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Kumari M, Jaiswal S, Shankar U, Gupta S, Pradeepkumar PI, Kumar A, Nayak D, Yadav V, Yadav P. Characterization of G-quadruplexes in the Helicobacter pylori genome and assessment of therapeutic potential of G4 ligands. Biotechnol Appl Biochem 2024. [PMID: 39041320 DOI: 10.1002/bab.2644] [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: 02/23/2024] [Accepted: 07/10/2024] [Indexed: 07/24/2024]
Abstract
Helicobacter pylori, a leading human pathogen associated with duodenal ulcer and gastric cancer, presents a significant threat to human health due to increasing antibiotic resistance rates. This study investigates G-quadruplexes (G4s), which are non-canonical secondary structures form in G-rich regions within the H. pylori genome. Extensive research on G4s in eukaryotes has revealed their role in epigenetically regulating cellular processes like gene transcription, DNA replication, and oncogene expression. However, understanding of G4-mediated gene regulation in other organisms, especially bacterial pathogens, remains limited. Although G4 motifs have been extensively studied in a few bacterial species such as Mycobacterium, Streptococci, and Helicobacter, research on G4 motifs in other bacterial species is still sparse. Like in other organisms such as archaea, mammals, and viruses, G4s in H. pylori display a non-random distribution primarily situated within open reading frames of various protein-coding genes. The occurrence of G4s in functional regions of the genome and their conservation across different species indicates that their placement is not random, suggesting an evolutionary pressure to maintain these sequences at specific genomic sites. Moreover, G-quadruplexes show enrichment in specific gene classes, suggesting their potential involvement in regulating the expression of genes related to cell wall/membrane/envelope biogenesis, amino acid transport, and metabolism. This indicates a probable regulatory role for G4s in controlling the expression of genes essential for H. pylori survival and virulence. Biophysical techniques such as Circular Dichroism spectroscopy and Nuclear Magnetic Resonance were used to characterize G4 motifs within selected H. pylori genes. The study revealed that G-quadruplex ligand inhibited the growth of H. pylori, with minimal inhibitory concentrations in the low micromolar range. This suggests that targeting G4 structures could offer a promising approach for developing novel anti-H. pylori drugs.
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Affiliation(s)
- Monika Kumari
- Department of Microbiology, Central University of Haryana, Mahendergarh, India
| | - Saumya Jaiswal
- Department of Biosciences and Biomedical Engineering, Indian Institute of Technology Indore, Indore, Madhya Pradesh, India
| | - Uma Shankar
- Department of Biosciences and Biomedical Engineering, Indian Institute of Technology Indore, Indore, Madhya Pradesh, India
| | - Sharad Gupta
- Department of Biosciences and Biomedical Engineering, Indian Institute of Technology Indore, Indore, Madhya Pradesh, India
| | | | - Amit Kumar
- Department of Biosciences and Biomedical Engineering, Indian Institute of Technology Indore, Indore, Madhya Pradesh, India
| | - Debasis Nayak
- Department of Biological Sciences, Indian Institute of Science Education and Research (IISER), Bhopal, Madhya Pradesh, India
| | - Vikas Yadav
- School of Life Sciences, Jawaharlal Nehru University, New Delhi, India
| | - Puja Yadav
- Department of Microbiology, Central University of Haryana, Mahendergarh, India
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2
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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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3
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Johnson S, Paul T, Sanford S, Schnable BL, Detwiler A, Thosar S, Van Houten B, Myong S, Opresko P. BG4 antibody can recognize telomeric G-quadruplexes harboring destabilizing base modifications and lesions. Nucleic Acids Res 2024; 52:1763-1778. [PMID: 38153143 PMCID: PMC10939409 DOI: 10.1093/nar/gkad1209] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2023] [Revised: 11/30/2023] [Accepted: 12/11/2023] [Indexed: 12/29/2023] Open
Abstract
BG4 is a single-chain variable fragment antibody shown to bind various G-quadruplex (GQ) topologies with high affinity and specificity, and to detect GQ in cells, including GQ structures formed within telomeric TTAGGG repeats. Here, we used ELISA and single-molecule pull-down (SiMPull) detection to test how various lengths and GQ destabilizing base modifications in telomeric DNA constructs alter BG4 binding. We observed high-affinity BG4 binding to telomeric GQ independent of telomere length, although three telomeric repeat constructs that cannot form stable intramolecular GQ showed reduced affinity. A single guanine substitution with 8-aza-7-deaza-G, T, A, or C reduced affinity to varying degrees depending on the location and base type, whereas two G substitutions in the telomeric construct dramatically reduced or abolished binding. Substitution with damaged bases 8-oxoguanine and O6-methylguanine failed to prevent BG4 binding although affinity was reduced depending on lesion location. SiMPull combined with FRET revealed that BG4 binding promotes folding of telomeric GQ harboring a G to T substitution or 8-oxoguanine. Atomic force microscopy revealed that BG4 binds telomeric GQ with a 1:1 stoichiometry. Collectively, our data suggest that BG4 can recognize partially folded telomeric GQ structures and promote telomeric GQ stability.
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Affiliation(s)
- Samuel A Johnson
- Department of Environmental and Occupational Health, University of Pittsburgh School of Public Health, Pittsburgh, PA 15261, USA
- UPMC Hillman Cancer Center, Pittsburgh, PA 15213, USA
- Molecular Biophysics and Structural Biology Graduate Program, University of Pittsburgh, PA 15260, USA
| | - Tapas Paul
- Department of Biophysics, Johns Hopkins University, Baltimore, MD 21218, USA
- Program in Cellular and Molecular Medicine, Boston Children's Hospital, Boston, MA 02115, USA
| | - Samantha L Sanford
- Department of Environmental and Occupational Health, University of Pittsburgh School of Public Health, Pittsburgh, PA 15261, USA
- UPMC Hillman Cancer Center, Pittsburgh, PA 15213, USA
| | - Brittani L Schnable
- UPMC Hillman Cancer Center, Pittsburgh, PA 15213, USA
- Molecular Biophysics and Structural Biology Graduate Program, University of Pittsburgh, PA 15260, USA
| | - Ariana C Detwiler
- Department of Environmental and Occupational Health, University of Pittsburgh School of Public Health, Pittsburgh, PA 15261, USA
- UPMC Hillman Cancer Center, Pittsburgh, PA 15213, USA
| | - Sanjana A Thosar
- Department of Environmental and Occupational Health, University of Pittsburgh School of Public Health, Pittsburgh, PA 15261, USA
- UPMC Hillman Cancer Center, Pittsburgh, PA 15213, USA
| | - Bennett Van Houten
- UPMC Hillman Cancer Center, Pittsburgh, PA 15213, USA
- Molecular Biophysics and Structural Biology Graduate Program, University of Pittsburgh, PA 15260, USA
- Department of Pharmacology and Chemical Biology, University of Pittsburgh School of Medicine, PA 15213, USA
| | - Sua Myong
- Department of Biophysics, Johns Hopkins University, Baltimore, MD 21218, USA
- Program in Cellular and Molecular Medicine, Boston Children's Hospital, Boston, MA 02115, USA
| | - Patricia L Opresko
- Department of Environmental and Occupational Health, University of Pittsburgh School of Public Health, Pittsburgh, PA 15261, USA
- UPMC Hillman Cancer Center, Pittsburgh, PA 15213, USA
- Molecular Biophysics and Structural Biology Graduate Program, University of Pittsburgh, PA 15260, USA
- Department of Pharmacology and Chemical Biology, University of Pittsburgh School of Medicine, PA 15213, USA
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4
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Shiekh S, Kodikara SG, Balci H. Structure, Topology, and Stability of Multiple G-quadruplexes in Long Telomeric Overhangs. J Mol Biol 2024; 436:168205. [PMID: 37481156 PMCID: PMC10799177 DOI: 10.1016/j.jmb.2023.168205] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2023] [Revised: 07/05/2023] [Accepted: 07/12/2023] [Indexed: 07/24/2023]
Abstract
Telomeres and their single stranded overhangs gradually shorten with successive cell divisions, as part of the natural aging process, but can be elongated by telomerase, a nucleoprotein complex which is activated in the majority of cancers. This prominent implication in cancer and aging has made the repetitive telomeric sequences (TTAGGG repeats) and the G-quadruplex structures that form in their overhangs the focus of intense research in the past several decades. However, until recently most in vitro efforts to understand the structure, stability, dynamics, and interactions of telomeric overhangs had been focused on short sequences that are not representative of longer sequences encountered in a physiological setting. In this review, we will provide a broad perspective about telomeres and associated factors, and introduce the agents and structural characteristics involved in organizing, maintaining, and protecting telomeric DNA. We will also present a summary of recent research performed on long telomeric sequences, nominally defined as those that can form two or more tandem G-quadruplexes, i.e., which contain eight or more TTAGGG repeats. Results of experimental studies using a broad array of experimental tools, in addition to recent computational efforts will be discussed, particularly in terms of their implications for the stability, folding topology, and compactness of the tandem G-quadruplexes that form in long telomeric overhangs.
