1
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Dobrovodsky D, Danhel A, Renciuk D, Mergny JL, Fojta M. N-methyl mesoporphyrin IX (NMM) as electrochemical probe for detection of guanine quadruplexes. Bioelectrochemistry 2024; 156:108611. [PMID: 37995502 DOI: 10.1016/j.bioelechem.2023.108611] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2023] [Revised: 11/13/2023] [Accepted: 11/16/2023] [Indexed: 11/25/2023]
Abstract
G-quadruplexes (G4) are stable alternative secondary structures of nucleic acids. With increasing understanding of their roles in biological processes and their application in bio- and nanotechnology, the exploration of novel methods for the analysis of these structures is becoming important. In this work, N-methyl mesoporphyrin IX (NMM) was used as a voltammetric probe for an easy electrochemical detection of G4s. Cyclic voltammetry on a hanging mercury drop electrode (HMDE) was used to detect NMM with a limit of detection (LOD) of 40 nM. Characteristic reduction signal of NMM was found to be substantially higher in the presence of G4 oligodeoxynucleotides (ODNs) than in the presence of single- or double-stranded ODNs and even ODNs susceptible to form G4s but in their unfolded, single-stranded forms. Gradual transition from unstructured single strand to G4, induced by increasing concentrations of the G4 stabilizing K+ ions, was detected by an electrochemical method for the first time. All obtained results were supported by circular dichroism spectroscopy. This work expands on the concept of electrochemical probes utilization in DNA secondary structure recognition and offers a proof of principle that can be potentially employed in the development of novel electroanalytical methods for nucleic acid structure studies.
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Affiliation(s)
- Daniel Dobrovodsky
- Institute of Biophysics, Czech Academy of Sciences, Královopolská 135, 612 00 Brno, Czech Republic
| | - Ales Danhel
- Institute of Biophysics, Czech Academy of Sciences, Královopolská 135, 612 00 Brno, Czech Republic
| | - Daniel Renciuk
- Institute of Biophysics, Czech Academy of Sciences, Královopolská 135, 612 00 Brno, Czech Republic
| | - Jean-Louis Mergny
- Institute of Biophysics, Czech Academy of Sciences, Královopolská 135, 612 00 Brno, Czech Republic
| | - Miroslav Fojta
- Institute of Biophysics, Czech Academy of Sciences, Královopolská 135, 612 00 Brno, Czech Republic.
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2
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Rekvig OP. The greatest contribution to medical science is the transformation from studying symptoms to studying their causes-the unrelenting legacy of Robert Koch and Louis Pasteur-and a causality perspective to approach a definition of SLE. Front Immunol 2024; 15:1346619. [PMID: 38361929 PMCID: PMC10867267 DOI: 10.3389/fimmu.2024.1346619] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2023] [Accepted: 01/10/2024] [Indexed: 02/17/2024] Open
Abstract
The basic initiative related to this study is derived from the fact that systemic lupus erythematosus (SLE) is a unique and fertile system science subject. We are, however, still far from understanding its nature. It may be fair to indicate that we are spending more time and resources on studying the complexity of classified SLE than studying the validity of classification criteria. This study represents a theoretical analysis of current instinctual SLE classification criteria based on "the causality principle." The discussion has its basis on the radical scientific traditions introduced by Robert Koch and Louis Pasteur. They announced significant changes in our thinking of disease etiology through the implementation of the modern version of "the causality principle." They influenced all aspects of today's medical concepts and research: the transformation of medical science from studies of symptoms to study their causes, relevant for monosymptomatic diseases as for syndromes. Their studies focused on bacteria as causes of infectious diseases and on how the immune system adapts to control and prevent contagious spreading. This is the most significant paradigm shift in the modern history of medicine and resulted in radical changes in our view of the immune system. They described acquired post-infection immunity and active immunization by antigen-specific vaccines. The paradigm "transformation" has a great theoretical impact also on current studies of autoimmune diseases like SLE: symptoms and their cause(s). In this study, the evolution of SLE classification and diagnostic criteria is discussed from "the causality principle" perspective, and if contemporary SLE classification criteria are as useful as believed today for SLE research. This skepticism is based on the fact that classification criteria are not selected based on cogent causal strategies. The SLE classification criteria do not harmonize with Koch's and Pasteur's causality principle paradigms and not with Witebsky's Koch-derived postulates for autoimmune and infectious diseases. It is not established whether the classification criteria can separate SLE as a "one disease entity" from "SLE-like non-SLE disorders"-the latter in terms of SLE imitations. This is discussed here in terms of weight, rank, and impact of the classification criteria: Do they all originate from "one basic causal etiology"? Probably not.
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Affiliation(s)
- Ole Petter Rekvig
- Section for Autoimmunity, Fürst Medical Laboratory, Oslo, Norway
- Department of Medical Biology, Faculty of Health Sciences, UiT The Arctic University of Norway, Tromsø, Norway
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3
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Robinson J, Stenspil SG, Maleckaite K, Bartlett M, Di Antonio M, Vilar R, Kuimova MK. Cellular Visualization of G-Quadruplex RNA via Fluorescence- Lifetime Imaging Microscopy. J Am Chem Soc 2024; 146:1009-1018. [PMID: 38151240 PMCID: PMC10786036 DOI: 10.1021/jacs.3c11908] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2023] [Revised: 12/06/2023] [Accepted: 12/07/2023] [Indexed: 12/29/2023]
Abstract
Over the past decade, appreciation of the roles of G-quadruplex (G4) structures in cellular regulation and maintenance has rapidly grown, making the establishment of robust methods to visualize G4s increasingly important. Fluorescent probes are commonly used for G4 detection in vitro; however, achieving sufficient selectivity to detect G4s in a dense and structurally diverse cellular environment is challenging. The use of fluorescent probes for G4 detection is further complicated by variations of probe uptake into cells, which may affect fluorescence intensity independently of G4 abundance. In this work, we report an alternative small-molecule approach to visualize G4s that does not rely on fluorescence intensity switch-on and, thus, does not require the use of molecules with exclusive G4 binding selectivity. Specifically, we have developed a novel thiazole orange derivative, TOR-G4, that exhibits a unique fluorescence lifetime when bound to G4s compared to other structures, allowing G4 binding to be sensitively distinguished from non-G4 binding, independent of the local probe concentration. Furthermore, TOR-G4 primarily colocalizes with RNA in the cytoplasm and nucleoli of cells, making it the first lifetime-based probe validated for exploring the emerging roles of RNA G4s in cellulo.
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Affiliation(s)
- Jenna Robinson
- Department
of Chemistry, Molecular Science Research Hub, Imperial College London, 82 Wood Lane, London W12
0BZ, U.K.
- Molecular
Science Research Hub, Institute of Chemical
Biology, 82 Wood Lane, London W12 0BZ, U.K.
- The
Francis Crick Institute, 1 Midland Road, London NW1 1AT, U.K.
| | - Stine G. Stenspil
- Department
of Chemistry, Molecular Science Research Hub, Imperial College London, 82 Wood Lane, London W12
0BZ, U.K.
| | - Karolina Maleckaite
- Department
of Chemistry, Molecular Science Research Hub, Imperial College London, 82 Wood Lane, London W12
0BZ, U.K.
| | - Molly Bartlett
- Department
of Chemistry, Molecular Science Research Hub, Imperial College London, 82 Wood Lane, London W12
0BZ, U.K.
| | - Marco Di Antonio
- Department
of Chemistry, Molecular Science Research Hub, Imperial College London, 82 Wood Lane, London W12
0BZ, U.K.
- Molecular
Science Research Hub, Institute of Chemical
Biology, 82 Wood Lane, London W12 0BZ, U.K.
- The
Francis Crick Institute, 1 Midland Road, London NW1 1AT, U.K.
| | - Ramon Vilar
- Department
of Chemistry, Molecular Science Research Hub, Imperial College London, 82 Wood Lane, London W12
0BZ, U.K.
- Molecular
Science Research Hub, Institute of Chemical
Biology, 82 Wood Lane, London W12 0BZ, U.K.
| | - Marina K. Kuimova
- Department
of Chemistry, Molecular Science Research Hub, Imperial College London, 82 Wood Lane, London W12
0BZ, U.K.
- Molecular
Science Research Hub, Institute of Chemical
Biology, 82 Wood Lane, London W12 0BZ, U.K.
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4
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Smirnov E, Molínová P, Chmúrčiaková N, Vacík T, Cmarko D. Non-canonical DNA structures in the human ribosomal DNA. Histochem Cell Biol 2023; 160:499-515. [PMID: 37750997 DOI: 10.1007/s00418-023-02233-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/15/2023] [Indexed: 09/27/2023]
Abstract
Non-canonical structures (NCS) refer to the various forms of DNA that differ from the B-conformation described by Watson and Crick. It has been found that these structures are usual components of the genome, actively participating in its essential functions. The present review is focused on the nine kinds of NCS appearing or likely to appear in human ribosomal DNA (rDNA): supercoiling structures, R-loops, G-quadruplexes, i-motifs, DNA triplexes, cruciform structures, DNA bubbles, and A and Z DNA conformations. We discuss the conditions of their generation, including their sequence specificity, distribution within the locus, dynamics, and beneficial and detrimental role in the cell.
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Affiliation(s)
- Evgeny Smirnov
- Laboratory of Cell Biology, Institute of Biology and Medical Genetics, First Faculty of Medicine, Charles University and General University Hospital in Prague, 128 00, Prague, Czech Republic.
| | - Pavla Molínová
- Laboratory of Cell Biology, Institute of Biology and Medical Genetics, First Faculty of Medicine, Charles University and General University Hospital in Prague, 128 00, Prague, Czech Republic
| | - Nikola Chmúrčiaková
- Laboratory of Cell Biology, Institute of Biology and Medical Genetics, First Faculty of Medicine, Charles University and General University Hospital in Prague, 128 00, Prague, Czech Republic
| | - Tomáš Vacík
- Laboratory of Cell Biology, Institute of Biology and Medical Genetics, First Faculty of Medicine, Charles University and General University Hospital in Prague, 128 00, Prague, Czech Republic
| | - Dušan Cmarko
- Laboratory of Cell Biology, Institute of Biology and Medical Genetics, First Faculty of Medicine, Charles University and General University Hospital in Prague, 128 00, Prague, Czech Republic
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5
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Mehra K, Khurana S, Kukreti S, Kaushik M. Nanomaterials and DNA multistranded structures: a treasure hunt for targeting specific biomedical applications. J Biomol Struct Dyn 2023; 41:11324-11340. [PMID: 36546729 DOI: 10.1080/07391102.2022.2159878] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2022] [Accepted: 12/13/2022] [Indexed: 12/24/2022]
Abstract
The advent in nanoscience and nanotechnology has enabled the successful synthesis and characterization of different nanomaterials with unique electrical, optical, magnetic and catalytic activities. However, with respect to sensing applications, nanomaterials intrinsically lack target recognition ability to selectively bind with the analyte. DNA, an important genetic material carrying biopolymer is polymorphic in nature and shows structural polymorphism, forming secondary/multistranded structures like hairpin, cruciform, pseudoknot, duplex, triplex, G-quadruplex and i-motif. Studies reported so far have suggested that these polymorphic structures have been targeted specifically for the treatment or diagnosis of various diseases. DNA is widely used in conjugation with nanomaterials for the development of nanoarchitectures due to its rigidity, sequence programmability and specific molecular recognition, which makes this biomolecule a treasure for designing of DNA based frameworks. These two entities (DNA and nanomaterials) can be used in association with each other, as their alliance can result into creation of novel assay platforms for different purposes, ranging from imaging, sensing and diagnostics to targeted delivery. In this review, we have discussed about the recent reports on association of various mutistranded/ polymorphic forms of DNA with nanomaterials. Furthermore, different applications using this versatile DNA-nanomaterial assembly has also been elaborated at length. This review aims to target the interests of scientists from various interdisciplinary fields, including biologists, chemists and nanotechnologists, who wish to gain an understanding of nano-fabrications using a plethora of DNA polymorphic forms.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Komal Mehra
- Nano-bioconjugate chemistry lab, Cluster Innovation Centre, University of Delhi, Delhi, India
- Nucleic acids research lab, Department of Chemistry, University of Delhi, Delhi, India
| | - Sonia Khurana
- Nano-bioconjugate chemistry lab, Cluster Innovation Centre, University of Delhi, Delhi, India
- Nucleic acids research lab, Department of Chemistry, University of Delhi, Delhi, India
| | - Shrikant Kukreti
- Nucleic acids research lab, Department of Chemistry, University of Delhi, Delhi, India
| | - Mahima Kaushik
- Nano-bioconjugate chemistry lab, Cluster Innovation Centre, University of Delhi, Delhi, India
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6
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Khan S, Singh A, Nain N, Kukreti S. Alkali cation-mediated topology displayed by an exonic G-rich sequence of TRPA1 gene. J Biomol Struct Dyn 2023; 41:9997-10008. [PMID: 36458452 DOI: 10.1080/07391102.2022.2150686] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2022] [Accepted: 11/17/2022] [Indexed: 12/04/2022]
Abstract
G-rich sequences are intrinsic parts of the genome, widespread in promoters, telomeres, or other regulatory regions. The in vivo existence and biological significance have established the functional aspect of G-quadruplex structures and thus have developed immense interest in exploring their therapeutic aspects. Herein, using biophysical methods, we examined the structural status and comprehensive cation-dependence of a 17-bp G-rich genomic sequence (SKGT17) located in the coding region of the human TRPA1 gene, known to be associated with various neurovascular, cardiovascular, and respiratory conditions. TRPA1 is primarily seen as a therapeutic target for the development of novel analgesics. Bioinformatics analysis has suggested that 17-bp quadruplex motif is a binding site for transcription factor 'Sp1'. The formation and recognition of SKGT17 G-quadruplex might impact its regulatory functioning. Biophysical studies confirmed that the presence of alkali metal ions facilitated the formation of G-quadruplex in parallel topology. Native gel further substantiated the formation of a biomolecular species. Circular dichroism (CD), UV-thermal melting (Tm), and CD melting confirmed the formation of parallel G-quadruplex with metal ion-dependent stability. The stability of the G-quadruplex formed is found to be significantly high in the presence of K+ ions than that of other ions. Intriguingly, we have also established that this segment of the TRAP1 gene favors G-quadruplex formation over its participation in the corresponding duplex formation under K+ ions conditions. This study attempts to explain the rationale for the stabilization of G-quadruplex in the presence of alkali metal ions and may add to a better understanding and insights into DNA-metal ions interactions.
