1
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Lin SM, Huang HT, Fang PJ, Chang CF, Satange R, Chang CK, Chou SH, Neidle S, Hou MH. Structural basis of water-mediated cis Watson-Crick/Hoogsteen base-pair formation in non-CpG methylation. Nucleic Acids Res 2024:gkae594. [PMID: 38989613 DOI: 10.1093/nar/gkae594] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2024] [Revised: 05/30/2024] [Accepted: 06/28/2024] [Indexed: 07/12/2024] Open
Abstract
Non-CpG methylation is associated with several cellular processes, especially neuronal development and cancer, while its effect on DNA structure remains unclear. We have determined the crystal structures of DNA duplexes containing -CGCCG- regions as CCG repeat motifs that comprise a non-CpG site with or without cytosine methylation. Crystal structure analyses have revealed that the mC:G base-pair can simultaneously form two alternative conformations arising from non-CpG methylation, including a unique water-mediated cis Watson-Crick/Hoogsteen, (w)cWH, and Watson-Crick (WC) geometries, with partial occupancies of 0.1 and 0.9, respectively. NMR studies showed that an alternative conformation of methylated mC:G base-pair at non-CpG step exhibits characteristics of cWH with a syn-guanosine conformation in solution. DNA duplexes complexed with the DNA binding drug echinomycin result in increased occupancy of the (w)cWH geometry in the methylated base-pair (from 0.1 to 0.3). Our structural results demonstrated that cytosine methylation at a non-CpG step leads to an anti→syntransition of its complementary guanosine residue toward the (w)cWH geometry as a partial population of WC, in both drug-bound and naked mC:G base pairs. This particular geometry is specific to non-CpG methylated dinucleotide sites in B-form DNA. Overall, the current study provides new insights into DNA conformation during epigenetic regulation.
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Affiliation(s)
- Shan-Meng Lin
- Graduate Institute of Genomics and Bioinformatics, National Chung Hsing University, Taichung 402, Taiwan
| | - Hsiang-Ti Huang
- Graduate Institute of Genomics and Bioinformatics, National Chung Hsing University, Taichung 402, Taiwan
| | - Pei-Ju Fang
- Genomics Research Center, Academia Sinica, Taipei 115, Taiwan
| | - Chi-Fon Chang
- Genomics Research Center, Academia Sinica, Taipei 115, Taiwan
| | - Roshan Satange
- Graduate Institute of Genomics and Bioinformatics, National Chung Hsing University, Taichung 402, Taiwan
| | - Chung-Ke Chang
- Taiwan Biobank, Institute of Biomedical Sciences, Academia Sinica, Taipei 115, Taiwan
| | - Shan-Ho Chou
- Institute of Biochemistry, National Chung Hsing University, Taichung 402, Taiwan
| | - Stephen Neidle
- School of Pharmacy, University College London, London WC1N 1AX, UK
| | - Ming-Hon Hou
- Graduate Institute of Genomics and Bioinformatics, National Chung Hsing University, Taichung 402, Taiwan
- Doctoral Program in Medical Biotechnology, National Chung Hsing University, Taichung 402, Taiwan
- Graduate Institute of Biotechnology, National Chung Hsing University, Taichung 402, Taiwan
- Department of Life Sciences, National Chung Hsing University, Taichung 402, Taiwan
- Biotechnology Center, National Chung Hsing University, Taichung 402, Taiwan
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2
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Gorb L, Voiteshenko I, Hurmach V, Zarudnaya M, Nyporko A, Shyryna T, Platonov M, Roszak S, Rasulev B. From RNA sequence to its three-dimensional structure: geometrical structure, stability and dynamics of selected fragments of SARS-CoV-2 RNA. NAR Genom Bioinform 2024; 6:lqae062. [PMID: 38835951 PMCID: PMC11148665 DOI: 10.1093/nargab/lqae062] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2023] [Revised: 04/26/2024] [Accepted: 05/16/2024] [Indexed: 06/06/2024] Open
Abstract
In this computational study, we explore the folding of a particular sequence using various computational tools to produce two-dimensional structures, which are then transformed into three-dimensional structures. We then study the geometry, energetics and dynamics of these structures using full electron quantum-chemical and classical molecular dynamics calculations. Our study focuses on the SARS-CoV-2 RNA fragment GGaGGaGGuguugcaGG and its various structures, including a G-quadruplex and five different hairpins. We examine the impact of two types of counterions (K+ and Na+) and flanking nucleotides on their geometrical characteristics, relative stability and dynamic properties. Our results show that the G-quadruplex structure is the most stable among the constructed hairpins. We confirm its topological stability through molecular dynamics simulations. Furthermore, we observe that the nucleotide loop consisting of seven nucleotides is the most flexible part of the RNA fragment. Additionally, we find that RNA networks of intermolecular hydrogen bonds are highly sensitive to the surrounding environment. Our findings reveal the loss of 79 old hydrogen bonds and the formation of 91 new ones in the case when the G-quadruplex containing flanking nucleotides is additionally stabilized by Na+ counterions.
