1
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Karam JAQ, Fréreux C, Mohanty BK, Dalton AC, Dincman TA, Palanisamy V, Howley BV, Howe PH. The RNA binding protein PCBP1 modulates transcription by recruiting the G-quadruplex-specific helicase DHX9. J Biol Chem 2024:107830. [PMID: 39342995 DOI: 10.1016/j.jbc.2024.107830] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2024] [Revised: 09/12/2024] [Accepted: 09/15/2024] [Indexed: 10/01/2024] Open
Abstract
PCBP1, polycytosine (poly(C)) binding protein 1, an RNA and single-stranded DNA (ssDNA) binding protein, binds poly(C) DNA tracts but it remains unclear whether its ability to bind ssDNA contributes to transcriptional regulation. Here, we report that PCBP1's DNA binding sites are enriched at transcription start sites and that by binding to promoter regions, PCBP1 regulates transcription in addition to splicing and translation. At PCBP1 target genes, we show that PCBP1 interacts with several RNA/DNA hybrid (R-loop) associated G-quadruplex resolving helicases. Furthermore, we find that PCBP1 interacts with RNA Helicase A (DHX9) to modulate transcription by regulating DHX9 accumulation and activity. PCBP1 depletion leads to defects in R-loop processing and dysregulation of transcription of PCBP1 target genes. PCBP1's high sequence specificity and interaction with helicases suggest that its mechanism in transcription involves guiding helicases to specific loci during transcription, thereby modulating their activity.
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Affiliation(s)
- Joseph A Q Karam
- Department of Biochemistry and Molecular Biology, College of Medicine, Medical University of South Carolina, Charleston, SC, 29425, United States
| | - Cécile Fréreux
- Department of Biochemistry and Molecular Biology, College of Medicine, Medical University of South Carolina, Charleston, SC, 29425, United States
| | - Bidyut K Mohanty
- Department of Biochemistry and Molecular Biology, College of Medicine, Medical University of South Carolina, Charleston, SC, 29425, United States; Department of Cell Biology and Physiology, Edward Via College of Osteopathic Medicine, Spartanburg, SC, United States
| | - Annamarie C Dalton
- Department of Biochemistry and Molecular Biology, College of Medicine, Medical University of South Carolina, Charleston, SC, 29425, United States
| | - Toros A Dincman
- Department of Biochemistry and Molecular Biology, College of Medicine, Medical University of South Carolina, Charleston, SC, 29425, United States; Department of Medicine, Division of Hematology and Oncology Medical University of South Carolina, Charleston, SC, 29425, United States
| | - Viswanathan Palanisamy
- Department of Biochemistry and Molecular Biology, College of Medicine, Medical University of South Carolina, Charleston, SC, 29425, United States; Division of Molecular Medicine, Department of Internal Medicine, UNM Comprehensive Cancer Center, University of New Mexico, Albuquerque, NM, 87131, USA
| | - Breege V Howley
- Department of Biochemistry and Molecular Biology, College of Medicine, Medical University of South Carolina, Charleston, SC, 29425, United States
| | - Philip H Howe
- Department of Biochemistry and Molecular Biology, College of Medicine, Medical University of South Carolina, Charleston, SC, 29425, United States; Hollings Cancer Center, Medical University of South Carolina, Charleston, SC, 29425, United States.
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2
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Guneri D, Alexandrou E, El Omari K, Dvořáková Z, Chikhale RV, Pike DTS, Waudby CA, Morris CJ, Haider S, Parkinson GN, Waller ZAE. Structural insights into i-motif DNA structures in sequences from the insulin-linked polymorphic region. Nat Commun 2024; 15:7119. [PMID: 39164244 PMCID: PMC11336075 DOI: 10.1038/s41467-024-50553-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2023] [Accepted: 07/12/2024] [Indexed: 08/22/2024] Open
Abstract
The insulin-linked polymorphic region is a variable number of tandem repeats region of DNA in the promoter of the insulin gene that regulates transcription of insulin. This region is known to form the alternative DNA structures, i-motifs and G-quadruplexes. Individuals have different sequence variants of tandem repeats and although previous work investigated the effects of some variants on G-quadruplex formation, there is not a clear picture of the relationship between the sequence diversity, the DNA structures formed, and the functional effects on insulin gene expression. Here we show that different sequence variants of the insulin linked polymorphic region form different DNA structures in vitro. Additionally, reporter genes in cellulo indicate that insulin expression may change depending on which DNA structures form. We report the crystal structure and dynamics of an intramolecular i-motif, which reveal sequences within the loop regions forming additional stabilising interactions that are critical to formation of stable i-motif structures. The outcomes of this work reveal the detail in formation of stable i-motif DNA structures, with potential for rational based drug design for compounds to target i-motif DNA.
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Affiliation(s)
- Dilek Guneri
- School of Pharmacy, University College London, 29-39 Brunswick Square, London, WC1N 1AX, UK
| | - Effrosyni Alexandrou
- School of Pharmacy, University College London, 29-39 Brunswick Square, London, WC1N 1AX, UK
| | - Kamel El Omari
- Diamond Light Source, Harwell Science and Innovation Campus, Chilton, Didcot, OX11 0DE, UK
| | - Zuzana Dvořáková
- Institute of Biophysics of the Czech Academy of Sciences, Královopolská 135, 612 00, Brno, Czech Republic
| | - Rupesh V Chikhale
- School of Pharmacy, University College London, 29-39 Brunswick Square, London, WC1N 1AX, UK
| | - Daniel T S Pike
- School of Pharmacy, University College London, 29-39 Brunswick Square, London, WC1N 1AX, UK
| | - Christopher A Waudby
- School of Pharmacy, University College London, 29-39 Brunswick Square, London, WC1N 1AX, UK
| | - Christopher J Morris
- School of Pharmacy, University College London, 29-39 Brunswick Square, London, WC1N 1AX, UK.
| | - Shozeb Haider
- School of Pharmacy, University College London, 29-39 Brunswick Square, London, WC1N 1AX, UK.
- UCL Centre for Advanced Research Computing, University College London, Gower Street, London, WC1E 6BT, UK.
| | - Gary N Parkinson
- School of Pharmacy, University College London, 29-39 Brunswick Square, London, WC1N 1AX, UK.
| | - Zoë A E Waller
- School of Pharmacy, University College London, 29-39 Brunswick Square, London, WC1N 1AX, UK.
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3
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Refael T, Sudman M, Golan G, Pnueli L, Naik S, Preger-Ben Noon E, Henn A, Kaplan A, Melamed P. An i-motif-regulated enhancer, eRNA and adjacent lncRNA affect Lhb expression through distinct mechanisms in a sex-specific context. Cell Mol Life Sci 2024; 81:361. [PMID: 39158745 PMCID: PMC11335282 DOI: 10.1007/s00018-024-05398-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2024] [Revised: 07/21/2024] [Accepted: 08/05/2024] [Indexed: 08/20/2024]
Abstract
Genome-wide studies have demonstrated regulatory roles for diverse non-coding elements, but their precise and interrelated functions have often remained enigmatic. Addressing the need for mechanistic insight, we studied their roles in expression of Lhb which encodes the pituitary gonadotropic hormone that controls reproduction. We identified a bi-directional enhancer in gonadotrope-specific open chromatin, whose functional eRNA (eRNA2) supports permissive chromatin at the Lhb locus. The central untranscribed region of the enhancer contains an iMotif (iM), and is bound by Hmgb2 which stabilizes the iM and directs transcription specifically towards the functional eRNA2. A distinct downstream lncRNA, associated with an inducible G-quadruplex (G4) and iM, also facilitates Lhb expression, following its splicing in situ. GnRH activates Lhb transcription and increased levels of all three RNAs, eRNA2 showing the highest response, while estradiol, which inhibits Lhb, repressed levels of eRNA2 and the lncRNA. The levels of these regulatory RNAs and Lhb mRNA correlate highly in female mice, though strikingly not in males, suggesting a female-specific function. Our findings, which shed new light on the workings of non-coding elements and non-canonical DNA structures, reveal novel mechanisms regulating transcription which have implications not only in the central control of reproduction but also for other inducible genes.
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Affiliation(s)
- Tal Refael
- Faculty of Biology, Technion-Israel Institute of Technology, Haifa, 3200003, Israel
| | - Maya Sudman
- Faculty of Biology, Technion-Israel Institute of Technology, Haifa, 3200003, Israel
| | - Gil Golan
- Faculty of Biology, Technion-Israel Institute of Technology, Haifa, 3200003, Israel
| | - Lilach Pnueli
- Faculty of Biology, Technion-Israel Institute of Technology, Haifa, 3200003, Israel
| | - Sujay Naik
- Department of Genetics and Developmental Biology, The Rappaport Faculty of Medicine and Research Institute, Technion-Israel Institute of Technology, Haifa, 3109601, Israel
| | - Ella Preger-Ben Noon
- Department of Genetics and Developmental Biology, The Rappaport Faculty of Medicine and Research Institute, Technion-Israel Institute of Technology, Haifa, 3109601, Israel
| | - Arnon Henn
- Faculty of Biology, Technion-Israel Institute of Technology, Haifa, 3200003, Israel
| | - Ariel Kaplan
- Faculty of Biology, Technion-Israel Institute of Technology, Haifa, 3200003, Israel
| | - Philippa Melamed
- Faculty of Biology, Technion-Israel Institute of Technology, Haifa, 3200003, Israel.
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4
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Guneri D, Waller ZAE. Utility of intercalator displacement assays for screening of ligands for i-motif DNA structures. Methods Enzymol 2024; 695:221-232. [PMID: 38521586 DOI: 10.1016/bs.mie.2023.12.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/25/2024]
Abstract
Cytosine rich sequences can form intercalated, i-motif DNA structures stabilized by hemi-protonated cytosine:cytosine base pairing. These sequences are often located in regulatory regions of genes such as promoters. Ligands targeting i-motif structures may provide potential leads for treatments for genetic disease. The focus on ligands interacting with i-motif DNA has been increasing in recent years. Here, we describe the fluorescent intercalator displacement (FID) assay using thiazole orange binding i-motif DNA and assess the binding affinity of a ligand to the i-motif DNA by displacing thiazole orange. This provides a time and cost-effective high throughput screening of ligands against secondary DNA structures for hit identification.
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Affiliation(s)
- Dilek Guneri
- School of Pharmacy, University College London, London, United Kingdom.
| | - Zoë A E Waller
- School of Pharmacy, University College London, London, United Kingdom.
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5
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El-Khoury R, Damha MJ. End-ligation can dramatically stabilize i-motifs at neutral pH. Chem Commun (Camb) 2023; 59:3715-3718. [PMID: 36883338 DOI: 10.1039/d2cc07063d] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/06/2023]
Abstract
Stabilizing i-motif structures at neutral pH and physiological temperature remains a major challenge. Here, we demonstrate the use of chemical end-ligation to stabilize intramolecular i-motifs at both acidic and neutral pH. We also demonstrate that combining 2'-deoxy-2'-fluoroarabinocytidine substitutions and end-ligation results in an i-motif with an unparalleled thermal stability of 54 °C at neutral pH. Overall, the ligated i-motifs presented herein may be used in screens for selective i-motif ligands and proteins and could find important applications in nanotechnology.
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Affiliation(s)
- Roberto El-Khoury
- Department of Chemistry, McGill University, Montréal, H3A0B8, Canada.
| | - Masad J Damha
- Department of Chemistry, McGill University, Montréal, H3A0B8, Canada.
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6
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Monsen RC, Chua ED, Hopkins J, Chaires J, Trent J. Structure of a 28.5 kDa duplex-embedded G-quadruplex system resolved to 7.4 Å resolution with cryo-EM. Nucleic Acids Res 2023; 51:1943-1959. [PMID: 36715343 PMCID: PMC9976903 DOI: 10.1093/nar/gkad014] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2022] [Revised: 12/16/2022] [Accepted: 01/04/2023] [Indexed: 01/31/2023] Open
Abstract
Genomic regions with high guanine content can fold into non-B form DNA four-stranded structures known as G-quadruplexes (G4s). Extensive in vivo investigations have revealed that promoter G4s are transcriptional regulators. Little structural information exists for these G4s embedded within duplexes, their presumed genomic environment. Here, we report the 7.4 Å resolution structure and dynamics of a 28.5 kDa duplex-G4-duplex (DGD) model system using cryo-EM, molecular dynamics, and small-angle X-ray scattering (SAXS) studies. The DGD cryo-EM refined model features a 53° bend induced by a stacked duplex-G4 interaction at the 5' G-tetrad interface with a persistently unstacked 3' duplex. The surrogate complement poly dT loop preferably stacks onto the 3' G-tetrad interface resulting in occlusion of both 5' and 3' tetrad interfaces. Structural analysis shows that the DGD model is quantifiably more druggable than the monomeric G4 structure alone and represents a new structural drug target. Our results illustrate how the integration of cryo-EM, MD, and SAXS can reveal complementary detailed static and dynamic structural information on DNA G4 systems.