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Affiliation(s)
- Shoaib Khan
- Nucleic Acid Research Laboratory, Department of Chemistry, University of Delhi, Delhi, India
| | - Anju Singh
- Department of Chemistry, Ramjas College, University of Delhi, Delhi, India
| | - Nishu Nain
- Nucleic Acid Research Laboratory, Department of Chemistry, University of Delhi, Delhi, India
| | - Shrikant Kukreti
- Nucleic Acid Research Laboratory, Department of Chemistry, University of Delhi, Delhi, India
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7
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Miranda de Souza Duarte-Filho LA, Ortega de Oliveira PC, Yanaguibashi Leal CE, de Moraes MC, Picot L. Ligand fishing as a tool to screen natural products with anticancer potential. J Sep Sci 2023:e2200964. [PMID: 36808885 DOI: 10.1002/jssc.202200964] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2022] [Revised: 02/07/2023] [Accepted: 02/07/2023] [Indexed: 02/23/2023]
Abstract
Cancer is the second leading cause of death in the world and its incidence is expected to increase with the aging of the world's population and globalization of risk factors. Natural products and their derivatives have provided a significant number of approved anticancer drugs and the development of robust and selective screening assays for the identification of lead anticancer natural products are essential in the challenge of developing personalized targeted therapies tailored to the genetic and molecular characteristics of tumors. To this end, a ligand fishing assay is a remarkable tool to rapidly and rigorously screen complex matrices, such as plant extracts, for the isolation and identification of specific ligands that bind to relevant pharmacological targets. In this paper, we review the application of ligand fishing with cancer-related targets to screen natural product extracts for the isolation and identification of selective ligands. We provide critical analysis of the system configurations, targets, and key phytochemical classes related to the field of anticancer research. Based on the data collected, ligand fishing emerges as a robust and powerful screening system for the rapid discovery of new anticancer drugs from natural resources. It is currently an underexplored strategy according to its considerable potential.
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Affiliation(s)
| | | | - Cíntia Emi Yanaguibashi Leal
- Departamento de Ciências Farmacêuticas, Pós-Graduação em Biociências (PGB) Universidade Federal do Vale do São Francisco, Petrolina, Brazil
| | - Marcela Cristina de Moraes
- Departamento de Química Orgânica, Laboratório BIOCROM, Instituto de Química, Universidade Federal Fluminense, Niterói, Brazil
| | - Laurent Picot
- UMR CNRS 7266 LIENSs, Département de Biotechnologie, La Rochelle Université, La Rochelle, France
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8
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Roy S, Bhattacharya S. Chemical Information and Computational Modeling of Targeting Hybrid Nucleic Acid Structures of PIM1 Sequences by Synthetic Pyrrole-Imidazole Carboxamide Drugs. J Chem Inf Model 2022; 62:6411-6422. [PMID: 35687766 DOI: 10.1021/acs.jcim.1c01500] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
DNA can adopt various distinct structural motifs, such as quadruplex, duplex, i-motifs, etc. which have multifarious applications in biomedical therapeutics. Quadruplex-duplex hybrids (QDHs) consist of the juxtaposed quadruplex and duplex motifs and are thermally stable and biologically relevant. Selective binding toward these secondary structures plays an important role in the evaluation of the structure-specific ligands. Herein, several small molecules containing anthraquinone conjugated oligopyrrole, oligoimidazole, and pyrrole-imidazole derivatives have been screened for the binding of the quadruplex-duplex nucleic acid hybrids formed in PIM1 sequences through docking and molecular dynamics (MD) simulation studies. The binding interaction of the anthraquinone polypyrrole ligands has also been checked by performing different biophysical experiments. PIM1, being a coactivator of the MYC oncogene, can be targeted by these small molecules to control MYC expression which is overexpressed in the majority of human cancer cells. Accordingly, these cancer cell-specific and blood-compatible anthraquinone conjugated oligopyrrole ligands can be employed for anticancer therapeutic applications. Thus, the structure-activity relationship (SAR) of the screened ligands manifested prudent structural information for designing PIM1 QDHs targeting small molecules.
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Affiliation(s)
- Soma Roy
- School of Applied & Interdisciplinary Sciences, Indian Association for the Cultivation of Science, Kolkata 700032, India
| | - Santanu Bhattacharya
- School of Applied & Interdisciplinary Sciences, Indian Association for the Cultivation of Science, Kolkata 700032, India.,Department of Organic Chemistry, Indian Institute of Science, Bangalore 560012, India
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9
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Shitikov EA, Bespiatykh DA, Bodoev IN, Zaychikova MV. G-Quadruplex Structures in Bacteria: Functional Properties and Prospects for Use as Biotargets. Biochem Moscow Suppl Ser B 2022. [DOI: 10.1134/s1990750822040084] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
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10
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Balasooriya GI, Spector DL. Allele-specific differential regulation of monoallelically expressed autosomal genes in the cardiac lineage. Nat Commun 2022; 13:5984. [PMID: 36216821 PMCID: PMC9550772 DOI: 10.1038/s41467-022-33722-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2021] [Accepted: 09/27/2022] [Indexed: 11/29/2022] Open
Abstract
Each mammalian autosomal gene is represented by two alleles in diploid cells. To our knowledge, no insights have been made in regard to allele-specific regulatory mechanisms of autosomes. Here we use allele-specific single cell transcriptomic analysis to elucidate the establishment of monoallelic gene expression in the cardiac lineage. We find that monoallelically expressed autosomal genes in mESCs and mouse blastocyst cells are differentially regulated based on the genetic background of the parental alleles. However, the genetic background of the allele does not affect the establishment of monoallelic genes in differentiated cardiomyocytes. Additionally, we observe epigenetic differences between deterministic and random autosomal monoallelic genes. Moreover, we also find a greater contribution of the maternal versus paternal allele to the development and homeostasis of cardiac tissue and in cardiac health, highlighting the importance of maternal influence in male cardiac tissue homeostasis. Our findings emphasize the significance of allele-specific insights into gene regulation in development, homeostasis and disease.
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11
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Abstract
A complete understanding of DNA double-helical structure discovered by James Watson and Francis Crick in 1953, unveil the importance and significance of DNA. For the last seven decades, this has been a leading light in the course of the development of modern biology and biomedical science. Apart from the predominant B-form, experimental shreds of evidence have revealed the existence of a sequence-dependent structural diversity, unusual non-canonical structures like hairpin, cruciform, Z-DNA, multistranded structures such as DNA triplex, G-quadruplex, i-motif forms, etc. The diversity in the DNA structure depends on various factors such as base sequence, ions, superhelical stress, and ligands. In response to these various factors, the polymorphism of DNA regulates various genes via different processes like replication, transcription, translation, and recombination. However, altered levels of gene expression are associated with many human genetic diseases including neurological disorders and cancer. These non-B-DNA structures are expected to play a key role in determining genetic stability, DNA damage and repair etc. The present review is a modest attempt to summarize the available literature, illustrating the occurrence of non-canonical structures at the molecular level in response to the environment and interaction with ligands and proteins. This would provide an insight to understand the biological functions of these unusual DNA structures and their recognition as potential therapeutic targets for diverse genetic diseases.
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Affiliation(s)
- Aparna Bansal
- Nucleic Acid Research Lab, Department of Chemistry, University of Delhi, Delhi, India
- Department of Chemistry, Hansraj College, University of Delhi, Delhi, India
| | - Shikha Kaushik
- Nucleic Acid Research Lab, Department of Chemistry, University of Delhi, Delhi, India
- Department of Chemistry, Rajdhani College, University of Delhi, New Delhi, India
| | - Shrikant Kukreti
- Nucleic Acid Research Lab, Department of Chemistry, University of Delhi, Delhi, India
- *Correspondence: Shrikant Kukreti,
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12
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Economos NG, Thapar U, Balasubramanian N, Karras GI, Glazer PM. An ELISA-based platform for rapid identification of structure-dependent nucleic acid-protein interactions detects novel DNA triplex interactors. J Biol Chem 2022; 298:102398. [PMID: 35988651 PMCID: PMC9493393 DOI: 10.1016/j.jbc.2022.102398] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2022] [Revised: 08/11/2022] [Accepted: 08/13/2022] [Indexed: 11/21/2022] Open
Abstract
Unusual nucleic acid structures play vital roles as intermediates in many cellular processes and, in the case of peptide nucleic acid (PNA)–mediated triplexes, are leveraged as tools for therapeutic gene editing. However, due to their transient nature, an understanding of the factors that interact with and process dynamic nucleic acid structures remains limited. Here, we developed snapELISA (structure-specific nucleic acid-binding protein ELISA), a rapid high-throughput platform to interrogate and compare up to 2688 parallel nucleic acid structure–protein interactions in vitro. We applied this system to both triplex-forming oligonucleotide–induced DNA triplexes and DNA-bound PNA heterotriplexes to describe the identification of previously known and novel interactors for both structures. For PNA heterotriplex recognition analyses, snapELISA identified factors implicated in nucleotide excision repair (XPA, XPC), single-strand annealing repair (RAD52), and recombination intermediate structure binding (TOP3A, BLM, MUS81). We went on to validate selected factor localization to genome-targeted PNA structures within clinically relevant loci in human cells. Surprisingly, these results demonstrated XRCC5 localization to PNA triplex-forming sites in the genome, suggesting the presence of a double-strand break intermediate. These results describe a powerful comparative approach for identifying structure-specific nucleic acid interactions and expand our understanding of the mechanisms of triplex structure recognition and repair.
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Affiliation(s)
- Nicholas G Economos
- Department of Therapeutic Radiology, Yale University School of Medicine, New Haven, CT; Department of Genetics, Yale University School of Medicine, New Haven, CT
| | - Upasna Thapar
- Department of Genetics, The University of Texas MD Anderson Cancer Center, Houston, TX
| | - Nanda Balasubramanian
- Department of Therapeutic Radiology, Yale University School of Medicine, New Haven, CT
| | - Georgios I Karras
- Department of Genetics, The University of Texas MD Anderson Cancer Center, Houston, TX; Genetics and Epigenetics Graduate Program, The University of Texas MD Anderson Cancer Center UTHealth Houston Graduate School of Biomedical Sciences, Houston, TX.
| | - Peter M Glazer
- Department of Therapeutic Radiology, Yale University School of Medicine, New Haven, CT; Department of Genetics, Yale University School of Medicine, New Haven, CT.