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Affiliation(s)
- Sajad Shiekh
- Department of Physics, Kent State University, Kent, OH 44242, USA
| | | | - Hamza Balci
- Department of Physics, Kent State University, Kent, OH 44242, USA.
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5
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Trizna L, Osif B, Víglaský V. G-QINDER Tool: Bioinformatically Predicted Formation of Different Four-Stranded DNA Motifs from (GT) n and (GA) n Repeats. Int J Mol Sci 2023; 24:ijms24087565. [PMID: 37108727 DOI: 10.3390/ijms24087565] [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: 03/31/2023] [Revised: 04/10/2023] [Accepted: 04/18/2023] [Indexed: 04/29/2023] Open
Abstract
The recently introduced semi-orthogonal system of nucleic acid imaging offers a greatly improved method of identifying DNA sequences that are capable of adopting noncanonical structures. This paper uses our newly developed G-QINDER tool to identify specific repeat sequences that adopt unique structural motifs in DNA: TG and AG repeats. The structures were found to adopt a left-handed G-quadruplex form under extreme crowding conditions and a unique tetrahelical motif under certain other conditions. The tetrahelical structure likely consists of stacked AGAG-tetrads but, unlike G-quadruplexes, their stability does not appear to be dependent on the type of monovalent cation present. The occurrence of TG and AG repeats in genomes is not rare, and they are also found frequently in the regulatory regions of nucleic acids, so it is reasonable to assume that putative structural motifs, like other noncanonical forms, could play an important regulatory role in cells. This hypothesis is supported by the structural stability of the AGAG motif; its unfolding can occur even at physiological temperatures since the melting temperature is primarily dependent on the number of AG repeats in the sequence.
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Affiliation(s)
- Lukáš Trizna
- Department of Biochemistry, Institute of Chemistry, Faculty of Sciences, Pavol Jozef Šafárik University, 04001 Košice, Slovakia
| | - Branislav Osif
- Department of Biochemistry, Institute of Chemistry, Faculty of Sciences, Pavol Jozef Šafárik University, 04001 Košice, Slovakia
| | - Viktor Víglaský
- Department of Biochemistry, Institute of Chemistry, Faculty of Sciences, Pavol Jozef Šafárik University, 04001 Košice, Slovakia
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6
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Bansal A, Kaushik S, Kukreti S. Non-canonical DNA structures: Diversity and disease association. Front Genet 2022; 13:959258. [PMID: 36134025 PMCID: PMC9483843 DOI: 10.3389/fgene.2022.959258] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2022] [Accepted: 07/25/2022] [Indexed: 11/18/2022] Open
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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7
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Rhodamine 6G-Ligand Influencing G-Quadruplex Stability and Topology. Int J Mol Sci 2021; 22:ijms22147639. [PMID: 34299257 PMCID: PMC8305571 DOI: 10.3390/ijms22147639] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2021] [Revised: 07/09/2021] [Accepted: 07/15/2021] [Indexed: 11/17/2022] Open
Abstract
The involvement of G-quadruplex (G4) structures in nucleic acids in various molecular processes in cells such as replication, gene-pausing, the expression of crucial cancer-related genes and DNA damage repair is well known. The compounds targeting G4 usually bind directly to the G4 structure, but some ligands can also facilitate the G4 folding of unfolded G-rich sequences and stabilize them even without the presence of monovalent ions such as sodium or potassium. Interestingly, some G4-ligand complexes can show a clear induced CD signal, a feature which is indirect proof of the ligand interaction. Based on the dichroic spectral profile it is not only possible to confirm the presence of a G4 structure but also to determine its topology. In this study we examine the potential of the commercially available Rhodamine 6G (RhG) as a G4 ligand. RhG tends to convert antiparallel G4 structures to parallel forms in a manner similar to that of Thiazole Orange. Our results confirm the very high selectivity of this ligand to the G4 structure. Moreover, the parallel topology of G4 can be verified unambiguously based on the specific induced CD profile of the G4-RhG complex. This feature has been verified on more than 50 different DNA sequences forming various non-canonical structural motifs.
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8
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Ogloblina AM, Iaccarino N, Capasso D, Di Gaetano S, Garzarella EU, Dolinnaya NG, Yakubovskaya MG, Pagano B, Amato J, Randazzo A. Toward G-Quadruplex-Based Anticancer Agents: Biophysical and Biological Studies of Novel AS1411 Derivatives. Int J Mol Sci 2020; 21:E7781. [PMID: 33096752 PMCID: PMC7590035 DOI: 10.3390/ijms21207781] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2020] [Revised: 10/17/2020] [Accepted: 10/19/2020] [Indexed: 12/16/2022] Open
Abstract
Certain G-quadruplex forming guanine-rich oligonucleotides (GROs), including AS1411, are endowed with cancer-selective antiproliferative activity. They are known to bind to nucleolin protein, resulting in the inhibition of nucleolin-mediated phenomena. However, multiple nucleolin-independent biological effects of GROs have also been reported, allowing them to be considered promising candidates for multi-targeted cancer therapy. Herein, with the aim of optimizing AS1411 structural features to find GROs with improved anticancer properties, we have studied a small library of AS1411 derivatives differing in the sequence length and base composition. The AS1411 derivatives were characterized by using circular dichroism and nuclear magnetic resonance spectroscopies and then investigated for their enzymatic resistance in serum and nuclear extract, as well as for their ability to bind nucleolin, inhibit topoisomerase I, and affect the viability of MCF-7 human breast adenocarcinoma cells. All derivatives showed higher thermal stability and inhibitory effect against topoisomerase I than AS1411. In addition, most of them showed an improved antiproliferative activity on MCF-7 cells compared to AS1411 despite a weaker binding to nucleolin. Our results support the hypothesis that the antiproliferative properties of GROs are due to multi-targeted effects.