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Affiliation(s)
- Robert C Monsen
- UofL Health Brown Cancer Center, University of Louisville, Louisville, KY 40202, USA
| | - Eugene Y D Chua
- National Center for CryoEM Access and Training (NCCAT), Simons Electron Microscopy Center, New York Structural Biology Center, NY 10027, USA
| | - Jesse B Hopkins
- The Biophysics Collaborative Access Team (BioCAT), Department of Biological, Chemical, and Physical Sciences, Illinois Institute of Technology, Chicago, IL 60616, USA
| | - Jonathan B Chaires
- UofL Health Brown Cancer Center, University of Louisville, Louisville, KY 40202, USA
- Department of Medicine, University of Louisville, Louisville, KY 40202, USA
- Department of Biochemistry and Molecular Genetics, University of Louisville, Louisville, KY 40202, USA
| | - John O Trent
- UofL Health Brown Cancer Center, University of Louisville, Louisville, KY 40202, USA
- Department of Medicine, University of Louisville, Louisville, KY 40202, USA
- Department of Biochemistry and Molecular Genetics, University of Louisville, Louisville, KY 40202, USA
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7
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Liu M, Yu K, Lian W, Zhou N, Wu C, Bao J. G-Quadruplex Structures as a "Switch" Regulate ATF4 Expression in Ferroptotic HepG2 Cells. ACS Chem Biol 2023; 18:273-284. [PMID: 36722101 DOI: 10.1021/acschembio.2c00615] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
G-quadruplex (G4) is a noncanonical structure folded in a widespread manner by guanine-rich tandem repeated sequences. As a key response factor, activating transcription factor 4 (ATF4) has dual functions in managing iron-dependent ferroptosis by regulating amino acid synthesis and antioxidant-related gene expression. In our study, the activity of ATF4 expression was elevated in HepG2 cells induced by erastin. Based on preliminary bioinformatics analyses, the G-tract region, named WT, had high potential to form G4, and it was found that PDS could markedly weaken the increase of ATF4 expression by reducing the sensitivity of HepG2 cells toward erastin. In circular dichroism spectra, WT oligonucleotides showed characteristic molar ellipticity at specific wavelengths of parallel G4 structures, while corresponding single-base mutants possessed a weaker ability to form G4, which were consistent with immunostaining results. In addition, endogenous G4 formed by the WT motif was significantly destroyed in HepG2 cells treated with erastin. After being transfected with WT oligonucleotides, the levels of ATF4 mRNA decreased significantly regardless of being treated with erastin or not. Meanwhile, mutations of G-tracts could advantageously impact the luciferase expression downstream of an ATF4 promoter in reporter assays, manifesting that the decrease of endogenous G4 in the ATF4 promoter was positively associated with the expression enhanced by erastin in HepG2 cells.
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Affiliation(s)
- Miaomiao Liu
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, Sichuan 610065, China
| | - Kangkang Yu
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, Sichuan 610065, China
| | - Weishao Lian
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, Sichuan 610065, China
| | - Nan Zhou
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, Sichuan 610065, China
| | - Chuanfang Wu
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, Sichuan 610065, China
| | - Jinku Bao
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, Sichuan 610065, China
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8
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Brush GS. Anomalies in dye-terminator DNA sequencing caused by a natural G-quadruplex. PLoS One 2022; 17:e0279423. [PMID: 36574393 PMCID: PMC9794070 DOI: 10.1371/journal.pone.0279423] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2021] [Accepted: 11/24/2022] [Indexed: 12/29/2022] Open
Abstract
A G-rich DNA sequence from yeast that can form a non-canonical G-quadruplex structure was cloned into a plasmid vector and subjected to Sanger sequencing using dye-labeled dideoxynucleotides. Two different effects were observed. In one, presence of the G4 sequence on the template strand led to incorrect incorporation of an A residue at an internal position in the G4 sequence. In the other, the nascent strand caused attenuation of the readout coincident with synthesis of the G-rich DNA. The two effects are novel examples of disruption in DNA synthesis caused by a G4 sequence. These results provide a new example of a DNA structure that could influence genomic stability in human cells.
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Affiliation(s)
- George S. Brush
- Department of Oncology, Molecular Therapeutics Program, Barbara Ann Karmanos Cancer Institute, Wayne State University School of Medicine,Detroit, MI, United States of America
- * E-mail:
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9
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Miglietta G, Marinello J, Russo M, Capranico G. Ligands stimulating antitumour immunity as the next G-quadruplex challenge. Mol Cancer 2022; 21:180. [PMID: 36114513 PMCID: PMC9482198 DOI: 10.1186/s12943-022-01649-y] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2022] [Accepted: 08/22/2022] [Indexed: 11/10/2022] Open
Abstract
AbstractG-quadruplex (G4) binders have been investigated to discover new anticancer drugs worldwide in past decades. As these ligands are generally not highly cytotoxic, the discovery rational was mainly based on increasing the cell-killing potency. Nevertheless, no G4 binder has been shown yet to be effective in cancer patients. Here, G4 binder activity at low dosages will be discussed as a critical feature to discover ligands with therapeutic effects in cancer patients. Specific effects of G4 binders al low doses have been reported to occur in cancer and normal cells. Among them, genome instability and the stimulation of cytoplasmic processes related to autophagy and innate immune response open to the use of G4 binders as immune-stimulating agents. Thus, we propose a new rational of drug discovery, which is not based on cytotoxic potency but rather on immune gene activation at non-cytotoxic dosage.
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10
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Chikhale RV, Guneri D, Yuan R, Morris CJ, Waller ZAE. Identification of sugar-containing natural products that interact with i-motif DNA. Bioorg Med Chem Lett 2022; 73:128886. [PMID: 35835380 DOI: 10.1016/j.bmcl.2022.128886] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2022] [Revised: 07/05/2022] [Accepted: 07/07/2022] [Indexed: 11/30/2022]
Abstract
There are thousands of compounds shown to interact with G-quadruplex DNA, yet very few which target i-motif (iM) DNA. Previous work showed that tobramycin can interact with iM- DNA, indicating the potential for sugar-molecules to target these structures. Computational approaches indicated that the sugar-containing natural products baicalin and geniposidic acid had potential to target iM-DNA. We assessed the DNA interacting properties of these compounds using FRET-based DNA melting and a fluorescence-based displacement assay using iM-DNA structures from the human telomere and the insulin linked polymorphic region (ILPR), as well as complementary G-quadruplex and double stranded DNA. Both baicalin and geniposidic acid show promise as iM-interacting compounds with potential for use in experiments into the structure and function of i-motif forming DNA sequences and present starting points for further synthetic development of these as probes for iM-DNA.
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Affiliation(s)
| | - Dilek Guneri
- UCL School of Pharmacy, 29-39 Brunswick Square, London WC1N 1AX, UK
| | - Robert Yuan
- UCL School of Pharmacy, 29-39 Brunswick Square, London WC1N 1AX, UK
| | | | - Zoë A E Waller
- UCL School of Pharmacy, 29-39 Brunswick Square, London WC1N 1AX, UK.
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11
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Adams DE, Zhen Y, Qi X, Shao WH. Axl Expression in Renal Mesangial Cells Is Regulated by Sp1, Ap1, MZF1, and Ep300, and the IL-6/miR-34a Pathway. Cells 2022; 11:cells11121869. [PMID: 35740998 PMCID: PMC9221537 DOI: 10.3390/cells11121869] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2022] [Revised: 05/31/2022] [Accepted: 06/06/2022] [Indexed: 12/10/2022] Open
Abstract
Axl receptor tyrosine kinase expression in the kidney contributes to a variety of inflammatory renal disease by promoting glomerular proliferation. Axl expression in the kidney is negligible in healthy individuals but upregulated under inflammatory conditions. Little is known about Axl transcriptional regulation. We analyzed the 4.4 kb mouse Axl promoter region and found that many transcription factor (TF)-binding sites and regulatory elements are located within a 600 bp fragment proximal to the translation start site. Among four TFs (Sp1, Ap1, MZF1, and Ep300) identified, Sp1 was the most potent TF that promotes Axl expression. Luciferase assays confirmed the siRNA results and revealed additional mechanisms that regulate Axl expression, including sequences encoding a 5'-UTR mini-intron and potential G-quadruplex forming regions. Deletion of the Axl 5'-UTR mini-intron resulted in a 3.2-fold increases in luciferase activity over the full-length UTR (4.4 kb Axl construct). The addition of TMPyP4, a G-quadruplex stabilizer, resulted in a significantly decreased luciferase activity. Further analysis of the mouse Axl 3'-UTR revealed a miRNA-34a binding site, which inversely regulates Axl expression. The inhibitory role of miRNA-34a in Axl expression was demonstrated in mesangial cells using miRNA-34a mimicry and in primary kidney cells with IL-6 stimulated STAT3 activation. Taken together, Axl expression in mouse kidney is synergistically regulated by multiple factors, including TFs and secondary structures, such as mini-intron and G-quadruplex. A unique IL6/STAT3/miRNA-34a pathway was revealed to be critical in inflammatory renal Axl expression.
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Affiliation(s)
- David E. Adams
- Division of Rheumatology, Allergy, and Immunology, Department of Internal Medicine, College of Medicine, University of Cincinnati, Cincinnati, OH 45267, USA; (D.E.A.); (Y.Z.)
| | - Yuxuan Zhen
- Division of Rheumatology, Allergy, and Immunology, Department of Internal Medicine, College of Medicine, University of Cincinnati, Cincinnati, OH 45267, USA; (D.E.A.); (Y.Z.)
| | - Xiaoyang Qi
- Division of Hematology/Oncology, Department of Internal Medicine, College of Medicine, University of Cincinnati, Cincinnati, OH 45267, USA;
| | - Wen-Hai Shao
- Division of Rheumatology, Allergy, and Immunology, Department of Internal Medicine, College of Medicine, University of Cincinnati, Cincinnati, OH 45267, USA; (D.E.A.); (Y.Z.)
- Correspondence:
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12
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CpG Methylation Altered the Stability and Structure of the i-Motifs Located in the CpG Islands. Int J Mol Sci 2022; 23:ijms23126467. [PMID: 35742916 PMCID: PMC9223787 DOI: 10.3390/ijms23126467] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2022] [Revised: 06/04/2022] [Accepted: 06/07/2022] [Indexed: 11/25/2022] Open
Abstract
Cytosine methylation within the 5′-C-phosphate-G-3′ sequence of nucleotides (called CpG methylation) is a well-known epigenetic modification of genomic DNA that plays an important role in gene expression and development. CpG methylation is likely to be altered in the CpG islands. CpG islands are rich in cytosine, forming a structure called the i-motif via cytosine-cytosine hydrogen bonding. However, little is known about the effect of CpG methylation on the i-motif. In this study, The CpG methylation-induced structural changes on the i-motif was examined by thermal stability, circular dichroism (CD) spectroscopy, and native-polyacrylamide gel electrophoresis (Native-PAGE) evaluation of five i-motif-forming DNAs from four cancer-related genes (VEGF, C-KIT, BCL2, and HRAS). This research shows that CpG methylation increased the transitional pH of several i-motif-forming DNAs and their thermal stability. When examining the effect of CpG methylation on the i-motif in the presence of opposite G4-forming DNAs, CpG methylation influenced the proportion of G4 and i-motif formation. This study showed that CpG methylation altered the stability and structure of the i-motif in CpG islands.
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13
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Frasson I, Pirota V, Richter SN, Doria F. Multimeric G-quadruplexes: A review on their biological roles and targeting. Int J Biol Macromol 2022; 204:89-102. [PMID: 35124022 DOI: 10.1016/j.ijbiomac.2022.01.197] [Citation(s) in RCA: 34] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2021] [Revised: 01/20/2022] [Accepted: 01/31/2022] [Indexed: 12/12/2022]
Abstract
In human cells, nucleic acids adopt several non-canonical structures that regulate key cellular processes. Among them, G-quadruplexes (G4s) are stable structures that form in guanine-rich regions in vitro and in cells. G4 folded/unfolded state shapes numerous cellular processes, including genome replication, transcription, and translation. Moreover, G4 folding is involved in genomic instability. G4s have been described to multimerize, forming high-order structures in both DNA and/or RNA strands. Multimeric G4s can be formed by adjacent intramolecular G4s joined by stacking interactions or connected by short loops. Multimeric G4s can also originate from the assembly of guanines embedded on independent DNA or RNA strands. Notably, crucial regions of the human genome, such as the 3'-terminal overhang of the telomeric DNA as well as the open reading frame of genes involved in the preservation of neuron viability in the human central and peripheral nervous system are prone to form multimeric G4s. The biological importance of such structures has been recently described, with multimeric G4s playing potentially protective or deleterious effects in the pathogenic cascade of various diseases. Here, we portray the multifaceted scenario of multimeric G4s, in terms of structural properties, biological roles, and targeting strategies.