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Georgakopoulos-Soares I, Chan CSY, Ahituv N, Hemberg M. High-throughput techniques enable advances in the roles of DNA and RNA secondary structures in transcriptional and post-transcriptional gene regulation. Genome Biol 2022; 23:159. [PMID: 35851062 DOI: 10.1186/s13059-022-02727-6] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2022] [Accepted: 07/07/2022] [Indexed: 12/27/2022] Open
Abstract
The most stable structure of DNA is the canonical right-handed double helix termed B DNA. However, certain environments and sequence motifs favor alternative conformations, termed non-canonical secondary structures. The roles of DNA and RNA secondary structures in transcriptional regulation remain incompletely understood. However, advances in high-throughput assays have enabled genome wide characterization of some secondary structures. Here, we describe their regulatory functions in promoters and 3’UTRs, providing insights into key mechanisms through which they regulate gene expression. We discuss their implication in human disease, and how advances in molecular technologies and emerging high-throughput experimental methods could provide additional insights.
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14
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Mosseri A, Sancho‐Albero M, Leone M, Nava D, Secundo F, Maggioni D, De Cola L, Romanelli A. Chiral Fibers Formation Upon Assembly of Tetraphenylalanine Peptide Conjugated to a PNA Dimer. Chemistry 2022; 28:e202200693. [PMID: 35474351 PMCID: PMC9325372 DOI: 10.1002/chem.202200693] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2022] [Indexed: 11/17/2022]
Abstract
Self‐assembly of biomolecules such as peptides, nucleic acids or their analogues affords supramolecular objects, exhibiting structures and physical properties dependent on the amino‐acid or nucleobase composition. Conjugation of the peptide diphenylalanine (FF) to peptide nucleic acids triggers formation of self‐assembled structures, mainly stabilized by interactions between FF. In this work we report formation of homogeneous chiral fibers upon self‐assembly of the hybrid composed of the tetraphenylalanine peptide (4F) conjugated to the PNA dimer adenine‐thymine (at). In this case nucleobases seem to play a key role in determining the morphology and chirality of the fibers. When the PNA “at” is replaced by guanine‐cytosine dimer “gc”, disordered structures are observed. Spectroscopic characterization of the self‐assembled hybrids, along with AFM and SEM studies is reported. Finally, a structural model consistent with the experimental evidence has also been obtained, showing how the building blocks of 4Fat arrange to give helical fibers.
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Affiliation(s)
- Andrea Mosseri
- Dipartimento di Scienze Farmaceutiche Università degli Studi di Milano via Venezian 21 20133 Milano Italy
| | - Maria Sancho‐Albero
- Department of Molecular Biochemistry and Pharmacology Istituto di Ricerche Farmacologiche Mario Negri IRCCS 20156 Milano Italy
| | - Marilisa Leone
- Istituto di Biostrutture e Bioimmagini – CNR via Mezzocannone 16 80134 Naples Italy
| | - Donatella Nava
- Dipartimento di Scienze Farmaceutiche Università degli Studi di Milano via Venezian 21 20133 Milano Italy
| | - Francesco Secundo
- Istituto di Scienze e Tecnologie Chimiche “Giulio Natta”, CNR via Mario Bianco 9 Milan 20131 Italy
| | - Daniela Maggioni
- Dipartimento di Chimica Università degli Studi di Milano Via Golgi 19 20133 Milano Italy
| | - Luisa De Cola
- Dipartimento di Scienze Farmaceutiche Università degli Studi di Milano via Venezian 21 20133 Milano Italy
- Department of Molecular Biochemistry and Pharmacology Istituto di Ricerche Farmacologiche Mario Negri IRCCS 20156 Milano Italy
| | - Alessandra Romanelli
- Dipartimento di Scienze Farmaceutiche Università degli Studi di Milano via Venezian 21 20133 Milano Italy
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15
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Ruggiero E, Lavezzo E, Grazioli M, Zanin I, Marušič M, Plavec J, Richter SN, Toppo S. Human Virus Genomes Are Enriched in Conserved Adenine/Thymine/Uracil Multiple Tracts That Pause Polymerase Progression. Front Microbiol 2022; 13:915069. [PMID: 35722311 PMCID: PMC9198555 DOI: 10.3389/fmicb.2022.915069] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2022] [Accepted: 05/02/2022] [Indexed: 11/13/2022] Open
Abstract
The DNA secondary structures that deviate from the classic Watson and Crick base pairing are increasingly being reported to form transiently in the cell and regulate specific cellular mechanisms. Human viruses are cell parasites that have evolved mechanisms shared with the host cell to support their own replication and spreading. Contrary to human host cells, viruses display a diverse array of nucleic acid types, which include DNA or RNA in single-stranded or double-stranded conformations. This heterogeneity improves the possible occurrence of non-canonical nucleic acid structures. We have previously shown that human virus genomes are enriched in G-rich sequences that fold in four-stranded nucleic acid secondary structures, the G-quadruplexes.Here, by extensive bioinformatics analysis on all available genomes, we showed that human viruses are enriched in highly conserved multiple A (and T or U) tracts, with such an array that they could in principle form quadruplex structures. By circular dichroism, NMR, and Taq polymerase stop assays, we proved that, while A/T/U-quadruplexes do not form, these tracts still display biological significance, as they invariably trigger polymerase pausing within two bases from the A/T/U tract. “A” bases display the strongest effect. Most of the identified A-tracts are in the coding strand, both at the DNA and RNA levels, suggesting their possible relevance during viral translation. This study expands on the presence and mechanism of nucleic acid secondary structures in human viruses and provides a new direction for antiviral research.
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Affiliation(s)
| | - Enrico Lavezzo
- Department of Molecular Medicine, University of Padua, Padua, Italy
| | - Marco Grazioli
- Department of Molecular Medicine, University of Padua, Padua, Italy
| | - Irene Zanin
- Department of Molecular Medicine, University of Padua, Padua, Italy
| | - Maja Marušič
- Slovenian NMR Centre, National Institute of Chemistry, Ljubljana, Slovenia
| | - Janez Plavec
- Slovenian NMR Centre, National Institute of Chemistry, Ljubljana, Slovenia
| | - Sara N Richter
- Department of Molecular Medicine, University of Padua, Padua, Italy
| | - Stefano Toppo
- Department of Molecular Medicine, University of Padua, Padua, Italy.,CRIBI Biotechnology Center, University of Padua, Padua, Italy
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16
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Georgakopoulos-Soares I, Parada GE, Wong HY, Medhi R, Furlan G, Munita R, Miska EA, Kwok CK, Hemberg M. Alternative splicing modulation by G-quadruplexes. Nat Commun 2022; 13:2404. [PMID: 35504902 PMCID: PMC9065059 DOI: 10.1038/s41467-022-30071-7] [Citation(s) in RCA: 26] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2019] [Accepted: 03/30/2022] [Indexed: 12/14/2022] Open
Abstract
Alternative splicing is central to metazoan gene regulation, but the regulatory mechanisms are incompletely understood. Here, we show that G-quadruplex (G4) motifs are enriched ~3-fold near splice junctions. The importance of G4s in RNA is emphasised by a higher enrichment for the non-template strand. RNA-seq data from mouse and human neurons reveals an enrichment of G4s at exons that were skipped following depolarisation induced by potassium chloride. We validate the formation of stable RNA G4s for three candidate splice sites by circular dichroism spectroscopy, UV-melting and fluorescence measurements. Moreover, we find that sQTLs are enriched at G4s, and a minigene experiment provides further support for their role in promoting exon inclusion. Analysis of >1,800 high-throughput experiments reveals multiple RNA binding proteins associated with G4s. Finally, exploration of G4 motifs across eleven species shows strong enrichment at splice sites in mammals and birds, suggesting an evolutionary conserved splice regulatory mechanism. Here the authors shows that G-quadruplexes, non-canonical DNA/RNA structures, can have a direct impact on alternative splicing and that binding of splicing regulators is affected by their presence.
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Affiliation(s)
- Ilias Georgakopoulos-Soares
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, CB10 1SA, UK.,Department of Bioengineering and Therapeutic Sciences, University of California San Francisco, San Francisco, CA, 94158, USA
| | - Guillermo E Parada
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, CB10 1SA, UK.,Wellcome Cancer Research UK Gurdon Institute, University of Cambridge, Tennis Court Road, Cambridge, CB2 1QN, UK.,Department of Genetics, University of Cambridge, Downing Street, Cambridge, CB2 3EH, UK.,Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, ON, M5S 3E1, Canada.,Department of Molecular Genetics, University of Toronto, Toronto, ON, M5A 1A8, Canada
| | - Hei Yuen Wong
- Department of Chemistry and State Key Laboratory of Marine Pollution, City University of Hong Kong, Kowloon Tong, Hong Kong SAR, China
| | - Ragini Medhi
- Wellcome Cancer Research UK Gurdon Institute, University of Cambridge, Tennis Court Road, Cambridge, CB2 1QN, UK.,Department of Genetics, University of Cambridge, Downing Street, Cambridge, CB2 3EH, UK
| | - Giulia Furlan
- Wellcome Cancer Research UK Gurdon Institute, University of Cambridge, Tennis Court Road, Cambridge, CB2 1QN, UK.,Department of Genetics, University of Cambridge, Downing Street, Cambridge, CB2 3EH, UK
| | - Roberto Munita
- Division of Molecular Hematology, Department of Laboratory Medicine, Lund Stem Cell Center, Faculty of Medicine, Lund University, Lund, Sweden
| | - Eric A Miska
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, CB10 1SA, UK.,Wellcome Cancer Research UK Gurdon Institute, University of Cambridge, Tennis Court Road, Cambridge, CB2 1QN, UK.,Department of Genetics, University of Cambridge, Downing Street, Cambridge, CB2 3EH, UK
| | - Chun Kit Kwok
- Department of Chemistry and State Key Laboratory of Marine Pollution, City University of Hong Kong, Kowloon Tong, Hong Kong SAR, China.,Shenzhen Research Institute of City University of Hong Kong, Shenzhen, China
| | - Martin Hemberg
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, CB10 1SA, UK. .,Wellcome Cancer Research UK Gurdon Institute, University of Cambridge, Tennis Court Road, Cambridge, CB2 1QN, UK. .,Evergrande Center for Immunologic Diseases, Harvard Medical School and Brigham and Women's Hospital, Boston, MA, 02115, USA.
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17
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Krajewski WA. Histone Modifications, Internucleosome Dynamics, and DNA Stresses: How They Cooperate to “Functionalize” Nucleosomes. Front Genet 2022; 13:873398. [PMID: 35571051 PMCID: PMC9096104 DOI: 10.3389/fgene.2022.873398] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2022] [Accepted: 03/28/2022] [Indexed: 12/25/2022] Open
Abstract
Tight packaging of DNA in chromatin severely constrains DNA accessibility and dynamics. In contrast, nucleosomes in active chromatin state are highly flexible, can exchange their histones, and are virtually “transparent” to RNA polymerases, which transcribe through gene bodies at rates comparable to that of naked DNA. Defining mechanisms that revert nucleosome repression, in addition to their value for basic science, is of key importance for the diagnosis and treatment of genetic diseases. Chromatin activity is largely regulated by histone posttranslational modifications, ranging from small chemical groups up to the yet understudied “bulky” ubiquitylation and sumoylation. However, it is to be revealed how histone marks are “translated” to permissive or repressive changes in nucleosomes: it is a general opinion that histone modifications act primarily as “signals” for recruiting the regulatory proteins or as a “neutralizer” of electrostatic shielding of histone tails. Here, we would like to discuss recent evidence suggesting that histone ubiquitylation, in a DNA stress–dependent manner, can directly regulate the dynamics of the nucleosome and their primary structure and can promote nucleosome decomposition to hexasome particles or additionally stabilize nucleosomes against unwrapping. In addition, nucleosome repression/ derepression studies are usually performed with single mononucleosomes as a model. We would like to review and discuss recent findings showing that internucleosomal interactions could strongly modulate the dynamics and rearrangements of nucleosomes. Our hypothesis is that bulky histone modifications, nucleosome inherent dynamics, internucleosome interactions, and DNA torsions could act in cooperation to orchestrate the formation of different dynamic states of arrayed nucleosomes and thus promote chromatin functionality and diversify epigenetic programming methods.
