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Minero GA, Møllebjerg A, Thiesen C, Johansen M, Jørgensen N, Birkedal V, Otzen DE, Meyer R. Extracellular G-quadruplexes and Z-DNA protect biofilms from DNase I, and G-quadruplexes form a DNAzyme with peroxidase activity. Nucleic Acids Res 2024; 52:1575-1590. [PMID: 38296834 PMCID: PMC10939358 DOI: 10.1093/nar/gkae034] [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: 06/30/2023] [Revised: 01/04/2024] [Accepted: 01/10/2024] [Indexed: 02/02/2024] Open
Abstract
Many bacteria form biofilms to protect themselves from predators or stressful environmental conditions. In the biofilm, bacteria are embedded in a protective extracellular matrix composed of polysaccharides, proteins and extracellular DNA (eDNA). eDNA most often is released from lysed bacteria or host mammalian cells, and it is the only matrix component most biofilms appear to have in common. However, little is known about the form DNA takes in the extracellular space, and how different non-canonical DNA structures such as Z-DNA or G-quadruplexes might contribute to its function in the biofilm. The aim of this study was to determine if non-canonical DNA structures form in eDNA-rich staphylococcal biofilms, and if these structures protect the biofilm from degradation by nucleases. We grew Staphylococcus epidermidis biofilms in laboratory media supplemented with hemin and NaCl to stabilize secondary DNA structures and visualized their location by immunolabelling and fluorescence microscopy. We furthermore visualized the macroscopic biofilm structure by optical coherence tomography. We developed assays to quantify degradation of Z-DNA and G-quadruplex DNA oligos by different nucleases, and subsequently investigated how these enzymes affected eDNA in the biofilms. Z-DNA and G-quadruplex DNA were abundant in the biofilm matrix, and were often present in a web-like structures. In vitro, the structures did not form in the absence of NaCl or mechanical shaking during biofilm growth, or in bacterial strains deficient in eDNA or exopolysaccharide production. We thus infer that eDNA and polysaccharides interact, leading to non-canonical DNA structures under mechanical stress when stabilized by salt. We also confirmed that G-quadruplex DNA and Z-DNA was present in biofilms from infected implants in a murine implant-associated osteomyelitis model. Mammalian DNase I lacked activity against Z-DNA and G-quadruplex DNA, while Micrococcal nuclease could degrade G-quadruplex DNA and S1 Aspergillus nuclease could degrade Z-DNA. Micrococcal nuclease, which originates from Staphylococcus aureus, may thus be key for dispersal of biofilm in staphylococci. In addition to its structural role, we show for the first time that the eDNA in biofilms forms a DNAzyme with peroxidase-like activity in the presence of hemin. While peroxidases are part of host defenses against pathogens, we now show that biofilms can possess intrinsic peroxidase activity in the extracellular matrix.
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Affiliation(s)
| | - Andreas Møllebjerg
- Interdisciplinary Nanoscience Center (iNANO), Aarhus University, Gustav Wieds Vej 14, 8000 Aarhus, Denmark
| | - Celine Thiesen
- Interdisciplinary Nanoscience Center (iNANO), Aarhus University, Gustav Wieds Vej 14, 8000 Aarhus, Denmark
| | - Mikkel Illemann Johansen
- Department Infectious Diseases, Aarhus University Hospital, Palle Juul-Jensens bvld 99, 8200 Aarhus N, Denmark
| | - Nis Pedersen Jørgensen
- Department Infectious Diseases, Aarhus University Hospital, Palle Juul-Jensens bvld 99, 8200 Aarhus N, Denmark
| | - Victoria Birkedal
- Interdisciplinary Nanoscience Center (iNANO), Aarhus University, Gustav Wieds Vej 14, 8000 Aarhus, Denmark
- Department of Chemistry, Aarhus University, Langelandsgade 140, 8000 Aarhus, Denmark
| | - Daniel Erik Otzen
- Interdisciplinary Nanoscience Center (iNANO), Aarhus University, Gustav Wieds Vej 14, 8000 Aarhus, Denmark
- Department of Molecular Biology and Genetics, Aarhus University, Universitetsbyen 81, 8000 Aarhus, Denmark
| | - Rikke Louise Meyer
- Interdisciplinary Nanoscience Center (iNANO), Aarhus University, Gustav Wieds Vej 14, 8000 Aarhus, Denmark
- Department of Biology, Aarhus University, Ny Munkegade 114, 8000 Aarhus, Denmark
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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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Russo G, Notarstefano V, Montik N, Gioacchini G, Giorgini E, Polidori AR, Candela FA, Ciavattini A, Cignitti M, Carnevali O. Evaluation of Controlled Ovarian Stimulation Protocols in Patients with Normal and Low Ovarian Reserve: Analyses of miRNAs and Selected Target Genes Involved in the Proliferation of Human Cumulus Cells and Oocyte Quality. Int J Mol Sci 2022; 23:ijms23031713. [PMID: 35163635 PMCID: PMC8836191 DOI: 10.3390/ijms23031713] [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: 11/08/2021] [Revised: 01/22/2022] [Accepted: 01/30/2022] [Indexed: 02/01/2023] Open
Abstract
The oocyte and the surrounding cumulus cells (CCs) are deeply linked by a complex bidirectional cross-talk. In this light, the molecular analysis of the CCs is nowadays considered to be precious in providing information on oocyte quality. It is now clear that miRNAs play a key role in several ovarian functions, such as folliculogenesis, steroidogenesis, and ovulation. Thus, in this study, specific miRNAs, together with their target genes, were selected and investigated in CCs to assess the response of patients with normal (NR) and low (LR) ovarian reserve to two different controlled ovarian stimulation (COS) protocols, based on rFSH and hMG. Moreover, a Fourier transform infrared microspectroscopy (FTIRM) analysis was performed to evaluate DNA conformational changes in CCs and to relate them with the two COS protocols. The results evidenced a modulation of the expression of miRNAs and related target genes involved in CCs’ proliferation, in vasculogenesis, angiogenesis, genomic integrity, and oocyte quality, with different effects according to the ovarian reserve of patients. Moreover, the COS protocols determined differences in DNA conformation and the methylation state. In particular, the results clearly showed that treatment with rFSH is the most appropriate in NR patients with normal ovarian reserve, while treatment with hMG appears to be the most suitable in LR patients with low ovarian reserve.
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Affiliation(s)
- Giulia Russo
- Department of Life and Environmental Sciences, Università Politecnica delle Marche, Via Brecce Bianche, 60131 Ancona, Italy; (G.R.); (V.N.); (G.G.); (E.G.)
| | - Valentina Notarstefano
- Department of Life and Environmental Sciences, Università Politecnica delle Marche, Via Brecce Bianche, 60131 Ancona, Italy; (G.R.); (V.N.); (G.G.); (E.G.)
| | - Nina Montik
- Clinica Ostetrica Ginecologica, Università Politecnica delle Marche, Ospedale G. Salesi, Via F. Corridoni 11, 60131 Ancona, Italy; (N.M.); (A.R.P.); (F.A.C.); (A.C.); (M.C.)
| | - Giorgia Gioacchini
- Department of Life and Environmental Sciences, Università Politecnica delle Marche, Via Brecce Bianche, 60131 Ancona, Italy; (G.R.); (V.N.); (G.G.); (E.G.)
| | - Elisabetta Giorgini
- Department of Life and Environmental Sciences, Università Politecnica delle Marche, Via Brecce Bianche, 60131 Ancona, Italy; (G.R.); (V.N.); (G.G.); (E.G.)
| | - Anna Rita Polidori
- Clinica Ostetrica Ginecologica, Università Politecnica delle Marche, Ospedale G. Salesi, Via F. Corridoni 11, 60131 Ancona, Italy; (N.M.); (A.R.P.); (F.A.C.); (A.C.); (M.C.)
| | - Fulvia Antonia Candela
- Clinica Ostetrica Ginecologica, Università Politecnica delle Marche, Ospedale G. Salesi, Via F. Corridoni 11, 60131 Ancona, Italy; (N.M.); (A.R.P.); (F.A.C.); (A.C.); (M.C.)
| | - Andrea Ciavattini
- Clinica Ostetrica Ginecologica, Università Politecnica delle Marche, Ospedale G. Salesi, Via F. Corridoni 11, 60131 Ancona, Italy; (N.M.); (A.R.P.); (F.A.C.); (A.C.); (M.C.)
| | - Maurizio Cignitti
- Clinica Ostetrica Ginecologica, Università Politecnica delle Marche, Ospedale G. Salesi, Via F. Corridoni 11, 60131 Ancona, Italy; (N.M.); (A.R.P.); (F.A.C.); (A.C.); (M.C.)
| | - Oliana Carnevali
- Department of Life and Environmental Sciences, Università Politecnica delle Marche, Via Brecce Bianche, 60131 Ancona, Italy; (G.R.); (V.N.); (G.G.); (E.G.)
- Correspondence: ; Tel.: +39-071-2204940
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Liu M, Cui Y, Zhang Y, An R, Li L, Park S, Sugiyama H, Liang X. Single base-modification reports and locates Z-DNA conformation on a Z-B-chimera formed by topological constraint. BULLETIN OF THE CHEMICAL SOCIETY OF JAPAN 2022. [DOI: 10.1246/bcsj.20210400] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Affiliation(s)
- Mengqin Liu
- College of Food Science and Engineering, Ocean University of China, Qingdao 266003, P. R. China
| | - Yixiao Cui
- College of Food Science and Engineering, Ocean University of China, Qingdao 266003, P. R. China
| | - Yaping Zhang
- College of Food Science and Engineering, Ocean University of China, Qingdao 266003, P. R. China
| | - Ran An
- College of Food Science and Engineering, Ocean University of China, Qingdao 266003, P. R. China
- Laboratory for Marine Drugs and Bioproducts, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266235, P. R. China
| | - Lin Li
- College of Food Science and Engineering, Ocean University of China, Qingdao 266003, P. R. China
| | - Soyoung Park
- Immunology Frontier Research Center, Osaka University, 3-1, Yamadaoka, Suita, Osaka 565-0871, Japan
| | - Hiroshi Sugiyama
- Department of Chemistry, Graduate School of Science, Kyoto University, Kitashirakawa-oiwakecho, Sakyo-ku, Kyoto 606-8502, Japan
| | - Xingguo Liang
- College of Food Science and Engineering, Ocean University of China, Qingdao 266003, P. R. China
- Laboratory for Marine Drugs and Bioproducts, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266235, P. R. China
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Kameda T, Awazu A, Togashi Y. Molecular dynamics analysis of biomolecular systems including nucleic acids. Biophys Physicobiol 2022; 19:e190027. [DOI: 10.2142/biophysico.bppb-v19.0027] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2022] [Accepted: 08/18/2022] [Indexed: 12/01/2022] Open
Affiliation(s)
| | - Akinori Awazu
- Graduate School of Integrated Sciences for Life, Hiroshima University
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Li L, Zhang Y, Ma W, Chen H, Liu M, An R, Cheng B, Liang X. Nonalternating purine pyrimidine sequences can form stable left-handed DNA duplex by strong topological constraint. Nucleic Acids Res 2021; 50:684-696. [PMID: 34967416 PMCID: PMC8789069 DOI: 10.1093/nar/gkab1283] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2021] [Revised: 12/01/2021] [Accepted: 12/16/2021] [Indexed: 11/14/2022] Open
Abstract
In vivo, left-handed DNA duplex (usually refers to Z-DNA) is mainly formed in the region of DNA with alternating purine pyrimidine (APP) sequence and plays significant biological roles. It is well known that d(CG)n sequence can form Z-DNA most easily under negative supercoil conditions, but its essence has not been well clarified. The study on sequence dependence of Z-DNA stability is very difficult without modification or inducers. Here, by the strong topological constraint caused by hybridization of two complementary short circular ssDNAs, left-handed duplex part was generated for various sequences, and their characteristics were investigated by using gel-shift after binding to specific proteins, CD and Tm analysis, and restriction enzyme cleavage. Under the strong topological constraint, non-APP sequences can also form left-handed DNA duplex as stable as that of APP sequences. As compared with non-APP sequences, the thermal stability difference for APP sequences between Z-form and B-form is smaller, which may be the reason that Z-DNA forms preferentially for APP ones. This result can help us to understand why nature selected APP sequences to regulate gene expression by transient Z-DNA formation, as well as why polymer with chirality can usually form both duplexes with left- or right-handed helix.