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Affiliation(s)
- Anna M. Ogloblina
- N.N. Blokhin National Medical Research Center of Oncology, Ministry of Health, 115478 Moscow, Russia; (A.M.O.); (M.G.Y.)
- Department of Pharmacy, University of Naples Federico II, Via D. Montesano 49, 80131 Naples, Italy; (N.I.); (E.U.G.); (A.R.)
| | - Nunzia Iaccarino
- Department of Pharmacy, University of Naples Federico II, Via D. Montesano 49, 80131 Naples, Italy; (N.I.); (E.U.G.); (A.R.)
| | - Domenica Capasso
- Center for Life Sciences and Technologies (CESTEV), University of Naples Federico II, Via A. De Amicis 95, 80145 Naples, Italy;
| | - Sonia Di Gaetano
- Institute of Biostructures and Bioimaging, National Research Council, Via Mezzocannone 16, 80134 Naples, Italy;
| | - Emanuele U. Garzarella
- Department of Pharmacy, University of Naples Federico II, Via D. Montesano 49, 80131 Naples, Italy; (N.I.); (E.U.G.); (A.R.)
| | - Nina G. Dolinnaya
- Department of Chemistry, Lomonosov Moscow State University, 119991 Moscow, Russia;
| | - Marianna G. Yakubovskaya
- N.N. Blokhin National Medical Research Center of Oncology, Ministry of Health, 115478 Moscow, Russia; (A.M.O.); (M.G.Y.)
| | - Bruno Pagano
- Department of Pharmacy, University of Naples Federico II, Via D. Montesano 49, 80131 Naples, Italy; (N.I.); (E.U.G.); (A.R.)
| | - Jussara Amato
- Department of Pharmacy, University of Naples Federico II, Via D. Montesano 49, 80131 Naples, Italy; (N.I.); (E.U.G.); (A.R.)
| | - Antonio Randazzo
- Department of Pharmacy, University of Naples Federico II, Via D. Montesano 49, 80131 Naples, Italy; (N.I.); (E.U.G.); (A.R.)
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Puig Lombardi E, Londoño-Vallejo A. A guide to computational methods for G-quadruplex prediction. Nucleic Acids Res 2020; 48:1-15. [PMID: 31754698 PMCID: PMC6943126 DOI: 10.1093/nar/gkz1097] [Citation(s) in RCA: 93] [Impact Index Per Article: 23.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2019] [Revised: 10/31/2019] [Accepted: 11/04/2019] [Indexed: 12/31/2022] Open
Abstract
Guanine-rich nucleic acids can fold into the non-B DNA or RNA structures called G-quadruplexes (G4). Recent methodological developments have allowed the characterization of specific G-quadruplex structures in vitro as well as in vivo, and at a much higher throughput, in silico, which has greatly expanded our understanding of G4-associated functions. Typically, the consensus motif G3+N1-7G3+N1-7G3+N1-7G3+ has been used to identify potential G-quadruplexes from primary sequence. Since, various algorithms have been developed to predict the potential formation of quadruplexes directly from DNA or RNA sequences and the number of studies reporting genome-wide G4 exploration across species has rapidly increased. More recently, new methodologies have also appeared, proposing other estimates which consider non-canonical sequences and/or structure propensity and stability. The present review aims at providing an updated overview of the current open-source G-quadruplex prediction algorithms and straightforward examples of their implementation.
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Affiliation(s)
- Emilia Puig Lombardi
- Telomeres and Cancer Laboratory, Institut Curie, PSL Research University, Sorbonne Universités, CNRS UMR3244, 75005 Paris, France
| | - Arturo Londoño-Vallejo
- Telomeres and Cancer Laboratory, Institut Curie, PSL Research University, Sorbonne Universités, CNRS UMR3244, 75005 Paris, France
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Belmonte-Reche E, Morales JC. G4-iM Grinder: when size and frequency matter. G-Quadruplex, i-Motif and higher order structure search and analysis tool. NAR Genom Bioinform 2019; 2:lqz005. [PMID: 33575559 PMCID: PMC7671307 DOI: 10.1093/nargab/lqz005] [Citation(s) in RCA: 35] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2019] [Revised: 08/08/2019] [Accepted: 09/10/2019] [Indexed: 11/15/2022] Open
Abstract
We present G4-iM Grinder, a system for the localization, characterization and selection of potential G4s, i-Motifs and higher order structures. A robust and highly adaptable search engine identifies all structures that fit the user’s quadruplex definitions. Their biological relevance, in vitro formation probability and presence of known-to-form structures are then used as filters. The outcome is an efficient methodology that helps select the best candidates for a subsequent in vitro analysis or a macroscopic genomic quadruplex assessment. As proof of the analytical capabilities of G4-iM Grinder, the human genome was analyzed for potential G4s and i-Motifs. Many known-to-form structures were identified. New candidates were selected considering their score and appearance frequency. We also focused on locating Potential Higher Order Quadruplex Sequences (PHOQS). We developed a new methodology to predict the most probable subunits of these assemblies and applied it to a PHOQS candidate. Taking the human average density as reference, we examined the genomes of several etiological causes of disease. This first of its class comparative study found many organisms to be very dense in these potential quadruplexes. Many presented already known-to-form-G4s and i-Motifs. These findings suggest the potential quadruplexes have as therapeutic targets for these diseases that currently kill millions worldwide.