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18
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Shitikov EA, Bespiatykh DA, Bodoev IN, Zaychikova MV. [G-quadruplex structures in bacteria: functional properties and prospects for use as biotargets]. Biomed Khim 2022; 68:93-103. [PMID: 35485483 DOI: 10.18097/pbmc20226802093] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
G-quadruplexes (G4), non-canonical secondary DNA structures, are intensively investigated for a long time. In eukaryotic organisms they play an important role in the regulation of gene expression and DNA repair. G4 have also been found in the genomes of numerous bacteria and archaea, but their functional role has not yet been fully explored. Nevertheless, their participation in the formation of antigenic variability, pathogenicity, antibiotic resistance and survival in extreme conditions has been established. Currently, many tools have been developed to detect potential G4 sequences and confirm their formation ability. Since the controlled formation and resolution of the quadruplex are significant means for the regulation of genes critical for survival, a promising direction is the search for ligands - compounds that can have a stabilizing effect on the quadruplex structure and thereby alter gene expression. Currently, a number of ligands are already known, their use stops the growth of pathogenic microorganisms. G4 ligands are of interest as potential antibiotics, which are extremely relevant due to the wide spread of drug resistant pathogens.
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Affiliation(s)
- E A Shitikov
- Federal Research and Clinical Center of Physical-Chemical Medicine, Moscow, Russia
| | - D A Bespiatykh
- Federal Research and Clinical Center of Physical-Chemical Medicine, Moscow, Russia
| | - I N Bodoev
- Federal Research and Clinical Center of Physical-Chemical Medicine, Moscow, Russia
| | - M V Zaychikova
- Federal Research and Clinical Center of Physical-Chemical Medicine, Moscow, Russia
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19
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Rekvig OP. The Anti-DNA Antibodies: Their Specificities for Unique DNA Structures and Their Unresolved Clinical Impact-A System Criticism and a Hypothesis. Front Immunol 2022; 12:808008. [PMID: 35087528 PMCID: PMC8786728 DOI: 10.3389/fimmu.2021.808008] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2021] [Accepted: 12/14/2021] [Indexed: 12/12/2022] Open
Abstract
Systemic lupus erythematosus (SLE) is diagnosed and classified by criteria, or by experience, intuition and traditions, and not by scientifically well-defined etiology(ies) or pathogenicity(ies). One central criterion and diagnostic factor is founded on theoretical and analytical approaches based on our imperfect definition of the term “The anti-dsDNA antibody”. “The anti-dsDNA antibody” holds an archaic position in SLE as a unique classification criterium and pathogenic factor. In a wider sense, antibodies to unique transcriptionally active or silent DNA structures and chromatin components may have individual and profound nephritogenic impact although not considered yet – not in theoretical nor in descriptive or experimental contexts. This hypothesis is contemplated here. In this analysis, our state-of-the-art conception of these antibodies is probed and found too deficient with respect to their origin, structural DNA specificities and clinical/pathogenic impact. Discoveries of DNA structures and functions started with Miescher’s Nuclein (1871), via Chargaff, Franklin, Watson and Crick, and continues today. The discoveries have left us with a DNA helix that presents distinct structures expressing unique operations of DNA. All structures are proven immunogenic! Unique autoimmune antibodies are described against e.g. ssDNA, elongated B DNA, bent B DNA, Z DNA, cruciform DNA, or individual components of chromatin. In light of the massive scientific interest in anti-DNA antibodies over decades, it is an unexpected observation that the spectrum of DNA structures has been known for decades without being implemented in clinical immunology. This leads consequently to a critical analysis of historical and contemporary evidence-based data and of ignored and one-dimensional contexts and hypotheses: i.e. “one antibody - one disease”. In this study radical viewpoints on the impact of DNA and chromatin immunity/autoimmunity are considered and discussed in context of the pathogenesis of lupus nephritis.
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Affiliation(s)
- Ole Petter Rekvig
- Section of Autoimmunity, Fürst Medical Laboratory, Oslo, Norway.,Department of Medical Biology, Faculty of Health Sciences, UiT The Arctic University of Norway, Tromsø, Norway
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20
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Vanaja A, Yella VR. Delineation of the DNA Structural Features of Eukaryotic Core Promoter Classes. ACS Omega 2022; 7:5657-5669. [PMID: 35224327 PMCID: PMC8867553 DOI: 10.1021/acsomega.1c04603] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/23/2021] [Accepted: 01/27/2022] [Indexed: 05/02/2023]
Abstract
The eukaryotic transcription is orchestrated from a chunk of the DNA region stated as the core promoter. Multifarious and punctilious core promoter signals, viz., TATA-box, Inr, BREs, and Pause Button, are associated with a subset of genes and regulate their spatiotemporal expression. However, the core promoter architecture linked with these signals has not been investigated exhaustively for several species. In this study, we attempted to envisage the adaptive binding landscape of the transcription initiation machinery as a function of DNA structure. To this end, we deployed a set of k-mer based DNA structural estimates and regular expression models derived from experiments, molecular dynamic simulations, and theoretical frameworks, and high-throughout promoter data sets retrieved from the eukaryotic promoter database. We categorized protein-coding gene core promoters based on characteristic motifs at precise locations and analyzed the B-DNA structural properties and non-B-DNA structural motifs for 15 different eukaryotic genomes. We observed that Inr, BREd, and no-motif classes display common patterns of DNA sequence and structural environment. TATA-containing, BREu, and Pause Button classes show a deviant behavior with the TATA class displaying varied axial and twisting flexibility while BREu and Pause Button leaned toward G-quadruplex motif enrichment. Intriguingly, DNA meltability and shape signals are conserved irrespective of the presence or absence of distinct core promoter motifs in the majority of species. Altogether, here we delineated the conserved DNA structural signals associated with several promoter classes that may contribute to the chromatin configuration, orchestration of transcription machinery, and DNA duplex melting during the transcription process.
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Affiliation(s)
- Akkinepally Vanaja
- Department
of Biotechnology, Koneru Lakshmaiah Education
Foundation, Vaddeswaram, Guntur 522502, Andhra
Pradesh, India
- KL
College of Pharmacy, Koneru Lakshmaiah Education
Foundation, Vaddeswaram, Guntur 522502, Andhra
Pradesh, India
| | - Venkata Rajesh Yella
- Department
of Biotechnology, Koneru Lakshmaiah Education
Foundation, Vaddeswaram, Guntur 522502, Andhra
Pradesh, India
- . Tel: +91-863-2399999, Extn-1021. Website: https://www.kluniversity.in/bt/faculty-list.aspx
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21
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Illodo S, Pérez-González C, Barcia R, Rodríguez-Prieto F, Al-Soufi W, Novo M. Spectroscopic Characterization of Mitochondrial G-Quadruplexes. Int J Mol Sci 2022; 23:925. [PMID: 35055110 DOI: 10.3390/ijms23020925] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2021] [Revised: 01/07/2022] [Accepted: 01/12/2022] [Indexed: 02/01/2023] Open
Abstract
Guanine quadruplexes (G4s) are highly polymorphic four-stranded structures formed within guanine-rich DNA and RNA sequences that play a crucial role in biological processes. The recent discovery of the first G4 structures within mitochondrial DNA has led to a small revolution in the field. In particular, the G-rich conserved sequence block II (CSB II) can form different types of G4s that are thought to play a crucial role in replication. In this study, we decipher the most relevant G4 structures that can be formed within CSB II: RNA G4 at the RNA transcript, DNA G4 within the non-transcribed strand and DNA:RNA hybrid between the RNA transcript and the non-transcribed strand. We show that the more abundant, but unexplored, G6AG7 (37%) and G6AG8 (35%) sequences in CSB II yield more stable G4s than the less profuse G5AG7 sequence. Moreover, the existence of a guanine located 1 bp upstream promotes G4 formation. In all cases, parallel G4s are formed, but their topology changes from a less ordered to a highly ordered G4 when adding small amounts of potassium or sodium cations. Circular dichroism was used due to discriminate different conformations and topologies of nucleic acids and was complemented with gel electrophoresis and fluorescence spectroscopy studies.
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22
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Khan S, Singh A, Nain N, Gulati S, Kukreti S. Sequence-specific recognition of a coding segment of human DACH1 gene via short pyrimidine/purine oligonucleotides. RSC Adv 2021; 11:40011-40021. [PMID: 35494143 PMCID: PMC9044637 DOI: 10.1039/d1ra06604h] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2021] [Accepted: 12/03/2021] [Indexed: 12/18/2022] Open
Abstract
With growing in vivo evidence of the roles of triplexes in biological processes, oligonucleotide-directed targeting of double-helical DNA for selective modulation of gene functions has become imperative in their therapeutic aspects. This study comprises a comparative investigation of 17-mer Py- and Pu-TFO for the formation of an intermolecular triplex with a 27-bp genomic homopurine–homopyrimidine track present in the transcriptional element of the human DACH1 gene. The biochemical and biophysical studies have revealed that triplex formation takes place only with Py-TFO and not with its Pu-counterpart. Non-denaturating gel electrophoresis indicated the formation of an intermolecular triplex in Py-motif with an increasing amount of Py-TFO, whereas no such interaction was observed for the Pu-counterpart. UV-thermal melting (Tm), circular dichroism (CD) and thermal difference spectra (TDS) studies confirmed the pyrimidine motif triplex formation, which was observed to be significantly pH-dependent and stable at acidic pH (5.2) in the presence of 100 mM Na+ ions. Contrarily, Pu-TFO was not found to bind to the target predominantly, owing to its self-association properties. Further studies have revealed that the GA-rich Pu-TFO adopts a homoduplex structure leading to a limit in its availability for triplex formation. These results may add to our understanding of sequence-specific gene targeting and give insight into designing more specific TFOs depending on genomic targets. Schematic representation of the proposed model of intermolecular triplex and homoduplex of used DNA sequences.![]()
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Affiliation(s)
- Shoaib Khan
- Nucleic Acid Research Laboratory, Department of Chemistry, University of Delhi Delhi-110007 India
| | - Anju Singh
- Department of Chemistry, Ramjas College, University of Delhi Delhi-110007 India
| | - Nishu Nain
- Nucleic Acid Research Laboratory, Department of Chemistry, University of Delhi Delhi-110007 India
| | - Srishty Gulati
- Nucleic Acid Research Laboratory, Department of Chemistry, University of Delhi Delhi-110007 India
| | - Shrikant Kukreti
- Nucleic Acid Research Laboratory, Department of Chemistry, University of Delhi Delhi-110007 India
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23
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Grytsyk N, Cianfarani D, Crégut O, Richert L, Boudier C, Humbert N, Didier P, Mély Y, Léonard J. Kinetics of protein-assisted nucleic acid interconversion monitored by transient time resolved fluorescence in microfluidic droplets. Nucleic Acids Res 2021; 49:e111. [PMID: 34450653 PMCID: PMC8565319 DOI: 10.1093/nar/gkab687] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2021] [Revised: 06/29/2021] [Accepted: 08/24/2021] [Indexed: 11/25/2022] Open
Abstract
Interconversions between nucleic acid structures play an important role in transcriptional and translational regulation and also in repair and recombination. These interconversions are frequently promoted by nucleic acid chaperone proteins. To monitor their kinetics, Förster resonance energy transfer (FRET) is widely exploited using ensemble fluorescence intensity measurements in pre-steady-state stopped-flow experiments. Such experiments only provide a weighted average of the emission of all species in solution and consume large quantities of materials. Herein, we lift these limitations by combining time-resolved fluorescence (TRF) with droplet microfluidics (DmF). We validate the innovative TRF-DmF approach by investigating the well characterized annealing of the HIV-1 (+)/(–) Primer Binding Sequences (PBS) promoted by a HIV-1 nucleocapsid peptide. Upon rapid mixing of the FRET-labelled (–)PBS with its complementary (+)PBS sequence inside microdroplets, the TRF-DmF set-up enables resolving the time evolution of sub-populations of reacting species and reveals an early intermediate with a ∼50 ps donor fluorescence lifetime never identified so far. TRF-DmF also favorably compares with single molecule experiments, as it offers an accurate control of concentrations with no upper limit, no need to graft one partner on a surface and no photobleaching issues.