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Affiliation(s)
- Lin Li
- College of Food Science and Engineering, Ocean University of China, Qingdao 266003, China
| | - Yaping Zhang
- College of Food Science and Engineering, Ocean University of China, Qingdao 266003, China
| | - Wanzhi Ma
- College of Food Science and Engineering, Ocean University of China, Qingdao 266003, China
| | - Hui Chen
- College of Food Science and Engineering, Ocean University of China, Qingdao 266003, China
| | - Mengqin Liu
- College of Food Science and Engineering, Ocean University of China, Qingdao 266003, China
| | - Ran An
- College of Food Science and Engineering, Ocean University of China, Qingdao 266003, China.,Laboratory for Marine Drugs and Bioproducts, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266235, China
| | - Bingxiao Cheng
- College of Food Science and Engineering, Ocean University of China, Qingdao 266003, China
| | - Xingguo Liang
- College of Food Science and Engineering, Ocean University of China, Qingdao 266003, China.,Laboratory for Marine Drugs and Bioproducts, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266235, China
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7
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Kanapeckaitė A, Burokienė N, Mažeikienė A, Cottrell GS, Widera D. Biophysics is reshaping our perception of the epigenome: from DNA-level to high-throughput studies. BIOPHYSICAL REPORTS 2021; 1:100028. [PMID: 36425454 PMCID: PMC9680810 DOI: 10.1016/j.bpr.2021.100028] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/26/2021] [Accepted: 09/24/2021] [Indexed: 06/16/2023]
Abstract
Epigenetic research holds great promise to advance our understanding of biomarkers and regulatory processes in health and disease. An increasing number of new approaches, ranging from molecular to biophysical analyses, enable identifying epigenetic changes on the level of a single gene or the whole epigenome. The aim of this review is to highlight how the field is shifting from completely molecular-biology-driven solutions to multidisciplinary strategies including more reliance on biophysical analysis tools. Biophysics not only offers technical advancements in imaging or structure analysis but also helps to explore regulatory interactions. New computational methods are also being developed to meet the demand of growing data volumes and their processing. Therefore, it is important to capture these new directions in epigenetics from a biophysical perspective and discuss current challenges as well as multiple applications of biophysical methods and tools. Specifically, we gradually introduce different biophysical research methods by first considering the DNA-level information and eventually higher-order chromatin structures. Moreover, we aim to highlight that the incorporation of bioinformatics, machine learning, and artificial intelligence into biophysical analysis allows gaining new insights into complex epigenetic processes. The gained understanding has already proven useful in translational and clinical research providing better patient stratification options or new therapeutic insights. Together, this offers a better readiness to transform bench-top experiments into industrial high-throughput applications with a possibility to employ developed methods in clinical practice and diagnostics.
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Affiliation(s)
- Austė Kanapeckaitė
- Algorithm379, Laisvės g. 7, LT 12007, Vilnius, Lithuania
- Reading School of Pharmacy, Whiteknights, Reading, UK, RG6 6UB
| | - Neringa Burokienė
- Clinics of Internal Diseases, Family Medicine and Oncology, Institute of Clinical Medicine, Faculty of Medicine, Vilnius University, M. K. Čiurlionio str. 21/27, LT-03101 Vilnius, Lithuania
| | - Asta Mažeikienė
- Department of Physiology, Biochemistry, Microbiology and Laboratory Medicine, Institute of Biomedical Sciences, Faculty of Medicine, M. K. Čiurlionio str. 21/27, LT-03101 Vilnius, Lithuania
| | | | - Darius Widera
- Reading School of Pharmacy, Whiteknights, Reading, UK, RG6 6UB
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Buzzo JR, Devaraj A, Gloag ES, Jurcisek JA, Robledo-Avila F, Kesler T, Wilbanks K, Mashburn-Warren L, Balu S, Wickham J, Novotny LA, Stoodley P, Bakaletz LO, Goodman SD. Z-form extracellular DNA is a structural component of the bacterial biofilm matrix. Cell 2021; 184:5740-5758.e17. [PMID: 34735796 DOI: 10.1016/j.cell.2021.10.010] [Citation(s) in RCA: 60] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2021] [Revised: 08/03/2021] [Accepted: 10/12/2021] [Indexed: 12/30/2022]
Abstract
Biofilms are community architectures adopted by bacteria inclusive of a self-formed extracellular matrix that protects resident bacteria from diverse environmental stresses and, in many species, incorporates extracellular DNA (eDNA) and DNABII proteins for structural integrity throughout biofilm development. Here, we present evidence that this eDNA-based architecture relies on the rare Z-form. Z-form DNA accumulates as biofilms mature and, through stabilization by the DNABII proteins, confers structural integrity to the biofilm matrix. Indeed, substances known to drive B-DNA into Z-DNA promoted biofilm formation whereas those that drive Z-DNA into B-DNA disrupted extant biofilms. Importantly, we demonstrated that the universal bacterial DNABII family of proteins stabilizes both bacterial- and host-eDNA in the Z-form in situ. A model is proposed that incorporates the role of Z-DNA in biofilm pathogenesis, innate immune response, and immune evasion.
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Affiliation(s)
- John R Buzzo
- Center for Microbial Pathogenesis, Abigail Wexner Research Institute at Nationwide Children's Hospital, Columbus, OH 43205, USA
| | - Aishwarya Devaraj
- Center for Microbial Pathogenesis, Abigail Wexner Research Institute at Nationwide Children's Hospital, Columbus, OH 43205, USA
| | - Erin S Gloag
- Department of Orthopedics, Ohio State University, Columbus, OH 43210, USA
| | - Joseph A Jurcisek
- Center for Microbial Pathogenesis, Abigail Wexner Research Institute at Nationwide Children's Hospital, Columbus, OH 43205, USA
| | - Frank Robledo-Avila
- Center for Microbial Pathogenesis, Abigail Wexner Research Institute at Nationwide Children's Hospital, Columbus, OH 43205, USA
| | - Theresa Kesler
- Center for Microbial Pathogenesis, Abigail Wexner Research Institute at Nationwide Children's Hospital, Columbus, OH 43205, USA
| | - Kathryn Wilbanks
- Center for Microbial Pathogenesis, Abigail Wexner Research Institute at Nationwide Children's Hospital, Columbus, OH 43205, USA
| | - Lauren Mashburn-Warren
- The Steve and Cindy Rasmussen Institute for Genomic Medicine, Abigail Wexner Research Institute at Nationwide Children's Hospital, Columbus, OH 43205, USA
| | - Sabarathnam Balu
- Center for Microbial Pathogenesis, Abigail Wexner Research Institute at Nationwide Children's Hospital, Columbus, OH 43205, USA
| | - Joseph Wickham
- Center for Microbial Pathogenesis, Abigail Wexner Research Institute at Nationwide Children's Hospital, Columbus, OH 43205, USA
| | - Laura A Novotny
- Center for Microbial Pathogenesis, Abigail Wexner Research Institute at Nationwide Children's Hospital, Columbus, OH 43205, USA
| | - Paul Stoodley
- Department of Orthopedics, Ohio State University, Columbus, OH 43210, USA; Department of Microbial Infection and Immunity, Ohio State University, Columbus, OH 43210, USA; National Centre for Advanced Tribology at Southampton, University of Southampton, Southampton S017 1BJ, UK
| | - Lauren O Bakaletz
- Center for Microbial Pathogenesis, Abigail Wexner Research Institute at Nationwide Children's Hospital, Columbus, OH 43205, USA; Department of Pediatrics, College of Medicine, Ohio State University, Columbus, OH 43210, USA.
| | - Steven D Goodman
- Center for Microbial Pathogenesis, Abigail Wexner Research Institute at Nationwide Children's Hospital, Columbus, OH 43205, USA; Department of Pediatrics, College of Medicine, Ohio State University, Columbus, OH 43210, USA.
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9
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Liang R, Li X, Li W, Zhu X, Li C. DNA methylation in lung cancer patients: Opening a "window of life" under precision medicine. Biomed Pharmacother 2021; 144:112202. [PMID: 34654591 DOI: 10.1016/j.biopha.2021.112202] [Citation(s) in RCA: 42] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2021] [Revised: 09/07/2021] [Accepted: 09/13/2021] [Indexed: 12/20/2022] Open
Abstract
DNA methylation is a work of adding a methyl group to the 5th carbon atom of cytosine in DNA sequence under the catalysis of DNA methyltransferase (DNMT) to produce 5-methyl cytosine. Some current studies have elucidated the mechanism of lung cancer occurrence and causes of lung cancer progression and metastasis from the perspective of DNA methylation. Moreover, many studies have shown that smoking can change the methylation status of some gene loci, leading to the occurrence of lung cancer, especially central lung cancer. This review mainly introduces the role of DNA methylation in the pathogenesis, early diagnosis and screening, progression and metastasis, treatment, and prognosis of lung cancer, as well as the latest progress. We point out that methylation markers, sample tests, and methylation detection limit the clinical application of DNA methylation. If the liquid biopsy is to become the main force in lung cancer diagnosis, it must make efficient use of limited samples and improve the sensitivity and specificity of the tests. In addition, we also put forward our views on the future development direction of DNA methylation.
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Affiliation(s)
- Runzhang Liang
- School of Laboratory Medicine, Hangzhou Medical College, Hangzhou 310053, China; Southern Marine Science and Engineering Guangdong Laboratory (Zhanjiang), Guangdong Medical University, Zhanjiang 524023, China
| | - Xiaosong Li
- Clinical Molecular Medicine Testing Center, The First Affiliated Hospital of Chongqing Medical University, Chongqing 400016, China
| | - Weiquan Li
- Southern Marine Science and Engineering Guangdong Laboratory (Zhanjiang), Guangdong Medical University, Zhanjiang 524023, China
| | - Xiao Zhu
- School of Laboratory Medicine, Hangzhou Medical College, Hangzhou 310053, China; Southern Marine Science and Engineering Guangdong Laboratory (Zhanjiang), Guangdong Medical University, Zhanjiang 524023, China.
| | - Chen Li
- Department of Biology, Chemistry, Pharmacy, Free University of Berlin, Berlin 14195, Germany.
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10
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Menzies GE, Prior IA, Brancale A, Reed SH, Lewis PD. Carcinogen-induced DNA structural distortion differences in the RAS gene isoforms; the importance of local sequence. BMC Chem 2021; 15:51. [PMID: 34521464 PMCID: PMC8439098 DOI: 10.1186/s13065-021-00777-8] [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: 05/05/2021] [Accepted: 08/17/2021] [Indexed: 11/12/2022] Open
Abstract
BACKGROUND Local sequence context is known to have an impact on the mutational pattern seen in cancer. The RAS genes and a smoking carcinogen, Benzo[a]pyrene diol epoxide (BPDE), have been utilised to explore these context effects. BPDE is known to form an adduct at the guanines in a number of RAS gene sites, KRAS codons 12, 13 and 14, NRAS codon 12, and HRAS codons 12 and 14. RESULTS Molecular modelling techniques, along with multivariate analysis, have been utilised to determine the sequence influenced differences between BPDE-adducted RAS gene sequences as well as the local distortion caused by the adducts. CONCLUSIONS We conclude that G:C > T:A mutations at KRAS codon 12 in the tumours of lung cancer patients (who smoke), proposed to be predominantly caused by BPDE, are due to the effect of the interaction methyl group at the C5 position of the thymine base in the KRAS sequence with the BPDE carcinogen investigated causing increased distortion. We further suggest methylated cytosine would have a similar effect, showing the importance of methylation in cancer development.
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Affiliation(s)
- Georgina E Menzies
- School of Biosciences and Dementia Research Institute at Cardiff, Cardiff University, Cardiff, CF10 3NX, UK.
| | - Ian A Prior
- Department of Cellular and Molecular Physiology, Institute of Translational Medicine, University of Liverpool, Liverpool, L69 3BX, UK
| | - Andrea Brancale
- School of Pharmacy and Pharmaceutical Sciences, Cardiff University, Cardiff, CF10 3NB, UK
| | - Simon H Reed
- Division of Cancer and Genetics, School of Medicine, Cardiff University, Cardiff, CF14 4XN, UK
| | - Paul D Lewis
- School of Management, Swansea University Bay Campus, Swansea, SA1 8EN, UK
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11
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Marini M, Legittimo F, Torre B, Allione M, Limongi T, Scaltrito L, Pirri CF, di Fabrizio E. DNA Studies: Latest Spectroscopic and Structural Approaches. MICROMACHINES 2021; 12:mi12091094. [PMID: 34577737 PMCID: PMC8465297 DOI: 10.3390/mi12091094] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/12/2021] [Revised: 08/28/2021] [Accepted: 09/04/2021] [Indexed: 11/16/2022]
Abstract
This review looks at the different approaches, techniques, and materials devoted to DNA studies. In the past few decades, DNA nanotechnology, micro-fabrication, imaging, and spectroscopies have been tailored and combined for a broad range of medical-oriented applications. The continuous advancements in miniaturization of the devices, as well as the continuous need to study biological material structures and interactions, down to single molecules, have increase the interdisciplinarity of emerging technologies. In the following paragraphs, we will focus on recent sensing approaches, with a particular effort attributed to cutting-edge techniques for structural and mechanical studies of nucleic acids.
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Affiliation(s)
- Monica Marini
- Dipartimento di Scienza Applicata e Tecnologia (DISAT), Politecnico di Torino, Corso Duca degli Abruzzi 24, 10129 Torino, Italy; (F.L.); (B.T.); (T.L.); (L.S.); (C.F.P.); (E.d.F.)