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Affiliation(s)
- Leonid Gorb
- Department of Molecular and Quantum Biophysics, Institute of Molecular Biology and Genetics, National Academy of Sciences of Ukraine, 150, Akademika Zabolotnoho Str., Kyiv 03143, Ukraine
| | - Ivan Voiteshenko
- Department of Molecular and Quantum Biophysics, Institute of Molecular Biology and Genetics, National Academy of Sciences of Ukraine, 150, Akademika Zabolotnoho Str., Kyiv 03143, Ukraine
- Taras Shevchenko National University of Kyiv, 60 Volodymyrska Street, Kyiv01033, Ukraine
| | - Vasyl Hurmach
- Department of Molecular and Quantum Biophysics, Institute of Molecular Biology and Genetics, National Academy of Sciences of Ukraine, 150, Akademika Zabolotnoho Str., Kyiv 03143, Ukraine
| | - Margarita Zarudnaya
- Department of Molecular and Quantum Biophysics, Institute of Molecular Biology and Genetics, National Academy of Sciences of Ukraine, 150, Akademika Zabolotnoho Str., Kyiv 03143, Ukraine
| | - Alex Nyporko
- Taras Shevchenko National University of Kyiv, 60 Volodymyrska Street, Kyiv01033, Ukraine
| | - Tetiana Shyryna
- Department of Molecular and Quantum Biophysics, Institute of Molecular Biology and Genetics, National Academy of Sciences of Ukraine, 150, Akademika Zabolotnoho Str., Kyiv 03143, Ukraine
| | - Maksym Platonov
- Department of Molecular and Quantum Biophysics, Institute of Molecular Biology and Genetics, National Academy of Sciences of Ukraine, 150, Akademika Zabolotnoho Str., Kyiv 03143, Ukraine
| | - Szczepan Roszak
- Faculty of Chemistry, University of Wrocław, 50-370Wrocław, Poland
| | - Bakhtiyor Rasulev
- Department of Coatings and Polymer Materials, North Dakota State University, NDSU Department 2760, PO Box 6050, Fargo, ND 58108, USA
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3
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Qiu Z, Huang R, Wu Y, Li X, Sun C, Ma Y. Decoding the Structural Diversity: A New Horizon in Antimicrobial Prospecting and Mechanistic Investigation. Microb Drug Resist 2024; 30:254-272. [PMID: 38648550 DOI: 10.1089/mdr.2023.0232] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/25/2024] Open
Abstract
The escalating crisis of antimicrobial resistance (AMR) underscores the urgent need for novel antimicrobials. One promising strategy is the exploration of structural diversity, as diverse structures can lead to diverse biological activities and mechanisms of action. This review delves into the role of structural diversity in antimicrobial discovery, highlighting its influence on factors such as target selectivity, binding affinity, pharmacokinetic properties, and the ability to overcome resistance mechanisms. We discuss various approaches for exploring structural diversity, including combinatorial chemistry, diversity-oriented synthesis, and natural product screening, and provide an overview of the common mechanisms of action of antimicrobials. We also describe techniques for investigating these mechanisms, such as genomics, proteomics, and structural biology. Despite significant progress, several challenges remain, including the synthesis of diverse compound libraries, the identification of active compounds, the elucidation of complex mechanisms of action, the emergence of AMR, and the translation of laboratory discoveries to clinical applications. However, emerging trends and technologies, such as artificial intelligence, high-throughput screening, next-generation sequencing, and open-source drug discovery, offer new avenues to overcome these challenges. Looking ahead, we envisage an exciting future for structural diversity-oriented antimicrobial discovery, with opportunities for expanding the chemical space, harnessing the power of nature, deepening our understanding of mechanisms of action, and moving toward personalized medicine and collaborative drug discovery. As we face the continued challenge of AMR, the exploration of structural diversity will be crucial in our search for new and effective antimicrobials.