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Affiliation(s)
- Ilaria Frasson
- Department of Molecular Medicine, University of Padova, via A. Gabelli 63, 35121 Padova, Italy
| | - Valentina Pirota
- Department of Chemistry, University of Pavia, v. le Taramelli 10, 27100 Pavia, Italy; G4-INTERACT, USERN, v. le Taramelli 10, 27100 Pavia, Italy
| | - Sara N Richter
- Department of Molecular Medicine, University of Padova, via A. Gabelli 63, 35121 Padova, Italy.
| | - Filippo Doria
- Department of Chemistry, University of Pavia, v. le Taramelli 10, 27100 Pavia, Italy.
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14
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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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15
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Kretzmann JA, Irving KL, Smith NM, Evans CW. Modulating gene expression in breast cancer via DNA secondary structure and the CRISPR toolbox. NAR Cancer 2022; 3:zcab048. [PMID: 34988459 PMCID: PMC8693572 DOI: 10.1093/narcan/zcab048] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2021] [Revised: 11/26/2021] [Accepted: 12/01/2021] [Indexed: 12/11/2022] Open
Abstract
Breast cancer is the most commonly diagnosed malignancy in women, and while the survival prognosis of patients with early-stage, non-metastatic disease is ∼75%, recurrence poses a significant risk and advanced and/or metastatic breast cancer is incurable. A distinctive feature of advanced breast cancer is an unstable genome and altered gene expression patterns that result in disease heterogeneity. Transcription factors represent a unique therapeutic opportunity in breast cancer, since they are known regulators of gene expression, including gene expression involved in differentiation and cell death, which are themselves often mutated or dysregulated in cancer. While transcription factors have traditionally been viewed as 'undruggable', progress has been made in the development of small-molecule therapeutics to target relevant protein-protein, protein-DNA and enzymatic active sites, with varying levels of success. However, non-traditional approaches such as epigenetic editing, transcriptional control via CRISPR/dCas9 systems, and gene regulation through non-canonical nucleic acid secondary structures represent new directions yet to be fully explored. Here, we discuss these new approaches and current limitations in light of new therapeutic opportunities for breast cancers.
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Affiliation(s)
- Jessica A Kretzmann
- Laboratory for Biomolecular Nanotechnology, Department of Physics, Technical University of Munich, Am Coulombwall 4a, 85748 Garching, Germany
| | - Kelly L Irving
- School of Molecular Sciences, The University of Western Australia, 35 Stirling Hwy, Crawley, WA 6009, Australia
| | - Nicole M Smith
- School of Molecular Sciences, The University of Western Australia, 35 Stirling Hwy, Crawley, WA 6009, Australia
| | - Cameron W Evans
- School of Molecular Sciences, The University of Western Australia, 35 Stirling Hwy, Crawley, WA 6009, Australia
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16
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Pandey S, Xiang Y, Friedrich D, Leng Y, Mao H. Direct Measurement of Intermolecular Mechanical Force for Nonspecific Interactions between Small Molecules. J Phys Chem Lett 2021; 12:11316-11322. [PMID: 34780182 PMCID: PMC8778946 DOI: 10.1021/acs.jpclett.1c03142] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
Mechanical force can evaluate intramolecular interactions in macromolecules. Because of the rapid motion of small molecules, it is extremely challenging to measure mechanical forces of nonspecific intermolecular interactions. Here, we used optical tweezers to directly examine the intermolecular mechanical force (IMMF) of nonspecific interactions between two cholesterols. We found that IMMFs of dimeric cholesterol complexes were dependent on the orientation of the interaction. The surprisingly high IMMF in cholesterol dimers (∼30 pN) is comparable to the mechanical stability of DNA secondary structures. Using Hess-like cycles, we quantified that changes in free energy of solubilizing cholesterol (ΔGsolubility) by β-cyclodextrin (βCD) and methylated βCD (Me-βCD) were as low as -16 and -27 kcal/mol, respectively. Compared to the ΔGsolubility of cholesterols in water (5.1 kcal/mol), these values indicated that cyclodextrins can easily solubilize cholesterols. Our results demonstrated that the IMMF can serve as a generic and multipurpose variable to dissect nonspecific intermolecular interactions among small molecules into orientational components.
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Affiliation(s)
- Shankar Pandey
- Department of Chemistry and Biochemistry, Kent State University, Kent, OH, 44242, USA
| | - Yuan Xiang
- Department of Mechanical and Aerospace Engineering, The George Washington University, Washington, DC 20052, USA
| | - Dirk Friedrich
- Department of Chemistry and Biochemistry, Kent State University, Kent, OH, 44242, USA
| | - Yongsheng Leng
- Department of Mechanical and Aerospace Engineering, The George Washington University, Washington, DC 20052, USA
| | - Hanbin Mao
- Department of Chemistry and Biochemistry, Kent State University, Kent, OH, 44242, USA
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17
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Grün JT, Schwalbe H. Folding dynamics of polymorphic G-quadruplex structures. Biopolymers 2021; 113:e23477. [PMID: 34664713 DOI: 10.1002/bip.23477] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2021] [Revised: 09/30/2021] [Accepted: 09/30/2021] [Indexed: 12/14/2022]
Abstract
G-quadruplexes (G4), found in numerous places within the human genome, are involved in essential processes of cell regulation. Chromosomal DNA G4s are involved for example, in replication and transcription as first steps of gene expression. Hence, they influence a plethora of downstream processes. G4s possess an intricate structure that differs from canonical B-form DNA. Identical DNA G4 sequences can adopt multiple long-lived conformations, a phenomenon known as G4 polymorphism. A detailed understanding of the molecular mechanisms that drive G4 folding is essential to understand their ambivalent regulatory roles. Disentangling the inherent dynamic and polymorphic nature of G4 structures thus is key to unravel their biological functions and make them amenable as molecular targets in novel therapeutic approaches. We here review recent experimental approaches to monitor G4 folding and discuss structural aspects for possible folding pathways. Substantial progress in the understanding of G4 folding within the recent years now allows drawing comprehensive models of the complex folding energy landscape of G4s that we herein evaluate based on computational and experimental evidence.
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Affiliation(s)
- J Tassilo Grün
- Department of Chemical and Biological Physics, Weizmann Institute of Science, Rehovot, Israel
| | - Harald Schwalbe
- Institute for Organic Chemistry and Chemical Biology, Johann Wolfgang Goethe-University, Frankfurt/M, Germany.,Center for Biomolecular Magnetic Resonance (BMRZ), Johann Wolfgang Goethe-University Frankfurt, Frankfurt/M, Germany
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18
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Teng FY, Jiang ZZ, Guo M, Tan XZ, Chen F, Xi XG, Xu Y. G-quadruplex DNA: a novel target for drug design. Cell Mol Life Sci 2021; 78:6557-6583. [PMID: 34459951 PMCID: PMC11072987 DOI: 10.1007/s00018-021-03921-8] [Citation(s) in RCA: 64] [Impact Index Per Article: 21.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2021] [Revised: 07/13/2021] [Accepted: 08/12/2021] [Indexed: 02/08/2023]
Abstract
G-quadruplex (G4) DNA is a type of quadruple helix structure formed by a continuous guanine-rich DNA sequence. Emerging evidence in recent years authenticated that G4 DNA structures exist both in cell-free and cellular systems, and function in different diseases, especially in various cancers, aging, neurological diseases, and have been considered novel promising targets for drug design. In this review, we summarize the detection method and the structure of G4, highlighting some non-canonical G4 DNA structures, such as G4 with a bulge, a vacancy, or a hairpin. Subsequently, the functions of G4 DNA in physiological processes are discussed, especially their regulation of DNA replication, transcription of disease-related genes (c-MYC, BCL-2, KRAS, c-KIT et al.), telomere maintenance, and epigenetic regulation. Typical G4 ligands that target promoters and telomeres for drug design are also reviewed, including ellipticine derivatives, quinoxaline analogs, telomestatin analogs, berberine derivatives, and CX-5461, which is currently in advanced phase I/II clinical trials for patients with hematologic cancer and BRCA1/2-deficient tumors. Furthermore, since the long-term stable existence of G4 DNA structures could result in genomic instability, we summarized the G4 unfolding mechanisms emerged recently by multiple G4-specific DNA helicases, such as Pif1, RecQ family helicases, FANCJ, and DHX36. This review aims to present a general overview of the field of G-quadruplex DNA that has progressed in recent years and provides potential strategies for drug design and disease treatment.
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Affiliation(s)
- Fang-Yuan Teng
- Experimental Medicine Center, The Affiliated Hospital of Southwest Medical University, Luzhou, 646000, Sichuan, China
- Department of Endocrinology and Metabolism, The Affiliated Hospital of Southwest Medical University, Luzhou, 646000, Sichuan, China
- Cardiovascular and Metabolic Diseases Key Laboratory of Luzhou, and Sichuan Clinical Research Center for Nephropathy, and Academician (Expert) Workstation of Sichuan Province, The Affiliated Hospital of Southwest Medical University, Luzhou, 646000, Sichuan, China
- State Key Laboratory of Crop Stress Biology for Arid Areas and College of Life Sciences, Northwest A&F University, Yangling, 712100, Shaanxi, China
| | - Zong-Zhe Jiang
- Experimental Medicine Center, The Affiliated Hospital of Southwest Medical University, Luzhou, 646000, Sichuan, China
- Department of Endocrinology and Metabolism, The Affiliated Hospital of Southwest Medical University, Luzhou, 646000, Sichuan, China
- Cardiovascular and Metabolic Diseases Key Laboratory of Luzhou, and Sichuan Clinical Research Center for Nephropathy, and Academician (Expert) Workstation of Sichuan Province, The Affiliated Hospital of Southwest Medical University, Luzhou, 646000, Sichuan, China
| | - Man Guo
- Department of Endocrinology and Metabolism, The Affiliated Hospital of Southwest Medical University, Luzhou, 646000, Sichuan, China
- Cardiovascular and Metabolic Diseases Key Laboratory of Luzhou, and Sichuan Clinical Research Center for Nephropathy, and Academician (Expert) Workstation of Sichuan Province, The Affiliated Hospital of Southwest Medical University, Luzhou, 646000, Sichuan, China
| | - Xiao-Zhen Tan
- Experimental Medicine Center, The Affiliated Hospital of Southwest Medical University, Luzhou, 646000, Sichuan, China
- Department of Endocrinology and Metabolism, The Affiliated Hospital of Southwest Medical University, Luzhou, 646000, Sichuan, China
- Cardiovascular and Metabolic Diseases Key Laboratory of Luzhou, and Sichuan Clinical Research Center for Nephropathy, and Academician (Expert) Workstation of Sichuan Province, The Affiliated Hospital of Southwest Medical University, Luzhou, 646000, Sichuan, China
| | - Feng Chen
- Experimental Medicine Center, The Affiliated Hospital of Southwest Medical University, Luzhou, 646000, Sichuan, China
| | - Xu-Guang Xi
- State Key Laboratory of Crop Stress Biology for Arid Areas and College of Life Sciences, Northwest A&F University, Yangling, 712100, Shaanxi, China.
- LBPA, Ecole Normale Supérieure Paris-Saclay, CNRS, Université Paris Saclay, 61, Avenue du Président Wilson, 94235, Cachan, France.
| | - Yong Xu
- Experimental Medicine Center, The Affiliated Hospital of Southwest Medical University, Luzhou, 646000, Sichuan, China.
- Department of Endocrinology and Metabolism, The Affiliated Hospital of Southwest Medical University, Luzhou, 646000, Sichuan, China.
- Cardiovascular and Metabolic Diseases Key Laboratory of Luzhou, and Sichuan Clinical Research Center for Nephropathy, and Academician (Expert) Workstation of Sichuan Province, The Affiliated Hospital of Southwest Medical University, Luzhou, 646000, Sichuan, China.