- Correspondence: ; Tel.: +39-011-090-43-22
| | - Francesca Legittimo
- Dipartimento di Scienza Applicata e Tecnologia (DISAT), Politecnico di Torino, Corso Duca degli Abruzzi 24, 10129 Torino, Italy; (F.L.); (B.T.); (T.L.); (L.S.); (C.F.P.); (E.d.F.)
| | - Bruno Torre
- Dipartimento di Scienza Applicata e Tecnologia (DISAT), Politecnico di Torino, Corso Duca degli Abruzzi 24, 10129 Torino, Italy; (F.L.); (B.T.); (T.L.); (L.S.); (C.F.P.); (E.d.F.)
| | - Marco Allione
- Istituto Italiano di Tecnologia (IIT), Via Livorno 60, 10144 Torino, Italy;
| | - Tania Limongi
- Dipartimento di Scienza Applicata e Tecnologia (DISAT), Politecnico di Torino, Corso Duca degli Abruzzi 24, 10129 Torino, Italy; (F.L.); (B.T.); (T.L.); (L.S.); (C.F.P.); (E.d.F.)
| | - Luciano Scaltrito
- Dipartimento di Scienza Applicata e Tecnologia (DISAT), Politecnico di Torino, Corso Duca degli Abruzzi 24, 10129 Torino, Italy; (F.L.); (B.T.); (T.L.); (L.S.); (C.F.P.); (E.d.F.)
| | - Candido Fabrizio Pirri
- Dipartimento di Scienza Applicata e Tecnologia (DISAT), Politecnico di Torino, Corso Duca degli Abruzzi 24, 10129 Torino, Italy; (F.L.); (B.T.); (T.L.); (L.S.); (C.F.P.); (E.d.F.)
- Istituto Italiano di Tecnologia (IIT), Via Livorno 60, 10144 Torino, Italy;
| | - Enzo di Fabrizio
- Dipartimento di Scienza Applicata e Tecnologia (DISAT), Politecnico di Torino, Corso Duca degli Abruzzi 24, 10129 Torino, Italy; (F.L.); (B.T.); (T.L.); (L.S.); (C.F.P.); (E.d.F.)
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12
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Balasubramaniyam T, Oh KI, Jin HS, Ahn HB, Kim BS, Lee JH. Non-Canonical Helical Structure of Nucleic Acids Containing Base-Modified Nucleotides. Int J Mol Sci 2021; 22:9552. [PMID: 34502459 PMCID: PMC8430589 DOI: 10.3390/ijms22179552] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2021] [Revised: 08/27/2021] [Accepted: 08/29/2021] [Indexed: 12/12/2022] Open
Abstract
Chemically modified nucleobases are thought to be important for therapeutic purposes as well as diagnosing genetic diseases and have been widely involved in research fields such as molecular biology and biochemical studies. Many artificially modified nucleobases, such as methyl, halogen, and aryl modifications of purines at the C8 position and pyrimidines at the C5 position, are widely studied for their biological functions. DNA containing these modified nucleobases can form non-canonical helical structures such as Z-DNA, G-quadruplex, i-motif, and triplex. This review summarizes the synthesis of chemically modified nucleotides: (i) methylation, bromination, and arylation of purine at the C8 position and (ii) methylation, bromination, and arylation of pyrimidine at the C5 position. Additionally, we introduce the non-canonical structures of nucleic acids containing these modifications.
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Affiliation(s)
- Thananjeyan Balasubramaniyam
- Department of Chemistry, Gyeongsang National University, Jinju 52828, Gyeongnam, Korea; (T.B.); (K.-I.O.); (H.-S.J.); (H.-B.A.)
- The Research Institute of Natural Science, Gyeongsang National University, Jinju 52828, Gyeongnam, Korea
| | - Kwnag-Im Oh
- Department of Chemistry, Gyeongsang National University, Jinju 52828, Gyeongnam, Korea; (T.B.); (K.-I.O.); (H.-S.J.); (H.-B.A.)
- The Research Institute of Natural Science, Gyeongsang National University, Jinju 52828, Gyeongnam, Korea
| | - Ho-Seong Jin
- Department of Chemistry, Gyeongsang National University, Jinju 52828, Gyeongnam, Korea; (T.B.); (K.-I.O.); (H.-S.J.); (H.-B.A.)
| | - Hye-Bin Ahn
- Department of Chemistry, Gyeongsang National University, Jinju 52828, Gyeongnam, Korea; (T.B.); (K.-I.O.); (H.-S.J.); (H.-B.A.)
| | - Byeong-Seon Kim
- The Research Institute of Natural Science, Gyeongsang National University, Jinju 52828, Gyeongnam, Korea
- Department of Chemistry Education, Gyeongsang National University, Jinju 52828, Gyeongnam, Korea
| | - Joon-Hwa Lee
- Department of Chemistry, Gyeongsang National University, Jinju 52828, Gyeongnam, Korea; (T.B.); (K.-I.O.); (H.-S.J.); (H.-B.A.)
- The Research Institute of Natural Science, Gyeongsang National University, Jinju 52828, Gyeongnam, Korea
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13
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Spencer DM, Reyna AG, Pisetsky DS. The Binding of Monoclonal and Polyclonal Anti-Z-DNA Antibodies to DNA of Various Species Origin. Int J Mol Sci 2021; 22:ijms22168931. [PMID: 34445637 PMCID: PMC8396244 DOI: 10.3390/ijms22168931] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2021] [Revised: 08/11/2021] [Accepted: 08/12/2021] [Indexed: 02/06/2023] Open
Abstract
DNA is a polymeric macromolecule that can display a variety of backbone conformations. While the classical B-DNA is a right-handed double helix, Z-DNA is a left-handed helix with a zig-zag orientation. The Z conformation depends upon the base sequence, base modification and supercoiling and is considered to be transient. To determine whether the presence of Z-DNA can be detected immunochemically, the binding of monoclonal and polyclonal anti-Z-DNA antibodies to a panel of natural DNA antigens was assessed by an ELISA using brominated poly(dG-dC) as a control for Z-DNA. As these studies showed, among natural DNA tested (Micrococcus luteus, calf thymus, Escherichiacoli, salmon sperm, lambda phage), micrococcal (MC) DNA showed the highest binding with both anti-Z-DNA preparations, and E. coli DNA showed binding with the monoclonal anti-DNA preparation. The specificity for Z-DNA conformation in MC DNA was demonstrated by an inhibition binding assay. An algorithm to identify propensity to form Z-DNA indicated that DNA from Mycobacterium tuberculosis could form Z-DNA, a prediction confirmed by immunoassay. Together, these findings indicate that anti-Z-DNA antibodies can serve as probes for the presence of Z-DNA in DNA of various species origin and that the content of Z-DNA varies significantly among DNA sources.
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Affiliation(s)
- Diane M. Spencer
- Department of Medicine and Immunology, Division of Rheumatology, Duke University Medical Center, Durham, NC 27710, USA;
- Medical Research Service, Veterans Administration Medical Center, Durham, NC 27705, USA
| | | | - David S. Pisetsky
- Department of Medicine and Immunology, Division of Rheumatology, Duke University Medical Center, Durham, NC 27710, USA;
- Medical Research Service, Veterans Administration Medical Center, Durham, NC 27705, USA
- Correspondence:
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14
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Notarstefano V, Belloni A, Sabbatini S, Pro C, Orilisi G, Monterubbianesi R, Tosco V, Byrne HJ, Vaccari L, Giorgini E. Cytotoxic Effects of 5-Azacytidine on Primary Tumour Cells and Cancer Stem Cells from Oral Squamous Cell Carcinoma: An In Vitro FTIRM Analysis. Cells 2021; 10:2127. [PMID: 34440896 PMCID: PMC8392608 DOI: 10.3390/cells10082127] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2021] [Revised: 08/10/2021] [Accepted: 08/17/2021] [Indexed: 01/05/2023] Open
Abstract
In the present study, the cytotoxic effects of 5-azacytidine on primary Oral Squamous Cell Carcinoma cells (OSCCs) from human biopsies, and on Cancer Stem Cells (CSCs) from the same samples, were investigated by an in vitro Fourier Transform InfraRed Microscospectroscopy (FTIRM) approach coupled with multivariate analysis. OSCC is an aggressive tumoral lesion of the epithelium, accounting for ~90% of all oral cancers. It is usually diagnosed in advanced stages, and this causes a poor prognosis with low success rates of surgical, as well as radiation and chemotherapy treatments. OSCC is frequently characterised by recurrence after chemotherapy and by the development of a refractoriness to some employed drugs, which is probably ascribable to the presence of CSCs niches, responsible for cancer growth, chemoresistance and metastasis. The spectral information from FTIRM was correlated with the outcomes of cytotoxicity tests and image-based cytometry, and specific spectral signatures attributable to 5-azacytidine treatment were identified, allowing us to hypothesise the demethylation of DNA and, hence, an increase in the transcriptional activity, together with a conformational transition of DNA, and a triggering of cell death by an apoptosis mechanism. Moreover, a different mechanism of action between OSSC and CSC cells was highlighted, probably due to possible differences between OSCCs and CSCs response.
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Affiliation(s)
- Valentina Notarstefano
- Department of Life and Environmental Sciences, Università Politecnica Delle Marche, 60131 Ancona, Italy; (V.N.); (A.B.); (C.P.)
| | - Alessia Belloni
- Department of Life and Environmental Sciences, Università Politecnica Delle Marche, 60131 Ancona, Italy; (V.N.); (A.B.); (C.P.)
| | - Simona Sabbatini
- Department of Material, Environmental Sciences and Urban Planning, Università Politecnica Delle Marche, 60131 Ancona, Italy;
| | - Chiara Pro
- Department of Life and Environmental Sciences, Università Politecnica Delle Marche, 60131 Ancona, Italy; (V.N.); (A.B.); (C.P.)
| | - Giulia Orilisi
- Department of Clinical Sciences and Stomatology, Università Politecnica Delle Marche, 60126 Ancona, Italy; (G.O.); (R.M.); (V.T.)
| | - Riccardo Monterubbianesi
- Department of Clinical Sciences and Stomatology, Università Politecnica Delle Marche, 60126 Ancona, Italy; (G.O.); (R.M.); (V.T.)
| | - Vincenzo Tosco
- Department of Clinical Sciences and Stomatology, Università Politecnica Delle Marche, 60126 Ancona, Italy; (G.O.); (R.M.); (V.T.)
| | - Hugh J. Byrne
- FOCAS Research Institute, Technological University Dublin, Dublin 8, Ireland;
| | - Lisa Vaccari
- Elettra Sincrotrone Trieste, SISSI Beamline, 34149 Basovizza, Italy;
| | - Elisabetta Giorgini
- Department of Life and Environmental Sciences, Università Politecnica Delle Marche, 60131 Ancona, Italy; (V.N.); (A.B.); (C.P.)
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15
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Bie LH, Fei JW, Gao J. Molecular mechanism of methyl-dependent and spatial-specific DNA recognition of c-Jun homodimer. J Mol Model 2021; 27:227. [PMID: 34264385 DOI: 10.1007/s00894-021-04840-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2021] [Accepted: 07/01/2021] [Indexed: 10/20/2022]
Abstract
DNA methylation is important in regulation of gene expression and normal development because it alters the interplay between protein and DNA. Experiments have shown that a single 5-methylcytosine at different CpG sites (mCpG) might have different effects on specific recognition, but the atomistic origin and dynamic details are largely unclear. In this work, we investigated the mechanism of monomethylation at different CpG sites in the cognate motif and the cooperativity of full methylation. By constructing four models of c-Jun/Jun protein binding to the 5[Formula: see text]-XGAGTCA-3[Formula: see text] (X represents C or methylated C) motif, we characterized the dynamics of the contact interface using the all-atom molecular dynamics method. Free energy analysis of MM/GBSA suggests that regardless of whether the C12pG13 site of the bottom strand is methylated, the effects from mC25 of the top strand are dominant and can moderately enhance the binding by [Formula: see text] 31 kcal/mol, whereas mC12 showed a relatively small contribution, in agreement with the experimental data. Remarkably, we found that this spatial-specific influence was induced by different regulatory rules. The influence of the mC25 site is mainly mediated by steric hindrance. The additional methyl group leads to the conformational changes in nearby residues and triggers an obvious structural bending in the protein, which results in the formation of a new T-Asn-C triad that enhances the specific recognition of TCA half-sites. The substitution of the methyl group at the mC12 site of the bottom strand breaks the original H-bonds directly. Such changes in electrostatic interactions also lead to the remote allosteric effects of protein by multifaceted interactions but have negligible contributions to binding. Although these two influence modes are different, they can both fine-tune the local environment, which might produce remote allosteric effects through protein-protein interactions. Further analysis reveals that the discrepancies in these two modes are primarily due to their location. Moreover, when both sites are methylated, the major determinant of binding specificity depends on the context and the location of the methylation site, which is the result of crosstalk and cooperativity.
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Affiliation(s)
- Li-Hua Bie
- Hubei Key Laboratory of Agricultural Bioinformatics, College of Informatics, Huazhong Agricultural University, Wuhan, 430070, People's Republic of China
| | - Jun-Wen Fei
- Hubei Key Laboratory of Agricultural Bioinformatics, College of Informatics, Huazhong Agricultural University, Wuhan, 430070, People's Republic of China
| | - Jun Gao
- Hubei Key Laboratory of Agricultural Bioinformatics, College of Informatics, Huazhong Agricultural University, Wuhan, 430070, People's Republic of China.