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Affiliation(s)
- Ziying Qiu
- School of Pharmacy, Binzhou Medical University, Yantai, China
| | - Rongkun Huang
- School of Pharmacy, Binzhou Medical University, Yantai, China
| | - Yuxuan Wu
- School of Pharmacy, Binzhou Medical University, Yantai, China
| | - Xinghao Li
- School of Pharmacy, Binzhou Medical University, Yantai, China
| | - Chunyu Sun
- School of Pharmacy, Binzhou Medical University, Yantai, China
| | - Yunqi Ma
- School of Pharmacy, Binzhou Medical University, Yantai, China
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4
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Gagna CE, Yodice AN, D'Amico J, Elkoulily L, Gill SM, DeOcampo FG, Rabbani M, Kaur J, Shah A, Ahmad Z, Lambert MW, Clark Lambert W. Novel B-DNA dermatophyte assay for demonstration of canonical DNA in dermatophytes: Histopathologic characterization by artificial intelligence. Clin Dermatol 2024; 42:233-258. [PMID: 38185195 DOI: 10.1016/j.clindermatol.2023.12.018] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2024]
Abstract
We describe a novel assay and artificial intelligence-driven histopathologic approach identifying dermatophytes in human skin tissue sections (ie, B-DNA dermatophyte assay) and demonstrate, for the first time, the presence of dermatophytes in tissue using immunohistochemistry to detect canonical right-handed double-stranded (ds) B-DNA. Immunohistochemistry was performed using anti-ds-B-DNA monoclonal antibodies with formalin-fixed paraffin-embedded tissues to determine the presence of dermatophytes. The B-DNA assay resulted in a more accurate identification of dermatophytes, nuclear morphology, dimensions, and gene expression of dermatophytes (ie, optical density values) than periodic acid-Schiff (PAS), Grocott methenamine silver (GMS), or hematoxylin and eosin (H&E) stains. The novel assay guided by artificial intelligence allowed for efficient identification of different types of dermatophytes (eg, hyphae, microconidia, macroconidia, and arthroconidia). Using the B-DNA dermatophyte assay as a clinical tool for diagnosing dermatophytes is an alternative to PAS, GMS, and H&E as a fast and inexpensive way to accurately detect dermatophytosis and reduce the number of false negatives. Our assay resulted in superior identification, sensitivity, life cycle stages, and morphology compared to H&E, PAS, and GMS stains. This method detects a specific structural marker (ie, ds-B-DNA), which can assist with diagnosis of dermatophytes. It represents a significant advantage over methods currently in use.
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Affiliation(s)
- Claude E Gagna
- Department of Biological and Chemical Sciences, College of Arts and Sciences, New York Institute of Technology, Old Westbury, New York, USA; Department of Pathology and Laboratory Medicine, Rutgers-New Jersey Medical School, Newark, New Jersey, USA; Department of Dermatology, Rutgers-New Jersey Medical School, Newark, New Jersey, USA; Department of Medicine, Rutgers-New Jersey Medical School, Newark, New Jersey, USA.
| | - Anthony N Yodice
- Department of Biological and Chemical Sciences, College of Arts and Sciences, New York Institute of Technology, Old Westbury, New York, USA
| | - Juliana D'Amico
- Department of Biological and Chemical Sciences, College of Arts and Sciences, New York Institute of Technology, Old Westbury, New York, USA
| | - Lina Elkoulily
- Department of Biological and Chemical Sciences, College of Arts and Sciences, New York Institute of Technology, Old Westbury, New York, USA
| | - Shaheryar M Gill
- Department of Biological and Chemical Sciences, College of Arts and Sciences, New York Institute of Technology, Old Westbury, New York, USA
| | - Francis G DeOcampo
- Department of Biological and Chemical Sciences, College of Arts and Sciences, New York Institute of Technology, Old Westbury, New York, USA
| | - Maryam Rabbani
- Department of Biological and Chemical Sciences, College of Arts and Sciences, New York Institute of Technology, Old Westbury, New York, USA
| | - Jai Kaur
- Department of Biological and Chemical Sciences, College of Arts and Sciences, New York Institute of Technology, Old Westbury, New York, USA
| | - Aangi Shah
- Department of Biological and Chemical Sciences, College of Arts and Sciences, New York Institute of Technology, Old Westbury, New York, USA
| | - Zainab Ahmad
- Department of Biological and Chemical Sciences, College of Arts and Sciences, New York Institute of Technology, Old Westbury, New York, USA
| | - Muriel W Lambert
- Department of Pathology and Laboratory Medicine, Rutgers-New Jersey Medical School, Newark, New Jersey, USA; Department of Dermatology, Rutgers-New Jersey Medical School, Newark, New Jersey, USA
| | - W Clark Lambert
- Department of Pathology and Laboratory Medicine, Rutgers-New Jersey Medical School, Newark, New Jersey, USA; Department of Dermatology, Rutgers-New Jersey Medical School, Newark, New Jersey, USA; Department of Medicine, Rutgers-New Jersey Medical School, Newark, New Jersey, USA
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5
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Chen E, Trajkovski M, Lee H, Nyovanie S, Martin K, Dean W, Tahiliani M, Plavec J, Yatsunyk L. Structure of native four-repeat satellite III sequence with non-canonical base interactions. Nucleic Acids Res 2024; 52:3390-3405. [PMID: 38381082 PMCID: PMC11014236 DOI: 10.1093/nar/gkae113] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2023] [Revised: 01/31/2024] [Accepted: 02/06/2024] [Indexed: 02/22/2024] Open
Abstract
Tandem-repetitive DNA (where two or more DNA bases are repeated numerous times) can adopt non-canonical secondary structures. Many of these structures are implicated in important biological processes. Human Satellite III (HSat3) is enriched for tandem repeats of the sequence ATGGA and is located in pericentromeric heterochromatin in many human chromosomes. Here, we investigate the secondary structure of the four-repeat HSat3 sequence 5'-ATGGA ATGGA ATGGA ATGGA-3' using X-ray crystallography, NMR, and biophysical methods. Circular dichroism spectroscopy, thermal stability, native PAGE, and analytical ultracentrifugation indicate that this sequence folds into a monomolecular hairpin with non-canonical base pairing and B-DNA characteristics at concentrations below 0.9 mM. NMR studies at 0.05-0.5 mM indicate that the hairpin is likely folded-over into a compact structure with high dynamics. Crystallographic studies at 2.5 mM reveal an antiparallel self-complementary duplex with the same base pairing as in the hairpin, extended into an infinite polymer. The non-canonical base pairing includes a G-G intercalation sandwiched by sheared A-G base pairs, leading to a cross-strand four guanine stack, so called guanine zipper. The guanine zippers are spaced throughout the structure by A-T/T-A base pairs. Our findings lend further insight into recurring structural motifs associated with the HSat3 and their potential biological functions.