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19
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Hur JH, Kang CY, Lee S, Parveen N, Yu J, Shamim A, Yoo W, Ghosh A, Bae S, Park CJ, Kim KK. AC-motif: a DNA motif containing adenine and cytosine repeat plays a role in gene regulation. Nucleic Acids Res 2021; 49:10150-10165. [PMID: 34469538 PMCID: PMC8464069 DOI: 10.1093/nar/gkab728] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2020] [Revised: 08/04/2021] [Accepted: 08/27/2021] [Indexed: 11/30/2022] Open
Abstract
I-motif or C4 is a four-stranded DNA structure with a protonated cytosine:cytosine base pair (C+:C) found in cytosine-rich sequences. We have found that oligodeoxynucleotides containing adenine and cytosine repeats form a stable secondary structure at a physiological pH with magnesium ion, which is similar to i-motif structure, and have named this structure ‘adenine:cytosine-motif (AC-motif)’. AC-motif contains C+:C base pairs intercalated with putative A+:C base pairs between protonated adenine and cytosine. By investigation of the AC-motif present in the CDKL3 promoter (AC-motifCDKL3), one of AC-motifs found in the genome, we confirmed that AC-motifCDKL3 has a key role in regulating CDKL3 gene expression in response to magnesium. This is further supported by confirming that genome-edited mutant cell lines, lacking the AC-motif formation, lost this regulation effect. Our results verify that adenine-cytosine repeats commonly present in the genome can form a stable non-canonical secondary structure with a non-Watson–Crick base pair and have regulatory roles in cells, which expand non-canonical DNA repertoires.
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Affiliation(s)
- Jeong Hwan Hur
- Department of Precision Medicine, Graduate Schoold of Basic Medical Science (GSBMS), Institute for Anti-microbial Resistance Research and Therapeutics, Sungkyunkwan University School of Medicine, Suwon 16419, Republic of Korea
| | - Chan Young Kang
- Department of Chemistry, Hanyang University, Seoul 04763, Republic of Korea
| | - Sungjin Lee
- Department of Chemistry, Gwangju Institute of Science and Technology, Gwangju 61005, Republic of Korea
| | - Nazia Parveen
- Department of Precision Medicine, Graduate Schoold of Basic Medical Science (GSBMS), Institute for Anti-microbial Resistance Research and Therapeutics, Sungkyunkwan University School of Medicine, Suwon 16419, Republic of Korea
| | - Jihyeon Yu
- Department of Chemistry, Hanyang University, Seoul 04763, Republic of Korea
| | - Amen Shamim
- Department of Precision Medicine, Graduate Schoold of Basic Medical Science (GSBMS), Institute for Anti-microbial Resistance Research and Therapeutics, Sungkyunkwan University School of Medicine, Suwon 16419, Republic of Korea.,Centre of Agricultural Biochemistry and Biotechnology, University of Agriculture, Faisalabad 38040, Pakistan
| | - Wanki Yoo
- Department of Precision Medicine, Graduate Schoold of Basic Medical Science (GSBMS), Institute for Anti-microbial Resistance Research and Therapeutics, Sungkyunkwan University School of Medicine, Suwon 16419, Republic of Korea
| | - Ambarnil Ghosh
- Department of Precision Medicine, Graduate Schoold of Basic Medical Science (GSBMS), Institute for Anti-microbial Resistance Research and Therapeutics, Sungkyunkwan University School of Medicine, Suwon 16419, Republic of Korea
| | - Sangsu Bae
- Department of Chemistry, Hanyang University, Seoul 04763, Republic of Korea
| | - Chin-Ju Park
- Department of Chemistry, Gwangju Institute of Science and Technology, Gwangju 61005, Republic of Korea
| | - Kyeong Kyu Kim
- Department of Precision Medicine, Graduate Schoold of Basic Medical Science (GSBMS), Institute for Anti-microbial Resistance Research and Therapeutics, Sungkyunkwan University School of Medicine, Suwon 16419, Republic of Korea.,Samsung Biomedical Research Institute, Samsung Advanced Institute for Health Sciences and Technology, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul 06351, Republic of Korea
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20
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Pavlova AV, Kubareva EA, Monakhova MV, Zvereva MI, Dolinnaya NG. Impact of G-Quadruplexes on the Regulation of Genome Integrity, DNA Damage and Repair. Biomolecules 2021; 11:1284. [PMID: 34572497 PMCID: PMC8472537 DOI: 10.3390/biom11091284] [Citation(s) in RCA: 31] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2021] [Revised: 08/19/2021] [Accepted: 08/25/2021] [Indexed: 12/13/2022] Open
Abstract
DNA G-quadruplexes (G4s) are known to be an integral part of the complex regulatory systems in both normal and pathological cells. At the same time, the ability of G4s to impede DNA replication plays a critical role in genome integrity. This review summarizes the results of recent studies of G4-mediated genomic and epigenomic instability, together with associated DNA damage and repair processes. Although the underlying mechanisms remain to be elucidated, it is known that, among the proteins that recognize G4 structures, many are linked to DNA repair. We analyzed the possible role of G4s in promoting double-strand DNA breaks, one of the most deleterious DNA lesions, and their repair via error-prone mechanisms. The patterns of G4 damage, with a focus on the introduction of oxidative guanine lesions, as well as their removal from G4 structures by canonical repair pathways, were also discussed together with the effects of G4s on the repair machinery. According to recent findings, there must be a delicate balance between G4-induced genome instability and G4-promoted repair processes. A broad overview of the factors that modulate the stability of G4 structures in vitro and in vivo is also provided here.
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Affiliation(s)
- Anzhela V. Pavlova
- Department of Chemistry, Lomonosov Moscow State University, Leninskie Gory 1, 119991 Moscow, Russia; (M.I.Z.); (N.G.D.)
| | - Elena A. Kubareva
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Leninskie Gory 1, 119991 Moscow, Russia; (E.A.K.); (M.V.M.)
| | - Mayya V. Monakhova
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Leninskie Gory 1, 119991 Moscow, Russia; (E.A.K.); (M.V.M.)
| | - Maria I. Zvereva
- Department of Chemistry, Lomonosov Moscow State University, Leninskie Gory 1, 119991 Moscow, Russia; (M.I.Z.); (N.G.D.)
| | - Nina G. Dolinnaya
- Department of Chemistry, Lomonosov Moscow State University, Leninskie Gory 1, 119991 Moscow, Russia; (M.I.Z.); (N.G.D.)
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21
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Buglione E, Salerno D, Marrano CA, Cassina V, Vesco G, Nardo L, Dacasto M, Rigo R, Sissi C, Mantegazza F. Nanomechanics of G-quadruplexes within the promoter of the KIT oncogene. Nucleic Acids Res 2021; 49:4564-4573. [PMID: 33849064 PMCID: PMC8096272 DOI: 10.1093/nar/gkab079] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2020] [Revised: 01/07/2021] [Accepted: 04/09/2021] [Indexed: 12/31/2022] Open
Abstract
G-quadruplexes (G4s) are tetrahelical DNA structures stabilized by four guanines paired via Hoogsteen hydrogen bonds into quartets. While their presence within eukaryotic DNA is known to play a key role in regulatory processes, their functional mechanisms are still under investigation. In the present work, we analysed the nanomechanical properties of three G4s present within the promoter of the KIT proto-oncogene from a single-molecule point of view through the use of magnetic tweezers (MTs). The study of DNA extension fluctuations under negative supercoiling allowed us to identify a characteristic fingerprint of G4 folding. We further analysed the energetic contribution of G4 to the double-strand denaturation process in the presence of negative supercoiling, and we observed a reduction in the energy required for strands separation.
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Affiliation(s)
- Enrico Buglione
- School of Medicine and Surgery, BioNanoMedicine Center NANOMIB, University of Milano-Bicocca, 20854 Vedano al Lambro (MB), Italy
| | - Domenico Salerno
- School of Medicine and Surgery, BioNanoMedicine Center NANOMIB, University of Milano-Bicocca, 20854 Vedano al Lambro (MB), Italy
| | - Claudia Adriana Marrano
- School of Medicine and Surgery, BioNanoMedicine Center NANOMIB, University of Milano-Bicocca, 20854 Vedano al Lambro (MB), Italy
| | - Valeria Cassina
- School of Medicine and Surgery, BioNanoMedicine Center NANOMIB, University of Milano-Bicocca, 20854 Vedano al Lambro (MB), Italy
| | - Guglielmo Vesco
- School of Medicine and Surgery, BioNanoMedicine Center NANOMIB, University of Milano-Bicocca, 20854 Vedano al Lambro (MB), Italy
| | - Luca Nardo
- School of Medicine and Surgery, BioNanoMedicine Center NANOMIB, University of Milano-Bicocca, 20854 Vedano al Lambro (MB), Italy
| | - Mauro Dacasto
- Department of Comparative Biomedicine and Food Science, University of Padova, 35020 Legnaro (PD), Italy
| | - Riccardo Rigo
- Department of Pharmaceutical and Pharmacological Sciences, University of Padova, 35131 Padova (PD), Italy
| | - Claudia Sissi
- Department of Pharmaceutical and Pharmacological Sciences, University of Padova, 35131 Padova (PD), Italy.,Interdepartmental Research Center for Innovative Biotechnologies (CRIBI), University of Padova, 35121 Padova (PD), Italy
| | - Francesco Mantegazza
- School of Medicine and Surgery, BioNanoMedicine Center NANOMIB, University of Milano-Bicocca, 20854 Vedano al Lambro (MB), Italy
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22
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Chaudhuri R, Fatma K, Dash J. Regulation of gene expression by targeting DNA secondary structures. J CHEM SCI 2021. [DOI: 10.1007/s12039-021-01898-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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23
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Tran P, Rieu M, Hodeib S, Joubert A, Ouellet J, Alberti P, Bugaut A, Allemand JF, Boulé JB, Croquette V. Folding and persistence times of intramolecular G-quadruplexes transiently embedded in a DNA duplex. Nucleic Acids Res 2021; 49:5189-5201. [PMID: 34009328 PMCID: PMC8136832 DOI: 10.1093/nar/gkab306] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2020] [Revised: 04/09/2021] [Accepted: 04/14/2021] [Indexed: 12/19/2022] Open
Abstract
G-quadruplex (G4) DNA structures have emerged as important regulatory elements during DNA metabolic transactions. While many in vitro studies have focused on the kinetics of G4 formation within DNA single-strands, G4 are found in vivo in double-stranded DNA regions, where their formation is challenged by the complementary strand. Since the energy of hybridization of Watson-Crick structures dominates the energy of G4 folding, this competition should play a critical role on G4 persistence. To address this, we designed a single-molecule assay allowing to measure G4 folding and persistence times in the presence of the complementary strand. We quantified both folding and unfolding rates of biologically relevant G4 sequences, such as the cMYC and cKIT oncogene promoters, human telomeres and an avian replication origin. We confirmed that G4s are found much more stable in tested replication origin and promoters than in human telomere repeats. In addition, we characterized how G4 dynamics was affected by G4 ligands and showed that both folding rate and persistence time increased. Our assay opens new perspectives for the measurement of G4 dynamics in double-stranded DNA mimicking a replication fork, which is important to understand their role in DNA replication and gene regulation at a mechanistic level.