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16
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Gurbanov R, Karadağ H, Karaçam S, Samgane G. Tapioca Starch Modulates Cellular Events in Oral Probiotic Streptococcus salivarius Strains. Probiotics Antimicrob Proteins 2021; 13:195-207. [PMID: 32601954 DOI: 10.1007/s12602-020-09678-z] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
Considering the implications of microbiota in health, scientists are in search of microbiota-oriented strategies for the effective prevention and/or treatment of a wide variety of serious diseases. A microbiota comprises diverse microorganisms with either probiotic or pathogenic properties. The fermentation of prebiotic carbohydrates by probiotic bacteria can affect host metabolism. Therefore, understanding the prebiotic-mediated metabolic modulations in probiotics is crucial to develop functional foods for the improvement of disturbed microbiota. Studies have emphasized the importance of prebiotics in probiotic therapies for mucosal diseases and highlighted the need for extensive research on oral bacteria. In the present study, the cellular events have been studied in batch cultures of probiotic Streptococcus salivarius exposed to the natural prebiotic, tapioca starch (TS). TS modulated the keystone metabolic events in Streptococcus salivarius in a dose-dependent manner. Besides increasing the live cell counts and altering the colony morphologies, TS affected the protein metabolism in terms of cellular expression and conformational changes in protein secondary structures. After treatment with TS, the nucleic acid synthesis increased and B-DNA was more than A- and Z-DNA, together with the diminished fatty acids and increased polysaccharide synthesis. The study results can be considered for the assessment of functional foods and probiotics in oral health.
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Affiliation(s)
- Rafig Gurbanov
- Department of Molecular Biology and Genetics, Bilecik Şeyh Edebali University, 11230, Bilecik, Turkey.
- Biotechnology Application and Research Center, Bilecik Şeyh Edebali University, 11230, Bilecik, Turkey.
| | - Hazel Karadağ
- Biotechnology Application and Research Center, Bilecik Şeyh Edebali University, 11230, Bilecik, Turkey
| | - Sevinç Karaçam
- Biotechnology Application and Research Center, Bilecik Şeyh Edebali University, 11230, Bilecik, Turkey
| | - Gizem Samgane
- Biotechnology Application and Research Center, Bilecik Şeyh Edebali University, 11230, Bilecik, Turkey
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17
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Mishra A, Siwach P, Misra P, Dhiman S, Pandey AK, Srivastava P, Jayaram B. Intron exon boundary junctions in human genome have in-built unique structural and energetic signals. Nucleic Acids Res 2021; 49:2674-2683. [PMID: 33621338 PMCID: PMC7969029 DOI: 10.1093/nar/gkab098] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2019] [Revised: 01/21/2021] [Accepted: 02/22/2021] [Indexed: 11/13/2022] Open
Abstract
Precise identification of correct exon–intron boundaries is a prerequisite to analyze the location and structure of genes. The existing framework for genomic signals, delineating exon and introns in a genomic segment, seems insufficient, predominantly due to poor sequence consensus as well as limitations of training on available experimental data sets. We present here a novel concept for characterizing exon–intron boundaries in genomic segments on the basis of structural and energetic properties. We analyzed boundary junctions on both sides of all the exons (3 28 368) of protein coding genes from human genome (GENCODE database) using 28 structural and three energy parameters. Study of sequence conservation at these sites shows very poor consensus. It is observed that DNA adopts a unique structural and energy state at the boundary junctions. Also, signals are somewhat different for housekeeping and tissue specific genes. Clustering of 31 parameters into four derived vectors gives some additional insights into the physical mechanisms involved in this biological process. Sites of structural and energy signals correlate well to the positions playing important roles in pre-mRNA splicing.
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Affiliation(s)
- Akhilesh Mishra
- Supercomputing Facility for Bioinformatics & Computational Biology, Indian Institute of Technology Delhi, India.,Kusuma School of Biological Sciences, Indian Institute of Technology, Delhi, India
| | - Priyanka Siwach
- Supercomputing Facility for Bioinformatics & Computational Biology, Indian Institute of Technology Delhi, India.,Department of Biotechnology, Chaudhary Devi Lal University, Sirsa, Haryana, India
| | - Pallavi Misra
- Supercomputing Facility for Bioinformatics & Computational Biology, Indian Institute of Technology Delhi, India
| | - Simran Dhiman
- Supercomputing Facility for Bioinformatics & Computational Biology, Indian Institute of Technology Delhi, India
| | | | - Parul Srivastava
- Supercomputing Facility for Bioinformatics & Computational Biology, Indian Institute of Technology Delhi, India
| | - B Jayaram
- Supercomputing Facility for Bioinformatics & Computational Biology, Indian Institute of Technology Delhi, India.,Kusuma School of Biological Sciences, Indian Institute of Technology, Delhi, India.,Department of Chemistry, Indian Institute of Technology, Delhi, India
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18
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Westwood MN, Ljunggren KD, Boyd B, Becker J, Dwyer TJ, Meints GA. Single-Base Lesions and Mismatches Alter the Backbone Conformational Dynamics in DNA. Biochemistry 2021; 60:873-885. [PMID: 33689312 DOI: 10.1021/acs.biochem.0c00784] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
DNA damage has been implicated in numerous human diseases, particularly cancer, and the aging process. Single-base lesions and mismatches in DNA can be cytotoxic or mutagenic and are recognized by a DNA glycosylase during the process of base excision repair. Altered local dynamics and conformational properties in damaged DNAs have previously been suggested to assist in recognition and specificity. Herein, we use solution nuclear magnetic resonance to quantify changes in BI-BII backbone conformational dynamics due to the presence of single-base lesions in DNA, including uracil, dihydrouracil, 1,N6-ethenoadenine, and T:G mismatches. Stepwise changes to the %BII and ΔG of the BI-BII dynamic equilibrium compared to those of unmodified sequences were observed. Additionally, the equilibrium skews toward endothermicity for the phosphates nearest the lesion/mismatched base pair. Finally, the phosphates with the greatest alterations correlate with those most relevant to the repair of enzyme binding. All of these results suggest local conformational rearrangement of the DNA backbone may play a role in lesion recognition by repair enzymes.
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Affiliation(s)
- M N Westwood
- Department of Chemistry, Missouri State University, 901 South National Avenue, Springfield, Missouri 65897, United States
| | - K D Ljunggren
- Department of Chemistry, Missouri State University, 901 South National Avenue, Springfield, Missouri 65897, United States
| | - Benjamin Boyd
- Department of Chemistry, Missouri State University, 901 South National Avenue, Springfield, Missouri 65897, United States
| | - Jaclyn Becker
- Department of Chemistry, Missouri State University, 901 South National Avenue, Springfield, Missouri 65897, United States
| | - Tammy J Dwyer
- Department of Chemistry and Biochemistry, University of San Diego, San Diego, California 92110, United States
| | - Gary A Meints
- Department of Chemistry, Missouri State University, 901 South National Avenue, Springfield, Missouri 65897, United States
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19
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Yang YJ, Dong HL, Qiang XW, Fu H, Zhou EC, Zhang C, Yin L, Chen XF, Jia FC, Dai L, Tan ZJ, Zhang XH. Cytosine Methylation Enhances DNA Condensation Revealed by Equilibrium Measurements Using Magnetic Tweezers. J Am Chem Soc 2020; 142:9203-9209. [DOI: 10.1021/jacs.9b11957] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Affiliation(s)
- Ya-Jun Yang
- College of Life Sciences, the Institute for Advanced Studies, State Key Laboratory of Virology, Hubei Key Laboratory of Cell Homeostasis, Wuhan University, Wuhan 430072, China
| | - Hai-Long Dong
- Department of Physics and Key Laboratory of Artificial Micro & Nano-structures of Ministry of Education, School of Physics and Technology, Wuhan University, Wuhan 430072, China
| | - Xiao-Wei Qiang
- Department of Physics and Key Laboratory of Artificial Micro & Nano-structures of Ministry of Education, School of Physics and Technology, Wuhan University, Wuhan 430072, China
| | - Hang Fu
- College of Life Sciences, the Institute for Advanced Studies, State Key Laboratory of Virology, Hubei Key Laboratory of Cell Homeostasis, Wuhan University, Wuhan 430072, China
| | - Er-Chi Zhou
- College of Life Sciences, the Institute for Advanced Studies, State Key Laboratory of Virology, Hubei Key Laboratory of Cell Homeostasis, Wuhan University, Wuhan 430072, China
| | - Chen Zhang
- College of Life Sciences, the Institute for Advanced Studies, State Key Laboratory of Virology, Hubei Key Laboratory of Cell Homeostasis, Wuhan University, Wuhan 430072, China
| | - Lei Yin
- College of Life Sciences, the Institute for Advanced Studies, State Key Laboratory of Virology, Hubei Key Laboratory of Cell Homeostasis, Wuhan University, Wuhan 430072, China
| | - Xue-Feng Chen
- College of Life Sciences, the Institute for Advanced Studies, State Key Laboratory of Virology, Hubei Key Laboratory of Cell Homeostasis, Wuhan University, Wuhan 430072, China
| | - Fu-Chao Jia
- Laboratory of Functional Molecules and Materials, School of Physics and Optoelectronic Engineering, Shandong University of Technology, Zibo 255000, China
| | - Liang Dai
- Department of Physics, City University of Hong Kong, Hong Kong 999077, China
| | - Zhi-Jie Tan
- Department of Physics and Key Laboratory of Artificial Micro & Nano-structures of Ministry of Education, School of Physics and Technology, Wuhan University, Wuhan 430072, China
| | - Xing-Hua Zhang
- College of Life Sciences, the Institute for Advanced Studies, State Key Laboratory of Virology, Hubei Key Laboratory of Cell Homeostasis, Wuhan University, Wuhan 430072, China
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20
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Oh KI, Kim J, Park CJ, Lee JH. Dynamics Studies of DNA with Non-canonical Structure Using NMR Spectroscopy. Int J Mol Sci 2020; 21:E2673. [PMID: 32290457 PMCID: PMC7216225 DOI: 10.3390/ijms21082673] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2020] [Revised: 04/07/2020] [Accepted: 04/09/2020] [Indexed: 12/11/2022] Open
Abstract
The non-canonical structures of nucleic acids are essential for their diverse functions during various biological processes. These non-canonical structures can undergo conformational exchange among multiple structural states. Data on their dynamics can illustrate conformational transitions that play important roles in folding, stability, and biological function. Here, we discuss several examples of the non-canonical structures of DNA focusing on their dynamic characterization by NMR spectroscopy: (1) G-quadruplex structures and their complexes with target proteins; (2) i-motif structures and their complexes with proteins; (3) triplex structures; (4) left-handed Z-DNAs and their complexes with various Z-DNA binding proteins. This review provides insight into how the dynamic features of non-canonical DNA structures contribute to essential biological processes.
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Affiliation(s)
- Kwang-Im Oh
- Department of Chemistry and RINS, Gyeongsang National University, Gyeongnam 52828, Korea;
| | - Jinwoo Kim
- Department of Chemistry, Gwangju Institute of Science and Technology, Gwangju 61005, Korea;
| | - Chin-Ju Park
- Department of Chemistry, Gwangju Institute of Science and Technology, Gwangju 61005, Korea;
| | - Joon-Hwa Lee
- Department of Chemistry and RINS, Gyeongsang National University, Gyeongnam 52828, Korea;
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21
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Gurbanov R, Tunçer S, Mingu S, Severcan F, Gozen AG. Methylation, sugar puckering and Z-form status of DNA from a heavy metal-acclimated freshwater Gordonia sp. JOURNAL OF PHOTOCHEMISTRY AND PHOTOBIOLOGY B-BIOLOGY 2019; 198:111580. [DOI: 10.1016/j.jphotobiol.2019.111580] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/02/2019] [Revised: 07/07/2019] [Accepted: 07/29/2019] [Indexed: 01/27/2023]
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22
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Zavarykina TM, Atkarskaya MV, Zhizhina GP. The Structural and Functional Properties of Z-DNA. Biophysics (Nagoya-shi) 2019. [DOI: 10.1134/s0006350919050270] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
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23
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Liebl K, Zacharias M. How methyl-sugar interactions determine DNA structure and flexibility. Nucleic Acids Res 2019; 47:1132-1140. [PMID: 30541032 PMCID: PMC6379717 DOI: 10.1093/nar/gky1237] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2018] [Revised: 11/26/2018] [Accepted: 11/30/2018] [Indexed: 12/18/2022] Open
Abstract
The sequence dependent structure and flexibility of the DNA double helix is of key importance for gene expression and DNA packing and it can be modulated by DNA modifications. The presence of a C5′-methyl group in thymine or the frequent C5′-methylated-cytosine affects the DNA fine structure, however, the underlying mechanism and steric origins have remained largely unexplained. Employing Molecular Dynamics free energy simulations that allow switching on or off interactions with the methyl groups in several DNA sequences, we systematically identified the physical origin of the coupling between methyl groups and DNA backbone fine structure. Whereas methyl-solvent and methyl–nucleobase interactions were found to be of minor importance, the methyl group interaction with the 5′ neighboring sugar was identified as main cause for influencing the population of backbone substates. The sterical methyl sugar clash prevents the formation of unconventional stabilizing hydrogen bonds between nucleobase and backbone. The technique was also used to study the contribution of methyl groups to DNA flexibility and served to explain why the presence of methyl sugar clashes in thymine and methyl-cytosine can result in an overall local increase of DNA flexibility.