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Affiliation(s)
- Erin Chen
- Department of Chemistry and Biochemistry, Swarthmore College, 500 College Ave, Swarthmore, PA 19081, USA
| | - Marko Trajkovski
- Slovenian NMR Centre, National Institute of Chemistry, Hajdrihova 19, 1000 Ljubljana, Slovenia
| | - Hyun Kyung Lee
- Department of Chemistry and Biochemistry, Swarthmore College, 500 College Ave, Swarthmore, PA 19081, USA
| | - Samantha Nyovanie
- Department of Chemistry and Biochemistry, Swarthmore College, 500 College Ave, Swarthmore, PA 19081, USA
| | - Kailey N Martin
- Department of Chemistry and Biochemistry, Swarthmore College, 500 College Ave, Swarthmore, PA 19081, USA
| | - William L Dean
- Structural Biology Program JG Brown Cancer Center, University of Louisville, Louisville, KY 40202, USA
| | - Mamta Tahiliani
- Department of Biology, New York University, New York, NY 10003, USA
| | - Janez Plavec
- Slovenian NMR Centre, National Institute of Chemistry, Hajdrihova 19, 1000 Ljubljana, Slovenia
| | - Liliya A Yatsunyk
- Department of Chemistry and Biochemistry, Swarthmore College, 500 College Ave, Swarthmore, PA 19081, USA
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6
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Manikandan M, Nicolini P, Hapala P. Computational Design of Photosensitive Polymer Templates To Drive Molecular Nanofabrication. ACS NANO 2024; 18:9969-9979. [PMID: 38545921 PMCID: PMC11008366 DOI: 10.1021/acsnano.3c10575] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/27/2023] [Revised: 03/15/2024] [Accepted: 03/21/2024] [Indexed: 04/10/2024]
Abstract
Molecular electronics promises the ultimate level of miniaturization of computers and other machines as organic molecules are the smallest known physical objects with nontrivial structure and function. But despite the plethora of molecular switches, memories, and motors developed during the almost 50-years long history of molecular electronics, mass production of molecular computers is still an elusive goal. This is mostly due to the lack of scalable nanofabrication methods capable of rapidly producing complex structures (similar to silicon chips or living cells) with atomic precision and a small number of defects. Living nature solves this problem by using linear polymer templates encoding large volumes of structural information into sequence of hydrogen bonded end groups which can be efficiently replicated and which can drive assembly of other molecular components into complex supramolecular structures. In this paper, we propose a nanofabrication method based on a class of photosensitive polymers inspired by these natural principles, which can operate in concert with UV photolithography used for fabrication of current microelectronic processors. We believe that such a method will enable a smooth transition from silicon toward molecular nanoelectronics and photonics. To demonstrate its feasibility, we performed a computational screening of candidate molecules that can selectively bind and therefore allow the deterministic assembly of molecular components. In the process, we unearthed trends and design principles applicable beyond the immediate scope of our proposed nanofabrication method, e.g., to biologically relevant DNA analogues and molecular recognition within hydrogen-bonded systems.
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Affiliation(s)
- Mithun Manikandan
- Institute of Physics (FZU), Czech
Academy of Sciences, Na Slovance 2, 182 00 Prague, Czech Republic
| | - Paolo Nicolini
- Institute of Physics (FZU), Czech
Academy of Sciences, Na Slovance 2, 182 00 Prague, Czech Republic
| | - Prokop Hapala
- Institute of Physics (FZU), Czech
Academy of Sciences, Na Slovance 2, 182 00 Prague, Czech Republic
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7
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Trizna L, Olajoš J, Víglaský V. DNA minicircles capable of forming a variety of non-canonical structural motifs. Front Chem 2024; 12:1384201. [PMID: 38595699 PMCID: PMC11002140 DOI: 10.3389/fchem.2024.1384201] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2024] [Accepted: 03/12/2024] [Indexed: 04/11/2024] Open
Abstract
Although more than 10% of the human genome has the potential to fold into non-B DNA, the formation of non-canonical structural motifs as part of long dsDNA chains are usually considered as unfavorable from a thermodynamic point of view. However, recent experiments have confirmed that non-canonical motifs do exist and are non-randomly distributed in genomic DNA. This distribution is highly dependent not only on the DNA sequence but also on various other factors such as environmental conditions, DNA topology and the expression of specific cellular factors in different cell types. In this study, we describe a new strategy used in the preparation of DNA minicircles containing different non-canonical motifs which arise as a result of imperfect base pairing between complementary strands. The approach exploits the fact that imperfections in the pairing of complementary strands thermodynamically weaken the dsDNA structure at the expense of enhancing the formation of non-canonical motifs. In this study, a completely different concept of stable integration of a non-canonical motif into dsDNA is presented. Our approach allows the integration of various types of non-canonical motifs into the dsDNA structure such as hairpin, cruciform, G-quadruplex and i-motif forms but also combinations of these forms. Small DNA minicircles have recently become the subject of considerable interest in both fundamental research and in terms of their potential therapeutic applications.