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Affiliation(s)
- Phong Lan Thao Tran
- Structure et Instabilité des Génomes, Museum National d’Histoire Naturelle, INSERM, CNRS, Alliance Sorbonne Université, 75005 Paris, France
| | - Martin Rieu
- Laboratoire de physique de L’École Normale Supérieure de Paris, CNRS, ENS, Université PSL, Sorbonne Université, Université de Paris, 75005 Paris, France
- Institut de Biologie de l’École Normale Supérieure (IBENS), Ecole Normale Supérieure, CNRS, INSERM, Université PSL, 75005 Paris, France
| | - Samar Hodeib
- Laboratoire de physique de L’École Normale Supérieure de Paris, CNRS, ENS, Université PSL, Sorbonne Université, Université de Paris, 75005 Paris, France
- Institut de Biologie de l’École Normale Supérieure (IBENS), Ecole Normale Supérieure, CNRS, INSERM, Université PSL, 75005 Paris, France
| | - Alexandra Joubert
- Structure et Instabilité des Génomes, Museum National d’Histoire Naturelle, INSERM, CNRS, Alliance Sorbonne Université, 75005 Paris, France
| | - Jimmy Ouellet
- Depixus SAS, 3-5 Impasse Reille, 75014 Paris, France
| | - Patrizia Alberti
- Structure et Instabilité des Génomes, Museum National d’Histoire Naturelle, INSERM, CNRS, Alliance Sorbonne Université, 75005 Paris, France
| | - Anthony Bugaut
- Structure et Instabilité des Génomes, Museum National d’Histoire Naturelle, INSERM, CNRS, Alliance Sorbonne Université, 75005 Paris, France
| | - Jean-François Allemand
- Laboratoire de physique de L’École Normale Supérieure de Paris, CNRS, ENS, Université PSL, Sorbonne Université, Université de Paris, 75005 Paris, France
- Institut de Biologie de l’École Normale Supérieure (IBENS), Ecole Normale Supérieure, CNRS, INSERM, Université PSL, 75005 Paris, France
| | - Jean-Baptiste Boulé
- Structure et Instabilité des Génomes, Museum National d’Histoire Naturelle, INSERM, CNRS, Alliance Sorbonne Université, 75005 Paris, France
| | - Vincent Croquette
- Laboratoire de physique de L’École Normale Supérieure de Paris, CNRS, ENS, Université PSL, Sorbonne Université, Université de Paris, 75005 Paris, France
- Institut de Biologie de l’École Normale Supérieure (IBENS), Ecole Normale Supérieure, CNRS, INSERM, Université PSL, 75005 Paris, France
- ESPCI Paris, Université PSL, 75005 Paris, France
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24
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Structural Biology for the Molecular Insight between Aptamers and Target Proteins. Int J Mol Sci 2021; 22:ijms22084093. [PMID: 33920991 PMCID: PMC8071422 DOI: 10.3390/ijms22084093] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2021] [Revised: 04/12/2021] [Accepted: 04/14/2021] [Indexed: 02/07/2023] Open
Abstract
Aptamers are promising therapeutic and diagnostic agents for various diseases due to their high affinity and specificity against target proteins. Structural determination in combination with multiple biochemical and biophysical methods could help to explore the interacting mechanism between aptamers and their targets. Regrettably, structural studies for aptamer–target interactions are still the bottleneck in this field, which are facing various difficulties. In this review, we first reviewed the methods for resolving structures of aptamer–protein complexes and for analyzing the interactions between aptamers and target proteins. We summarized the general features of the interacting nucleotides and residues involved in the interactions between aptamers and proteins. Challenges and perspectives in current methodologies were discussed. Approaches for determining the binding affinity between aptamers and target proteins as well as modification strategies for stabilizing the binding affinity of aptamers to target proteins were also reviewed. The review could help to understand how aptamers interact with their targets and how alterations such as chemical modifications in the structures affect the affinity and function of aptamers, which could facilitate the optimization and translation of aptamers-based theranostics.
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25
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Gao B, Hou XM. Opposite Effects of Potassium Ions on the Thermal Stability of i-Motif DNA in Different Buffer Systems. ACS OMEGA 2021; 6:8976-8985. [PMID: 33842768 PMCID: PMC8028132 DOI: 10.1021/acsomega.0c06350] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/30/2020] [Accepted: 03/11/2021] [Indexed: 05/12/2023]
Abstract
i-motifs are noncanonical DNA structures formed via the stack of intercalating hemi-protonated C+: C base pairs in C-rich DNA strands and play essential roles in the regulation of gene expression. Here, we systematically investigated the impacts of K+ on i-motif DNA folding using different buffer systems. We found that i-motif structures display very different T m values at the same pH and ion strength in different buffer systems. More importantly, K+ disrupts the i-motif formed in the MES and Bis-Tris buffer; however, K+ stabilizes the i-motif in phosphate, citrate, and sodium cacodylate buffers. Next, we selected phosphate buffer and confirmed by single-molecule fluorescence resonance energy transfer that K+ indeed has the stabilizing effect on the folding of i-motif DNA from pH 5.8 to 8.0. Nonetheless, circular dichroism spectra further indicate that the structures formed by i-motif sequences at high K+ concentrations at neutral and alkaline pH are not i-motif but other types of higher-order structures and most likely C-hairpins. We finally proposed the mechanisms of how K+ plays the opposite roles in different buffer systems. The present study may provide new insights into our understanding of the formation and stability of i-motif DNA.
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Affiliation(s)
| | - Xi-Miao Hou
- . Phone: +86 29 8708 1664. Fax: +86 29 8708 1664
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26
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Megalathan A, Wijesinghe KM, Ranson L, Dhakal S. Single-Molecule Analysis of Nanocircle-Embedded I-Motifs under Crowding. J Phys Chem B 2021; 125:2193-2201. [PMID: 33629846 DOI: 10.1021/acs.jpcb.0c09640] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Cytosine (C)-rich regions of single-stranded DNA or RNA can fold into a tetraplex structure called i-motifs, which are typically stable under acidic pHs due to the need for protons to stabilize C-C interactions. While new studies have shown evidence for the formation of i-motifs at neutral and even physiological pH, it is not clear whether i-motifs can stably form in cells where DNA experiences topological constraint and crowding. Similarly, several studies have shown that a molecularly crowded environment promotes the formation of i-motifs at physiological pH; however, whether the intracellular crowding counteracts the topological destabilization of i-motifs is yet to be investigated. In this manuscript, using fluorescence resonance energy transfer (FRET)-based single-molecule analyses of human telomeric (hTel) i-motifs embedded in nanocircles as a proof-of-concept platform, we investigated the overall effects of crowding and topological constraint on the i-motif behavior. The smFRET analysis of the nanoassembly showed that the i-motif remains folded at pH 5.5 but unfolds at higher pHs. However, in the presence of a crowder (30% PEG 6000), i-motifs are formed at physiological pH overcoming the topological constraint imposed by the DNA nanocircles. Analysis of FRET-time traces show that the hTel sequence primarily assumes the folded state at pH ≤7.0 under crowding, but it undergoes slow conformational transitions between the folded and unfolded states at physiological pH. Our demonstration that the i-motif can form under cell-mimic crowding and topologically constrained environments may provide new insights into the potential biological roles of i-motifs and also into the design and development of i-motif-based biosensors, therapy, and other nanotechnological applications.
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Affiliation(s)
- Anoja Megalathan
- Department of Chemistry, Virginia Commonwealth University, Richmond, Virginia 23284, United States
| | - Kalani M Wijesinghe
- Department of Chemistry, Virginia Commonwealth University, Richmond, Virginia 23284, United States
| | - Leslie Ranson
- Department of Chemistry, Virginia Commonwealth University, Richmond, Virginia 23284, United States
| | - Soma Dhakal
- Department of Chemistry, Virginia Commonwealth University, Richmond, Virginia 23284, United States
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27
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Sengupta P, Bose D, Chatterjee S. The Molecular Tête-à-Tête between G-Quadruplexes and the i-motif in the Human Genome. Chembiochem 2021; 22:1517-1537. [PMID: 33355980 DOI: 10.1002/cbic.202000703] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2020] [Revised: 12/16/2020] [Indexed: 12/22/2022]
Abstract
G-Quadruplex (GQ) and i-motif structures are the paradigmatic examples of nonclassical tetrastranded nucleic acids having multifarious biological functions and widespread applications in therapeutics and material science. Recently, tetraplexes emerged as promising anticancer targets due to their structural robustness, gene-regulatory roles, and predominant distribution at specific loci of oncogenes. However, it is arguable whether the i-motif evolves in the complementary single-stranded region after GQ formation in its opposite strand and vice versa. In this review, we address the prerequisites and significance of the simultaneous and/or mutually exclusive formation of GQ and i-motif structures at complementary and sequential positions in duplexes in the cellular milieu. We discussed how their dynamic interplay Sets up cellular homeostasis and exacerbates carcinogenesis. The review gives insights into the spatiotemporal formation of GQ and i-motifs that could be harnessed to design different types of reporter systems and diagnostic platforms for potential bioanalytical and therapeutic intervention.
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Affiliation(s)
- Pallabi Sengupta
- Department of Biophysics, Bose Institute, Centenary Campus, P-1/12, C.I.T. Scheme VIIM, Kankurgachi, Kolkata, 700054, West Bengal, India
| | - Debopriya Bose
- Department of Biophysics, Bose Institute, Centenary Campus, P-1/12, C.I.T. Scheme VIIM, Kankurgachi, Kolkata, 700054, West Bengal, India
| | - Subhrangsu Chatterjee
- Department of Biophysics, Bose Institute, Centenary Campus, P-1/12, C.I.T. Scheme VIIM, Kankurgachi, Kolkata, 700054, West Bengal, India
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28
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Chen H, Sun H, Zhang W, Zhang Q, Ma J, Li Q, Guo X, Xu K, Tang Y. Chelerythrine as a fluorescent light-up ligand for an i-motif DNA structure. NEW J CHEM 2021. [DOI: 10.1039/d0nj04863a] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
A fluorescent light-up ligand for an i-motif structure has been reported in this study.
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Affiliation(s)
- Hongbo Chen
- Shenzhou Space Biology Science and Technology Coorporation, Ltd
- China Academy of Space Technology
- Beijing
- P. R. China
- Space Biology Research and Technology Center
| | - Hongxia Sun
- National Laboratory for Molecular Sciences
- Center for Molecular Sciences
- State Key Laboratory for Structural Chemistry of Unstable and Stable Species
- Institute of Chemistry Chinese Academy of Sciences
- Beijing
| | - Wende Zhang
- Shenzhou Space Biology Science and Technology Coorporation, Ltd
- China Academy of Space Technology
- Beijing
- P. R. China
- Space Biology Research and Technology Center
| | - Qin Zhang
- Shenzhou Space Biology Science and Technology Coorporation, Ltd
- China Academy of Space Technology
- Beijing
- P. R. China
- Space Biology Research and Technology Center
| | - Jun Ma
- Shenzhou Space Biology Science and Technology Coorporation, Ltd
- China Academy of Space Technology
- Beijing
- P. R. China
- Space Biology Research and Technology Center
| | - Qian Li
- National Laboratory for Molecular Sciences
- Center for Molecular Sciences
- State Key Laboratory for Structural Chemistry of Unstable and Stable Species
- Institute of Chemistry Chinese Academy of Sciences
- Beijing
| | - Xiaomeng Guo
- National Laboratory for Molecular Sciences
- Center for Molecular Sciences
- State Key Laboratory for Structural Chemistry of Unstable and Stable Species
- Institute of Chemistry Chinese Academy of Sciences
- Beijing
| | - Kanyan Xu
- Shenzhou Space Biology Science and Technology Coorporation, Ltd
- China Academy of Space Technology
- Beijing
- P. R. China
- Space Biology Research and Technology Center
| | - Yalin Tang
- National Laboratory for Molecular Sciences
- Center for Molecular Sciences
- State Key Laboratory for Structural Chemistry of Unstable and Stable Species
- Institute of Chemistry Chinese Academy of Sciences
- Beijing
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29
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MD-TSPC4: Computational Method for Predicting the Thermal Stability of I-Motif. Int J Mol Sci 2020; 22:ijms22010061. [PMID: 33374624 PMCID: PMC7793491 DOI: 10.3390/ijms22010061] [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: 11/24/2020] [Revised: 12/16/2020] [Accepted: 12/17/2020] [Indexed: 11/23/2022] Open
Abstract
I-Motif is a tetrameric cytosine-rich DNA structure with hemi-protonated cytosine: cytosine base pairs. Recent evidence showed that i-motif structures in human cells play regulatory roles in the genome. Therefore, characterization of novel i-motifs and investigation of their functional implication are urgently needed for comprehensive understanding of their roles in gene regulation. However, considering the complications of experimental investigation of i-motifs and the large number of putative i-motifs in the genome, development of an in silico tool for the characterization of i-motifs in the high throughput scale is necessary. We developed a novel computation method, MD-TSPC4, to predict the thermal stability of i-motifs based on molecular modeling and molecular dynamic simulation. By assuming that the flexibility of loops in i-motifs correlated with thermal stability within certain temperature ranges, we evaluated the correlation between the root mean square deviations (RMSDs) of model structures and the thermal stability as the experimentally obtained melting temperature (Tm). Based on this correlation, we propose an equation for Tm prediction from RMSD. We expect this method can be useful for estimating the overall structure and stability of putative i-motifs in the genome, which can be a starting point of further structural and functional studies of i-motifs.
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30
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Miglietta G, Russo M, Capranico G. G-quadruplex-R-loop interactions and the mechanism of anticancer G-quadruplex binders. Nucleic Acids Res 2020; 48:11942-11957. [PMID: 33137181 PMCID: PMC7708042 DOI: 10.1093/nar/gkaa944] [Citation(s) in RCA: 79] [Impact Index Per Article: 19.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2020] [Revised: 10/05/2020] [Accepted: 10/08/2020] [Indexed: 12/17/2022] Open
Abstract
Genomic DNA and cellular RNAs can form a variety of non-B secondary structures, including G-quadruplex (G4) and R-loops. G4s are constituted by stacked guanine tetrads held together by Hoogsteen hydrogen bonds and can form at key regulatory sites of eukaryote genomes and transcripts, including gene promoters, untranslated exon regions and telomeres. R-loops are 3-stranded structures wherein the two strands of a DNA duplex are melted and one of them is annealed to an RNA. Specific G4 binders are intensively investigated to discover new effective anticancer drugs based on a common rationale, i.e.: the selective inhibition of oncogene expression or specific impairment of telomere maintenance. However, despite the high number of known G4 binders, such a selective molecular activity has not been fully established and several published data point to a different mode of action. We will review published data that address the close structural interplay between G4s and R-loops in vitro and in vivo, and how these interactions can have functional consequences in relation to G4 binder activity. We propose that R-loops can play a previously-underestimated role in G4 binder action, in relation to DNA damage induction, telomere maintenance, genome and epigenome instability and alterations of gene expression programs.