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Affiliation(s)
- Efres Belmonte-Reche
- Department of Biochemistry and Molecular Pharmacology, Instituto de Parasitología y Biomedicina López Neyra, CSIC, PTS Granada, Avda. del Conocimiento, 17, 18016 Armilla, Granada, Spain.,Life Sciences Department, International Iberian Nanotechnology Laboratory, Av. Mestre José Veiga, 4715-330 Braga, Portugal
| | - Juan Carlos Morales
- Department of Biochemistry and Molecular Pharmacology, Instituto de Parasitología y Biomedicina López Neyra, CSIC, PTS Granada, Avda. del Conocimiento, 17, 18016 Armilla, Granada, Spain
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11
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Bansal A, Kukreti S. The four repeat Giardia lamblia telomere forms tetramolecular G-quadruplex with antiparallel topology. J Biomol Struct Dyn 2019; 38:1975-1983. [DOI: 10.1080/07391102.2019.1623074] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Affiliation(s)
- Aparna Bansal
- Nucleic Acids Research Lab, Department of Chemistry, University of Delhi (North Campus), Delhi, India
- Department of Chemistry, Hansraj College, University of Delhi (North Campus), Delhi, India
| | - Shrikant Kukreti
- Nucleic Acids Research Lab, Department of Chemistry, University of Delhi (North Campus), Delhi, India
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12
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Huang S, Liang Y, Cui J, Xie J, Liu Y, Hu B, Xiao Q. Comparative investigation of binding interactions with three steroidal derivatives of d(GGGT) 4 G-quadruplex aptamer. Steroids 2018; 132:46-55. [PMID: 29458054 DOI: 10.1016/j.steroids.2018.02.003] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/26/2017] [Revised: 02/04/2018] [Accepted: 02/13/2018] [Indexed: 11/19/2022]
Abstract
Steroidal derivatives have attracted tremendous attentions in biological and biomedical areas, due to their variety biological activities. The investigation of structural influences helps in understanding their biological activities. The interactions of steroidal derivatives with DNA may play important roles in biological activities, however only a few investigations were reported on this issue. Herein, the structural influences of three steroidal derivatives were investigated based on their binding interactions with d(GGGT)4 G-quadruplex aptamer by spectroscopic approaches, nuclear magnetic resonance (NMR), electrochemical methods, and molecular modeling techniques. Three compounds were found to selectively bind with parallel G-quadruplex aptamer to form three complexes through end-stacking binding modes. Three compounds stabilized the G-quadruplex structure of the aptamer at different levels, which enhanced the biological activity of this aptamer to some extent. The space steric hindrance was responsible for differences in the binding interactions between d(GGGT)4 G-quadruplex aptamer and three compounds. These results provide new information for the molecular understanding of binding interactions of steroidal derivatives with DNA and the strategy for research of structural influences.
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Affiliation(s)
- Shan Huang
- College of Chemistry and Materials Science, Guangxi Key Laboratory of Natural Polymer Chemistry and Physics, Guangxi Teachers Education University, Nanning 530001, PR China; Key Laboratory of Beibu Gulf Environment Change and Resources Utilization (Guangxi Teachers Education University), Ministry of Education, Nanning 530001, PR China
| | - Yu Liang
- College of Chemistry and Materials Science, Guangxi Key Laboratory of Natural Polymer Chemistry and Physics, Guangxi Teachers Education University, Nanning 530001, PR China
| | - Jianguo Cui
- College of Chemistry and Materials Science, Guangxi Key Laboratory of Natural Polymer Chemistry and Physics, Guangxi Teachers Education University, Nanning 530001, PR China.
| | - Jiangning Xie
- College of Chemistry and Materials Science, Guangxi Key Laboratory of Natural Polymer Chemistry and Physics, Guangxi Teachers Education University, Nanning 530001, PR China
| | - Yi Liu
- College of Chemistry and Materials Science, Guangxi Key Laboratory of Natural Polymer Chemistry and Physics, Guangxi Teachers Education University, Nanning 530001, PR China; College of Chemistry and Molecular Sciences, Wuhan University, Wuhan 430072, PR China
| | - Baoqing Hu
- Key Laboratory of Beibu Gulf Environment Change and Resources Utilization (Guangxi Teachers Education University), Ministry of Education, Nanning 530001, PR China
| | - Qi Xiao
- College of Chemistry and Materials Science, Guangxi Key Laboratory of Natural Polymer Chemistry and Physics, Guangxi Teachers Education University, Nanning 530001, PR China; College of Chemistry and Molecular Sciences, Wuhan University, Wuhan 430072, PR China; Key Laboratory of Beibu Gulf Environment Change and Resources Utilization (Guangxi Teachers Education University), Ministry of Education, Nanning 530001, PR China.
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Dolinnaya NG, Ogloblina AM, Yakubovskaya MG. Structure, Properties, and Biological Relevance of the DNA and RNA G-Quadruplexes: Overview 50 Years after Their Discovery. BIOCHEMISTRY (MOSCOW) 2017; 81:1602-1649. [PMID: 28260487 PMCID: PMC7087716 DOI: 10.1134/s0006297916130034] [Citation(s) in RCA: 47] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
G-quadruplexes (G4s), which are known to have important roles in regulation of key biological processes in both normal and pathological cells, are the most actively studied non-canonical structures of nucleic acids. In this review, we summarize the results of studies published in recent years that change significantly scientific views on various aspects of our understanding of quadruplexes. Modern notions on the polymorphism of DNA quadruplexes, on factors affecting thermodynamics and kinetics of G4 folding–unfolding, on structural organization of multiquadruplex systems, and on conformational features of RNA G4s and hybrid DNA–RNA G4s are discussed. Here we report the data on location of G4 sequence motifs in the genomes of eukaryotes, bacteria, and viruses, characterize G4-specific small-molecule ligands and proteins, as well as the mechanisms of their interactions with quadruplexes. New information on the structure and stability of G4s in telomeric DNA and oncogene promoters is discussed as well as proof being provided on the occurrence of G-quadruplexes in cells. Prominence is given to novel experimental techniques (single molecule manipulations, optical and magnetic tweezers, original chemical approaches, G4 detection in situ, in-cell NMR spectroscopy) that facilitate breakthroughs in the investigation of the structure and functions of G-quadruplexes.
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Affiliation(s)
- N G Dolinnaya
- Lomonosov Moscow State University, Department of Chemistry, Moscow, 119991, Russia.
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14
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Wen LN, Xie MX. Spectroscopic investigation of the interaction between G-quadruplex of KRAS promoter sequence and three isoquinoline alkaloids. SPECTROCHIMICA ACTA PART A-MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2017; 171:287-296. [PMID: 27565766 DOI: 10.1016/j.saa.2016.08.013] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/11/2016] [Revised: 08/02/2016] [Accepted: 08/10/2016] [Indexed: 12/21/2022]
Affiliation(s)
- Li-Na Wen
- Medical Science & Research Center of Beijing Shijitan Hospital Affiliated to Capital Medical University, Beijing 100038, People's Republic of China
| | - Meng-Xia Xie
- Analytical & Testing Center of Beijing Normal University, Beijing 100875, People's Republic of China.
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15
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Rigo R, Palumbo M, Sissi C. G-quadruplexes in human promoters: A challenge for therapeutic applications. Biochim Biophys Acta Gen Subj 2016; 1861:1399-1413. [PMID: 28025083 DOI: 10.1016/j.bbagen.2016.12.024] [Citation(s) in RCA: 83] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2016] [Revised: 12/21/2016] [Accepted: 12/22/2016] [Indexed: 12/19/2022]
Abstract
BACKGROUND G-rich sequences undergo unique structural equilibria to form G-quadruplexes (G4) both in vitro and in cell systems. Several pathologies emerged to be directly related to G4 occurrence at defined genomic portions. Additionally, G-rich sequences are significantly represented around transcription start sites (TSS) thus leading to the hypothesis of a gene regulatory function for G4. Thus, the tuning of G4 formation has been proposed as a new powerful tool to regulate gene expression to treat related pathologies. However, up-to date this approach did not provide any new really efficient treatment. SCOPE OF REVIEW Here, we summarize the most recent advances on the correlation between the structural features of G4 in human promoters and the role these systems physiologically exert. In particular we focus on the effect of G4 localization among cell compartments and along the promoters in correlation with protein interaction networks and epigenetic state. Finally the intrinsic structural features of G4 at promoters are discussed to unveil the contribution of different G4 structural modules in this complex architecture. MAJOR CONCLUSIONS It emerges that G4s play several roles in the intriguing and complex mechanism of gene expression, being able to produce opposite effects on the same target. This reflects the occurrence of a highly variegate network of several components working simultaneously. GENERAL SIGNIFICANCE The resulting picture is still fuzzy but some points of strength are definitely emerging, which prompts all of us to strengthen our efforts in view of a selective control of gene expression through G4 modulation. This article is part of a Special Issue entitled "G-quadruplex" Guest Editor: Dr. Concetta Giancola and Dr. Daniela Montesarchio.