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Affiliation(s)
- Natalia Grytsyk
- Institut de Physique et Chimie des Matériaux de Strasbourg, Université de Strasbourg & CNRS, 67034 Strasbourg, France.,Laboratoire de Bioimagerie et Pathologies, UMR 7021 CNRS, Université de Strasbourg, Faculté de Pharmacie, 67401 Illkirch, France
| | - Damien Cianfarani
- Institut de Physique et Chimie des Matériaux de Strasbourg, Université de Strasbourg & CNRS, 67034 Strasbourg, France
| | - Olivier Crégut
- Institut de Physique et Chimie des Matériaux de Strasbourg, Université de Strasbourg & CNRS, 67034 Strasbourg, France
| | - Ludovic Richert
- Laboratoire de Bioimagerie et Pathologies, UMR 7021 CNRS, Université de Strasbourg, Faculté de Pharmacie, 67401 Illkirch, France
| | - Christian Boudier
- Laboratoire de Bioimagerie et Pathologies, UMR 7021 CNRS, Université de Strasbourg, Faculté de Pharmacie, 67401 Illkirch, France
| | - Nicolas Humbert
- Laboratoire de Bioimagerie et Pathologies, UMR 7021 CNRS, Université de Strasbourg, Faculté de Pharmacie, 67401 Illkirch, France
| | - Pascal Didier
- Laboratoire de Bioimagerie et Pathologies, UMR 7021 CNRS, Université de Strasbourg, Faculté de Pharmacie, 67401 Illkirch, France
| | - Yves Mély
- Laboratoire de Bioimagerie et Pathologies, UMR 7021 CNRS, Université de Strasbourg, Faculté de Pharmacie, 67401 Illkirch, France
| | - Jérémie Léonard
- Institut de Physique et Chimie des Matériaux de Strasbourg, Université de Strasbourg & CNRS, 67034 Strasbourg, France
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24
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Camarillo R, Jimeno S, Huertas P. The Effect of Atypical Nucleic Acids Structures in DNA Double Strand Break Repair: A Tale of R-loops and G-Quadruplexes. Front Genet 2021; 12:742434. [PMID: 34691154 PMCID: PMC8531813 DOI: 10.3389/fgene.2021.742434] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2021] [Accepted: 09/28/2021] [Indexed: 01/08/2023] Open
Abstract
The fine tuning of the DNA double strand break repair pathway choice relies on different regulatory layers that respond to environmental and local cues. Among them, the presence of non-canonical nucleic acids structures seems to create challenges for the repair of nearby DNA double strand breaks. In this review, we focus on the recently published effects of G-quadruplexes and R-loops on DNA end resection and homologous recombination. Finally, we hypothesized a connection between those two atypical DNA structures in inhibiting the DNA end resection step of HR.
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Affiliation(s)
- Rosa Camarillo
- Departamento de Genética, Universidad de Sevilla, Sevilla, Spain.,Centro Andaluz de Biología Molecular y Medicina Regenerativa-CABIMER, Universidad de Sevilla-CSIC-Universidad Pablo de Olavide, Sevilla, Spain
| | - Sonia Jimeno
- Departamento de Genética, Universidad de Sevilla, Sevilla, Spain.,Centro Andaluz de Biología Molecular y Medicina Regenerativa-CABIMER, Universidad de Sevilla-CSIC-Universidad Pablo de Olavide, Sevilla, Spain
| | - Pablo Huertas
- Departamento de Genética, Universidad de Sevilla, Sevilla, Spain.,Centro Andaluz de Biología Molecular y Medicina Regenerativa-CABIMER, Universidad de Sevilla-CSIC-Universidad Pablo de Olavide, Sevilla, Spain
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25
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Figueiredo J, Santos T, Miranda A, Alexandre D, Teixeira B, Simões P, Lopes-Nunes J, Cruz C. Ligands as Stabilizers of G-Quadruplexes in Non-Coding RNAs. Molecules 2021; 26:6164. [PMID: 34684745 DOI: 10.3390/molecules26206164] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2021] [Revised: 10/03/2021] [Accepted: 10/06/2021] [Indexed: 11/16/2022] Open
Abstract
The non-coding RNAs (ncRNA) are RNA transcripts with different sizes, structures and biological functions that do not encode functional proteins. RNA G-quadruplexes (rG4s) have been found in small and long ncRNAs. The existence of an equilibrium between rG4 and stem-loop structures in ncRNAs and its effect on biological processes remains unexplored. For example, deviation from the stem-loop leads to deregulated mature miRNA levels, demonstrating that miRNA biogenesis can be modulated by ions or small molecules. In light of this, we report several examples of rG4s in certain types of ncRNAs, and the implications of G4 stabilization using small molecules, also known as G4 ligands, in the regulation of gene expression, miRNA biogenesis, and miRNA-mRNA interactions. Until now, different G4 ligands scaffolds were synthesized for these targets. The regulatory role of the above-mentioned rG4s in ncRNAs can be used as novel therapeutic approaches for adjusting miRNA levels.
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26
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Bandyopadhyay D, Mishra PP. Decoding the Structural Dynamics and Conformational Alternations of DNA Secondary Structures by Single-Molecule FRET Microspectroscopy. Front Mol Biosci 2021; 8:725541. [PMID: 34540899 PMCID: PMC8446445 DOI: 10.3389/fmolb.2021.725541] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2021] [Accepted: 07/30/2021] [Indexed: 12/02/2022] Open
Abstract
In addition to the canonical double helix form, DNA is known to be extrapolated into several other secondary structural patterns involving themselves in inter- and intramolecular type hydrogen bonding. The secondary structures of nucleic acids go through several stages of multiple, complex, and interconvertible heterogeneous conformations. The journey of DNA through these conformers has significant importance and has been monitored thoroughly to establish qualitative and quantitative information about the transition between the unfolded, folded, misfolded, and partially folded states. During this structural interconversion, there always exist specific populations of intermediates, which are short-lived or sometimes even do not accumulate within a heterogeneous population and are challenging to characterize using conventional ensemble techniques. The single-molecule FRET(sm-FRET) microspectroscopic method has the advantages to overcome these limitations and monitors biological phenomena transpiring at a measurable high rate and balanced stochastically over time. Thus, tracing the time trajectory of a particular molecule enables direct measurement of the rate constant of each transition step, including the intermediates that are hidden in the ensemble level due to their low concentrations. This review is focused on the advantages of the employment of single-molecule Forster's resonance energy transfer (sm-FRET), which is worthwhile to access the dynamic architecture and structural transition of various secondary structures that DNA adopts, without letting the donor of one molecule to cross-talk with the acceptor of any other. We have emphasized the studies performed to explore the states of folding and unfolding of several nucleic acid secondary structures, for example, the DNA hairpin, Holliday junction, G-quadruplex, and i-motif.
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Affiliation(s)
- Debolina Bandyopadhyay
- Single-Molecule Biophysics Lab, Chemical Sciences Division, Saha Institute of Nuclear Physics, Kolkata, India
- HBNI, Mumbai, India
| | - Padmaja P. Mishra
- Single-Molecule Biophysics Lab, Chemical Sciences Division, Saha Institute of Nuclear Physics, Kolkata, India
- HBNI, Mumbai, India
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Seidu YS, Roy HA, Rodgers MT. Influence of 5-Methylation and the 2'- and 3'-Hydroxy Substituents on the Base Pairing Energies of Protonated Cytidine Nucleoside Analogue Base Pairs: Implications for the Stabilities of i-Motif Structures. J Phys Chem A 2021; 125:5939-5955. [PMID: 34228469 DOI: 10.1021/acs.jpca.1c04303] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Abstract
Repetitive nucleic acid sequences, which occur in abundance throughout the mammalian genome, are of enormous research interest due to their potential to adopt fascinating and unusual molecular structures such as the i-motif. In remarkable contrast to the DNA double helix, i-motif conformations are stabilized by protonated cytosine base pairs, (Cyt)H+(Cyt), that are centrally located in the core of the i-motif and intercalated vertically in an antiparallel fashion. An in-depth understanding of how modifications influence the stability of i-motif conformations is a prerequisite to understanding their biological functions and the development of effective means of tuning their stability for specific medical and technological applications. Here, the influence of the 2'- and 3'-hydroxy substituents of the sugar moieties and 5-methylation of the cytosine nucleobases on the base-pairing interactions of protonated cytidine nucleoside analogue base pairs, (xCyd)H+(xCyd), are examined by complementary threshold collision-induced dissociation techniques and computational methods. The xCyd nucleosides examined include the canonical DNA and RNA cytidine nucleosides, 2'-deoxycytidine (dCyd) and cytidine (Cyd), as well as several modified cytidine nucleoside analogues, 2',3'-dideoxycytidine (ddCyd), 5-methyl-2'-deoxycytidine (m5dCyd), and 5-methylcytidine (m5Cyd). Comparisons among these model base pairs indicate that the 2'- and 3'-hydroxy substituents of the sugar moieties have very little influence on the strength of the base-pairing interactions, whereas 5-methylation of the cytosine nucleobases is found to enhance the strength of the base-pairing interactions. The increase in stability resulting from 5-methylation is only modest but is more than twice as large for the DNA than RNA protonated cytidine base pair. Overall, present results suggest that canonical DNA i-motif conformations should be more stable than analogous RNA i-motif conformations and that 5-methylation of cytosine residues, a significant epigenetic marker, provides greater stabilization to DNA than RNA i-motif conformations.
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Affiliation(s)
- Yakubu S Seidu
- Department of Chemistry, Wayne State University, Detroit, Michigan 48202, United States
| | - H A Roy
- Department of Chemistry, Wayne State University, Detroit, Michigan 48202, United States
| | - M T Rodgers
- Department of Chemistry, Wayne State University, Detroit, Michigan 48202, United States
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Bush J, Hu C, Veneziano R. Mechanical Properties of DNA Hydrogels: Towards Highly Programmable Biomaterials. Applied Sciences 2021; 11:1885. [DOI: 10.3390/app11041885] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
DNA hydrogels are self-assembled biomaterials that rely on Watson–Crick base pairing to form large-scale programmable three-dimensional networks of nanostructured DNA components. The unique mechanical and biochemical properties of DNA, along with its biocompatibility, make it a suitable material for the assembly of hydrogels with controllable mechanical properties and composition that could be used in several biomedical applications, including the design of novel multifunctional biomaterials. Numerous studies that have recently emerged, demonstrate the assembly of functional DNA hydrogels that are responsive to stimuli such as pH, light, temperature, biomolecules, and programmable strand-displacement reaction cascades. Recent studies have investigated the role of different factors such as linker flexibility, functionality, and chemical crosslinking on the macroscale mechanical properties of DNA hydrogels. In this review, we present the existing data and methods regarding the mechanical design of pure DNA hydrogels and hybrid DNA hydrogels, and their use as hydrogels for cell culture. The aim of this review is to facilitate further study and development of DNA hydrogels towards utilizing their full potential as multifeatured and highly programmable biomaterials with controlled mechanical properties.
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Fik-Jaskółka MA, Pospieszna-Markiewicz I, Roviello GN, Kubicki M, Radecka-Paryzek W, Patroniak V. Synthesis and Spectroscopic Investigation of a Hexaaza Lanthanum(III) Macrocycle with a Hybrid-Type G4 DNA Stabilizing Effect. Inorg Chem 2021; 60:2122-2126. [PMID: 33528248 PMCID: PMC7888264 DOI: 10.1021/acs.inorgchem.0c03260] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Herein we present a mononuclear lanthanum(III) complex obtained in a template cyclocondensation reaction of lanthanum(III) nitrate salt, 1,2-propanediamine, and 2,6-diacetylpyridine (LaPA complex). A preliminary investigation of the biological potential of this compound was conducted using a biomedically relevant target Tel26. We found that, different from parallel G4, antiparallel G4, and duplex DNA, only a hybrid-type G4 structure of Tel26 in a K+ solution was significantly stabilized by ≥7 °C, which emerged in our UV melting studies. Moreover, LaPA induced structural changes in the Tel26 structure in a K+-deprived solution, suggesting that it may also lead to conformational changes in "non-G4" telomeric DNA.
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Affiliation(s)
- Marta A Fik-Jaskółka
- Faculty of Chemistry, Adam Mickiewicz University in Poznań, Uniwersytetu Poznańskiego 8, 61-614 Poznań, Poland.,Centre for Advanced Technology, Adam Mickiewicz University in Poznań, Uniwersytetu Poznańskiego 10, 61-614 Poznań, Poland
| | | | - Giovanni N Roviello
- Institute of Biostructures and Bioimaging, National Research Council, Mezzocannone 16, 80134 Napoli, Italy
| | - Maciej Kubicki
- Faculty of Chemistry, Adam Mickiewicz University in Poznań, Uniwersytetu Poznańskiego 8, 61-614 Poznań, Poland
| | - Wanda Radecka-Paryzek
- Faculty of Chemistry, Adam Mickiewicz University in Poznań, Uniwersytetu Poznańskiego 8, 61-614 Poznań, Poland
| | - Violetta Patroniak
- Faculty of Chemistry, Adam Mickiewicz University in Poznań, Uniwersytetu Poznańskiego 8, 61-614 Poznań, Poland
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Brown SL, Kendrick S. The i-Motif as a Molecular Target: More Than a Complementary DNA Secondary Structure. Pharmaceuticals (Basel) 2021; 14:ph14020096. [PMID: 33513764 PMCID: PMC7911047 DOI: 10.3390/ph14020096] [Citation(s) in RCA: 40] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2020] [Revised: 01/20/2021] [Accepted: 01/22/2021] [Indexed: 12/25/2022] Open
Abstract
Stretches of cytosine-rich DNA are capable of adopting a dynamic secondary structure, the i-motif. When within promoter regions, the i-motif has the potential to act as a molecular switch for controlling gene expression. However, i-motif structures in genomic areas of repetitive nucleotide sequences may play a role in facilitating or hindering expansion of these DNA elements. Despite research on the i-motif trailing behind the complementary G-quadruplex structure, recent discoveries including the identification of a specific i-motif antibody are pushing this field forward. This perspective reviews initial and current work characterizing the i-motif and providing insight into the biological function of this DNA structure, with a focus on how the i-motif can serve as a molecular target for developing new therapeutic approaches to modulate gene expression and extension of repetitive DNA.