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Affiliation(s)
- Giulia Miglietta
- Department of Pharmacy and Biotechnology, Alma Mater Studiorum University of Bologna, via Selmi 3, 40126 Bologna, Italy
| | - Marco Russo
- Department of Pharmacy and Biotechnology, Alma Mater Studiorum University of Bologna, via Selmi 3, 40126 Bologna, Italy
| | - Giovanni Capranico
- Department of Pharmacy and Biotechnology, Alma Mater Studiorum University of Bologna, via Selmi 3, 40126 Bologna, Italy
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31
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King JJ, Irving KL, Evans CW, Chikhale RV, Becker R, Morris CJ, Peña Martinez CD, Schofield P, Christ D, Hurley LH, Waller ZAE, Iyer KS, Smith NM. DNA G-Quadruplex and i-Motif Structure Formation Is Interdependent in Human Cells. J Am Chem Soc 2020; 142:20600-20604. [PMID: 33253551 DOI: 10.1021/jacs.0c11708] [Citation(s) in RCA: 53] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
Guanine- and cytosine-rich nucleic acid sequences have the potential to form secondary structures such as G-quadruplexes and i-motifs, respectively. We show that stabilization of G-quadruplexes using small molecules destabilizes the i-motifs, and vice versa, indicating these gene regulatory controllers are interdependent in human cells. This has important implications as these structures are predominately considered as isolated structural targets for therapy, but their interdependency highlights the interplay of both structures as an important gene regulatory switch.
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Affiliation(s)
- Jessica J King
- School of Molecular Sciences, University of Western Australia, Crawley, Western Australia 6009, Australia
| | - Kelly L Irving
- School of Molecular Sciences, University of Western Australia, Crawley, Western Australia 6009, Australia
| | - Cameron W Evans
- School of Molecular Sciences, University of Western Australia, Crawley, Western Australia 6009, Australia
| | - Rupesh V Chikhale
- School of Pharmacy, University of East Anglia, Norwich Research Park, Norwich NR4 7TJ, U.K.,UCL School of Pharmacy, 29-39 Brunswick Square, London WC1N 1AX, U.K
| | - Rouven Becker
- School of Pharmacy, University of East Anglia, Norwich Research Park, Norwich NR4 7TJ, U.K
| | - Christopher J Morris
- School of Pharmacy, University of East Anglia, Norwich Research Park, Norwich NR4 7TJ, U.K
| | - Cristian D Peña Martinez
- Kinghorn Centre for Clinical Genomics, Garvan Institute of Medical Research, Darlinghurst, Sydney New South Wales 2010, Australia
| | - Peter Schofield
- Kinghorn Centre for Clinical Genomics, Garvan Institute of Medical Research, Darlinghurst, Sydney New South Wales 2010, Australia.,St Vincent's Clinical School, Faculty of Medicine, University of New South Wales, Kensington, Sydney, New South Wales 2052, Australia
| | - Daniel Christ
- Kinghorn Centre for Clinical Genomics, Garvan Institute of Medical Research, Darlinghurst, Sydney New South Wales 2010, Australia.,St Vincent's Clinical School, Faculty of Medicine, University of New South Wales, Kensington, Sydney, New South Wales 2052, Australia
| | - Laurence H Hurley
- College of Pharmacy, University of Arizona, 1703 East Mabel Street, Tucson, Arizona 85721, United States
| | - Zoë A E Waller
- School of Pharmacy, University of East Anglia, Norwich Research Park, Norwich NR4 7TJ, U.K.,UCL School of Pharmacy, 29-39 Brunswick Square, London WC1N 1AX, U.K
| | - K Swaminathan Iyer
- School of Molecular Sciences, University of Western Australia, Crawley, Western Australia 6009, Australia
| | - Nicole M Smith
- School of Molecular Sciences, University of Western Australia, Crawley, Western Australia 6009, Australia
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32
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Zhang X, Zhang Y, Zhang W. Dynamic topology of double-stranded telomeric DNA studied by single-molecule manipulation in vitro. Nucleic Acids Res 2020; 48:6458-6470. [PMID: 32496520 PMCID: PMC7337930 DOI: 10.1093/nar/gkaa479] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2019] [Revised: 05/17/2020] [Accepted: 05/27/2020] [Indexed: 12/18/2022] Open
Abstract
The dynamic topological structure of telomeric DNA is closely related to its biological function; however, no such structural information on full-length telomeric DNA has been reported due to difficulties synthesizing long double-stranded telomeric DNA. Herein, we developed an EM-PCR and TA cloning-based approach to synthesize long-chain double-stranded tandem repeats of telomeric DNA. Using mechanical manipulation assays based on single-molecule atomic force microscopy, we found that mechanical force can trigger the melting of double-stranded telomeric DNA and the formation of higher-order structures (G-quadruplexes or i-motifs). Our results show that only when both the G-strand and C-strand of double-stranded telomeric DNA form higher-order structures (G-quadruplexes or i-motifs) at the same time (e.g. in the presence of 100 mM KCl under pH 4.7), that the higher-order structure(s) can remain after the external force is removed. The presence of monovalent K+, single-wall carbon nanotubes (SWCNTs), acidic conditions, or short G-rich fragments (∼30 nt) can shift the transition from dsDNA to higher-order structures. Our results provide a new way to regulate the topology of telomeric DNA.
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Affiliation(s)
- Xiaonong Zhang
- State Key Laboratory of Supramolecular Structure and Materials, Jilin University, Changchun 130012, People's Republic of China
| | - Yingqi Zhang
- State Key Laboratory of Supramolecular Structure and Materials, Jilin University, Changchun 130012, People's Republic of China
| | - Wenke Zhang
- State Key Laboratory of Supramolecular Structure and Materials, Jilin University, Changchun 130012, People's Republic of China
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33
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Fleming AM, Zhu J, Jara-Espejo M, Burrows CJ. Cruciform DNA Sequences in Gene Promoters Can Impact Transcription upon Oxidative Modification of 2'-Deoxyguanosine. Biochemistry 2020; 59:2616-2626. [PMID: 32567845 DOI: 10.1021/acs.biochem.0c00387] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Sequences of DNA typically adopt B-form duplexes in genomes, although noncanonical structures such as G-quadruplexes, i-motifs, Z-DNA, and cruciform structures can occur. A challenge is to determine the functions of these various structures in cellular processes. We and others have hypothesized that G-rich G-quadruplex-forming sequences in human genome promoters serve to sense oxidative damage generated during oxidative stress impacting gene regulation. Herein, chemical tools and a cell-based assay were used to study the oxidation of guanine to 8-oxo-7,8-dihydroguanine (OG) in the context of a cruciform-forming sequence in a gene promoter to determine the impact on transcription. We found that OG in the nontemplate strand in the loop of a cruciform-forming sequence could induce gene expression; conversely when OG was in the same sequence on the template strand, gene expression was inhibited. A model for the transcriptional changes observed is proposed in which OG focuses the DNA repair process on the promoter to impact expression. Our cellular and biophysical studies and literature sources support the idea that removal of OG from duplex DNA by OGG1 yields an abasic site (AP) that triggers a structural shift to the cruciform fold. The AP-bearing cruciform structure is presented to APE1, which functions as a conduit between DNA repair and gene regulation. The significance is enhanced by a bioinformatic study of all human gene promoters and transcription termination sites for inverted repeats (IRs). Comparison of the two regions showed that promoters have stable and G-rich IRs at a low frequency and termination sites have many AT-rich IRs with low stability.
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Affiliation(s)
- Aaron M Fleming
- Department of Chemistry, University of Utah, 315 South 1400 East, Salt Lake City, Utah 84112-0850, United States
| | - Judy Zhu
- Department of Chemistry, University of Utah, 315 South 1400 East, Salt Lake City, Utah 84112-0850, United States
| | - Manuel Jara-Espejo
- Department of Chemistry, University of Utah, 315 South 1400 East, Salt Lake City, Utah 84112-0850, United States.,Department of Morphology, Piracicaba Dental School, University of Campinas-UNICAMP, Av. Limeira 901, Piracicaba, CEP 13414-018 Sao Paulo, Brazil
| | - Cynthia J Burrows
- Department of Chemistry, University of Utah, 315 South 1400 East, Salt Lake City, Utah 84112-0850, United States
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34
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Liu L, Ma C, Wells JW, Chalikian TV. Conformational Preferences of DNA Strands from the Promoter Region of the c-MYC Oncogene. J Phys Chem B 2020; 124:751-762. [PMID: 31923361 DOI: 10.1021/acs.jpcb.9b10518] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
We characterized the conformational preferences of DNA in an equimolar mixture of complementary G-rich and C-rich strands from the promoter region of the c-MYC oncogene. Our CD-based approach presupposes that the CD spectrum of such a mixture is the spectral sum of the constituent duplex, G-quadruplex, i-motif, and coiled conformations. Spectra were acquired over a range of temperatures at different pHs and concentrations of KCl. Each spectrum was unmixed in terms of the predetermined spectra of the constituent conformational states to obtain the corresponding weighting factors for their fractional contributions to the total population of DNA. The temperature dependences of those contributions then were analyzed in concert according to a model based on a thermodynamic representation of the underlying equilibria. Fitted estimates of the melting enthalpy and temperature obtained for the duplex, G-quadruplex, and i-motif imply that the driving force behind dissociation of the duplex and the concomitant formation of tetrahelical structures is the folding of the G-strand into the G-quadruplex. The liberated C-strand adopts the i-motif conformation at acidic pH and exists in the coiled state at neutral pH. The i-motif alone cannot induce dissociation of the duplex even at pH 5.0, at which it is most stable. Under the physiological conditions of neutral pH, elevated potassium, and room temperature, the duplex and G-quadruplex conformations coexist with the C-strand in the coiled state. Taken together, our results suggest a novel, thermodynamically controlled mechanism for the regulation of gene expression.
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Affiliation(s)
- Lutan Liu
- Department of Pharmaceutical Sciences, Leslie Dan Faculty of Pharmacy , University of Toronto , 144 College Street , Toronto , Ontario M5S 3M2 , Canada
| | - Congshan Ma
- Department of Pharmaceutical Sciences, Leslie Dan Faculty of Pharmacy , University of Toronto , 144 College Street , Toronto , Ontario M5S 3M2 , Canada
| | - James W Wells
- Department of Pharmaceutical Sciences, Leslie Dan Faculty of Pharmacy , University of Toronto , 144 College Street , Toronto , Ontario M5S 3M2 , Canada
| | - Tigran V Chalikian
- Department of Pharmaceutical Sciences, Leslie Dan Faculty of Pharmacy , University of Toronto , 144 College Street , Toronto , Ontario M5S 3M2 , Canada
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35
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Chasing Particularities of Guanine- and Cytosine-Rich DNA Strands. Molecules 2020; 25:molecules25030434. [PMID: 31972988 PMCID: PMC7037129 DOI: 10.3390/molecules25030434] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2019] [Revised: 01/17/2020] [Accepted: 01/20/2020] [Indexed: 01/17/2023] Open
Abstract
By substitution of natural nucleotides by their abasic analogs (i.e., 1',2'-dideoxyribose phosphate residue) at critically chosen positions within 27-bp DNA constructs originating from the first intron of N-myc gene, we hindered hybridization within the guanine- and cytosine-rich central region and followed formation of non-canonical structures. The impeded hybridization between the complementary strands leads to time-dependent structural transformations of guanine-rich strand that are herein characterized with the use of solution-state NMR, CD spectroscopy, and native polyacrylamide gel electrophoresis. Moreover, the DNA structural changes involve transformation of intra- into inter-molecular G-quadruplex structures that are thermodynamically favored. Intriguingly, the transition occurs in the presence of complementary cytosine-rich strands highlighting the inability of Watson-Crick base-pairing to preclude the transformation between G-quadruplex structures that occurs via intertwining mechanism and corroborates a role of G-quadruplex structures in DNA recombination processes.