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Affiliation(s)
| | | | - Viktor Víglaský
- Department of Biochemistry, Institute of Chemistry, Faculty of Sciences, P. J. Šafárik University, Košice, Slovakia
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8
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Palma E, Santos JF, Fernandes C, Paulo A. DNA-Targeted Complexes of Tc and Re for Biomedical Applications. Chemistry 2024; 30:e202303591. [PMID: 38038361 DOI: 10.1002/chem.202303591] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2023] [Revised: 11/30/2023] [Accepted: 12/01/2023] [Indexed: 12/02/2023]
Abstract
Due to their favorable chemical features, Re and Tc complexes have been widely used for the development of new therapeutic agents and imaging probes to solve problems of biomedical relevance. This review provides an update of the most relevant research efforts towards the development of novel cancer theranostic agents using Re and Tc-based compounds interacting with specific DNA structures. This includes a variety of homometallic complexes, namely those containing M(CO)3 (M=Re, Tc) moieties, that exhibit different modes of interaction with DNA, such as covalent binding, intercalation, groove binding or G-quadruplex DNA binding. Additionally, heterometallic complexes, designed to potentiate synergistic effects of different metal centers to improve DNA-targeting, cytotoxicity and fluorescence properties, are also reviewed. Particular attention is also given to 99m Tc- and 188 Re-labeled oligonucleotides that have been widely explored to develop imaging and therapeutic radiopharmaceuticals through the in vivo hybridization with a specific complementary DNA or RNA target sequence to provide useful molecular tools in precision medicine for cancer diagnosis and treatment. Finally, the need for further improvement of DNA-targeted Re and Tc-based compounds as potential therapeutic and diagnostic agents is highlighted, and future directions are discussed.
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Affiliation(s)
- Elisa Palma
- C2TN - Centro de Ciências e Tecnologias, Nucleares Instituto Superior Técnico, Universidade de Lisboa, Portugal
| | - Joana F Santos
- C2TN - Centro de Ciências e Tecnologias, Nucleares Instituto Superior Técnico, Universidade de Lisboa, Portugal
| | - Célia Fernandes
- C2TN - Centro de Ciências e Tecnologias, Nucleares Instituto Superior Técnico, Universidade de Lisboa, Portugal
- DECN - Departamento de Engenharia e Ciências Nucleares, Instituto Superior Técnico, Universidade de Lisboa, Portugal
| | - António Paulo
- C2TN - Centro de Ciências e Tecnologias, Nucleares Instituto Superior Técnico, Universidade de Lisboa, Portugal
- DECN - Departamento de Engenharia e Ciências Nucleares, Instituto Superior Técnico, Universidade de Lisboa, Portugal
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9
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Hardikar S, Ren R, Ying Z, Horton JR, Bramble MD, Liu B, Lu Y, Liu B, Dan J, Zhang X, Cheng X, Chen T. The ICF syndrome protein CDCA7 harbors a unique DNA-binding domain that recognizes a CpG dyad in the context of a non-B DNA. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.12.15.571946. [PMID: 38168392 PMCID: PMC10760177 DOI: 10.1101/2023.12.15.571946] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/05/2024]
Abstract
CDCA7 , encoding a protein with a C-terminal cysteine-rich domain (CRD), is mutated in immunodeficiency, centromeric instability and facial anomalies (ICF) syndrome, a disease related to hypomethylation of juxtacentromeric satellite DNA. How CDCA7 directs DNA methylation to juxtacentromeric regions is unknown. Here, we show that the CDCA7 CRD adopts a unique zinc-binding structure that recognizes a CpG dyad in a non-B DNA formed by two sequence motifs. CDCA7, but not ICF mutants, preferentially binds the non-B DNA with strand-specific CpG hemi-methylation. The unmethylated sequence motif is highly enriched at centromeres of human chromosomes, whereas the methylated motif is distributed throughout the genome. At S phase, CDCA7, but not ICF mutants, is concentrated in constitutive heterochromatin foci, and the formation of such foci can be inhibited by exogenous hemi-methylated non-B DNA bound by the CRD. Binding of the non-B DNA formed in juxtacentromeric regions during DNA replication provides a mechanism by which CDCA7 controls the specificity of DNA methylation.
