorimetry approach correlating spectroscopic to thermodynamic changes, we propose a molecular mechanism of hydrophilic hydration driving GMP self-assembly as a function of temperature. The free energy contribution of hydrophilic hydration is shown as a decisive factor in guanine-quadruplex formation. Our findings spotlight the role of hydration in the formation of macromolecular structures and suggest the potential of hydration tuning for regulating DNA transcription and replication.
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Affiliation(s)
- Yu Heng Tao
- Department of Physics, The University of Western Australia, Crawley, WA, Australia
| | - Simon Schulke
- Department of Physical Chemistry II, Ruhr University Bochum, Bochum, Germany
| | - Gerhard Schwaab
- Department of Physical Chemistry II, Ruhr University Bochum, Bochum, Germany
| | - Gareth L Nealon
- School of Molecular Sciences, The University of Western Australia, Crawley, WA, Australia; Centre for Microscopy, Characterisation and Analysis, The University of Western Australia, Crawley, WA, Australia
| | - Simone Pezzotti
- Department of Physical Chemistry II, Ruhr University Bochum, Bochum, Germany
| | - Stuart I Hodgetts
- School of Human Sciences, The University of Western Australia, Crawley, WA, Australia; Perron Institute for Neurological and Translational Science, Nedlands, WA, Australia
| | - Alan R Harvey
- School of Human Sciences, The University of Western Australia, Crawley, WA, Australia; Perron Institute for Neurological and Translational Science, Nedlands, WA, Australia
| | - Martina Havenith
- Department of Physical Chemistry II, Ruhr University Bochum, Bochum, Germany.
| | - Vincent P Wallace
- Department of Physics, The University of Western Australia, Crawley, WA, Australia.
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Dong T, Yu P, Zhao J, Wang J. Site specifically probing the unfolding process of human telomere i-motif DNA using vibrationally enhanced alkynyl stretch. Phys Chem Chem Phys 2024; 26:3857-3868. [PMID: 38224126 DOI: 10.1039/d3cp05328h] [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: 01/16/2024]
Abstract
The microscopic unfolding process of a cytosine-rich DNA forming i-motif by hemi-protonated base pairs is related to gene regulation. However, the detailed thermal unfolding mechanism and the protonation/deprotonation status of site-specific cytosine in DNA in a physiological environment are still obscure. To address this issue, a vibration-enhanced CC probe tagged on 5'E terminal cytosine of human telomere i-motif DNA was examined using linear and nonlinear infrared (IR) spectroscopies and quantum-chemistry calculations. The CC probe extended into the major groove of the i-motif was found using nonlinear IR results only to introduce a minor steric effect on both steady-state structure and local structure dynamics; however, its IR absorption profile effectively reports the cleavage of the hemi-protonated base pair of C1-C13 upon the unfolding with C1 remaining protonated. The temperature mid-point (Tm) of the local transition reported using the CC tag was slightly lower than the Tm of global transition, and the enthalpy of the former exceeds 60% of the global transition. It is shown that the base-pair unraveling is noncooperative, with outer base pairs breaking first and being likely the rate limiting step. Our results offered an in-depth understanding of the macroscopic unfolding characteristics of the i-motif DNA and provided a nonlinear IR approach to monitoring the local structural transition and dynamics of DNA and its complexes.
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Affiliation(s)
- Tiantian Dong
- Beijing National Laboratory for Molecular Sciences, Molecular Reaction Dynamics Laboratory, CAS Research/Education Center for Excellence in Molecular Sciences, Institute of Chemistry, Chinese Academy of Sciences, Beijing, 100190, P. R. China.
- University of Chinese Academy of Sciences, Beijing 100049, P. R. China
| | - Pengyun Yu
- Beijing National Laboratory for Molecular Sciences, Molecular Reaction Dynamics Laboratory, CAS Research/Education Center for Excellence in Molecular Sciences, Institute of Chemistry, Chinese Academy of Sciences, Beijing, 100190, P. R. China.