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36
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Chaudhary S, Kaushik M, Ahmed S, Kukreti S. Exploring potential of i-motif DNA formed in the promoter region of GRIN1 gene for nanotechnological applications. RESULTS IN CHEMISTRY 2020. [DOI: 10.1016/j.rechem.2020.100086] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023] Open
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37
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Megalathan A, Cox BD, Wilkerson PD, Kaur A, Sapkota K, Reiner JE, Dhakal S. Single-molecule analysis of i-motif within self-assembled DNA duplexes and nanocircles. Nucleic Acids Res 2019; 47:7199-7212. [PMID: 31287873 PMCID: PMC6698746 DOI: 10.1093/nar/gkz565] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2018] [Revised: 06/13/2019] [Accepted: 07/04/2019] [Indexed: 12/20/2022] Open
Abstract
The cytosine (C)-rich sequences that can fold into tetraplex structures known as i-motif are prevalent in genomic DNA. Recent studies of i-motif-forming sequences have shown increasing evidence of their roles in gene regulation. However, most of these studies have been performed in short single-stranded oligonucleotides, far from the intracellular environment. In cells, i-motif-forming sequences are flanked by DNA duplexes and packed in the genome. Therefore, exploring the conformational dynamics and kinetics of i-motif under such topologically constrained environments is highly relevant in predicting their biological roles. Using single-molecule fluorescence analysis of self-assembled DNA duplexes and nanocircles, we show that the topological environments play a key role on i-motif stability and dynamics. While the human telomere sequence (C3TAA)3C3 assumes i-motif structure at pH 5.5 regardless of topological constraint, it undergoes conformational dynamics among unfolded, partially folded and fully folded states at pH 6.5. The lifetimes of i-motif and the partially folded state at pH 6.5 were determined to be 6 ± 2 and 31 ± 11 s, respectively. Consistent with the partially folded state observed in fluorescence analysis, interrogation of current versus time traces obtained from nanopore analysis at pH 6.5 shows long-lived shallow blockades with a mean lifetime of 25 ± 6 s. Such lifetimes are sufficient for the i-motif and partially folded states to interact with proteins to modulate cellular processes.
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Affiliation(s)
- Anoja Megalathan
- Department of Chemistry, Virginia Commonwealth University, 1001 West Main Street, Richmond, VA 23284, USA
| | - Bobby D Cox
- Department of Physics, Virginia Commonwealth University, 701 West Grace Street, Richmond, VA 23284, USA
| | - Peter D Wilkerson
- Department of Physics, Virginia Commonwealth University, 701 West Grace Street, Richmond, VA 23284, USA
| | - Anisa Kaur
- Department of Chemistry, Virginia Commonwealth University, 1001 West Main Street, Richmond, VA 23284, USA
| | - Kumar Sapkota
- Department of Chemistry, Virginia Commonwealth University, 1001 West Main Street, Richmond, VA 23284, USA
| | - Joseph E Reiner
- Department of Physics, Virginia Commonwealth University, 701 West Grace Street, Richmond, VA 23284, USA
| | - Soma Dhakal
- Department of Chemistry, Virginia Commonwealth University, 1001 West Main Street, Richmond, VA 23284, USA
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38
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Dvoráková Z, Renciuk D, Kejnovská I, Školáková P, Bednárová K, Sagi J, Vorlícková M. i-Motif of cytosine-rich human telomere DNA fragments containing natural base lesions. Nucleic Acids Res 2019; 46:1624-1634. [PMID: 29378012 PMCID: PMC5829569 DOI: 10.1093/nar/gky035] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2017] [Accepted: 01/15/2018] [Indexed: 12/01/2022] Open
Abstract
i-Motif (iM) is a four stranded DNA structure formed by cytosine-rich sequences, which are often present in functionally important parts of the genome such as promoters of genes and telomeres. Using electronic circular dichroism and UV absorption spectroscopies and electrophoretic methods, we examined the effect of four naturally occurring DNA base lesions on the folding and stability of the iM formed by the human telomere DNA sequence (C3TAA)3C3T. The results demonstrate that the TAA loop lesions, the apurinic site and 8-oxoadenine substituting for adenine, and the 5-hydroxymethyluracil substituting for thymine only marginally disturb the formation of iM. The presence of uracil, which is formed by enzymatic or spontaneous deamination of cytosine, shifts iM formation towards substantially more acidic pH values and simultaneously distinctly reduces iM stability. This effect depends on the position of the damage sites in the sequence. The results have enabled us to formulate additional rules for iM formation.
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Affiliation(s)
- Zuzana Dvoráková
- Institute of Biophysics of the Czech Academy of Sciences, Královopolská 135, 612 65 Brno, Czech Republic
| | - Daniel Renciuk
- Institute of Biophysics of the Czech Academy of Sciences, Královopolská 135, 612 65 Brno, Czech Republic
| | - Iva Kejnovská
- Institute of Biophysics of the Czech Academy of Sciences, Královopolská 135, 612 65 Brno, Czech Republic
| | - Petra Školáková
- Institute of Biophysics of the Czech Academy of Sciences, Královopolská 135, 612 65 Brno, Czech Republic
| | - Klára Bednárová
- Institute of Biophysics of the Czech Academy of Sciences, Královopolská 135, 612 65 Brno, Czech Republic
| | - Janos Sagi
- Rimstone Laboratory, RLI, Carlsbad, CA 92010, USA
| | - Michaela Vorlícková
- Institute of Biophysics of the Czech Academy of Sciences, Královopolská 135, 612 65 Brno, Czech Republic
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39
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Panczyk T, Wojton P, Wolski P. Mechanism of unfolding and relative stabilities of G-quadruplex and I-motif noncanonical DNA structures analyzed in biased molecular dynamics simulations. Biophys Chem 2019; 250:106173. [DOI: 10.1016/j.bpc.2019.106173] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2019] [Revised: 04/12/2019] [Accepted: 04/12/2019] [Indexed: 12/01/2022]
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40
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Abou Assi H, Garavís M, González C, Damha MJ. i-Motif DNA: structural features and significance to cell biology. Nucleic Acids Res 2019; 46:8038-8056. [PMID: 30124962 PMCID: PMC6144788 DOI: 10.1093/nar/gky735] [Citation(s) in RCA: 242] [Impact Index Per Article: 48.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2018] [Accepted: 08/13/2018] [Indexed: 12/20/2022] Open
Abstract
The i-motif represents a paradigmatic example of the wide structural versatility of nucleic acids. In remarkable contrast to duplex DNA, i-motifs are four-stranded DNA structures held together by hemi- protonated and intercalated cytosine base pairs (C:C+). First observed 25 years ago, and considered by many as a mere structural oddity, interest in and discussion on the biological role of i-motifs have grown dramatically in recent years. In this review we focus on structural aspects of i-motif formation, the factors leading to its stabilization and recent studies describing the possible role of i-motifs in fundamental biological processes.
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Affiliation(s)
- Hala Abou Assi
- Department of Chemistry, McGill University, Montreal, QC H3A 0B8, Canada
| | - Miguel Garavís
- Instituto de Química Física 'Rocasolano', CSIC, C/Serrano 119, 28006 Madrid, Spain
| | - Carlos González
- Instituto de Química Física 'Rocasolano', CSIC, C/Serrano 119, 28006 Madrid, Spain
| | - Masad J Damha
- Department of Chemistry, McGill University, Montreal, QC H3A 0B8, Canada
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41
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Sengupta P, Bhattacharya A, Sa G, Das T, Chatterjee S. Truncated G-Quadruplex Isomers Cross-Talk with the Transcription Factors To Maintain Homeostatic Equilibria in c-MYC Transcription. Biochemistry 2019; 58:1975-1991. [PMID: 30920805 DOI: 10.1021/acs.biochem.9b00030] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The nuclease hypersensitive element III1 (NHE III1) upstream c-MYC promoter harbors a transcription-silencing G-quadruplex (Pu27) element. Dynamic turnover of various transcription factors (TFs) across Pu27 to control c-MYC transcription homeostasis is enigmatic. Here, we reveal that native Pu27 evolves truncated G-quadruplex isomers (Pu19, Pu22, Pu24, and Pu25) in cells that are optimal intracellular targets of specific TFs in a sequence- and structure-dependent manner. Nuclear magnetic resonance and isothermal titration calorimetry envisaged that NM23-H2 (nucleoside diphosphate kinase) and nucleolin induce conformational fluctuations in Pu27 to sample specific conformationally restricted conformer(s). Structural investigations revealed that the flanking guanines at 5'-Pu27 control solvent exposure at G-quartets upon NM23-H2 and nucleolin binding driving Pu27 unfolding and folding, respectively. Transient chromatin immunoprecipitations confirmed that NM23-H2 drives the conformation switch to Pu24 that outcompetes nucleolin recruitment. Similarly, nucleolin arrests Pu27 in the Pu22 conformer minimizing NM23-H2 binding at Pu27. hnRNPK (heterogeneous nuclear ribonucleoprotein K) positively regulates NM23-H2 and nucleolin association at Pu27 despite their antagonism. On the basis of these results, we simulated the transcription kinetics in a feed-forward loop in which the transcription output responds to hnRNPK-induced early activation via NM23-H2 association, which favors Pu24 formation at NHE III1 reducing nucleolin occupancy and driving quadruplex unfolding to initiate transcription. NM23-H2 further promotes hnRNPK deposition across NHE III1 altering Pu27 plasticity that finally enriches the nucleolin abundance to drive Pu22 formation and weaken NM23-H2 binding to extinguish transcription. This mechanism involves three positive feedback loops (NM23-H2-hnRNPK, NM23-H2-CNBP, and hnRNPK-nucleolin) and one negative feedback loop (NM23-H2-nucleolin) controlling optimal turnover and residence time of TFs at Pu27 to homeostatically regulate c-MYC transcription.
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Affiliation(s)
- Pallabi Sengupta
- Department of Biophysics , Bose Institute , P 1/12, C. I. T. Road, Scheme-VIIM , Kolkata 700054 , West Bengal , India
| | - Apoorva Bhattacharya
- Division of Molecular Medicine , Bose Institute , P 1/12, C. I. T. Road, Scheme-VIIM , Kolkata 700054 , West Bengal , India
| | - Gaurisankar Sa
- Division of Molecular Medicine , Bose Institute , P 1/12, C. I. T. Road, Scheme-VIIM , Kolkata 700054 , West Bengal , India
| | - Tanya Das
- Division of Molecular Medicine , Bose Institute , P 1/12, C. I. T. Road, Scheme-VIIM , Kolkata 700054 , West Bengal , India
| | - Subhrangsu Chatterjee
- Department of Biophysics , Bose Institute , P 1/12, C. I. T. Road, Scheme-VIIM , Kolkata 700054 , West Bengal , India
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42
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Debnath M, Fatma K, Dash J. Chemical Regulation of DNA i‐Motifs for Nanobiotechnology and Therapeutics. Angew Chem Int Ed Engl 2019. [DOI: 10.1002/ange.201813288] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Affiliation(s)
- Manish Debnath
- School of Chemical SciencesIndian Association for the Cultivation of Science Jadavpur Kolkata- 700032 India
| | - Khushnood Fatma
- School of Chemical SciencesIndian Association for the Cultivation of Science Jadavpur Kolkata- 700032 India
| | - Jyotirmayee Dash
- School of Chemical SciencesIndian Association for the Cultivation of Science Jadavpur Kolkata- 700032 India
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Debnath M, Fatma K, Dash J. Chemical Regulation of DNA i-Motifs for Nanobiotechnology and Therapeutics. Angew Chem Int Ed Engl 2019; 58:2942-2957. [PMID: 30600876 DOI: 10.1002/anie.201813288] [Citation(s) in RCA: 55] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2018] [Revised: 12/27/2018] [Indexed: 12/20/2022]
Abstract
DNA sequences rich in cytosine have the propensity, under acidic pH, to fold into four-stranded intercalated DNA structures called i-motifs. Recent studies have provided significant breakthroughs that demonstrate how chemists can manipulate these structures for nanobiotechnology and therapeutics. The first section of this Minireview discusses the development of advanced functional nanostructures by synthetic conjugation of i-motifs with organic scaffolds and metal nanoparticles and their role in therapeutics. The second section highlights the therapeutic targeting of i-motifs with chemical scaffolds and their significance in biology. For this, first we shed light on the long-lasting debate regarding the stability of i-motifs under physiological conditions. Next, we present a comparative analysis of recently reported small molecules for specifically targeting i-motifs over other abundant DNA structures and modulating their function in cellular systems. These advances provide new insights into i-motif-targeted regulation of gene expression, telomere maintenance, and therapeutic applications.