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10
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Duardo RC, Guerra F, Pepe S, Capranico G. Non-B DNA structures as a booster of genome instability. Biochimie 2023; 214:176-192. [PMID: 37429410 DOI: 10.1016/j.biochi.2023.07.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2023] [Revised: 07/04/2023] [Accepted: 07/06/2023] [Indexed: 07/12/2023]
Abstract
Non-canonical secondary structures (NCSs) are alternative nucleic acid structures that differ from the canonical B-DNA conformation. NCSs often occur in repetitive DNA sequences and can adopt different conformations depending on the sequence. The majority of these structures form in the context of physiological processes, such as transcription-associated R-loops, G4s, as well as hairpins and slipped-strand DNA, whose formation can be dependent on DNA replication. It is therefore not surprising that NCSs play important roles in the regulation of key biological processes. In the last years, increasing published data have supported their biological role thanks to genome-wide studies and the development of bioinformatic prediction tools. Data have also highlighted the pathological role of these secondary structures. Indeed, the alteration or stabilization of NCSs can cause the impairment of transcription and DNA replication, modification in chromatin structure and DNA damage. These events lead to a wide range of recombination events, deletions, mutations and chromosomal aberrations, well-known hallmarks of genome instability which are strongly associated with human diseases. In this review, we summarize molecular processes through which NCSs trigger genome instability, with a focus on G-quadruplex, i-motif, R-loop, Z-DNA, hairpin, cruciform and multi-stranded structures known as triplexes.
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Affiliation(s)
- Renée C Duardo
- Department of Pharmacy and Biotechnology, Alma Mater Studiorum University of Bologna, via Selmi 3, 40126, Bologna, Italy
| | - Federico Guerra
- Department of Pharmacy and Biotechnology, Alma Mater Studiorum University of Bologna, via Selmi 3, 40126, Bologna, Italy
| | - Simona Pepe
- Department of Pharmacy and Biotechnology, Alma Mater Studiorum University of Bologna, via Selmi 3, 40126, Bologna, Italy
| | - Giovanni Capranico
- Department of Pharmacy and Biotechnology, Alma Mater Studiorum University of Bologna, via Selmi 3, 40126, Bologna, Italy.
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11
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Kaur S, Kundu N, Sharma T, Shankaraswamy J, Saxena S. Identification of G4 motifs of various stem cell markers and their biophysical and biochemical characterization. J Biomol Struct Dyn 2023:1-10. [PMID: 37837414 DOI: 10.1080/07391102.2023.2259478] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2023] [Accepted: 09/09/2023] [Indexed: 10/16/2023]
Abstract
Regulatory regions in the human genome, enriched in guanine-rich DNA sequences have a remarkable enrichment of G-rich sequences having a tendency to fold into G-quadruplex structures. To identify the G-quadruplex forming motifs in regulatory regions of stem cell markers, gene sequences of various stem cell markers were downloaded and analyzed to see the abundance of G-rich sequences. We observed the enrichment of G-rich sequences in stem cell markers (CD13, CD19, CD24 and CD38) which could possibly play a critical role in its regulation. We used Circular Dichroism (CD), UV-Thermal denaturation (UV-Tm) and polyacrylamide gel electrophoresis (PAGE) to demonstrate the formation of a G-quadruplex by G-rich sequences present in these stem cell markers. We observed that these G-rich sequences containing minimum consecutive G3 stretch separated by loop length ranging from one to three bases long adopt G-quadruplexes with different molecularity involving two-strands, three-strand and four-strand with parallel and antiparallel conformation. Interestingly, we proposed the formation of three-stranded G-quadruplex by CD13 in 100 mM Na+, CD19 in 100 mM K+, 100 mM K+ with 40 wt% PEG 200, and CD38 in 100 mM K+ + 40 wt% PEG 200. The formation of such diverse G-quadruplex structures in the regulatory regions leaves the fair possibility of recognition by regulatory factors to modulate the gene expression. First time, this study may give insight into the structural polymorphism of G4 forming motifs in different stem cell markers to design the best suitable ligand and to target them for therapeutic development.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Sarvpreet Kaur
- Amity Institute of Biotechnology, Amity University Uttar Pradesh, Noida, India
| | - Nikita Kundu
- Amity Institute of Biotechnology, Amity University Uttar Pradesh, Noida, India
| | - Taniya Sharma
- Amity Institute of Biotechnology, Amity University Uttar Pradesh, Noida, India
| | - Jadala Shankaraswamy
- Department of Fruit Science, College of Horticulture, Sri Konda Laxman Telangana State Horticultural University, Mojerla, Telangana, India
| | - Sarika Saxena
- Amity Institute of Biotechnology, Amity University Uttar Pradesh, Noida, India
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12
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Derewenda ZS. C-H Groups as Donors in Hydrogen Bonds: A Historical Overview and Occurrence in Proteins and Nucleic Acids. Int J Mol Sci 2023; 24:13165. [PMID: 37685972 PMCID: PMC10488043 DOI: 10.3390/ijms241713165] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2023] [Revised: 08/21/2023] [Accepted: 08/23/2023] [Indexed: 09/10/2023] Open
Abstract
Hydrogen bonds constitute a unique type of non-covalent interaction, with a critical role in biology. Until fairly recently, the canonical view held that these bonds occur between electronegative atoms, typically O and N, and that they are mostly electrostatic in nature. However, it is now understood that polarized C-H groups may also act as hydrogen bond donors in many systems, including biological macromolecules. First recognized from physical chemistry studies, C-H…X bonds were visualized with X-ray crystallography sixty years ago, although their true significance has only been recognized in the last few decades. This review traces the origins of the field and describes the occurrence and significance of the most important C-H…O bonds in proteins and nucleic acids.