- University of Chinese Academy of Sciences, Beijing 100049, P. R. China
| | - Juan Zhao
- Beijing National Laboratory for Molecular Sciences, Molecular Reaction Dynamics Laboratory, CAS Research/Education Center for Excellence in Molecular Sciences, Institute of Chemistry, Chinese Academy of Sciences, Beijing, 100190, P. R. China.
- University of Chinese Academy of Sciences, Beijing 100049, P. R. China
| | - Jianping Wang
- Beijing National Laboratory for Molecular Sciences, Molecular Reaction Dynamics Laboratory, CAS Research/Education Center for Excellence in Molecular Sciences, Institute of Chemistry, Chinese Academy of Sciences, Beijing, 100190, P. R. China.
- University of Chinese Academy of Sciences, Beijing 100049, P. R. China
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Lawler NB, Ou A, King JJ, Evans CW, Iyer KS, Smith NM. G4-DNA formation and chromatin remodelling are interdependent in human cells. Chem Sci 2023; 14:7681-7687. [PMID: 37476710 PMCID: PMC10355101 DOI: 10.1039/d3sc02533k] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2023] [Accepted: 06/18/2023] [Indexed: 07/22/2023] Open
Abstract
DNA G-quadruplexes (G4s) have been identified as important biological targets for transcriptional, translational, and epigenetic regulation. The stabilisation of G4s with small molecule ligands has emerged as a technique to regulate gene expression and as a potential therapeutic approach for human diseases. Here, we demonstrate that ligand stabilisation of G4s causes altered chromatin accessibility dependent on the targeting specificity of the molecule. In particular, stabilisation of a target G4 using the highly specific GTC365 ligand resulted in differential accessibility of 61 genomic regions, while the broad-targeting G4 ligand, GQC-05, stabilised many G4s and induced a global shift towards increased accessibility of gene promoter regions. Interestingly, while we observed distinct effects of each ligand on RNA expression levels and the induction of DNA double-stranded breaks, both ligands modified DNA damage response pathways. Our work represents the dual possibility of G4-stabilising ligands for specific or global chromatin modulation via unique targeting characteristics.
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Affiliation(s)
- Nicholas B Lawler
- School of Molecular Sciences, The University of Western Australia Perth WA Australia
- School of Physics, Mathematics and Computing, The University of Western Australia Perth WA Australia
| | - Arnold Ou
- School of Molecular Sciences, The University of Western Australia Perth WA Australia
| | - Jessica J King
- School of Molecular Sciences, The University of Western Australia Perth WA Australia
| | - Cameron W Evans
- School of Molecular Sciences, The University of Western Australia Perth WA Australia
| | - K Swaminathan Iyer
- School of Molecular Sciences, The University of Western Australia Perth WA Australia
| | - Nicole M Smith
- School of Molecular Sciences, The University of Western Australia Perth WA Australia
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Wang J, Zhang X, You Z, Meng Y, Fan X, Qiao G, Pang D. RNA atlas and competing endogenous RNA regulation in tissue-derived exosomes from luminal B and triple-negative breast cancer patients. Front Oncol 2023; 13:1113115. [PMID: 37483500 PMCID: PMC10361514 DOI: 10.3389/fonc.2023.1113115] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2022] [Accepted: 01/26/2023] [Indexed: 07/25/2023] Open
Abstract
Background Luminal B and triple-negative breast cancer (TNBC) are malignant subtypes of breast cancer (BC), which can be attributed to the multifaceted roles of tissue-derived exosomes (T-exos). Competing endogenous RNA (ceRNA) networks can regulate gene expression post-transcriptionally. Methods RNAs in T-exos from luminal B BC (n=8) and TNBC (n=8) patients were compared with those from persons with benign breast disease (n=8). The differentially expressed (DE) mRNA, microRNA (miRNA), and long noncoding RNA (lncRNA) target genes were annotated using Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) to reveal the relevant biological processes.The ceRNA networks were constructed to show distinct regulation, and the mRNAs involved were annotated. The miRNAs involved in the ceRNA networks were screened with the Kaplan-Meier Plotter database to identify dysregulated ceRNAs with prognostic power. Results In total, 802 DE mRNAs, 441 DE lncRNAs, and 104 DE miRNAs were identified in luminal B BC T-exos, while 1699 DE mRNAs, 590 DE lncRNAs, and 277 DE miRNAs were identified in TNBC T-exos. Gene annotation revealed that the RAS-MAPK pathway was the primary biological process in luminal B BC T-exos, while endocrine system development and growth were the main processes in TNBC T-exos. Survival analysis established seven survival-related lncRNA/miRNA/mRNA regulations in luminal B BC T-exos, and nineteen survival-related lncRNA/miRNA/mRNA regulations in TNBC T-exos. Conclusion In addition to survival-related ceRNA regulations, ceRNA regulation of RAS-MAPK in luminal B and endocrine system development and growth regulation in TNBC might contribute to the tumorigenesis of BC.