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Bartas M, Červeň J, Guziurová S, Slychko K, Pečinka P. Amino Acid Composition in Various Types of Nucleic Acid-Binding Proteins. Int J Mol Sci 2021; 22:ijms22020922. [PMID: 33477647 PMCID: PMC7831508 DOI: 10.3390/ijms22020922] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2020] [Revised: 01/15/2021] [Accepted: 01/16/2021] [Indexed: 12/20/2022] Open
Abstract
Nucleic acid-binding proteins are traditionally divided into two categories: With the ability to bind DNA or RNA. In the light of new knowledge, such categorizing should be overcome because a large proportion of proteins can bind both DNA and RNA. Another even more important features of nucleic acid-binding proteins are so-called sequence or structure specificities. Proteins able to bind nucleic acids in a sequence-specific manner usually contain one or more of the well-defined structural motifs (zinc-fingers, leucine zipper, helix-turn-helix, or helix-loop-helix). In contrast, many proteins do not recognize nucleic acid sequence but rather local DNA or RNA structures (G-quadruplexes, i-motifs, triplexes, cruciforms, left-handed DNA/RNA form, and others). Finally, there are also proteins recognizing both sequence and local structural properties of nucleic acids (e.g., famous tumor suppressor p53). In this mini-review, we aim to summarize current knowledge about the amino acid composition of various types of nucleic acid-binding proteins with a special focus on significant enrichment and/or depletion in each category.
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Santos IC, Brodbelt JS. Recent developments in the characterization of nucleic acids by liquid chromatography, capillary electrophoresis, ion mobility, and mass spectrometry (2010-2020). J Sep Sci 2021; 44:340-372. [PMID: 32974962 PMCID: PMC8378248 DOI: 10.1002/jssc.202000833] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2020] [Revised: 09/18/2020] [Accepted: 09/21/2020] [Indexed: 12/25/2022]
Abstract
The development of new strategies for the analysis of nucleic acids has gained momentum due to the increased interest in using these biomolecules as drugs or drug targets. The application of new mass spectrometry ion activation techniques and the optimization of separation methods including liquid chromatography, capillary electrophoresis, and ion mobility have allowed more detailed characterization of nucleic acids and oligonucleotide therapeutics including confirmation of sequence, localization of modifications and interaction sites, and structural analysis as well as identification of failed sequences and degradation products. This review will cover tandem mass spectrometry methods as well as the recent developments in liquid chromatography, capillary electrophoresis, and ion mobility coupled to mass spectrometry for the analysis of nucleic acids and oligonucleotides.
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Affiliation(s)
- Inês C Santos
- Department of Chemistry, University of Texas at Austin, Austin, Texas, USA
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Kolenko P, Svoboda J, Černý J, Charnavets T, Schneider B. Structural variability of CG-rich DNA 18-mers accommodating double T-T mismatches. Acta Crystallogr D Struct Biol 2020; 76:1233-1243. [PMID: 33263329 PMCID: PMC7709200 DOI: 10.1107/s2059798320014151] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2020] [Accepted: 10/23/2020] [Indexed: 11/26/2022] Open
Abstract
Solution and crystal data are reported for DNA 18-mers with sequences related to those of bacterial noncoding single-stranded DNA segments called repetitive extragenic palindromes (REPs). Solution CD and melting data showed that the CG-rich, near-palindromic REPs from various bacterial species exhibit dynamic temperature-dependent and concentration-dependent equilibria, including architectures compatible with not only hairpins, which are expected to be biologically relevant, but also antiparallel duplexes and bimolecular tetraplexes. Three 18-mer oligonucleotides named Hpar-18 (PDB entry 6rou), Chom-18 (PDB entry 6ros) and its brominated variant Chom-18Br (PDB entry 6ror) crystallized as isomorphic right-handed A-like duplexes. The low-resolution crystal structures were solved with the help of experimental phases for Chom-18Br. The center of the duplexes is formed by two successive T-T noncanonical base pairs (mismatches). They do not deform the double-helical geometry. The presence of T-T mismatches prompted an analysis of the geometries of these and other noncanonical pairs in other DNA crystals in terms of their fit to the experimental electron densities (RSCC) and their geometric fit to the NtC (dinucleotide conformational) classes (https://dnatco.datmos.org/). Throughout this work, knowledge of the NtC classes was used to refine and validate the crystal structures, and to analyze the mismatches.
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Affiliation(s)
- Petr Kolenko
- Faculty of Nuclear Sciences and Physical Engineering, Czech Technical University in Prague, Brehova 7, 11519 Prague 1, Czech Republic
- Institute of Biotechnology of the Czech Academy of Sciences, BIOCEV, Prumyslova 595, 252 50 Vestec, Czech Republic
| | - Jakub Svoboda
- Institute of Biotechnology of the Czech Academy of Sciences, BIOCEV, Prumyslova 595, 252 50 Vestec, Czech Republic
| | - Jiří Černý
- Institute of Biotechnology of the Czech Academy of Sciences, BIOCEV, Prumyslova 595, 252 50 Vestec, Czech Republic
| | - Tatsiana Charnavets
- Institute of Biotechnology of the Czech Academy of Sciences, BIOCEV, Prumyslova 595, 252 50 Vestec, Czech Republic
| | - Bohdan Schneider
- Institute of Biotechnology of the Czech Academy of Sciences, BIOCEV, Prumyslova 595, 252 50 Vestec, Czech Republic
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Lenarčič Živković M, Rozman J, Plavec J. Structure of a DNA G-Quadruplex Related to Osteoporosis with a G-A Bulge Forming a Pseudo-loop. Molecules 2020; 25:E4867. [PMID: 33096904 PMCID: PMC7588008 DOI: 10.3390/molecules25204867] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2020] [Revised: 10/19/2020] [Accepted: 10/19/2020] [Indexed: 11/30/2022] Open
Abstract
Bone remodeling is a fine-tuned process principally regulated by a cascade triggered by interaction of receptor activator of NF-κB (RANK) and RANK ligand (RANKL). Excessive activity of the RANKL gene leads to increased bone resorption and can influence the incidence of osteoporosis. Although much has been learned about the intracellular signals activated by RANKL/RANK complex, significantly less is known about the molecular mechanisms of regulation of RANKL expression. Here, we report on the structure of an unprecedented DNA G-quadruplex, well-known secondary structure-mediated gene expression regulator, formed by a G-rich sequence found in the regulatory region of a RANKL gene. Solution-state NMR structural study reveals the formation of a three-layered parallel-type G-quadruplex characterized by an unique features, including a G-A bulge. Although a guanine within a G-tract occupies syn glycosidic conformation, bulge-forming residues arrange in a pseudo-loop conformation to facilitate partial 5/6-ring stacking, typical of G-quadruplex structures with parallel G-tracts orientation. Such distinctive structural features protruding from the core of the structure can represent a novel platform for design of highly specific ligands with anti-osteoporotic function. Additionally, our study suggests that the expression of RANKL gene may be regulated by putative folding of its G-rich region into non-B-DNA structure(s).
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Affiliation(s)
- Martina Lenarčič Živković
- Slovenian NMR Centre, National Institute of Chemistry, Hajdrihova 19, 1000 Ljubljana, Slovenia;
- Central European Institute of Technology, Masaryk University, Kamenice 753/5, 62500 Brno, Czech Republic
| | - Jan Rozman
- Slovenian NMR Centre, National Institute of Chemistry, Hajdrihova 19, 1000 Ljubljana, Slovenia;
| | - Janez Plavec
- Slovenian NMR Centre, National Institute of Chemistry, Hajdrihova 19, 1000 Ljubljana, Slovenia;
- EN-FIST Centre of Excellence, Trg OF 13, 1000 Ljubljana, Slovenia
- Faculty of Chemistry and Chemical Technology, University of Ljubljana, Večna pot 113, 1000 Ljubljana, Slovenia
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Gorb L, Pekh A, Nyporko A, Ilchenko M, Golius A, Zubatiuk T, Zubatyuk R, Dubey I, Hovorun DM, Leszczynski J. Effect of Microenvironment on the Geometrical Structure of d(A)5 d(T)5 and d(G)5 d(C)5 DNA Mini-Helixes and the Dickerson Dodecamer: A Density Functional Theory Study. J Phys Chem B 2020; 124:9343-9353. [DOI: 10.1021/acs.jpcb.0c06154] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Affiliation(s)
- Leonid Gorb
- Department of Molecular and Quantum Biophysics, Institute of Molecular Biology and Genetics, National Academy of Sciences of Ukraine, 150 Vul. Zabolotnogo, Kyiv 03143, Ukraine
- Interdisciplinary Center for Nanotoxicity, Department of Chemistry, Physics and Atmospheric Sciences, Jackson State University, P.O. Box 17910, 1325 Lynch Street, Jackson, Mississippi 39217, United States
| | - Anatolii Pekh
- Department of Molecular Biotechnology and Bioinformatics, Institute of High Technologies, Taras Shevchenko National University of Kyiv, Kyiv 03022, Ukraine
| | - Alexey Nyporko
- Department of Molecular Biotechnology and Bioinformatics, Institute of High Technologies, Taras Shevchenko National University of Kyiv, Kyiv 03022, Ukraine
| | - Mykola Ilchenko
- Department of Synthetic Bioregulators, Institute of Molecular Biology and Genetics, National Academy of Sciences of Ukraine, 150 Vul. Zabolotnogo, Kyiv 03143, Ukraine
| | - Anastasiia Golius
- Interdisciplinary Center for Nanotoxicity, Department of Chemistry, Physics and Atmospheric Sciences, Jackson State University, P.O. Box 17910, 1325 Lynch Street, Jackson, Mississippi 39217, United States
| | - Tetiana Zubatiuk
- Interdisciplinary Center for Nanotoxicity, Department of Chemistry, Physics and Atmospheric Sciences, Jackson State University, P.O. Box 17910, 1325 Lynch Street, Jackson, Mississippi 39217, United States
| | - Roman Zubatyuk
- Interdisciplinary Center for Nanotoxicity, Department of Chemistry, Physics and Atmospheric Sciences, Jackson State University, P.O. Box 17910, 1325 Lynch Street, Jackson, Mississippi 39217, United States
| | - Igor Dubey
- Department of Synthetic Bioregulators, Institute of Molecular Biology and Genetics, National Academy of Sciences of Ukraine, 150 Vul. Zabolotnogo, Kyiv 03143, Ukraine
| | - Dmytro M. Hovorun
- Department of Molecular and Quantum Biophysics, Institute of Molecular Biology and Genetics, National Academy of Sciences of Ukraine, 150 Vul. Zabolotnogo, Kyiv 03143, Ukraine
| | - Jerzy Leszczynski
- Interdisciplinary Center for Nanotoxicity, Department of Chemistry, Physics and Atmospheric Sciences, Jackson State University, P.O. Box 17910, 1325 Lynch Street, Jackson, Mississippi 39217, United States
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Bua G, Tedesco D, Conti I, Reggiani A, Bartolini M, Gallinella G. No G-Quadruplex Structures in the DNA of Parvovirus B19: Experimental Evidence versus Bioinformatic Predictions. Viruses 2020; 12:v12090935. [PMID: 32854437 PMCID: PMC7552014 DOI: 10.3390/v12090935] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2020] [Revised: 08/20/2020] [Accepted: 08/21/2020] [Indexed: 12/11/2022] Open
Abstract
Parvovirus B19 (B19V), an ssDNA virus in the family Parvoviridae, is a human pathogenic virus, responsible for a wide range of clinical manifestations, still in need of effective and specific antivirals. DNA structures, including G-quadruplex (G4), have been recognised as relevant functional features in viral genomes, and small-molecule ligands binding to these structures are promising antiviral compounds. Bioinformatic tools predict the presence of potential G4 forming sequences (PQSs) in the genome of B19V, raising interest as targets for antiviral strategies. Predictions locate PQSs in the genomic terminal regions, in proximity to replicative origins. The actual propensity of these PQSs to form G4 structures was investigated by circular dichroism spectroscopic analysis on synthetic oligonucleotides of corresponding sequences. No signature of G4 structures was detected, and the interaction with the G4 ligand BRACO-19 (N,N'-(9-{[4-(dimethylamino)phenyl]amino}acridine-3,6-diyl)bis(3-pyrrolidin-1-ylpropanamide) did not appear consistent with the stabilisation of G4 structures. Any potential role of PQSs in the viral lifecycle was then assessed in an in vitro infection model system, by evaluating any variation in replication or expression of B19V in the presence of the G4 ligands BRACO-19 and pyridostatin. Neither showed a significant inhibitory activity on B19V replication or expression. Experimental challenge did not support bioinformatic predictions. The terminal regions of B19V are characterised by relevant sequence and symmetry constraints, which are functional to viral replication. Our experiments suggest that these impose a stringent requirement prevailing over the propensity of forming actual G4 structures.