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Affiliation(s)
- Riccardo Rigo
- Dept. of Pharmaceutical and Pharmacological Sciences, University of Padova, v. Marzolo, 5, 35131 Padova, Italy
| | - Manlio Palumbo
- Dept. of Pharmaceutical and Pharmacological Sciences, University of Padova, v. Marzolo, 5, 35131 Padova, Italy
| | - Claudia Sissi
- Dept. of Pharmaceutical and Pharmacological Sciences, University of Padova, v. Marzolo, 5, 35131 Padova, Italy.
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16
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Bugaut A, Alberti P. Understanding the stability of DNA G-quadruplex units in long human telomeric strands. Biochimie 2015; 113:125-33. [PMID: 25888167 DOI: 10.1016/j.biochi.2015.04.003] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2015] [Accepted: 04/03/2015] [Indexed: 10/23/2022]
Abstract
Human telomeric DNA is composed of GGGTTA repeats. The presence of consecutive guanines makes the telomeric G-strand prone to fold into contiguous (or tandem) G-quadruplexes (G4s). The aim of this study was to provide a clarified picture of the stability of telomeric tandem G4 structures as a function of the number of G4 units and of boundary sequences, and an understanding of the diversity of their melting behaviors in terms of the single G4 units composing them. To this purpose we undertook an UV-spectroscopic investigation of the structure and stability of telomeric repeats potentially able to fold into up to four contiguous G4s, flanked or not by TTA sequences at their 5' and 3' extremities. We explain why the stability of (GGGTTA)4m-1GGG structures (m = 2, 3, 4 …) decreases with increasing the number m of G4 units, whereas the stability of TTA-(GGGTTA)4m-1GGG-TTA structures does not. Our results support that the inner G4 units have similar stabilities, whereas the stabilities of the terminal G4 units are modulated by their flanking nucleotides: in a TTA-(GGGTTA)4m-1GGG-TTA tandem context, the terminal G4 units are roughly as stable as the inner G4 units; while in a (GGGTTA)4m-1GGG tandem context, the G4 at the 5' extremity is more stable than the G4 at the 3' extremity, which in turn is more stable than an inner G4. Our study provides new information about the global and local stability of telomeric tandem G4 structures under near physiological conditions.
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Affiliation(s)
- Anthony Bugaut
- Muséum National d'Histoire Naturelle, Sorbonne Universités, 57 rue Cuvier, CP 26, 75005 Paris, France; CNRS UMR 7196, 57 rue Cuvier, CP 26, 75005 Paris, France; Inserm U 1154, 57 rue Cuvier, CP 26, 75005 Paris, France
| | - Patrizia Alberti
- Muséum National d'Histoire Naturelle, Sorbonne Universités, 57 rue Cuvier, CP 26, 75005 Paris, France; CNRS UMR 7196, 57 rue Cuvier, CP 26, 75005 Paris, France; Inserm U 1154, 57 rue Cuvier, CP 26, 75005 Paris, France.
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17
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Li Y, Jia G, Wang C, Cheng M, Li C. Higher-Order Human Telomeric G-Quadruplex DNA Metalloenzymes Enhance Enantioselectivity in the Diels-Alder Reaction. Chembiochem 2015; 16:618-24. [DOI: 10.1002/cbic.201402692] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2014] [Indexed: 12/12/2022]
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18
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Li Y, Sugiyama H. Photoreactivity of the linker region of two consecutive G-quadruplexes formed by human telomeric DNA. Chem Commun (Camb) 2015; 51:8861-4. [DOI: 10.1039/c5cc01812a] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
The photoreaction method was applied to probe the linker region of two consecutive G-quadruplexes.
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Affiliation(s)
- Yue Li
- Department of Chemistry, Graduate School of Science
- Kyoto University
- Kyoto 606-8502
- Japan
| | - Hiroshi Sugiyama
- Department of Chemistry, Graduate School of Science
- Kyoto University
- Kyoto 606-8502
- Japan
- Institute for Integrated Cell-Material Sciences (WPI-iCeMS)
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19
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A tetrahelical DNA fold adopted by tandem repeats of alternating GGG and GCG tracts. Nat Commun 2014; 5:5831. [PMID: 25500730 PMCID: PMC4275592 DOI: 10.1038/ncomms6831] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2014] [Accepted: 11/12/2014] [Indexed: 01/21/2023] Open
Abstract
DNA can form diverse higher-order structures, whose details are greatly dependent on nucleotide sequence. G-rich sequences containing four or more repeats of three guanines are expected to form G-quadruplexes. Here we show that DNA sequences with GGGAGCG repeats found in the regulatory region of the PLEKHG3 gene are capable of forming tetrahelical DNA structures that are distinct from G-quadruplexes. The d(GGGAGCGAGGGAGCG) sequence, VK1, forms a dimer. Two VK1 sequences connected by an adenine residue, VK2, fold into a monomer, which shares identical structural characteristics with the VK1 fold. Their four-stranded architectures are stabilized by four G-C, four G-A and six G-G base pairs. No G-quartets or Hoogsteen-type hydrogen-bonded guanine residues are present and the overall topology is conserved in the presence of Li(+), Na(+), K(+) and NH4(+) ions. Unique structural features include two edgewise loops on each side of the structure stabilized by three G-G base pairs in N1-carbonyl symmetric geometry.
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20
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Tóthová P, Krafčíková P, Víglaský V. Formation of highly ordered multimers in G-quadruplexes. Biochemistry 2014; 53:7013-27. [PMID: 25347520 DOI: 10.1021/bi500773c] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
G-Rich DNA and RNA have a higher propensity to form G-quadruplex structures, but the presence of G-runs alone is not sufficient to prove that such sequences can form stable G-quadruplexes. While G-rich sequences are essential for G-quadruplex formation, not all G-rich sequences have the propensity to form G-quadruplex structures. In addition, monovalent metal ions, dehydrating agents, and loop sequences connecting the G-runs also play important roles in the topology of G-quadruplex folding. To date, no quantitative analysis of the CD spectra of G-quadruplexes in confrontation with the electrophoretic results has been performed. Therefore, in this study, we use information gained through the analysis of a series of well-known G-quadruplex-forming sequences to evaluate other less-studied sets of aptameric sequences. A simple and cost-effective methodology that can verify the formation of G-quadruplex motifs from oligomeric DNA sequences and a technique to determine the molecularity of these structures are also described. This methodology could be of great use in the prediction of G-quadruplex assembly, and the basic principles of our techniques can be extrapolated for any G-rich DNA sequences. This study also presents a model that can predict the multimerization of G-quadruplexes; the predictions offered by this model are shown to match the results obtained using circular dichroism.