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Affiliation(s)
- Ji Wang
- Medical Translational Research Institute, Guangzhou KingMed Center for Clinical Laboratory Co., Ltd, Guangzhou, China
- Department of Breast Surgery, Yantai Yuhuangding Hospital, Yantai, China
| | - Xianyu Zhang
- Department of Breast Surgery, Harbin Medical University Cancer Hospital, Harbin, China
| | - Zilong You
- Medical Translational Research Institute, Guangzhou KingMed Center for Clinical Laboratory Co., Ltd, Guangzhou, China
| | - Yuhuan Meng
- Medical Translational Research Institute, Guangzhou KingMed Center for Clinical Laboratory Co., Ltd, Guangzhou, China
| | - Xijie Fan
- Medical Translational Research Institute, Guangzhou KingMed Center for Clinical Laboratory Co., Ltd, Guangzhou, China
| | - Guangdong Qiao
- Department of Breast Surgery, Yantai Yuhuangding Hospital, Yantai, China
| | - Da Pang
- Department of Breast Surgery, Harbin Medical University Cancer Hospital, Harbin, China
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Luo X, Zhang J, Gao Y, Pan W, Yang Y, Li X, Chen L, Wang C, Wang Y. Emerging roles of i-motif in gene expression and disease treatment. Front Pharmacol 2023; 14:1136251. [PMID: 37021044 PMCID: PMC10067743 DOI: 10.3389/fphar.2023.1136251] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2023] [Accepted: 02/27/2023] [Indexed: 03/22/2023] Open
Abstract
As non-canonical nucleic acid secondary structures consisting of cytosine-rich nucleic acids, i-motifs can form under certain conditions. Several i-motif sequences have been identified in the human genome and play important roles in biological regulatory functions. Due to their physicochemical properties, these i-motif structures have attracted attention and are new targets for drug development. Herein, we reviewed the characteristics and mechanisms of i-motifs located in gene promoters (including c-myc, Bcl-2, VEGF, and telomeres), summarized various small molecule ligands that interact with them, and the possible binding modes between ligands and i-motifs, and described their effects on gene expression. Furthermore, we discussed diseases closely associated with i-motifs. Among these, cancer is closely associated with i-motifs since i-motifs can form in some regions of most oncogenes. Finally, we introduced recent advances in the applications of i-motifs in multiple areas.
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Affiliation(s)
| | | | | | | | | | | | | | - Chang Wang
- *Correspondence: Chang Wang, ; Yuqing Wang,
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Ten Years of CRISPRing Cancers In Vitro. Cancers (Basel) 2022; 14:cancers14235746. [PMID: 36497228 PMCID: PMC9738354 DOI: 10.3390/cancers14235746] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2022] [Revised: 11/21/2022] [Accepted: 11/22/2022] [Indexed: 11/24/2022] Open
Abstract
Cell lines have always constituted a good investigation tool for cancer research, allowing scientists to understand the basic mechanisms underlying the complex network of phenomena peculiar to the transforming path from a healthy to cancerous cell. The introduction of CRISPR in everyday laboratory activity and its relative affordability greatly expanded the bench lab weaponry in the daily attempt to better understand tumor biology with the final aim to mitigate cancer's impact in our lives. In this review, we aim to report how this genome editing technique affected in the in vitro modeling of different aspects of tumor biology, its several declinations, and analyze the advantages and drawbacks of each of them.