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Affiliation(s)
- Korbinian Liebl
- Physics Department T38, Technical University of Munich, James-Franck-Str. 1, 85748 Garching, Germany
| | - Martin Zacharias
- Physics Department T38, Technical University of Munich, James-Franck-Str. 1, 85748 Garching, Germany
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24
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Matyášek R, Kuderová A, Kutílková E, Kučera M, Kovařík A. Intragenomic heterogeneity of intergenic ribosomal DNA spacers in Cucurbita moschata is determined by DNA minisatellites with variable potential to form non-canonical DNA conformations. DNA Res 2019; 26:273-286. [PMID: 31231763 PMCID: PMC6589552 DOI: 10.1093/dnares/dsz008] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2018] [Accepted: 04/03/2019] [Indexed: 11/26/2022] Open
Abstract
The intergenic spacer (IGS) of rDNA is frequently built of long blocks of tandem repeats. To estimate the intragenomic variability of such knotty regions, we employed PacBio sequencing of the Cucurbita moschata genome, in which thousands of rDNA copies are distributed across a number of loci. The rRNA coding regions are highly conserved, indicating intensive interlocus homogenization and/or high selection pressure. However, the IGS exhibits high intragenomic structural diversity. Two repeated blocks, R1 (300–1250 bp) and R2 (290–643 bp), account for most of the IGS variation. They exhibit minisatellite-like features built of multiple periodically spaced short GC-rich sequence motifs with the potential to adopt non-canonical DNA conformations, G-quadruplex-folded and left-handed Z-DNA. The mutual arrangement of these motifs can be used to classify IGS variants into five structural families. Subtle polymorphisms exist within each family due to a variable number of repeats, suggesting the coexistence of an enormous number of IGS variants. The substantial length and structural heterogeneity of IGS minisatellites suggests that the tempo of their divergence exceeds the tempo of the homogenization of rDNA arrays. As frequently occurring among plants, we hypothesize that their instability may influence transcription regulation and/or destabilize rDNA units, possibly spreading them across the genome.
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Affiliation(s)
- Roman Matyášek
- Institute of Biophysics of the Czech Academy of Sciences, CZ Brno, Czech Republic
| | - Alena Kuderová
- Institute of Biophysics of the Czech Academy of Sciences, CZ Brno, Czech Republic
| | - Eva Kutílková
- Institute of Biophysics of the Czech Academy of Sciences, CZ Brno, Czech Republic
| | - Marek Kučera
- Institute of Biophysics of the Czech Academy of Sciences, CZ Brno, Czech Republic
| | - Aleš Kovařík
- Institute of Biophysics of the Czech Academy of Sciences, CZ Brno, Czech Republic
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25
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Molecular mechanisms of the protein-protein interaction-regulated binding specificity of basic-region leucine zipper transcription factors. J Mol Model 2019; 25:246. [PMID: 31342181 DOI: 10.1007/s00894-019-4138-9] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2019] [Accepted: 07/14/2019] [Indexed: 10/26/2022]
Abstract
It is well known that the DNA-binding specificity of transcription factors (TFs) is influenced by protein-protein interactions (PPIs). However, the underlying molecular mechanisms remain largely unknown. In this work, we adopted the cAMP-response element-binding protein (CREB) of the basic leucine zipper (bZIP) TF family as a model system, and a workflow of combined bioinformatics and molecular modeling analysis of protein-DNA interaction was tested. First, the multiple sequence alignment and SDPsite method were used to find potential bZIP family binding specificity determining positions (SDPs) within the protein-protein interaction region. Second, the mutation system was analyzed using molecular dynamics simulation. Molecular mechanics Poisson-Boltzmann surface area (MM/PBSA) free energy calculations confirmed the enhancement of the binding affinity of the mutation, which was in agreement with experimental results. The root mean square fluctuation (RMSF) and hydrogen bonding changes suggested an open and close protein dimerization process after the system was mutated, which resulted in the change of the hydrogen bonding of the protein-DNA interface and a slight conformational change. We believe that this work will contribute to understanding the protein-protein interaction-regulated binding specificity of bZIP transcription factors.
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26
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Gruber DR, Toner JJ, Miears HL, Shernyukov AV, Kiryutin AS, Lomzov AA, Endutkin AV, Grin IR, Petrova DV, Kupryushkin MS, Yurkovskaya AV, Johnson EC, Okon M, Bagryanskaya EG, Zharkov DO, Smirnov SL. Oxidative damage to epigenetically methylated sites affects DNA stability, dynamics and enzymatic demethylation. Nucleic Acids Res 2019; 46:10827-10839. [PMID: 30289469 PMCID: PMC6237784 DOI: 10.1093/nar/gky893] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2018] [Accepted: 09/20/2018] [Indexed: 01/20/2023] Open
Abstract
DNA damage can affect various regulatory elements of the genome, with the consequences for DNA structure, dynamics, and interaction with proteins remaining largely unexplored. We used solution NMR spectroscopy, restrained and free molecular dynamics to obtain the structures and investigate dominant motions for a set of DNA duplexes containing CpG sites permuted with combinations of 5-methylcytosine (mC), the primary epigenetic base, and 8-oxoguanine (oxoG), an abundant DNA lesion. Guanine oxidation significantly changed the motion in both hemimethylated and fully methylated DNA, increased base pair breathing, induced BI→BII transition in the backbone 3′ to the oxoG and reduced the variability of shift and tilt helical parameters. UV melting experiments corroborated the NMR and molecular dynamics results, showing significant destabilization of all methylated contexts by oxoG. Notably, some dynamic and thermodynamic effects were not additive in the fully methylated oxidized CpG, indicating that the introduced modifications interact with each other. Finally, we show that the presence of oxoG biases the recognition of methylated CpG dinucleotides by ROS1, a plant enzyme involved in epigenetic DNA demethylation, in favor of the oxidized DNA strand. Thus, the conformational and dynamic effects of spurious DNA oxidation in the regulatory CpG dinucleotide can have far-reaching biological consequences.
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Affiliation(s)
- David R Gruber
- Chemistry Department, Western Washington University, 516 High St., Bellingham, WA 98225-9150, USA
| | - Joanna J Toner
- Chemistry Department, Western Washington University, 516 High St., Bellingham, WA 98225-9150, USA
| | - Heather L Miears
- Chemistry Department, Western Washington University, 516 High St., Bellingham, WA 98225-9150, USA
| | - Andrey V Shernyukov
- N. N. Vorozhtsov Novosibirsk Institute of Organic Chemistry SB RAS, 9 Lavrentieva Ave., Novosibirsk 630090, Russia.,Novosibirsk State University, 2 Pirogova St., Novosibirsk 630090, Russia
| | - Alexey S Kiryutin
- Novosibirsk State University, 2 Pirogova St., Novosibirsk 630090, Russia.,SB RAS International Tomography Center, 3a Institutskaya St., Novosibirsk 630090, Russia
| | - Alexander A Lomzov
- Novosibirsk State University, 2 Pirogova St., Novosibirsk 630090, Russia.,SB RAS Institute of Chemical Biology and Fundamental Medicine, 8 Lavrentieva Ave., Novosibirsk 630090, Russia
| | - Anton V Endutkin
- Novosibirsk State University, 2 Pirogova St., Novosibirsk 630090, Russia.,SB RAS Institute of Chemical Biology and Fundamental Medicine, 8 Lavrentieva Ave., Novosibirsk 630090, Russia
| | - Inga R Grin
- Novosibirsk State University, 2 Pirogova St., Novosibirsk 630090, Russia.,SB RAS Institute of Chemical Biology and Fundamental Medicine, 8 Lavrentieva Ave., Novosibirsk 630090, Russia
| | - Darya V Petrova
- Novosibirsk State University, 2 Pirogova St., Novosibirsk 630090, Russia.,SB RAS Institute of Chemical Biology and Fundamental Medicine, 8 Lavrentieva Ave., Novosibirsk 630090, Russia
| | - Maxim S Kupryushkin
- SB RAS Institute of Chemical Biology and Fundamental Medicine, 8 Lavrentieva Ave., Novosibirsk 630090, Russia
| | - Alexandra V Yurkovskaya
- Novosibirsk State University, 2 Pirogova St., Novosibirsk 630090, Russia.,SB RAS International Tomography Center, 3a Institutskaya St., Novosibirsk 630090, Russia
| | | | - Mark Okon
- Department of Biochemistry and Molecular Biology, Department of Chemistry, and Michael Smith Laboratories, University of British Columbia, Vancouver BC, V6T 1Z3, Canada
| | - Elena G Bagryanskaya
- N. N. Vorozhtsov Novosibirsk Institute of Organic Chemistry SB RAS, 9 Lavrentieva Ave., Novosibirsk 630090, Russia.,Novosibirsk State University, 2 Pirogova St., Novosibirsk 630090, Russia
| | - Dmitry O Zharkov
- Novosibirsk State University, 2 Pirogova St., Novosibirsk 630090, Russia.,SB RAS Institute of Chemical Biology and Fundamental Medicine, 8 Lavrentieva Ave., Novosibirsk 630090, Russia
| | - Serge L Smirnov
- Chemistry Department, Western Washington University, 516 High St., Bellingham, WA 98225-9150, USA
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27
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Teng X, Hwang W. Effect of Methylation on Local Mechanics and Hydration Structure of DNA. Biophys J 2019; 114:1791-1803. [PMID: 29694859 DOI: 10.1016/j.bpj.2018.03.022] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2017] [Revised: 03/03/2018] [Accepted: 03/14/2018] [Indexed: 12/31/2022] Open
Abstract
Cytosine methylation affects mechanical properties of DNA and potentially alters the hydration fingerprint for recognition by proteins. The atomistic origin for these effects is not well understood, and we address this via all-atom molecular dynamics simulations. We find that the stiffness of the methylated dinucleotide step changes marginally, whereas the neighboring steps become stiffer. Stiffening is further enhanced for consecutively methylated steps, providing a mechanistic origin for the effect of hypermethylation. Steric interactions between the added methyl groups and the nonpolar groups of the neighboring nucleotides are responsible for the stiffening in most cases. By constructing hydration maps, we found that methylation also alters the surface hydration structure in distinct ways. Its resistance to deformation may contribute to the stiffening of DNA for deformational modes lacking steric interactions. These results highlight the sequence- and deformational-mode-dependent effects of cytosine methylation.
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Affiliation(s)
- Xiaojing Teng
- Department of Biomedical Engineering, Texas A&M University, College Station, Texas
| | - Wonmuk Hwang
- Department of Biomedical Engineering, Texas A&M University, College Station, Texas; Department of Materials Science & Engineering, Texas A&M University, College Station, Texas; School of Computational Sciences, Korea Institute for Advanced Study, Seoul, Korea.
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28
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Zhang Y, Cui Y, An R, Liang X, Li Q, Wang H, Wang H, Fan Y, Dong P, Li J, Cheng K, Wang W, Wang S, Wang G, Xue C, Komiyama M. Topologically Constrained Formation of Stable Z-DNA from Normal Sequence under Physiological Conditions. J Am Chem Soc 2019; 141:7758-7764. [PMID: 30844265 DOI: 10.1021/jacs.8b13855] [Citation(s) in RCA: 33] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
Z-DNA, a left-handed duplex, has been shown to form in vivo and regulate expression of the corresponding gene. However, its biological roles have not been satisfactorily understood, mainly because Z-DNA is easily converted to the thermodynamically favorable B-DNA. Here we present a new idea to form stable Z-DNA under normal physiological conditions and achieve detailed analysis on its fundamental features. Simply by mixing two complementary minicircles of single-stranded DNA with no chemical modification, the hybridization spontaneously induces topological constraint which twines one-half of the double-stranded DNA into stable Z-DNA. The formation of Z-conformation with high stability has been proved by using circular dichroism spectroscopy, Z-DNA-specific antibody binding assay, nuclease digestion, etc. Even at a concentration of MgCl2 as low as 0.5 mM, Z-DNA was successfully obtained, avoiding the use of high salt conditions, limited sequences, ancillary additives, or chemical modifications, criteria which have hampered Z-DNA research. The resultant Z-DNA has the potential to be used as a canonical standard sample in Z-DNA research. By using this approach, further developments of Z-DNA science and its applications become highly promising.