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Affiliation(s)
- Petra Tóthová
- Department of Biochemistry, Institute of Chemistry, Faculty of Sciences, P. J. Šafárik University , 04001 Košice, Slovakia
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21
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Hwang H, Kreig A, Calvert J, Lormand J, Kwon Y, Daley JM, Sung P, Opresko PL, Myong S. Telomeric overhang length determines structural dynamics and accessibility to telomerase and ALT-associated proteins. Structure 2014; 22:842-53. [PMID: 24836024 DOI: 10.1016/j.str.2014.03.013] [Citation(s) in RCA: 53] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2013] [Revised: 02/07/2014] [Accepted: 03/04/2014] [Indexed: 02/03/2023]
Abstract
The G-rich single-stranded DNA at the 3' end of human telomeres can self-fold into G-quaduplex (GQ). However, telomere lengthening by telomerase or the recombination-based alternative lengthening of telomere (ALT) mechanism requires protein loading on the overhang. Using single-molecule fluorescence spectroscopy, we discovered that lengthening the telomeric overhang also increased the rate of dynamic exchanges between structural conformations. Overhangs with five to seven TTAGGG repeats, compared with four repeats, showed much greater dynamics and accessibility to telomerase binding and activity and loading of the ALT-associated proteins RAD51, WRN, and BLM. Although the eight repeats are highly dynamic, they can fold into two GQs, which limited protein accessibility. In contrast, the telomere-specific protein POT1 is unique in that it binds independently of repeat number. Our results suggest that the telomeric overhang length and dynamics may contribute to the regulation of telomere extension via telomerase action and the ALT mechanism.
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Affiliation(s)
- Helen Hwang
- Bioengineering Department, University of Illinois, 1304 West Springfield Avenue, Urbana, IL 61801, USA; Medical Scholars Program, University of Illinois, 506 South Matthews Avenue, Urbana, IL 61801, USA
| | - Alex Kreig
- Bioengineering Department, University of Illinois, 1304 West Springfield Avenue, Urbana, IL 61801, USA
| | - Jacob Calvert
- Bioengineering Department, University of Illinois, 1304 West Springfield Avenue, Urbana, IL 61801, USA
| | - Justin Lormand
- Department of Environmental and Occupational Health, University of Pittsburgh, 100 Technology Drive, Suite 326, BRIDG, Pittsburgh, PA 15219, USA
| | - Yongho Kwon
- Department of Molecular Biophysics and Biochemistry, Yale University, 333 Cedar Street, P.O. Box 208024, New Haven, CT 06520, USA
| | - James M Daley
- Department of Molecular Biophysics and Biochemistry, Yale University, 333 Cedar Street, P.O. Box 208024, New Haven, CT 06520, USA
| | - Patrick Sung
- Department of Molecular Biophysics and Biochemistry, Yale University, 333 Cedar Street, P.O. Box 208024, New Haven, CT 06520, USA
| | - Patricia L Opresko
- Department of Environmental and Occupational Health, University of Pittsburgh, 100 Technology Drive, Suite 326, BRIDG, Pittsburgh, PA 15219, USA
| | - Sua Myong
- Bioengineering Department, University of Illinois, 1304 West Springfield Avenue, Urbana, IL 61801, USA; Institute for Genomic Biology, University of Illinois, 1206 West Gregory Street, Urbana, IL 61801, USA; Physics Frontier Center (Center of Physics for Living Cells), University of Illinois, 1110 West Green Street, Urbana, IL 61801, USA.
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22
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Timmer CM, Michmerhuizen NL, Witte AB, Van Winkle M, Zhou D, Sinniah K. An Isothermal Titration and Differential Scanning Calorimetry Study of the G-Quadruplex DNA–Insulin Interaction. J Phys Chem B 2014; 118:1784-90. [DOI: 10.1021/jp411293r] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Affiliation(s)
- Christine M. Timmer
- Department
of Chemistry and Biochemistry, Calvin College, 3201 Burton Street Southeast, Grand Rapids, Michigan 49546, United States
| | - Nicole L. Michmerhuizen
- Department
of Chemistry and Biochemistry, Calvin College, 3201 Burton Street Southeast, Grand Rapids, Michigan 49546, United States
| | - Amanda B. Witte
- Department
of Chemistry and Biochemistry, Calvin College, 3201 Burton Street Southeast, Grand Rapids, Michigan 49546, United States
| | - Margaret Van Winkle
- Department
of Chemistry and Biochemistry, Calvin College, 3201 Burton Street Southeast, Grand Rapids, Michigan 49546, United States
| | - Dejian Zhou
- School
of Chemistry and Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds LS2 9JT, U.K
| | - Kumar Sinniah
- Department
of Chemistry and Biochemistry, Calvin College, 3201 Burton Street Southeast, Grand Rapids, Michigan 49546, United States
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23
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Kim KT, Kim BH. A fluorescent probe for the 3'-overhang of telomeric DNA based on competition between two interstrand G-quadruplexes. Chem Commun (Camb) 2013; 49:1717-9. [PMID: 23344213 DOI: 10.1039/c3cc37504h] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
A 6-mer oligonucleotide containing a fluorescent (Bod)U moiety has been used as a novel fluorescent probe for the 3'-overhang of telomeric DNA based on competition between non-fluorescent tetramolecular and fluorescent (3+1) intermolecular G-quadruplexes.
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Affiliation(s)
- Ki Tae Kim
- Department of Chemistry, BK School of Molecular Science, Pohang University of Science and Technology, Pohang 790-784, South Korea
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24
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Zhao P, Lu JZ, Hong FY, Ou BH, Zhang FD, Ma LN, Guo HM. Shedding light on the interactions of guanine quadruplexes with tricationic metalloporphyrins. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2013; 108:1-7. [PMID: 23434614 DOI: 10.1016/j.saa.2013.01.074] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/20/2012] [Revised: 01/24/2013] [Accepted: 01/28/2013] [Indexed: 06/01/2023]
Abstract
G-quadruplex DNA presents a potential target for the design and development of novel anticancer drugs. The porphyrin TMPyP4 was early reported to be a suitable motif for G-quadruplex DNA interaction. We inserted various metal ions such as Zn(II), Cu(II), Co(III) in the center of the aromatic core of tricationic TMPyP4-like porphyrin and examined their interactions with an antiparallel G-quadruplex DNA by a combination of spectroscopy and Job plot methods. Porphyrin metallation allowed the conclusion that the presence of one axial ligand perpendicular to the aromatic plane did not hamper π-π stacking interactions between quadruplex and the aromatic parts of porphyrin on the other face while porphyrin with two axial ligands was unable to undergo such interaction due to geometrical factors. Free base porphyrin and porphyrin without axial ligands are able to stabilize the quadruplex structure to a greater extent than the other metal complexes and thus may be potential anti-cancer drugs.