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Abstract
BACKGROUND Fusion transcripts are involved in tumourigenesis and play a crucial role in tumour heterogeneity, tumour evolution and cancer treatment resistance. However, fusion transcripts have not been studied at high spatial resolution in tissue sections due to the lack of full-length transcripts with spatial information. New high-throughput technologies like spatial transcriptomics measure the transcriptome of tissue sections on almost single-cell level. While this technique does not allow for direct detection of fusion transcripts, we show that they can be inferred using the relative poly(A) tail abundance of the involved parental genes. METHOD We present a new method STfusion, which uses spatial transcriptomics to infer the presence and absence of poly(A) tails. A fusion transcript lacks a poly(A) tail for the 5' gene and has an elevated number of poly(A) tails for the 3' gene. Its expression level is defined by the upstream promoter of the 5' gene. STfusion measures the difference between the observed and expected number of poly(A) tails with a novel C-score. RESULTS We verified the STfusion ability to predict fusion transcripts on HeLa cells with known fusions. STfusion and C-score applied to clinical prostate cancer data revealed the spatial distribution of the cis-SAGe SLC45A3-ELK4 in 12 tissue sections with almost single-cell resolution. The cis-SAGe occurred in disease areas, e.g. inflamed, prostatic intraepithelial neoplastic, or cancerous areas, and occasionally in normal glands. CONCLUSIONS STfusion detects fusion transcripts in cancer cell line and clinical tissue data, and distinguishes chimeric transcripts from chimeras caused by trans-splicing events. With STfusion and the use of C-scores, fusion transcripts can be spatially localised in clinical tissue sections on almost single cell level.
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Affiliation(s)
- Stefanie Friedrich
- Science for Life Laboratory, Department of Biochemistry and Biophysics, Stockholm University, Box 1031, 17121, Solna, Sweden.
| | - Erik L L Sonnhammer
- Science for Life Laboratory, Department of Biochemistry and Biophysics, Stockholm University, Box 1031, 17121, Solna, Sweden
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Yakimova LS, Nugmanova AR, Mostovaya OA, Vavilova AA, Shurpik DN, Mukhametzyanov TA, Stoikov II. Nanostructured Polyelectrolyte Complexes Based on Water-Soluble Thiacalix[4]Arene and Pillar[5]Arene: Self-Assembly in Micelleplexes and Polyplexes at Packaging DNA. Nanomaterials (Basel) 2020; 10:E777. [PMID: 32316551 DOI: 10.3390/nano10040777] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/24/2020] [Revised: 04/14/2020] [Accepted: 04/15/2020] [Indexed: 01/27/2023]
Abstract
Controlling the self-assembly of polyfunctional compounds in interpolyelectrolyte aggregates is an extremely challenging task. The use of macrocyclic compounds offers new opportunities in design of a new generation of mixed nanoparticles. This approach allows creating aggregates with multivalent molecular recognition, improved binding efficiency and selectivity. In this paper, we reported a straightforward approach to the synthesis of interpolyelectrolytes by co-assembling of the thiacalix[4]arene with four negatively charged functional groups on the one side of macrocycle, and pillar[5]arene with 10 ammonium groups located on both sides. Nanostructured polyelectrolyte complexes show effective packaging of high-molecular DNA from calf thymus. The interaction of co-interpolyelectrolytes with the DNA is completely different from the interaction of the pillar[5]arene with the DNA. Two different complexes with DNA, i.e., micelleplex- and polyplex-type, were formed. The DNA in both cases preserved its secondary structure in native B form without distorting helicity. The presented approach provides important advantage for the design of effective biomolecular gene delivery systems.
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Didier P, Kuchlyan J, Martinez-Fernandez L, Gosset P, Léonard J, Tor Y, Improta R, Mély Y. Deciphering the pH-dependence of ground- and excited-state equilibria of thienoguanine. Phys Chem Chem Phys 2020; 22:7381-7391. [PMID: 32211689 DOI: 10.1039/c9cp06931c] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
The thienoguanine nucleobase (thGb) is an isomorphic fluorescent analogue of guanine. In aqueous buffer at neutral pH, thGb exists as a mixture of two ground-state H1 and H3 keto-amino tautomers with distinct absorption and emission spectra and high quantum yield. In this work, we performed the first systematic photophysical characterization of thGb as a function of pH (2 to 12). Steady-state and time-resolved fluorescence spectroscopies, supplemented with theoretical calculations, enabled us to identify three additional thGb forms, resulting from pH-dependent ground-state and excited-state reactions. Moreover, a thorough analysis allowed us to retrieve their individual absorption and emission spectra as well as the equilibrium constants which govern their interconversion. From these data, the complete photoluminescence pathway of thGb in aqueous solution and its dependence as a function of pH was deduced. As the identified forms differ by their spectra and fluorescence lifetime, thGb could be used as a probe for sensing local pH changes under acidic conditions.
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Affiliation(s)
- Pascal Didier
- Laboratoire de Bioimagerie et Pathologies, UMR 7021 CNRS Université de Strasbourg, Faculté de Pharmacie, 74 route du Rhin, 67401 Illkirch, France.
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40
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Michel BY, Dziuba D, Benhida R, Demchenko AP, Burger A. Probing of Nucleic Acid Structures, Dynamics, and Interactions With Environment-Sensitive Fluorescent Labels. Front Chem 2020; 8:112. [PMID: 32181238 PMCID: PMC7059644 DOI: 10.3389/fchem.2020.00112] [Citation(s) in RCA: 49] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2019] [Accepted: 02/06/2020] [Indexed: 12/13/2022] Open
Abstract
Fluorescence labeling and probing are fundamental techniques for nucleic acid analysis and quantification. However, new fluorescent probes and approaches are urgently needed in order to accurately determine structural and conformational dynamics of DNA and RNA at the level of single nucleobases/base pairs, and to probe the interactions between nucleic acids with proteins. This review describes the means by which to achieve these goals using nucleobase replacement or modification with advanced fluorescent dyes that respond by the changing of their fluorescence parameters to their local environment (altered polarity, hydration, flipping dynamics, and formation/breaking of hydrogen bonds).
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Affiliation(s)
- Benoît Y. Michel
- Université Côte d'Azur, CNRS, Institut de Chimie de Nice, UMR 7272 – Parc Valrose, Nice, France
| | - Dmytro Dziuba
- Université Côte d'Azur, CNRS, Institut de Chimie de Nice, UMR 7272 – Parc Valrose, Nice, France
- Laboratoire de Bioimagerie et Pathologies, UMR 7021 CNRS, Faculté de Pharmacie, Université de Strasbourg, Illkirch, France
| | - Rachid Benhida
- Université Côte d'Azur, CNRS, Institut de Chimie de Nice, UMR 7272 – Parc Valrose, Nice, France
- Mohamed VI Polytechnic University, UM6P, Ben Guerir, Morocco
| | - Alexander P. Demchenko
- Laboratory of Nanobiotechnologies, Palladin Institute of Biochemistry, Kyiv, Ukraine
- Institute of Physical, Technical and Computer Science, Yuriy Fedkovych National University, Chernivtsi, Ukraine
| | - Alain Burger
- Université Côte d'Azur, CNRS, Institut de Chimie de Nice, UMR 7272 – Parc Valrose, Nice, France
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41
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Kaushik S, Kaushik M, Barthwal R, Kukreti S. Self-association of Coralyne: An ordered thermal destacking. Results in Chemistry 2020. [DOI: 10.1016/j.rechem.2020.100043] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022] Open
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42
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Goodman LD, Bonini NM. New Roles for Canonical Transcription Factors in Repeat Expansion Diseases. Trends Genet 2019; 36:81-92. [PMID: 31837826 DOI: 10.1016/j.tig.2019.11.003] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2019] [Revised: 11/05/2019] [Accepted: 11/08/2019] [Indexed: 12/11/2022]
Abstract
The presence of microsatellite repeat expansions within genes is associated with >30 neurological diseases. Of interest, (GGGGCC)>30-repeats within C9orf72 are associated with amyotrophic lateral sclerosis and frontotemporal dementia (ALS/FTD). These expansions can be 100s to 1000s of units long. Thus, it is perplexing how RNA-polymerase II (RNAPII) can successfully transcribe them. Recent investigations focusing on GGGGCC-transcription have identified specific, canonical complexes that may promote RNAPII-transcription at these GC-rich microsatellites: the DSIF complex and PAF1C. These complexes may be important for resolving the unique secondary structures formed by GGGGCC-DNA during transcription. Importantly, this process can produce potentially toxic repeat-containing RNA that can encode potentially toxic peptides, impacting neuron function and health. Understanding how transcription of these repeats occurs has implications for therapeutics in multiple diseases.
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Affiliation(s)
- Lindsey D Goodman
- Department of Molecular and Human Genetics, Neurological Research Institute, Baylor College of Medicine, Houston, TX 77030, USA
| | - Nancy M Bonini
- Department of Biology, University of Pennsylvania, Philadelphia, PA 19104, USA.
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43
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Krajewski WA. "Direct" and "Indirect" Effects of Histone Modifications: Modulation of Sterical Bulk as a Novel Source of Functionality. Bioessays 2019; 42:e1900136. [PMID: 31805213 DOI: 10.1002/bies.201900136] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2019] [Revised: 10/17/2019] [Indexed: 12/26/2022]
Abstract
The chromatin-regulatory principles of histone post-translational modifications (PTMs) are discussed with a focus on the potential alterations in chromatin functional state due to steric and mechanical constraints imposed by bulky histone modifications such as ubiquitin and SUMO. In the classical view, PTMs operate as recruitment platforms for histone "readers," and as determinants of chromatin array compaction. Alterations of histone charges by "small" chemical modifications (e.g., acetylation, phosphorylation) could regulate nucleosome spontaneous dynamics without globally affecting nucleosome structure. These fluctuations in nucleosome wrapping can be exploited by chromatin-processing machinery. In contrast, ubiquitin and SUMO are comparable in size to histones, and it seems logical that these PTMs could conflict with canonical nucleosome organization. An experimentally testable hypothesis that by adding sterical bulk these PTMs can robustly alter nucleosome primary structure is proposed. The model presented here stresses the diversity of mechanisms by which histone PTMs regulate chromatin dynamics, primary structure and, hence, functionality.
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Affiliation(s)
- Wladyslaw A Krajewski
- N. K. Koltsov Institute of Developmental Biology of Russian Academy of Sciences, Vavilova str. 26, Moscow, 119334, Russia
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44
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Del Mundo IMA, Vasquez KM, Wang G. Modulation of DNA structure formation using small molecules. Biochim Biophys Acta Mol Cell Res 2019; 1866:118539. [PMID: 31491448 DOI: 10.1016/j.bbamcr.2019.118539] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/08/2019] [Revised: 08/20/2019] [Accepted: 08/24/2019] [Indexed: 02/06/2023]
Abstract
Genome integrity is essential for proper cell function such that genetic instability can result in cellular dysfunction and disease. Mutations in the human genome are not random, and occur more frequently at "hotspot" regions that often co-localize with sequences that have the capacity to adopt alternative (i.e. non-B) DNA structures. Non-B DNA-forming sequences are mutagenic, can stimulate the formation of DNA double-strand breaks, and are highly enriched at mutation hotspots in human cancer genomes. Thus, small molecules that can modulate the conformations of these structure-forming sequences may prove beneficial in the prevention and/or treatment of genetic diseases. Further, the development of molecular probes to interrogate the roles of non-B DNA structures in modulating DNA function, such as genetic instability in cancer etiology are warranted. Here, we discuss reported non-B DNA stabilizers, destabilizers, and probes, recent assays to identify ligands, and the potential biological applications of these DNA structure-modulating molecules.