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Affiliation(s)
- Yaping Zhang
- College of Food Science and Engineering , Ocean University of China , No. 5 Yushan Road , Qingdao , People's Republic of China
| | - Yixiao Cui
- College of Food Science and Engineering , Ocean University of China , No. 5 Yushan Road , Qingdao , People's Republic of China
| | - Ran An
- College of Food Science and Engineering , Ocean University of China , No. 5 Yushan Road , Qingdao , People's Republic of China
| | - Xingguo Liang
- College of Food Science and Engineering , Ocean University of China , No. 5 Yushan Road , Qingdao , People's Republic of China.,Laboratory for Marine Drugs and Bioproducts , Qingdao National Laboratory for Marine Science and Technology , No. 1 Wenhai Road , Qingdao , People's Republic of China
| | - Qi Li
- College of Food Science and Engineering , Ocean University of China , No. 5 Yushan Road , Qingdao , People's Republic of China
| | - Haiting Wang
- College of Food Science and Engineering , Ocean University of China , No. 5 Yushan Road , Qingdao , People's Republic of China
| | - Hao Wang
- College of Food Science and Engineering , Ocean University of China , No. 5 Yushan Road , Qingdao , People's Republic of China
| | - Yiqiao Fan
- College of Food Science and Engineering , Ocean University of China , No. 5 Yushan Road , Qingdao , People's Republic of China
| | - Ping Dong
- College of Food Science and Engineering , Ocean University of China , No. 5 Yushan Road , Qingdao , People's Republic of China
| | - Jing Li
- College of Food Science and Engineering , Ocean University of China , No. 5 Yushan Road , Qingdao , People's Republic of China
| | - Kai Cheng
- College of Food Science and Engineering , Ocean University of China , No. 5 Yushan Road , Qingdao , People's Republic of China
| | - Weinan Wang
- College of Food Science and Engineering , Ocean University of China , No. 5 Yushan Road , Qingdao , People's Republic of China
| | - Sai Wang
- College of Food Science and Engineering , Ocean University of China , No. 5 Yushan Road , Qingdao , People's Republic of China
| | - Guoqing Wang
- College of Food Science and Engineering , Ocean University of China , No. 5 Yushan Road , Qingdao , People's Republic of China.,Laboratory for Marine Drugs and Bioproducts , Qingdao National Laboratory for Marine Science and Technology , No. 1 Wenhai Road , Qingdao , People's Republic of China
| | - Changhu Xue
- College of Food Science and Engineering , Ocean University of China , No. 5 Yushan Road , Qingdao , People's Republic of China.,Laboratory for Marine Drugs and Bioproducts , Qingdao National Laboratory for Marine Science and Technology , No. 1 Wenhai Road , Qingdao , People's Republic of China
| | - Makoto Komiyama
- College of Food Science and Engineering , Ocean University of China , No. 5 Yushan Road , Qingdao , People's Republic of China
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29
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Fleming AM, Zhu J, Ding Y, Esders S, Burrows CJ. Oxidative Modification of Guanine in a Potential Z-DNA-Forming Sequence of a Gene Promoter Impacts Gene Expression. Chem Res Toxicol 2019; 32:899-909. [PMID: 30821442 DOI: 10.1021/acs.chemrestox.9b00041] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
One response to oxidation of guanine (G) to 8-oxo-7,8-dihydroguanine (OG) in a gene promoter is regulation of mRNA expression suggesting an epigenetic-like role for OG. A proposed mechanism involves G oxidation within a potential G-quadruplex-forming sequence (PQS) in the promoter, enabling a structural shift from B-DNA to a G-quadruplex fold (G4). When OG was located in the coding vs template strand, base excision repair led to an on/off transcriptional switch. Herein, a G-rich, potential Z-DNA-forming sequence (PZS) comprised of a d(GC) n repeat was explored to determine whether oxidation in this motif was also a transcriptional switch. Bioinformatic analysis found 1650 PZSs of length >10 nts in the human genome that were overrepresented in promoters and 5'-UTRs. Studies in human cells transfected with a luciferase reporter plasmid in which OG was synthesized in a PZS context in the promoter found that a coding strand OG increased expression and a template strand OG decreased expression. The initial base excision repair product of OG, an abasic site (AP), was also found to yield similar expression changes as OG. Biophysical studies on model Z-DNA strands found OG favored a shift in the equilibrium to Z-DNA from B-DNA, while an AP disrupted Z-DNA to favor a hairpin, placing AP in the loop where it is a poor substrate for the endonuclease APE1. Overall, the impact of OG and AP in a PZS on gene expression was similar to that in a PQS but reduced in magnitude.
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Affiliation(s)
- Aaron M Fleming
- Department of Chemistry , University of Utah , 315S 1400 East , Salt Lake City , Utah 84112-0850 , United States
| | - Judy Zhu
- Department of Chemistry , University of Utah , 315S 1400 East , Salt Lake City , Utah 84112-0850 , United States
| | - Yun Ding
- Department of Chemistry , University of Utah , 315S 1400 East , Salt Lake City , Utah 84112-0850 , United States
| | - Selma Esders
- Department of Chemistry , University of Utah , 315S 1400 East , Salt Lake City , Utah 84112-0850 , United States
| | - Cynthia J Burrows
- Department of Chemistry , University of Utah , 315S 1400 East , Salt Lake City , Utah 84112-0850 , United States
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30
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Tunçer S, Gurbanov R, Sheraj I, Solel E, Esenturk O, Banerjee S. Low dose dimethyl sulfoxide driven gross molecular changes have the potential to interfere with various cellular processes. Sci Rep 2018; 8:14828. [PMID: 30287873 PMCID: PMC6172209 DOI: 10.1038/s41598-018-33234-z] [Citation(s) in RCA: 59] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2018] [Accepted: 09/25/2018] [Indexed: 12/18/2022] Open
Abstract
Dimethyl sulfoxide (DMSO) is a small molecule with polar, aprotic and amphiphilic properties. It serves as a solvent for many polar and nonpolar molecules and continues to be one of the most used solvents (vehicle) in medical applications and scientific research. To better understand the cellular effects of DMSO within the concentration range commonly used as a vehicle (0.1-1.5%, v/v) for cellular treatments, we applied Attenuated Total Reflectance (ATR) Fourier Transform Infrared (FT-IR) spectroscopy to DMSO treated and untreated epithelial colon cancer cells. Both unsupervised (Principal Component Analysis-PCA) and supervised (Linear Discriminant Analysis-LDA) pattern recognition/modelling algorithms applied to the IR data revealed total segregation and prominent differences between DMSO treated and untreated cells at whole, lipid and nucleic acid regions. Several of these data were supported by other independent techniques. Further IR data analyses of macromolecular profile indicated comprehensive alterations especially in proteins and nucleic acids. Protein secondary structure analysis showed predominance of β-sheet over α-helix in DMSO treated cells. We also observed for the first time, a reduction in nucleic acid level upon DMSO treatment accompanied by the formation of Z-DNA. Molecular docking and binding free energy studies indicated a stabilization of Z-DNA in the presence of DMSO. This alternate DNA form may be related with the specific actions of DMSO on gene expression, differentiation, and epigenetic alterations. Using analytical tools combined with molecular and cellular biology techniques, our data indicate that even at very low concentrations, DMSO induces a number of changes in all macromolecules, which may affect experimental outcomes where DMSO is used as a solvent.
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Affiliation(s)
- Sinem Tunçer
- Department of Biological Sciences, Orta Dogu Teknik Universitesi (ODTU/METU), Ankara, 06800, Turkey
- Vocational School of Health Services, Department of Medical Laboratory Techniques, Bilecik Şeyh Edebali University, Bilecik, 11230, Turkey
| | - Rafig Gurbanov
- Department of Molecular Biology and Genetics, Bilecik Şeyh Edebali University, Bilecik, 11230, Turkey
| | - Ilir Sheraj
- Department of Biological Sciences, Orta Dogu Teknik Universitesi (ODTU/METU), Ankara, 06800, Turkey
| | - Ege Solel
- Department of Biological Sciences, Orta Dogu Teknik Universitesi (ODTU/METU), Ankara, 06800, Turkey
- Department of Biomedicine, University of Bergen, Postbox 7804, Bergen, N-5020, Norway
| | - Okan Esenturk
- Department of Chemistry, Orta Dogu Teknik Universitesi (ODTU/METU), Ankara, 06800, Turkey
| | - Sreeparna Banerjee
- Department of Biological Sciences, Orta Dogu Teknik Universitesi (ODTU/METU), Ankara, 06800, Turkey.
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31
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Mishra A, Siwach P, Misra P, Jayaram B, Bansal M, Olson WK, Thayer KM, Beveridge DL. Toward a Universal Structural and Energetic Model for Prokaryotic Promoters. Biophys J 2018; 115:1180-1189. [PMID: 30172386 DOI: 10.1016/j.bpj.2018.08.002] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2018] [Revised: 07/28/2018] [Accepted: 08/02/2018] [Indexed: 01/04/2023] Open
Abstract
With almost no consensus promoter sequence in prokaryotes, recruitment of RNA polymerase (RNAP) to precise transcriptional start sites (TSSs) has remained an unsolved puzzle. Uncovering the underlying mechanism is critical for understanding the principle of gene regulation. We attempted to search the hidden code in ∼16,500 promoters of 12 prokaryotes representing two kingdoms in their structure and energetics. Twenty-eight fundamental parameters of DNA structure including backbone angles, basepair axis, and interbasepair and intrabasepair parameters were used, and information was extracted from x-ray crystallography data. Three parameters (solvation energy, hydrogen-bond energy, and stacking energy) were selected for creating energetics profiles using in-house programs. DNA of promoter regions was found to be inherently designed to undergo a change in every parameter undertaken for the study, in all prokaryotes. The change starts from some distance upstream of TSSs and continues past some distance from TSS, hence giving a signature state to promoter regions. These signature states might be the universal hidden codes recognized by RNAP. This observation was reiterated when randomly selected promoter sequences (with little sequence conservation) were subjected to structure generation; all developed into very similar three-dimensional structures quite distinct from those of conventional B-DNA and coding sequences. Fine structural details at important motifs (viz. -11, -35, and -75 positions relative to TSS) of promoters reveal novel to our knowledge and pointed insights for RNAP interaction at these locations; it could be correlated with how some particular structural changes at the -11 region may allow insertion of RNAP amino acids in interbasepair space as well as facilitate the flipping out of bases from the DNA duplex.
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Affiliation(s)
- Akhilesh Mishra
- Supercomputing Facility for Bioinformatics & Computational Biology; Kusuma School of Biological Sciences, Indian Institute of Technology, Delhi, India
| | - Priyanka Siwach
- Supercomputing Facility for Bioinformatics & Computational Biology; Department of Biotechnology, Chaudhary Devi Lal University, Sirsa, Haryana, India
| | - Pallavi Misra
- Supercomputing Facility for Bioinformatics & Computational Biology
| | - Bhyravabhotla Jayaram
- Supercomputing Facility for Bioinformatics & Computational Biology; Kusuma School of Biological Sciences, Indian Institute of Technology, Delhi, India; Department of Chemistry, Indian Institute of Technology, Delhi, India.
| | - Manju Bansal
- Molecular Biophysics Unit, Indian Institute of Science, Bangalore, Karnataka, India
| | - Wilma K Olson
- Department of Chemistry & Chemical Biology and BioMaPS Institute for Quantitative Biology, Rutgers, Piscataway, New Jersey
| | - Kelly M Thayer
- Department of Chemistry, Vassar College, Poughkeepsie, New York
| | - David L Beveridge
- Departments of Chemistry, Molecular Biology, and Biochemistry and Molecular Biophysics Program, Wesleyan University, Middletown, Connecticut
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32
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Bie L, Du L, Yuan Q, Gao J. How a single 5-methylation of cytosine regulates the recognition of C/EBPβ transcription factor: a molecular dynamic simulation study. J Mol Model 2018; 24:159. [PMID: 29892907 DOI: 10.1007/s00894-018-3678-8] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2017] [Accepted: 05/15/2018] [Indexed: 12/23/2022]
Abstract
CpG methylation can regulate gene expression by altering the specific binding of protein and DNA. In order to understand how a single 5mC regulates protein-DNA interactions, we have compared the structures and dynamics of CEBP/βprotein-DNA complexes before and after methylation, and the results indicate that even a single 5mC can regulate protein-DNA recognition by steric-hindrance effect of methyl group and changing the hydrogen bond interactions. The interactions between the methyl group, mCpG motif, and the conserved residue arginine make the protein read out the variation of local environment, which further enhances the specific recognition and affects the base pair stacking. The stacking interactions can propagate along the backbone of DNA and lead to long-range allosteric effects, including obvious conformational variations for DNA base pairs.
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Affiliation(s)
- Lihua Bie
- Agricultural Bioinformatics Key Laboratory of Hubei Province, College of Informatics, Huazhong Agricultural University, Wuhan, 430070, People's Republic of China
| | - Likai Du
- Agricultural Bioinformatics Key Laboratory of Hubei Province, College of Informatics, Huazhong Agricultural University, Wuhan, 430070, People's Republic of China
| | - Qiaoxia Yuan
- College of Engineering, Huazhong Agricultural University, Wuhan, 430070, People's Republic of China.
| | - Jun Gao
- Agricultural Bioinformatics Key Laboratory of Hubei Province, College of Informatics, Huazhong Agricultural University, Wuhan, 430070, People's Republic of China.
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33
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Abstract
The complex conformational change from B-DNA to Z-DNA requires inversion of helix-handedness. Multiple degrees of freedom are intricately coupled during this transition, and formulating an appropriate reaction coordinate that captures the underlying complexity would be problematic. In this contribution, we adopt an alternative approach, based on the potential energy landscape perspective, to construct a kinetic transition network. Microscopic insight into the B → Z transition is provided in terms of geometrically defined discrete paths consisting of local minima and the transition states that connect them. We find that the inversion of handedness can occur via two competing mechanisms, either involving stretched intermediates, or a B-Z junction, in agreement with previous predictions. The organisation of the free energy landscape further suggests that this process is likely to be slow under physiological conditions. Our results represent a key step towards decoding the more intriguing features of the B → Z transition, such as the role of ionic strength and negative supercoiling in reshaping the landscape.
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Affiliation(s)
- Debayan Chakraborty
- Department of Chemistry, University of Cambridge, Lensfield Road, CB2 1EW, UK.
| | - David J Wales
- Department of Chemistry, University of Cambridge, Lensfield Road, CB2 1EW, UK.