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Affiliation(s)
- Ping Zhao
- School of Chemistry and Chemical Engineering, Guangdong Pharmaceutical University, No. 280, Waihuandong Road, Education Mega Centre, Guangzhou 510006, PR China.
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25
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Hänsel R, Löhr F, Trantirek L, Dötsch V. High-resolution insight into G-overhang architecture. J Am Chem Soc 2013; 135:2816-24. [PMID: 23339582 DOI: 10.1021/ja312403b] [Citation(s) in RCA: 90] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
NMR and fluorescence spectroscopy were used to address the effect of intracellular molecular crowding and related hydration on a model telomeric G-quadruplex (G4) DNA structure (d(AG(3)(TTAGGG)(3))). d(AG(3)(TTAGGG)(3)) prevalently adopted the hybrid-1 conformation in vivo, ex vivo, and in dilute potassium-based solution, while it formed the parallel propeller fold in water-depleted potassium-based solution, a commonly used model system for studying intracellular molecular crowding. The dilute potassium-based solution appeared to imitate the properties of the cellular environment required for d(AG(3)(TTAGGG)(3)) folding under in vivo and ex vivo conditions. High-resolution NMR investigations of site-specifically (15)N-labeled G4 units in native-like single-stranded telomeric DNA revealed that the 3'-terminal and internal G4 unit predominantly coexist in 2-tetrad antiparallel basket and hybrid-2 structures that are arranged in "beads-on-a-string"-like fashion. Our data provide the first high-resolution insight into the telomeric G-overhang architecture under essentially physiological conditions and identify the 2-tetrad antiparallel basket and hybrid-2 topologies as the structural targets for the development of telomere-specific G4 ligands.
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Affiliation(s)
- Robert Hänsel
- Institute of Biophysical Chemistry and Center for Biomolecular Magnetic Resonance, Goethe University, Frankfurt/Main, Germany.
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26
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Yu H, Gu X, Nakano SI, Miyoshi D, Sugimoto N. Beads-on-a-string structure of long telomeric DNAs under molecular crowding conditions. J Am Chem Soc 2012; 134:20060-9. [PMID: 22934853 DOI: 10.1021/ja305384c] [Citation(s) in RCA: 88] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The structure and stability of long telomeric DNAs, (T(2)AG(3))(n) (n = 4-20), were studied under dilute and molecular crowding conditions in the presence of Na(+) and K(+). Structural analysis showed that the long telomeric DNAs formed intramolecular G-quadruplexes under all conditions. In the presence of Na(+), the telomeric DNAs formed an antiparallel G-quadruplex under both dilute and molecular crowding conditions. However, in the presence of K(+), molecular crowding induced a conformational change from mixed to parallel. These results are consistent with numerous structural studies for G-quadruplex units under molecular crowding conditions. Thermodynamic analysis showed that G-quadruplexes under the molecular crowding conditions were obviously more stable than under dilute condition. Interestingly, this stabilization effect of molecular crowding was reduced for the longer telomeric DNAs, indicating that the G-quadruplex structure of long telomeric DNAs is not as stable under molecular crowding conditions, as implied from the large stabilization of isolated G-quadruplex units as previously reported. Moreover, a hydration study revealed that upon structure folding, the interior of a G-quadruplex unit was dehydrated, whereas the linker between two units was more hydrated. It is thus possible to propose that the linkers between G-quadruplex units are ordered structures but not random coils, which could have an important influence on the stability of the entire structure of long telomeric DNAs. These results are significant to elucidate the biological characteristics of telomeres, and can aid in the rational design of ligands and drugs targeting the telomere and related proteins.
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Affiliation(s)
- Haiqing Yu
- FIBER (Frontier Institute for Biomolecular Engineering Research), Konan University, 7-1-20 Minatijima-Minatomachi, Chuo-ku, Kobe 650-0047, Japan
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27
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G-ruption: the third international meeting on G-quadruplex and G-assembly. Biochimie 2012; 94:2475-83. [PMID: 22974982 DOI: 10.1016/j.biochi.2012.09.002] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2012] [Accepted: 09/04/2012] [Indexed: 12/31/2022]
Abstract
A three and a half day conference focusing on nucleic acid structures called G-quadruplexes (G4s) and other guanine-based assemblies was held in Sorrento, Italy (June 28-July 1, 2011) and featured 35 invited talks and over 89 posters. The G-quadruplex field continues to expand at an explosive rate with the emergence of new connections to biology, chemistry, physics, and nanotechnology. Following the trend established by the previous two international G4 meetings, the conference touched upon all these areas and facilitated productive exchanges of ideas between researchers from all over the world.
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28
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Payet L, Huppert JL. Stability and structure of long intramolecular G-quadruplexes. Biochemistry 2012; 51:3154-61. [PMID: 22417391 DOI: 10.1021/bi201750g] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
G-quadruplexes are formed from guanine-rich sequences of DNA and RNA. They consist of stacks of square arrangements of guanines called G-quartets. Increasing evidence suggests that these structures are involved in cellular processes such as transcription or translation. Knowing their structure and their stability in vitro should help to predict their formation in vivo and to understand their biological functions. Many studies have been performed on isolated G-quadruplexes, but little attention has been given to their interactions. Here, we present non-denaturing gel electrophoresis, UV melting, and circular dichroism data obtained for long sequences of DNA which are capable of forming two simultaneous G-quadruplexes, namely, d(TG(3)T(3)G(3)T(3)G(3)T(3)G(3)T(n)G(3)T(3)G(3)T(3)G(3)T(3)G(3)T), with n varying from one to seven. These sequences can form up to two separate G-quadruplexes. We also study mutated versions of these sequences designed to form one G-quadruplex at specific positions on the strand. Comparing results from the original sequences and their mutated versions, we show that for the former different folded states coexist: either with six stacked G-quartets or only three, in various combinations. Which ones are favored depends on n. Moreover, for n greater than three, the thermodynamic stability stays constant, contrary to an expected decrease in stability if the six G-quartets were stacked together in a single structure. This result agrees with a beads-on-a-string folding model for long sequences of G-quadruplexes, where two adjacent G-quadruplexes fold independently.
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Affiliation(s)
- Linda Payet
- Cavendish Laboratory, University of Cambridge, Cambridge CB3 OHE, UK.
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29
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Circular dichroism and guanine quadruplexes. Methods 2012; 57:64-75. [PMID: 22450044 DOI: 10.1016/j.ymeth.2012.03.011] [Citation(s) in RCA: 311] [Impact Index Per Article: 25.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2012] [Revised: 03/08/2012] [Accepted: 03/09/2012] [Indexed: 11/22/2022] Open
Abstract
Circular dichroism (CD) is remarkably sensitive to the conformational states of nucleic acids; therefore, CD spectroscopy has been used to study most features of DNA and RNA structures. Quadruplexes are among the significant noncanonical nucleic acids architectures that have received special attentions recently. This article presents examples on the contribution of CD spectroscopy to our knowledge of quadruplex structures and their polymorphism. The examples were selected to demonstrate the potential of this simple method in the quadruplex field. As CD spectroscopy detects only the global feature of a macromolecule, it should preferably be used in combination with other techniques. On the other hand, CD spectroscopy, often as a pioneering approach, can reveal the formation of particular structural arrangements, to search for the conditions stabilizing the structures, to follow the transitions between various structural states, to explore kinetics of their appearance, to determine thermodynamic parameters and also detect formation of higher order structures. This article aims to show that CD spectroscopy is an important complementary technique to NMR spectroscopy and X-ray diffraction in quadruplex studies.