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Affiliation(s)
- Imee M A Del Mundo
- Division of Pharmacology and Toxicology, College of Pharmacy, The University of Texas at Austin, Dell Pediatric Research Institute, 1400 Barbara Jordan Blvd., Austin, TX 78723, USA
| | - Karen M Vasquez
- Division of Pharmacology and Toxicology, College of Pharmacy, The University of Texas at Austin, Dell Pediatric Research Institute, 1400 Barbara Jordan Blvd., Austin, TX 78723, USA.
| | - Guliang Wang
- Division of Pharmacology and Toxicology, College of Pharmacy, The University of Texas at Austin, Dell Pediatric Research Institute, 1400 Barbara Jordan Blvd., Austin, TX 78723, USA
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45
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Singh A, Kukreti R, Saso L, Kukreti S. Oxidative Stress: Role and Response of Short Guanine Tracts at Genomic Locations. Int J Mol Sci 2019; 20:E4258. [PMID: 31480304 DOI: 10.3390/ijms20174258] [Citation(s) in RCA: 35] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2019] [Revised: 07/20/2019] [Accepted: 07/26/2019] [Indexed: 12/21/2022] Open
Abstract
Over the decades, oxidative stress has emerged as a major concern to biological researchers. It is involved in the pathogenesis of various lifestyle-related diseases such as hypertension, diabetes, atherosclerosis, and neurodegenerative diseases. The connection between oxidative stress and telomere shortening via oxidative guanine lesion is well documented. Telomeres are confined to guanine rich ends of chromosomes. Owing to its self-association properties, it adopts G-quadruplex structures and hampers the overexpression of telomerase in the cancer cells. Guanine, being the most oxidation prone nucleobase, when structured in G-quadruplex entity, is found to respond peculiarly towards oxidative stress. Interestingly, this non-Watson-Crick structural feature exists abundantly in promoters of various oncogenes, exons and other genomic locations. The involvement of G-quadruplex architecture in oncogene promoters is well recognized in gene regulation processes. Development of small molecules aimed to target G-quadruplex structures, have found to alter the overexpression of oncogenes. The interaction may lead to the obstruction of diseased cell having elevated level of reactive oxygen species (ROS). Thus, presence of short guanine tracts (Gn) forming G-quadruplexes suggests its critical role in oxidative genome damage. Present review is a modest attempt to gain insight on the association of oxidative stress and G-quadruplexes, in various biological processes.
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Satange R, Chang CK, Hou MH. A survey of recent unusual high-resolution DNA structures provoked by mismatches, repeats and ligand binding. Nucleic Acids Res 2019; 46:6416-6434. [PMID: 29945186 PMCID: PMC6061790 DOI: 10.1093/nar/gky561] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2018] [Accepted: 06/08/2018] [Indexed: 12/20/2022] Open
Abstract
The structure of the DNA duplex is arguably one of the most important biological structures elucidated in modern history. DNA duplex structure is closely associated with essential biological functions such as DNA replication and RNA transcription. In addition to the classical A-, B- and Z-DNA conformations, DNA duplexes are capable of assuming a variety of alternative conformations depending on the sequence and environmental context. A considerable number of these unusual DNA duplex structures have been identified in the past decade, and some of them have been found to be closely associated with different biological functions and pathological conditions. In this manuscript, we review a selection of unusual DNA duplex structures, particularly those originating from base pair mismatch, repetitive sequence motifs and ligand-induced structures. Although the biological significance of these novel structures has not yet been established in most cases, the illustrated conformational versatility of DNA could have relevance for pharmaceutical or nanotechnology development. A perspective on the future directions of this field is also presented.
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Affiliation(s)
- Roshan Satange
- Institute of Genomics and Bioinformatics, National Chung Hsing University, Taichung, Taiwan.,Ph.D. Program in Medical Biotechnology, National Chung Hsing University, Taichung, Taiwan
| | - Chung-Ke Chang
- Institute of Biomedical Sciences, Academia Sinica, Taipei, Taiwan
| | - Ming-Hon Hou
- Institute of Genomics and Bioinformatics, National Chung Hsing University, Taichung, Taiwan.,Ph.D. Program in Medical Biotechnology, National Chung Hsing University, Taichung, Taiwan
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Porter JE, Chapagain P, Fernandez-Lima F. Single-stranded DNA structural diversity: TAGGGT from monomers to dimers to tetramer formation. Rapid Commun Mass Spectrom 2019; 33 Suppl 2:60-65. [PMID: 30506977 DOI: 10.1002/rcm.8367] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/06/2018] [Revised: 11/27/2018] [Accepted: 11/27/2018] [Indexed: 06/09/2023]
Abstract
RATIONALE DNA quadruplex structures have emerged as novel drug targets due to their role in preventing abnormal gene transcription and maintaining telomere stability. Trapped Ion Mobility Spectrometry-Mass Spectrometry (TIMS-MS), combined with theoretical modeling, is a powerful tool for studying the kinetic intermediates of DNA complexes formed in solution and interrogated in the gas phase after desolvation. METHODS A TAGGGT ssDNA sequence was purchased and studied in 10 mM ammonium acetate using nanospray electrospray ionization (nESI)-TIMS-MS in positive and negative ion mode. Collisional cross section (CCS) profiles were measured using internal calibration (Tune Mix). Theoretical structures were proposed based on molecular dynamics, charge location and geometry optimization for the most intense IMS bands based on the number of TAGGGT units, adduct form and charge states. RESULTS A distribution of monomeric, dimeric and tetrameric TAGGGT structures were formed in solution and separated in the gas phase based on their mobility and m/z value (e.g., [M + 2H]+2 , [2M + 3H]+3 , [M - 2H]-2 , [2M - 3H]-3 , [4M + 4H]+4 , [4M + 3H + NH4 ]+4 , [4M + 2H + 2NH4 ]+4 and [4M + H + 3NH4 ]+4 ). The high mobility resolution of the TIMS-MS analyzer permitted the observation of multiple CCS bands per molecular ion form. Comparison with theoretical candidate structures suggests that monomeric TAGGGT species are stabilized by A-T and G+ -G interactions, with the size of the conformer influenced by the proton location. In the case of the TAGGGT quadruplex, the protonated species displayed a broad CCS distribution, while six discrete conformers were stabilized by the presence of ammonium ions (n = 1-3). CONCLUSIONS This is the first observation of multiple conformations of TAGGGT complexes (n = 1, 2 and 4) in 10 mM ammonium acetate. Candidate structures with intramolecular interactions of the form of G+ -G and traditional A-T base pairing agreed with the experimental trends. Our results demonstrate the structural diversity of TAGGGT monomers, dimers and tetramers in the gas phase beyond the previously reported solution structure, using 10 mM ammonium acetate to replicate biological conditions.
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Affiliation(s)
- Jacob E Porter
- Department of Chemistry & Biochemistry, Florida International University, Miami, FL, USA
| | - Prem Chapagain
- Department of Physics, Florida International University, Miami, FL, USA
- Biomolecular Sciences Institute, Florida International University, Miami, FL, USA
| | - Francisco Fernandez-Lima
- Department of Chemistry & Biochemistry, Florida International University, Miami, FL, USA
- Biomolecular Sciences Institute, Florida International University, Miami, FL, USA
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48
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Affiliation(s)
- Pei Guo
- Department of Chemistry, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong
| | - Sik Lok Lam
- Department of Chemistry, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong
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49
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Martinez-Fernandez L, Gavvala K, Sharma R, Didier P, Richert L, Segarra Martì J, Mori M, Mely Y, Improta R. Excited-State Dynamics of Thienoguanosine, an Isomorphic Highly Fluorescent Analogue of Guanosine. Chemistry 2019; 25:7375-7386. [PMID: 30882930 DOI: 10.1002/chem.201900677] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2019] [Revised: 03/15/2019] [Indexed: 12/27/2022]
Abstract
Thienoguanosine (th G) is an isomorphic analogue of guanosine with promising potentialities as fluorescent DNA label. As a free probe in protic solvents, th G exists in two tautomeric forms, identified as the H1, being the only one observed in nonprotic solvents, and H3 keto-amino tautomers. We herein investigate the photophysics of th G in solvents of different polarity, from water to dioxane, by combining time-resolved fluorescence with PCM/TD-DFT and CASSCF calculations. Fluorescence lifetimes of 14.5-20.5 and 7-13 ns were observed for the H1 and H3 tautomers, respectively, in the tested solvents. In methanol and ethanol, an additional fluorescent decay lifetime (≈3 ns) at the blue emission side (λ≈430 nm) as well as a 0.5 ns component with negative amplitude at the red edge of the spectrum, typical of an excited-state reaction, were observed. Our computational analysis explains the solvent effects observed on the tautomeric equilibrium. The main radiative and nonradiative deactivation routes have been mapped by PCM/TD-DFT calculations in solution and CASSCF in the gas phase. The most easily accessible conical intersection, involving an out-of plane motion of the sulfur atom in the five-membered ring of th G, is separated by a sizeable energy barrier (≥0.4 eV) from the minimum of the spectroscopic state, which explains the large experimental fluorescence quantum yield.
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Affiliation(s)
- Lara Martinez-Fernandez
- Departamento de Química, Facultad de Ciencias, Modúlo13, Universidad Autónoma de Madrid, Campus de Excelencia UAM-CSIC, Cantoblanco, 28049 Madrid, Spain
| | - Krishna Gavvala
- Laboratoire de Bioimagerie et Pathologies, UMR 7021 CNRS, Université de Strasbourg, Faculté de pharmacie, 74 route du Rhin, 67401, Illkirch, France
| | - Rajhans Sharma
- Laboratoire de Bioimagerie et Pathologies, UMR 7021 CNRS, Université de Strasbourg, Faculté de pharmacie, 74 route du Rhin, 67401, Illkirch, France
| | - Pascal Didier
- Laboratoire de Bioimagerie et Pathologies, UMR 7021 CNRS, Université de Strasbourg, Faculté de pharmacie, 74 route du Rhin, 67401, Illkirch, France
| | - Ludovic Richert
- Laboratoire de Bioimagerie et Pathologies, UMR 7021 CNRS, Université de Strasbourg, Faculté de pharmacie, 74 route du Rhin, 67401, Illkirch, France
| | - Javier Segarra Martì
- Department of Chemistry, Molecular Sciences Research Hub, Imperial College London, White City Campus, 80 Wood Lane, W12 0BZ, London, UK
| | - Mattia Mori
- Dipartimento di Biotecnologie, Chimica e Farmacia, Università degli Studi di Siena, 53100, Siena, Italy
| | - Yves Mely
- Laboratoire de Bioimagerie et Pathologies, UMR 7021 CNRS, Université de Strasbourg, Faculté de pharmacie, 74 route du Rhin, 67401, Illkirch, France
| | - Roberto Improta
- Consiglio Nazionale delle Ricerche, Istituto Biostrutture e Bioimmagini, Via Mezzocannone 16, 80134, Napoli, Italy
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50
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Cristofari C, Rigo R, Greco ML, Ghezzo M, Sissi C. pH-driven conformational switch between non-canonical DNA structures in a C-rich domain of EGFR promoter. Sci Rep 2019; 9:1210. [PMID: 30718769 DOI: 10.1038/s41598-018-37968-8] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2018] [Accepted: 12/17/2018] [Indexed: 01/10/2023] Open
Abstract
EGFR is an oncogene that encodes for a trans-membrane tyrosine kinase receptor. Its mis-regulation is associated to several human cancers that, consistently, can be treated by selective tyrosine kinase inhibitors. The proximal promoter of EGFR contains a G-rich domain located at 272 bases upstream the transcription start site. We previously proved it folds into two main interchanging G-quadruplex structures, one of parallel and one of hybrid topology. Here we present the first evidences supporting the ability of the complementary C-rich strand (EGFR-272_C) to assume an intramolecular i-Motif (iM) structure that, according to the experimental conditions (pH, presence of co-solvent and salts), can coexist with a different arrangement we referred to as a hairpin. The herein identified iM efficiently competes with the canonical pairing of the two complementary strands, indicating it as a potential novel target for anticancer therapies. A preliminary screening for potential binders identified some phenanthroline derivatives as able to target EGFR-272_C at multiple binding sites when it is folded into an iM.
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