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34
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Sunami T, Chatake T, Kono H. DNA conformational transitions inferred from re-evaluation of m|F o| - D|F c| electron-density maps. Acta Crystallogr D Struct Biol 2017; 73:600-608. [PMID: 28695860 PMCID: PMC5505156 DOI: 10.1107/s2059798317007707] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2016] [Accepted: 05/24/2017] [Indexed: 11/30/2022] Open
Abstract
Conformational flexibility of DNA plays important roles in biological processes such as transcriptional regulation and DNA packaging etc. To understand the mechanisms of these processes, it is important to analyse when, where and how DNA shows conformational variations. Recent analyses have indicated that conventional refinement methods do not always provide accurate models of crystallographic heterogeneities and that some information on polymorphism has been overlooked in previous crystallographic studies. In the present study, the m|Fo| - D|Fc| electron-density maps of double-helical DNA crystal structures were calculated at a resolution equal to or better than 1.5 Å and potential conformational transitions were found in 27% of DNA phosphates. Detailed analyses of the m|Fo| - D|Fc| peaks indicated that some of these unassigned densities correspond to ZI ↔ ZII or A/B → BI conformational transitions. A relationship was also found between ZI/ZII transitions and metal coordination in Z-DNA from the detected peaks. The present study highlights that frequent transitions of phosphate backbones occur even in crystals and that some of these transitions are affected by the local molecular environment.
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Affiliation(s)
- Tomoko Sunami
- Molecular Modeling and Simulation Group, National Institutes for Quantum and Radiological Science and Technology, 8-1-7 Umemidai, Kizugawa 619-0215, Japan
| | - Toshiyuki Chatake
- Research Reactor Institute, Kyoto University, 2 Asashironishi, Kumatori, Osaka 590-0494, Japan
| | - Hidetoshi Kono
- Molecular Modeling and Simulation Group, National Institutes for Quantum and Radiological Science and Technology, 8-1-7 Umemidai, Kizugawa 619-0215, Japan
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35
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Martinez-Fernandez L, Banyasz A, Esposito L, Markovitsi D, Improta R. UV-induced damage to DNA: effect of cytosine methylation on pyrimidine dimerization. Signal Transduct Target Ther 2017; 2:17021. [PMID: 29263920 PMCID: PMC5661629 DOI: 10.1038/sigtrans.2017.21] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2016] [Revised: 01/24/2017] [Accepted: 03/30/2017] [Indexed: 11/09/2022] Open
Abstract
Methylation/demethylation of cytosine plays an important role in epigenetic signaling, the reversibility of epigenetic modifications offering important opportunities for targeted therapies. Actually, methylated sites have been correlated with mutational hotspots detected in skin cancers. The present brief review discusses the physicochemical parameters underlying the specific ultraviolet-induced reactivity of methylated cytosine. It focuses on dimerization reactions giving rise to cyclobutane pyrimidine dimers and pyrimidine (6–4) pyrimidone adducts. According to recent studies, four conformational and electronic factors that are affected by cytosine methylation may control these reactions: the red-shift of the absorption spectrum, the lengthening of the excited state lifetime, changes in the sugar puckering modifying the stacking between reactive pyrimidines and an increase in the rigidity of duplexes favoring excitation energy transfer toward methylated pyrimidines.
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Affiliation(s)
| | - Akos Banyasz
- LIDYL, CEA, CNRS, Université Paris-Saclay, Gif-sur-Yvette, France
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36
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Mahmoud AA, Farouk A, Goneim A, Hafez MFA, Saleem TH. Ornithine decarboxylase gene expression and activity in lung cancer. GENE REPORTS 2016. [DOI: 10.1016/j.genrep.2016.09.012] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
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37
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Manderville RA, Wetmore SD. C-Linked 8-aryl guanine nucleobase adducts: biological outcomes and utility as fluorescent probes. Chem Sci 2016; 7:3482-3493. [PMID: 29997840 PMCID: PMC6007177 DOI: 10.1039/c6sc00053c] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2016] [Accepted: 02/23/2016] [Indexed: 12/18/2022] Open
Abstract
Aryl radical species derived from enzymatic transformations of aromatic mutagens preferentially react at the 8-site of the guanine (G) nucleobase to afford carbon-linked 8arylG adducts. The resulting lesions possess altered biophysical and genetic coding properties compared to the precursor G nucleoside in B-form DNA. Unlike other adducts, these lesions also possess useful fluorescent properties, since direct attachment of the 8aryl ring extends the purine π-system to afford G mimics with red-shifted excitation maxima and emission that can be sensitive to the microenvironment of the 8arylG base within nucleic acid structures. In B-form DNA, 8arylG adducts are disruptive to duplex formation because they prefer to adopt the syn-conformation about the bond connecting the nucleobase to the deoxyribose backbone, which perturbs Watson-Crick (WC) H-bonding with the opposing cytosine (C). Thus, in a B-form duplex, the emissive properties of 8arylG adducts can be employed as a tool to provide insight into adduct conformation, which can be related to their biological outcomes. However, since Gs preferentially adopt the syn-conformation in left-handed Z-DNA and antiparallel G-quadruplex (GQ) structures, 8arylG lesions can be inserted into syn-G positions without disrupting H-bonding interactions. In fact, 8arylG lesions can serve as ideal fluorescent probes in an antiparallel GQ because their emission is sensitive to GQ folding. This perspective outlines recent developments in the biological implications of 8arylG formation together with their utility as fluorescent G analogs for use in DNA-based diagnostic systems.
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Affiliation(s)
- Richard A Manderville
- Department of Chemistry & Toxicology , University of Guelph , Guelph , ON , Canada N1G 2W1 .
| | - Stacey D Wetmore
- Department of Chemistry & Biochemistry , University of Lethbridge , Lethbridge , AB , Canada T1K 3M4 .
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Shruthi Sureshan C, Habeeb SKM. Identification and conformational analysis of putative microRNAs in Maruca vitrata (Lepidoptera: Pyralidae). Appl Transl Genom 2015; 7:2-12. [PMID: 27054079 PMCID: PMC4803788 DOI: 10.1016/j.atg.2015.10.003] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2015] [Revised: 08/21/2015] [Accepted: 10/14/2015] [Indexed: 11/29/2022]
Abstract
MicroRNAs (miRNAs) are a class of small RNAs, evolutionarily conserved endogenous non-coding RNAs that regulate their target mRNA expression by either inactivating or degrading mRNA genes; thus playing an important role in the growth and development of an organism. Maruca vitrata is an insect pest of leguminous plants like pigeon pea, cowpea and mung bean and is pantropical. In this study, we perform BLAST on all known miRNAs against the transcriptome data of M. vitrata and thirteen miRNAs were identified. These miRNAs were characterised and their target genes were identified using TargetScan and were functionally annotated using FlyBase. The importance of the structure of pre-miRNA in the Drosha activity led to study the backbone torsion angles of predicted pre-miRNAs (mvi-miR-9751, mvi-miR-649-3p, mvi-miR-4057 and mvi-miR-1271) to identify various nucleotide triplets that contribute to the variation of torsion angle values at various structural motifs of a pre-miRNA.
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Affiliation(s)
- C Shruthi Sureshan
- Department of Bioinformatics, School of Bioengineering, SRM University, Kattankulathur 603203, Tamil Nadu, India
| | - S K M Habeeb
- Department of Bioinformatics, School of Bioengineering, SRM University, Kattankulathur 603203, Tamil Nadu, India
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Qi J, Govind N, Anantram MP. The role of cytosine methylation on charge transport through a DNA strand. J Chem Phys 2015; 143:094306. [DOI: 10.1063/1.4929909] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
- Jianqing Qi
- Department of Electrical Engineering, University of Washington, Seattle, Washington 98195-2500, USA
| | - Niranjan Govind
- William R. Wiley Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, Washington 99352, USA
| | - M. P. Anantram
- Department of Electrical Engineering, University of Washington, Seattle, Washington 98195-2500, USA
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Wang J, Wang S, Zhong C, Tian T, Zhou X. Novel insights into a major DNA oxidative lesion: its effects on Z-DNA stabilization. Org Biomol Chem 2015; 13:8996-9. [PMID: 26242474 DOI: 10.1039/c5ob01340b] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Here, we have provided novel insights into the effects of 8-oxodG substitutions on B-Z transitions of CpG dinucleotide DNAs. A combination of different techniques including a CD study, a PAGE analysis, DFT calculations and molecular modeling has been collectively used.
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Affiliation(s)
- Jiaqi Wang
- College of Chemistry and Molecular Sciences, Key Laboratory of Biomedical Polymers of Ministry of Education, State Key Laboratory of Virology, Wuhan University, Wuhan, Hubei 430072, P. R. China.
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41
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Carvalho ATP, Gouveia L, Kanna CR, Wärmländer SKTS, Platts JA, Kamerlin SCL. Understanding the structural and dynamic consequences of DNA epigenetic modifications: computational insights into cytosine methylation and hydroxymethylation. Epigenetics 2015; 9:1604-12. [PMID: 25625845 PMCID: PMC4622728 DOI: 10.4161/15592294.2014.988043] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023] Open
Abstract
We report a series of molecular dynamics (MD) simulations of up to a microsecond combined simulation time designed to probe epigenetically modified DNA sequences. More specifically, by monitoring the effects of methylation and hydroxymethylation of cytosine in different DNA sequences, we show, for the first time, that DNA epigenetic modifications change the molecule's dynamical landscape, increasing the propensity of DNA toward different values of twist and/or roll/tilt angles (in relation to the unmodified DNA) at the modification sites. Moreover, both the extent and position of different modifications have significant effects on the amount of structural variation observed. We propose that these conformational differences, which are dependent on the sequence environment, can provide specificity for protein binding.
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Key Words
- AFM, Atomic Force Microscopy
- DDD, Dickerson-Drew Dodecamer
- DFT, Density Functional Theory
- DNA methylation
- DNA, Deoxyribonucleic Acid
- DNMT, DNA Methyltransferase
- LINEs, Long Interspred Transposable Elements
- MD, Molecular Dynamics
- MM, Molecular Mechanics
- MeCP, Methylated CpG-binding proteins
- PBC, Periodic Boundary Conditions
- QM, Quantum Mechanics
- RDF, Radial Distribution Functions
- RESP, Restrained Electrostatic Potentials Model
- SINEs, Short Interspred Transposable Elements
- SPME, Smooth Particle-Mesh Ewald
- TET, Translocation Proteins
- WT, Wild Type
- epigenetics
- indirect readout
- molecular dynamics
- recognition
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Affiliation(s)
- Alexandra T P Carvalho
- a Science for Life Laboratory; Department of Cell and Molecular Biology ; Uppsala University ; Uppsala , Sweden
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42
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Hamm CA, Costa FF. Epigenomes as therapeutic targets. Pharmacol Ther 2015; 151:72-86. [PMID: 25797698 DOI: 10.1016/j.pharmthera.2015.03.003] [Citation(s) in RCA: 83] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2015] [Accepted: 03/06/2015] [Indexed: 12/19/2022]
Abstract
Epigenetics is a molecular phenomenon that pertains to heritable changes in gene expression that do not involve changes in the DNA sequence. Epigenetic modifications in a whole genome, known as the epigenome, play an essential role in the regulation of gene expression in both normal development and disease. Traditional epigenetic changes include DNA methylation and histone modifications. Recent evidence reveals that other players, such as non-coding RNAs, may have an epigenetic regulatory role. Aberrant epigenetic signaling is becoming to be known as a central component of human disease, and the reversible nature of the epigenetic modifications provides an exciting opportunity for the development of clinically relevant therapeutics. Current epigenetic therapies provide a clinical benefit through disrupting DNA methyltransferases or histone deacetylases. However, the emergence of next-generation epigenetic therapies provides an opportunity to more effectively disrupt epigenetic disease states. Novel epigenetic therapies may improve drug targeting and drug delivery, optimize dosing schedules, and improve the efficacy of preexisting treatment modalities (chemotherapy, radiation, and immunotherapy). This review discusses the epigenetic mechanisms that contribute to the disease, available epigenetic therapies, epigenetic therapies currently in development, and the potential future use of epigenetic therapeutics in a clinical setting.
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Affiliation(s)
- Christopher A Hamm
- Cancer Biology and Epigenomics Program, Ann & Robert H Lurie Children's Hospital of Chicago Research Center and Department of Pediatrics, Northwestern University's Feinberg School of Medicine, 225 E. Chicago Avenue, Box 220, Chicago, IL 60611-2605, USA.
| | - Fabricio F Costa
- Cancer Biology and Epigenomics Program, Ann & Robert H Lurie Children's Hospital of Chicago Research Center and Department of Pediatrics, Northwestern University's Feinberg School of Medicine, 225 E. Chicago Avenue, Box 220, Chicago, IL 60611-2605, USA; StartUp Health Academy, 2000 Broadway St, 18th Floor, New York, NY 10.023, USA; Genomic Enterprise, 2405 N. Sheffield Av., # 14088, Chicago, IL 60.614, USA; Genomic Sciences and Biotechnology Program, UCB - Brasilia, SGAN 916 Modulo B, Bloco C, 70.790-160 Brasilia, Brazil.