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Affiliation(s)
- Zygmunt Stanislaw Derewenda
- Department of Molecular Physiology and Biological Physics, School of Medicine, University of Virginia, Charlottesville, VA 22903-2628, USA
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13
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Iglesias BA, Peranzoni NP, Faria SI, Trentin LB, Schuch AP, Chaves OA, Bertoloni RR, Nikolaou S, de Oliveira KT. DNA-Interactive and Damage Study with meso-Tetra(2-thienyl)porphyrins Coordinated with Polypyridyl Pd(II) and Pt(II) Complexes. Molecules 2023; 28:5217. [PMID: 37446879 DOI: 10.3390/molecules28135217] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2023] [Revised: 06/17/2023] [Accepted: 06/30/2023] [Indexed: 07/15/2023] Open
Abstract
We report the DNA-binding properties of three porphyrins with peripheral thienyl substituents (TThPor, PdTThPor and PtTThPor). The binding capacity of each porphyrin with DNA was determined by UV-Vis and steady-state fluorescence emission spectroscopy combined with molecular docking calculations. The results suggest that the interaction of these compounds probably occurs via secondary interactions via external grooves (minor grooves) around the DNA macromolecule. Moreover, porphyrins containing peripheral Pd(II) or Pt(II) complexes (PdTThPor and PtTThPor) were able to promote photo-damage in the DNA.
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Affiliation(s)
- Bernardo Almeida Iglesias
- Bioinorganic and Porphyrinoids Materials Laboratory, Department of Chemistry, Federal University of Santa Maria (UFSM), Santa Maria 97105-900, RS, Brazil
| | - Níckolas Pippi Peranzoni
- Laboratory of Photobiology, Department of Biochemistry and Molecular Biology, Federal University of Santa Maria (UFSM), Santa Maria 97105-900, RS, Brazil
| | - Sophia Iwersen Faria
- Laboratory of Photobiology, Department of Biochemistry and Molecular Biology, Federal University of Santa Maria (UFSM), Santa Maria 97105-900, RS, Brazil
| | - Luana Belo Trentin
- Laboratory of Photobiology, Department of Biochemistry and Molecular Biology, Federal University of Santa Maria (UFSM), Santa Maria 97105-900, RS, Brazil
| | - André Passaglia Schuch
- Laboratory of Photobiology, Department of Biochemistry and Molecular Biology, Federal University of Santa Maria (UFSM), Santa Maria 97105-900, RS, Brazil
| | - Otávio Augusto Chaves
- CQC-IMS, Department of Chemistry, University of Coimbra, Rua Larga, 3004-535 Coimbra, Portugal
| | - Renan Ribeiro Bertoloni
- Laboratory of Biological Activity and Supramolecular Chemical of Coordination Compounds (LABiQSC2), Department of Chemistry, FFCLRP, University of São Paulo, Ribeirão Preto 14040-901, SP, Brazil
| | - Sofia Nikolaou
- Laboratory of Biological Activity and Supramolecular Chemical of Coordination Compounds (LABiQSC2), Department of Chemistry, FFCLRP, University of São Paulo, Ribeirão Preto 14040-901, SP, Brazil
| | - Kleber Thiago de Oliveira
- Department of Chemistry, Federal University of São Carlos, Rod. Washington Luiz, km 235, São Carlos 13565-905, SP, Brazil
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14
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Mu ZC, Tan YL, Liu J, Zhang BG, Shi YZ. Computational Modeling of DNA 3D Structures: From Dynamics and Mechanics to Folding. Molecules 2023; 28:4833. [PMID: 37375388 DOI: 10.3390/molecules28124833] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2023] [Revised: 06/11/2023] [Accepted: 06/14/2023] [Indexed: 06/29/2023] Open
Abstract
DNA carries the genetic information required for the synthesis of RNA and proteins and plays an important role in many processes of biological development. Understanding the three-dimensional (3D) structures and dynamics of DNA is crucial for understanding their biological functions and guiding the development of novel materials. In this review, we discuss the recent advancements in computer methods for studying DNA 3D structures. This includes molecular dynamics simulations to analyze DNA dynamics, flexibility, and ion binding. We also explore various coarse-grained models used for DNA structure prediction or folding, along with fragment assembly methods for constructing DNA 3D structures. Furthermore, we also discuss the advantages and disadvantages of these methods and highlight their differences.