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Affiliation(s)
- Manish Debnath
- School of Chemical Sciences, Indian Association for the Cultivation of Science, Jadavpur, Kolkata-, 700032, India
| | - Khushnood Fatma
- School of Chemical Sciences, Indian Association for the Cultivation of Science, Jadavpur, Kolkata-, 700032, India
| | - Jyotirmayee Dash
- School of Chemical Sciences, Indian Association for the Cultivation of Science, Jadavpur, Kolkata-, 700032, India
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Endo M, Xing X, Sugiyama H. Direct Observation of the Formation and Dissociation of Double-Stranded DNA Containing G-Quadruplex/i-Motif Sequences in the DNA Origami Frame Using High-Speed AFM. Methods Mol Biol 2019; 2035:299-308. [PMID: 31444757 DOI: 10.1007/978-1-4939-9666-7_17] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
We demonstrate the single-molecule operation and observation of the formation and resolution of double-stranded DNA (dsDNA) containing G-quadruplex (GQ)- and counterpart i-motif-forming sequences in the DNA nanostructure. Sequential manipulation of DNA strands in the DNA frame was performed to prepare a topologically controlled GQ/i-motif dsDNA. Using the strand displacement and the addition and removal of K+, the topologically controlled GQ/i-motif dsDNA in the DNA frame was obtained in high yield. The dsDNA was resolved into the single-stranded DNA, GQ, and i-motif by the addition of K+ and operation under acidic conditions. The dissociation of the dsDNA under the GQ and i-motif formation conditions was monitored by high-speed atomic force microscopy. The results indicate that the dsDNA containing the GQ- and i-motif sequence is effectively dissolved when the duplex is helically loosened in the DNA nanoscaffold.
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Affiliation(s)
- Masayuki Endo
- Department of Chemistry, Graduate School of Science, Kyoto University, Kyoto, Japan
- Institute for Integrated Cell-Material Sciences, Kyoto University, Kyoto, Japan
| | - Xiwen Xing
- Department of Chemistry, Graduate School of Science, Kyoto University, Kyoto, Japan
- Department of Biotechnology, Key Laboratory of Virology of Guangzhou College of Life Science and Technology, Jinan University, Guangzhou, P. R. China
| | - Hiroshi Sugiyama
- Department of Chemistry, Graduate School of Science, Kyoto University, Kyoto, Japan.
- Institute for Integrated Cell-Material Sciences, Kyoto University, Kyoto, Japan.
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45
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Wolski P, Nieszporek K, Panczyk T. G-Quadruplex and I-Motif Structures within the Telomeric DNA Duplex. A Molecular Dynamics Analysis of Protonation States as Factors Affecting Their Stability. J Phys Chem B 2018; 123:468-479. [DOI: 10.1021/acs.jpcb.8b11547] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Pawel Wolski
- Institute of Catalysis and Surface Chemistry, Polish Academy of Sciences, ul. Niezapominajek 8, 30239 Cracow, Poland
| | - Krzysztof Nieszporek
- Department of Chemistry, Maria Curie-Sklodowska University, pl. M. Curie-Sklodowskiej 3, 20031 Lublin, Poland
| | - Tomasz Panczyk
- Institute of Catalysis and Surface Chemistry, Polish Academy of Sciences, ul. Niezapominajek 8, 30239 Cracow, Poland
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Sedghi Masoud S, Nagasawa K. i-Motif-Binding Ligands and Their Effects on the Structure and Biological Functions of i-Motif. Chem Pharm Bull (Tokyo) 2018; 66:1091-1103. [DOI: 10.1248/cpb.c18-00720] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Affiliation(s)
- Shadi Sedghi Masoud
- Department of Life Science and Biotechnology, Faculty of Technology, Tokyo University of Agriculture and Technology
| | - Kazuo Nagasawa
- Department of Life Science and Biotechnology, Faculty of Technology, Tokyo University of Agriculture and Technology
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47
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Masai H, Kakusho N, Fukatsu R, Ma Y, Iida K, Kanoh Y, Nagasawa K. Molecular architecture of G-quadruplex structures generated on duplex Rif1-binding sequences. J Biol Chem 2018; 293:17033-17049. [PMID: 30217821 DOI: 10.1074/jbc.ra118.005240] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2018] [Revised: 09/06/2018] [Indexed: 01/07/2023] Open
Abstract
G-quadruplexes (G4s) are four-stranded DNA structures comprising stacks of four guanines, are prevalent in genomes, and have diverse biological functions in various chromosomal structures. A conserved protein, Rap1-interacting factor 1 (Rif1) from fission yeast (Schizosaccharomyces pombe), binds to Rif1-binding sequence (Rif1BS) and regulates DNA replication timing. Rif1BS is characterized by the presence of multiple G-tracts, often on both strands, and their unusual spacing. Although previous studies have suggested generation of G4-like structures on duplex Rif1BS, its precise molecular architecture remains unknown. Using gel-shift DNA binding assays and DNA footprinting with various nuclease probes, we show here that both of the Rif1BS strands adopt specific higher-order structures upon heat denaturation. We observed that the structure generated on the G-strand is consistent with a G4 having unusually long loop segments and that the structure on the complementary C-strand does not have an intercalated motif (i-motif). Instead, we found that the formation of the C-strand structure depends on the G4 formation on the G-strand. Thus, the higher-order structure generated at Rif1BS involved both DNA strands, and in some cases, G4s may form on both of these strands. The presence of multiple G-tracts permitted the formation of alternative structures when some G-tracts were mutated or disrupted by deazaguanine replacement, indicating the robust nature of DNA higher-order structures generated at Rif1BS. Our results provide general insights into DNA structures generated at G4-forming sequences on duplex DNA.
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Affiliation(s)
- Hisao Masai
- From the Department of Genome Medicine, Tokyo Metropolitan Institute of Medical Science, Kamikitazawa, Setagaya-ku, Tokyo 156-8506, Japan,
| | - Naoko Kakusho
- From the Department of Genome Medicine, Tokyo Metropolitan Institute of Medical Science, Kamikitazawa, Setagaya-ku, Tokyo 156-8506, Japan
| | - Rino Fukatsu
- From the Department of Genome Medicine, Tokyo Metropolitan Institute of Medical Science, Kamikitazawa, Setagaya-ku, Tokyo 156-8506, Japan
| | - Yue Ma
- the Department of Biotechnology and Life Science, Faculty of Technology, Tokyo University of Agriculture and Technology, Tokyo 184-8588, Japan, and
| | - Keisuke Iida
- the Molecular Chirality Research Center, Synthetic Organic Chemistry, Department of Chemistry, Graduate School of Science, Chiba University, Chiba 263-8522, Japan
| | - Yutaka Kanoh
- From the Department of Genome Medicine, Tokyo Metropolitan Institute of Medical Science, Kamikitazawa, Setagaya-ku, Tokyo 156-8506, Japan
| | - Kazuo Nagasawa
- the Department of Biotechnology and Life Science, Faculty of Technology, Tokyo University of Agriculture and Technology, Tokyo 184-8588, Japan, and
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48
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Bartas M, Brázda V, Karlický V, Červeň J, Pečinka P. Bioinformatics analyses and in vitro evidence for five and six stacked G-quadruplex forming sequences. Biochimie 2018; 150:70-75. [PMID: 29733879 DOI: 10.1016/j.biochi.2018.05.002] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2018] [Accepted: 05/02/2018] [Indexed: 02/08/2023]
Abstract
Quadruplexes are noncanonical DNA structures that arise in guanine rich loci and have important biological functions. Classically, quadruplexes contain four stacked intramolecular G-tetrads. Surprisingly, although some algorithms allow searching for longer than 4G tracts for quadruplex formation, these have not yet been systematically studied. Therefore, we analyzed the human genome for sequences that are predicted to adopt stacked intramolecular G-tetrads with greater than four stacks. The data provide evidence for numerous G-quadruplexes that contain five or six stacked intramolecular G-tetrads. These sequences are predominantly found in known gene regulatory regions. Electrophoretic mobility assays and circular dichroism spectroscopy indicate that these sequences form quadruplex structures in vitro under physiological conditions. The localization and in vitro stability of these G-quadruplexes indicate their potentially important roles in gene regulation and their potential for therapeutic applications.
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Affiliation(s)
- Martin Bartas
- Department of Biology and Ecology/Institute of Environmental Technologies, Faculty of Science, University of Ostrava, Chittussiho 10, Ostrava, CZ, 71000, Czech Republic
| | - Václav Brázda
- Department of Biophysical Chemistry and Molecular Oncology, Institute of Biophysics, The Czech Academy of Sciences, Brno, CZ, 61265, Czech Republic
| | - Václav Karlický
- Department of Physics, Faculty of Science, University of Ostrava, Chittussiho 10, Ostrava, CZ, 71000, Czech Republic; Global Change Research Institute CAS, V. V. I., Bělidla 986/4a, Brno, CZ, 60300, Czech Republic
| | - Jiří Červeň
- Department of Biology and Ecology/Institute of Environmental Technologies, Faculty of Science, University of Ostrava, Chittussiho 10, Ostrava, CZ, 71000, Czech Republic
| | - Petr Pečinka
- Department of Biology and Ecology/Institute of Environmental Technologies, Faculty of Science, University of Ostrava, Chittussiho 10, Ostrava, CZ, 71000, Czech Republic.
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49
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Kaulage MH, Bhattacharya S, Muniyappa K. Structural Characterization of i-Motif Structure in the Human Acetyl-CoA Carboxylase 1 Gene Promoters and Their Role in the Regulation of Gene Expression. Chembiochem 2018; 19:1078-1087. [DOI: 10.1002/cbic.201800021] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2018] [Indexed: 12/26/2022]
Affiliation(s)
- Mangesh H. Kaulage
- Department of Biochemistry; Indian Institute of Science; Bengaluru 560012 India
- Department of Organic Chemistry; Indian Institute of Science; Bengaluru 560012 India
| | - Santanu Bhattacharya
- Department of Organic Chemistry; Indian Institute of Science; Bengaluru 560012 India
| | - K. Muniyappa
- Department of Biochemistry; Indian Institute of Science; Bengaluru 560012 India
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50
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Chang S, Kilic T, Lee CK, Avci H, Bae H, Oskui SM, Jung SM, Shin SR, Kim SJ. Reversible Redox Activity by Ion-pH Dually Modulated Duplex Formation of i-Motif DNA with Complementary G-DNA. NANOMATERIALS 2018; 8:nano8040226. [PMID: 29642472 PMCID: PMC5923556 DOI: 10.3390/nano8040226] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/06/2018] [Revised: 03/28/2018] [Accepted: 04/01/2018] [Indexed: 01/12/2023]
Abstract
The unique biological features of supramolecular DNA have led to an increasing interest in biomedical applications such as biosensors. We have developed an i-motif and G-rich DNA conjugated single-walled carbon nanotube hybrid materials, which shows reversible conformational switching upon external stimuli such as pH (5 and 8) and presence of ions (Li⁺ and K⁺). We observed reversible electrochemical redox activity upon external stimuli in a quick and robust manner. Given the ease and the robustness of this method, we believe that pH- and ion-driven reversible DNA structure transformations will be utilized for future applications for developing novel biosensors.
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Affiliation(s)
- Soyoung Chang
- Center for Bio-Artificial Muscle and Department of Biomedical Engineering, Hanyang University, Seoul 04763, Korea.
| | - Tugba Kilic
- Division of Engineering in Medicine, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Cambridge, MA 02139, USA.
- Harvard-MIT Division of Health Sciences and Technology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA.
- Department of Biomedical Engineering, Izmir Katip Celebi University, Izmir 35620, Turkey.
| | - Chang Kee Lee
- Korea Packaging Center, Korea Institute of Industrial Technology, Bucheon 14449, Korea.
| | - Huseyin Avci
- Division of Engineering in Medicine, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Cambridge, MA 02139, USA.
- Harvard-MIT Division of Health Sciences and Technology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA.
- Department of Metallurgical and Materials Engineering, Eskisehir Osmangazi University, Eskisehir 26040, Turkey.
| | - Hojae Bae
- KU Convergence Science and Technology Institute, Department of Stem Cell and Regenerative Biotechnology, Konkuk University, Seoul 05029, Korea.
| | - Shirin Mesbah Oskui
- Division of Engineering in Medicine, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Cambridge, MA 02139, USA.
- Harvard-MIT Division of Health Sciences and Technology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA.
| | - Sung Mi Jung
- Future Environmental Research Center, Korea Institute of Toxicology, Jinju 52834, Korea.
| | - Su Ryon Shin
- Center for Bio-Artificial Muscle and Department of Biomedical Engineering, Hanyang University, Seoul 04763, Korea.
- Division of Engineering in Medicine, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Cambridge, MA 02139, USA.
- Harvard-MIT Division of Health Sciences and Technology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA.
| | - Seon Jeong Kim
- Center for Bio-Artificial Muscle and Department of Biomedical Engineering, Hanyang University, Seoul 04763, Korea.
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