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43
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Sawaya S, Boocock J, Black MA, Gemmell NJ. Exploring possible DNA structures in real-time polymerase kinetics using Pacific Biosciences sequencer data. BMC Bioinformatics 2015; 16:21. [PMID: 25626999 PMCID: PMC4384361 DOI: 10.1186/s12859-014-0449-0] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2014] [Accepted: 12/30/2014] [Indexed: 12/01/2022] Open
Abstract
Background Pausing of DNA polymerase can indicate the presence of a DNA structure that differs from the canonical double-helix. Here we detail a method to investigate how polymerase pausing in the Pacific Biosciences sequencer reads can be related to DNA sequences. The Pacific Biosciences sequencer uses optics to view a polymerase and its interaction with a single DNA molecule in real-time, offering a unique way to detect potential alternative DNA structures. Results We have developed a new way to examine polymerase kinetics data and relate it to the DNA sequence by using a wavelet transform of read information from the sequencer. We use this method to examine how polymerase kinetics are related to nucleotide base composition. We then examine tandem repeat sequences known for their ability to form different DNA structures: (CGG)n and (CG)n repeats which can, respectively, form G-quadruplex DNA and Z-DNA. We find pausing around the (CGG)n repeat that may indicate the presence of G-quadruplexes in some of the sequencer reads. The (CG)n repeat does not appear to cause polymerase pausing, but its kinetics signature nevertheless suggests the possibility that alternative nucleotide conformations may sometimes be present. Conclusion We discuss the implications of using our method to discover DNA sequences capable of forming alternative structures. The analyses presented here can be reproduced on any Pacific Biosciences kinetics data for any DNA pattern of interest using an R package that we have made publicly available.
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Affiliation(s)
- Sterling Sawaya
- Institute for Behavioral Genetics, University of Colorado, Boulder, USA. .,Department of Anatomy, and Allan Wilson Centre for Molecular Ecology and Evolution, University of Otago, Dunedin, New Zealand.
| | - James Boocock
- Department of Biochemistry, University of Otago, Dunedin, New Zealand.
| | - Michael A Black
- Department of Biochemistry, University of Otago, Dunedin, New Zealand.
| | - Neil J Gemmell
- Department of Anatomy, and Allan Wilson Centre for Molecular Ecology and Evolution, University of Otago, Dunedin, New Zealand.
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44
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Karolak A, van der Vaart A. Enhanced sampling simulations of DNA step parameters. J Comput Chem 2014; 35:2297-304. [PMID: 25303338 DOI: 10.1002/jcc.23751] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2014] [Revised: 09/03/2014] [Accepted: 09/14/2014] [Indexed: 12/14/2022]
Abstract
A novel approach for the selection of step parameters as reaction coordinates in enhanced sampling simulations of DNA is presented. The method uses three atoms per base and does not require coordinate overlays or idealized base pairs. This allowed for a highly efficient implementation of the calculation of all step parameters and their Cartesian derivatives in molecular dynamics simulations. Good correlation between the calculated and actual twist, roll, tilt, shift, and slide parameters is obtained, while the correlation with rise is modest. The method is illustrated by its application to the methylated and unmethylated 5'-CATGTGACGTCACATG-3' double stranded DNA sequence. One-dimensional umbrella simulations indicate that the flexibility of the central CG step is only marginally affected by methylation.
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Affiliation(s)
- Aleksandra Karolak
- Department of Chemistry, University of South Florida, 4202 East Fowler Avenue, CHE 205, Tampa, Florida, 33620
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45
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Babbitt GA, Alawad MA, Schulze KV, Hudson AO. Synonymous codon bias and functional constraint on GC3-related DNA backbone dynamics in the prokaryotic nucleoid. Nucleic Acids Res 2014; 42:10915-26. [PMID: 25200075 PMCID: PMC4176184 DOI: 10.1093/nar/gku811] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
While mRNA stability has been demonstrated to control rates of translation, generating both global and local synonymous codon biases in many unicellular organisms, this explanation cannot adequately explain why codon bias strongly tracks neighboring intergene GC content; suggesting that structural dynamics of DNA might also influence codon choice. Because minor groove width is highly governed by 3-base periodicity in GC, the existence of triplet-based codons might imply a functional role for the optimization of local DNA molecular dynamics via GC content at synonymous sites (≈GC3). We confirm a strong association between GC3-related intrinsic DNA flexibility and codon bias across 24 different prokaryotic multiple whole-genome alignments. We develop a novel test of natural selection targeting synonymous sites and demonstrate that GC3-related DNA backbone dynamics have been subject to moderate selective pressure, perhaps contributing to our observation that many genes possess extreme DNA backbone dynamics for their given protein space. This dual function of codons may impose universal functional constraints affecting the evolution of synonymous and non-synonymous sites. We propose that synonymous sites may have evolved as an 'accessory' during an early expansion of a primordial genetic code, allowing for multiplexed protein coding and structural dynamic information within the same molecular context.
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Affiliation(s)
- Gregory A Babbitt
- Thomas H. Gosnell School of Life Sciences, Rochester Institute of Technology, Rochester NY, USA 14623
| | - Mohammed A Alawad
- B. Thomas Golisano College of Computing and Information Sciences, Rochester Institute of Technology, Rochester NY, USA 14623
| | - Katharina V Schulze
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston TX, USA 77030
| | - André O Hudson
- Thomas H. Gosnell School of Life Sciences, Rochester Institute of Technology, Rochester NY, USA 14623
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46
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van der Vaart A. Coupled binding-bending-folding: The complex conformational dynamics of protein-DNA binding studied by atomistic molecular dynamics simulations. Biochim Biophys Acta Gen Subj 2014; 1850:1091-1098. [PMID: 25161164 DOI: 10.1016/j.bbagen.2014.08.009] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2014] [Revised: 08/14/2014] [Accepted: 08/18/2014] [Indexed: 12/21/2022]
Abstract
BACKGROUND Protein-DNA binding often involves dramatic conformational changes such as protein folding and DNA bending. While thermodynamic aspects of this behavior are understood, and its biological function is often known, the mechanism by which the conformational changes occur is generally unclear. By providing detailed structural and energetic data, molecular dynamics simulations have been helpful in elucidating and rationalizing protein-DNA binding. SCOPE OF REVIEW This review will summarize recent atomistic molecular dynamics simulations of the conformational dynamics of DNA and protein-DNA binding. A brief overview of recent developments in DNA force fields is given as well. MAJOR CONCLUSIONS Simulations have been crucial in rationalizing the intrinsic flexibility of DNA, and have been instrumental in identifying the sequence of binding events, the triggers for the conformational motion, and the mechanism of binding for a number of important DNA-binding proteins. GENERAL SIGNIFICANCE Molecular dynamics simulations are an important tool for understanding the complex binding behavior of DNA-binding proteins. With recent advances in force fields and rapid increases in simulation time scales, simulations will become even more important for future studies. This article is part of a Special Issue entitled Recent developments of molecular dynamics.
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Affiliation(s)
- Arjan van der Vaart
- Department of Chemistry, University of South Florida, 4202 East Fowler Avenue CHE 205, Tampa, FL 33620, USA.
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47
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Esposito L, Banyasz A, Douki T, Perron M, Markovitsi D, Improta R. Effect of C5-Methylation of Cytosine on the Photoreactivity of DNA: A Joint Experimental and Computational Study of TCG Trinucleotides. J Am Chem Soc 2014; 136:10838-41. [DOI: 10.1021/ja5040478] [Citation(s) in RCA: 49] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Luciana Esposito
- Istituto di Biostrutture e Bioimmagini—CNR, Via Mezzocannone 16, I-80134 Napoli, Italy
| | - Akos Banyasz
- CNRS, IRAMIS, LIDYL, Laboratoire Francis Perrin, URA 2453, F-91191 Gif-sur-Yvette, France
| | - Thierry Douki
- INAC-LCIB,
LAN, and CEA, INAC-SCIB, LAN Université Grenoble Alpes, F-38000 Grenoble, France
| | - Marion Perron
- CNRS, IRAMIS, LIDYL, Laboratoire Francis Perrin, URA 2453, F-91191 Gif-sur-Yvette, France
| | - Dimitra Markovitsi
- CNRS, IRAMIS, LIDYL, Laboratoire Francis Perrin, URA 2453, F-91191 Gif-sur-Yvette, France
| | - Roberto Improta
- Istituto di Biostrutture e Bioimmagini—CNR, Via Mezzocannone 16, I-80134 Napoli, Italy
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Vargas-Caraveo A, Castillo-Michel H, Mejia-Carmona GE, Pérez-Ishiwara DG, Cotte M, Martínez-Martínez A. Preliminary studies of the effects of psychological stress on circulating lymphocytes analyzed by synchrotron radiation based-Fourier transform infrared microspectroscopy. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2014; 128:141-146. [PMID: 24667417 DOI: 10.1016/j.saa.2014.02.148] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/18/2013] [Revised: 02/13/2014] [Accepted: 02/23/2014] [Indexed: 06/03/2023]
Abstract
Psychological stress is a condition that not only generates behavioral disorders but also disrupts homeostasis and immune activity that can exacerbate or lead to inflammatory diseases. The aim of this work was to study biochemical changes in circulating immune cells from rats under psychological stress by using vibrational spectroscopy. A stress model was used, where exposure to a stressor was repeated for 5 days. Subsequently, circulating lymphocytes were examined for their biomolecular vibrational fingerprints with synchrotron radiation based-Fourier transform infrared microspectroscopy. The results showed an increased absorption at the ester lipid region (1720-1755 cm(-1)) in lymphocytes from stressed rats, suggesting lipid peroxidation. Statistical significant changes in wavenumber peak position and absorbance in the nucleic acid region were also observed (915-950 cm(-1) Z-DNA, 1090-1150 cm(-1) symmetric stretching of P-O-C, 1200-1260 cm(-1) asymmetric PO2 and 1570-1510 cm(-1) methylated nucleotides) which suggest a reduction of transcriptional activity in lymphocytes from stressed rat. These results unravel part of the mechanisms by which psychological stress may affect the immune system leading to systemic consequences.
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Affiliation(s)
- Alejandra Vargas-Caraveo
- Escuela Nacional de Medicina y Homeopatía, Instituto Politécnico Nacional, Guillermo Massieu Helguera, No. 239, Fraccionamiento "La Escalera", Ticomán, C.P. 07320 México DF, Mexico; Departamento de Ciencias Químico Biológicas, Instituto de Ciencias Biomédicas, Universidad Autónoma de Ciudad Juárez, Anillo envolvente Pronaf y Estocolmo s/n, 32310 Cd. Juárez, Mexico.
| | - Hiram Castillo-Michel
- ID21, European Synchrotron Radiation Facility, 6 Rue Jules Horowitz, 38000 Grenoble, France.
| | - Gloria Erika Mejia-Carmona
- Escuela Nacional de Medicina y Homeopatía, Instituto Politécnico Nacional, Guillermo Massieu Helguera, No. 239, Fraccionamiento "La Escalera", Ticomán, C.P. 07320 México DF, Mexico; Departamento de Ciencias Químico Biológicas, Instituto de Ciencias Biomédicas, Universidad Autónoma de Ciudad Juárez, Anillo envolvente Pronaf y Estocolmo s/n, 32310 Cd. Juárez, Mexico.
| | - David Guillermo Pérez-Ishiwara
- Escuela Nacional de Medicina y Homeopatía, Instituto Politécnico Nacional, Guillermo Massieu Helguera, No. 239, Fraccionamiento "La Escalera", Ticomán, C.P. 07320 México DF, Mexico.
| | - Marine Cotte
- ID21, European Synchrotron Radiation Facility, 6 Rue Jules Horowitz, 38000 Grenoble, France.
| | - Alejandro Martínez-Martínez
- Departamento de Ciencias Químico Biológicas, Instituto de Ciencias Biomédicas, Universidad Autónoma de Ciudad Juárez, Anillo envolvente Pronaf y Estocolmo s/n, 32310 Cd. Juárez, Mexico.
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49
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Gioacchini G, Giorgini E, Vaccari L, Ferraris P, Sabbatini S, Bianchi V, Borini A, Carnevali O. A new approach to evaluate aging effects on human oocytes: Fourier transform infrared imaging spectroscopy study. Fertil Steril 2014; 101:120-7. [DOI: 10.1016/j.fertnstert.2013.09.012] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2013] [Revised: 09/03/2013] [Accepted: 09/09/2013] [Indexed: 01/21/2023]
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50
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Wang S, Long Y, Wang J, Ge Y, Guo P, Liu Y, Tian T, Zhou X. Systematic investigations of different cytosine modifications on CpG dinucleotide sequences: the effects on the B-Z transition. J Am Chem Soc 2013; 136:56-9. [PMID: 24364741 DOI: 10.1021/ja4107012] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
We have first demonstrated the distinctive effects of three newly reported epigenetic modifications, including 5hmC, 5fC, and 5caC, on B-Z transition of CpG dinucleotide DNAs. We have performed detailed assays and compared their effects. We further studied the regulation of B-Z transition of CpG dinucleotide dodecamers by alternating oxidation and alternating reduction.
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Affiliation(s)
- Shaoru Wang
- College of Chemistry and Molecular Sciences, Key Laboratory of Biomedical Polymers of Ministry of Education, Wuhan University , Wuhan, Hubei 430072, P. R. China
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