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Affiliation(s)
- Zi-Chun Mu
- Research Center of Nonlinear Science, School of Mathematical & Physical Sciences, Wuhan Textile University, Wuhan 430073, China
- School of Computer Science and Artificial Intelligence, Wuhan Textile University, Wuhan 430073, China
| | - Ya-Lan Tan
- Research Center of Nonlinear Science, School of Mathematical & Physical Sciences, Wuhan Textile University, Wuhan 430073, China
| | - Jie Liu
- Research Center of Nonlinear Science, School of Mathematical & Physical Sciences, Wuhan Textile University, Wuhan 430073, China
| | - Ben-Gong Zhang
- Research Center of Nonlinear Science, School of Mathematical & Physical Sciences, Wuhan Textile University, Wuhan 430073, China
| | - Ya-Zhou Shi
- Research Center of Nonlinear Science, School of Mathematical & Physical Sciences, Wuhan Textile University, Wuhan 430073, China
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15
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Xu Q, Kowalski J. NBBC: a non-B DNA burden explorer in cancer. Nucleic Acids Res 2023:7177884. [PMID: 37224529 DOI: 10.1093/nar/gkad379] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2023] [Revised: 04/16/2023] [Accepted: 05/12/2023] [Indexed: 05/26/2023] Open
Abstract
Alternate (non-B) DNA-forming structures, such as Z-DNA, G-quadruplex, triplex have demonstrated a potential role in cancer etiology. It has been found that non-B DNA-forming sequences can stimulate genetic instability in human cancer genomes, implicating them in the development of cancer and other genetic diseases. While there exist several non-B prediction tools and databases, they lack the ability to both analyze and visualize non-B data within a cancer context. Herein, we introduce NBBC, a non-B DNA burden explorer in cancer, that offers analyses and visualizations for non-B DNA forming motifs. To do so, we introduce 'non-B burden' as a metric to summarize the prevalence of non-B DNA motifs at the gene-, signature- and genomic site-levels. Using our non-B burden metric, we developed two analyses modules within a cancer context to assist in exploring both gene- and motif-level non-B type heterogeneity among gene signatures. NBBC is designed to serve as a new analysis and visualization platform for the exploration of non-B DNA, guided by non-B burden as a novel marker.
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Affiliation(s)
- Qi Xu
- Department of Oncology, Dell Medical School, The University of Texas at Austin, Austin, TX 78712, USA
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX 78712, USA
| | - Jeanne Kowalski
- Department of Oncology, Dell Medical School, The University of Texas at Austin, Austin, TX 78712, USA
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16
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DNA Base Excision Repair Intermediates Influence Duplex-Quadruplex Equilibrium. Molecules 2023; 28:molecules28030970. [PMID: 36770637 PMCID: PMC9920732 DOI: 10.3390/molecules28030970] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2022] [Revised: 01/12/2023] [Accepted: 01/13/2023] [Indexed: 01/21/2023] Open
Abstract
Although genomic DNA is predominantly duplex under physiological conditions, particular sequence motifs can favor the formation of alternative secondary structures, including the G-quadruplex. These structures can exist within gene promoters, telomeric DNA, and regions of the genome frequently found altered in human cancers. DNA is also subject to hydrolytic and oxidative damage, and its local structure can influence the type of damage and its magnitude. Although the repair of endogenous DNA damage by the base excision repair (BER) pathway has been extensively studied in duplex DNA, substantially less is known about repair in non-duplex DNA structures. Therefore, we wanted to better understand the effect of DNA damage and repair on quadruplex structure. We first examined the effect of placing pyrimidine damage products uracil, 5-hydroxymethyluracil, the chemotherapy agent 5-fluorouracil, and an abasic site into the loop region of a 22-base telomeric repeat sequence known to form a G-quadruplex. Quadruplex formation was unaffected by these analogs. However, the activity of the BER enzymes were negatively impacted. Uracil DNA glycosylase (UDG) and single-strand selective monofunctional uracil DNA glycosylase (SMUG1) were inhibited, and apurinic/apyrimidinic endonuclease 1 (APE1) activity was completely blocked. Interestingly, when we performed studies placing DNA repair intermediates into the strand opposite the quadruplex, we found that they destabilized the duplex and promoted quadruplex formation. We propose that while duplex is the preferred configuration, there is kinetic conversion between duplex and quadruplex. This is supported by our studies using a quadruplex stabilizing molecule, pyridostatin, that is able to promote quadruplex formation starting from duplex DNA. Our results suggest how DNA damage and repair intermediates can alter duplex-quadruplex equilibrium.
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17
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Bowater RP, Brázda V. Impacts of Molecular Structure on Nucleic Acid-Protein Interactions. Int J Mol Sci 2022; 24:ijms24010407. [PMID: 36613851 PMCID: PMC9820666 DOI: 10.3390/ijms24010407] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2022] [Accepted: 12/21/2022] [Indexed: 12/28/2022] Open
Abstract
Interactions between nucleic acids and proteins are some of the most important interactions in biology because they are the cornerstones for fundamental biological processes, such as replication, transcription, and recombination [...].
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Affiliation(s)
- Richard P. Bowater
- School of Biological Sciences, University of East Anglia, Norwich Research Park, Norwich NR4 7TJ, UK
- Correspondence: (R.P.B.); (V.B.)
| | - Václav Brázda
- Institute of Biophysics of the Czech Academy of Sciences, Královopolská 135, 612 00 Brno, Czech Republic
- Correspondence: (R.P.B.); (V.B.)
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