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30
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Trajkovski M, da Silva MW, Plavec J. Unique structural features of interconverting monomeric and dimeric G-quadruplexes adopted by a sequence from the intron of the N-myc gene. J Am Chem Soc 2012; 134:4132-41. [PMID: 22303871 DOI: 10.1021/ja208483v] [Citation(s) in RCA: 62] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
A multidimensional heteronuclear NMR study has demonstrated that a guanine-rich DNA oligonucleotide originating from the N-myc gene folds into G-quadruplex structures in the presence of K(+), NH(4)(+), and Na(+) ions. A monomeric G-quadruplex formed in K(+) ion containing solution exhibits three G-quartets and flexible propeller-type loops. The 3D structure with three single nucleotide loops represents a missing element in structures of parallel G-quadruplexes. The structural features together with the high temperature stability are suggestive of the specific biological role of G-quadruplex formation within the intron of the N-myc gene. An increase in K(+) ion and oligonucleotide concentrations resulted in transformation of the monomeric G-quadruplex into a dimeric form. The dimeric G-quadruplex exhibits six stacked G-quartets, parallel strand orientations, and propeller-type loops. A link between the third and the fourth G-quartets consists of two adenine residues that are flipped out to facilitate consecutive stacking of six G-quartets.
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Affiliation(s)
- Marko Trajkovski
- Slovenian NMR Center, National Institute of Chemistry, Hajdrihova 19, SI-1000 Ljubljana, Slovenia
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Abstract
Structural studies have shown that four G-tracts along a DNA strand are the minimal requirement for intramolecular G-quadruplex formation. Longer DNA sequences containing multiples of four G-tracts could, in principle, form higher-order structures based on multiple G-quadruplex blocks. This latter condition is abundantly verified for the telomeric single-stranded overhang (~200 nt) consisting of tens of TTAGGG repeats, thus opening new interesting questions about the structure of the "real" telomeric DNA. How many quadruplex units form in the human telomeric overhang? Which type of quadruplex topologies? Do they interact or not? What about their binding properties? Although many of these questions are still unanswered, recent experimental and computational studies have begun to address them. The existence and relevance of these higher-order quadruplex structures in the human genome is now an interesting and stimulating research topic in the quadruplex field. The recent results, the unsolved problems, and the future prospects for understanding higher-order telomeric quadruplex structures are the main topics of this review. Other studies on long telomeric RNA sequences and on other intramolecular (non telomeric) DNA higher order quadruplex structures are also presented.
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Petraccone L, Spink C, Trent JO, Garbett NC, Mekmaysy CS, Giancola C, Chaires JB. Structure and stability of higher-order human telomeric quadruplexes. J Am Chem Soc 2011; 133:20951-61. [PMID: 22082001 PMCID: PMC3244555 DOI: 10.1021/ja209192a] [Citation(s) in RCA: 151] [Impact Index Per Article: 11.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
G-quadruplex formation in the sequences 5'-(TTAGGG)(n) and 5'(TTAGGG)(n)TT (n = 4, 8, 12) was studied using circular dichroism, sedimentation velocity, differential scanning calorimetry, and molecular dynamics simulations. Sequences containing 8 and 12 repeats formed higher-order structures with two and three contiguous quadruplexes, respectively. Plausible structures for these sequences were determined by molecular dynamics simulations followed by experimental testing of predicted hydrodynamic properties by sedimentation velocity. These structures featured folding of the strand into contiguous quadruplexes with mixed hybrid conformations. Thermodynamic studies showed the strands folded spontaneous to contain the maximum number contiguous quadruplexes. For the sequence 5'(TTAGGG)(12)TT, more than 90% of the strands contained completely folded structures with three quadruplexes. Statistical mechanical-based deconvolution of thermograms for three quadruplex structures showed that each quadruplex melted independently with unique thermodynamic parmameters. Thermodynamic analysis revealed further that quadruplexes in higher-ordered structures were destabilized relative to their monomeric counterparts, with unfavorable coupling free energies. Quadruplex stability thus depends critically on the sequence and structural context.
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Affiliation(s)
- Luigi Petraccone
- Dept. Chimica “P. Corradini”, University of Naples “Federico II”, 80122 Naples, Italy
- Department of Medicine, James Graham Brown Cancer Center, University of Louisville, 505 S. Hancock St., Louisville, KY 40202
| | - Charles Spink
- Department of Chemistry, SUNY-Cortland, Cortland, NY 13045
| | - John O. Trent
- Department of Medicine, James Graham Brown Cancer Center, University of Louisville, 505 S. Hancock St., Louisville, KY 40202
| | - Nichola C. Garbett
- Department of Medicine, James Graham Brown Cancer Center, University of Louisville, 505 S. Hancock St., Louisville, KY 40202
| | - Chongkham S. Mekmaysy
- Department of Medicine, James Graham Brown Cancer Center, University of Louisville, 505 S. Hancock St., Louisville, KY 40202
| | - Concetta Giancola
- Dept. Chimica “P. Corradini”, University of Naples “Federico II”, 80122 Naples, Italy
| | - Jonathan B. Chaires
- Department of Medicine, James Graham Brown Cancer Center, University of Louisville, 505 S. Hancock St., Louisville, KY 40202
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33
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Stefan L, Denat F, Monchaud D. Deciphering the DNAzyme activity of multimeric quadruplexes: insights into their actual role in the telomerase activity evaluation assay. J Am Chem Soc 2011; 133:20405-15. [PMID: 22050329 DOI: 10.1021/ja208145d] [Citation(s) in RCA: 89] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
The end of human telomeres is comprised of a long G-rich single-stranded DNA (known as 3'-overhang) able to adopt an unusual three-dimensional "beads-on-the-string" organization made of consecutively stacked G-quadruplex units (so-called quadruplex multimers). It has been widely demonstrated that, upon interaction with hemin, discrete quadruplexes acquire peroxidase-mimicking properties, oxidizing several organic probes in H(2)O(2)-rich conditions; this property, known as DNAzyme, has found tens of applications in the last two decades. However, little is known about the DNAzyme activity of multimeric quadruplexes; this is an important question to address, especially in light of recent reports that exploit the DNAzyme process to optically assess the activity of an enzyme that elongates the telomeric overhang, the telomerase. Herein, we thoroughly investigate the DNAzyme activity of long telomeric fragments, with a particular focus on both the nature of the hemin/multimeric quadruplex interactions and the putative higher-order fold of the studied fragments; in light of our results, we also propose possible ways that may be followed to improve the use of DNAzyme to evaluate the telomerase activity.
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Affiliation(s)
- Loic Stefan
- Institut de Chimie Moléculaire, Université de Bourgogne (ICMUB), CNRS UMR5260, 9, avenue Alain Savary, 21000 Dijon, France
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