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Mondal M, Gao YQ. Microscopic Insight into pH-Dependent Conformational Dynamics and Noncanonical Base Pairing in Telomeric i-Motif DNA. J Phys Chem Lett 2022; 13:5109-5115. [PMID: 35657602 DOI: 10.1021/acs.jpclett.2c00640] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Gene regulatory functions of noncanonical i-motif DNA are associated with dynamic i-motif formation in the cellular environment and pH variation. With atomistic simulations, we show the dramatic influence of solvent pH on the conformational dynamics of biologically relevant telomeric i-motif DNA coupled with protonation of cytosine bases in different conformations. We rationalized the pH-dependent dynamics and conformational variability of the i-motif in terms of base pairing and specific loop motions. The human telomeric i-motif is found to acquire various metastable folded conformations at pH values near the pKa of cytosine with the formation of a noncanonical C:C W:W trans base pair along with the hemiprotonated C:C+ pairs in the i-motif core. pH-dependent dynamics and the local solvent structure of i-motif DNA imply that the presence of a cosolvent or molecular crowding can promote i-motif formation in vivo by changing the conformational fluctuations and hydration state of the structure.
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Affiliation(s)
- Manas Mondal
- Institute of Systems and Physical Biology, Shenzhen Bay Laboratory, 518107 Shenzhen, China
| | - Yi Qin Gao
- Institute of Systems and Physical Biology, Shenzhen Bay Laboratory, 518107 Shenzhen, China
- Beijing National Laboratory for Molecular Sciences, College of Chemistry and Molecular Engineering, Peking University, 100871 Beijing, China
- Biomedical Pioneering Innovation Center, Peking University, 100871 Beijing, China
- Beijing Advanced Innovation Center for Genomics, Peking University, 100871 Beijing, China
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Stability and context of intercalated motifs (i-motifs) for biological applications. Biochimie 2022; 198:33-47. [PMID: 35259471 DOI: 10.1016/j.biochi.2022.03.001] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2021] [Revised: 02/21/2022] [Accepted: 03/03/2022] [Indexed: 11/24/2022]
Abstract
DNA is naturally dynamic and can self-assemble into alternative secondary structures including the intercalated motif (i-motif), a four-stranded structure formed in cytosine-rich DNA sequences. Until recently, i-motifs were thought to be unstable in physiological cellular environments. Studies demonstrating their existence in the human genome and role in gene regulation are now shining light on their biological relevance. Herein, we review the effects of epigenetic modifications on i-motif structure and stability, and biological factors that affect i-motif formation within cells. Furthermore, we highlight recent progress in targeting i-motifs with structure-specific ligands for biotechnology and therapeutic purposes.
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Affiliation(s)
- Danzhou Yang
- Purdue University, College of Pharmacy, Medicinal Chemistry and Molecular Pharmacology, 575 W Stadium Ave., West Lafayette, IN 47907, USA,Purdue University Center for Cancer Research, 201 S University St, West Lafayette, IN 47906, USA,Purdue University, Department of Chemistry, West Lafayette, IN, USA,Purdue Institute for Drug Discovery, West Lafayette, IN, USA
| | - Jonathan Dickerhoff
- Purdue University, College of Pharmacy, Medicinal Chemistry and Molecular Pharmacology, 575 W Stadium Ave., West Lafayette, IN 47907, USA
| | - William S Dynan
- Emory University School of Medicine, Department of Radiation Oncology, Department of Biochemistry, and Winship Cancer Institute, 1510 Clifton Rd NE, Atlanta GA 30322, USA
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