1
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Sun X, Zhang W, Gou C, Wang X, Wang X, Shao X, Chen X, Chen Z. AS1411 binds to nucleolin via its parallel structure and disrupts the exos-miRNA-27a-mediated reciprocal activation loop between glioma and astrocytes. Biochim Biophys Acta Mol Basis Dis 2024; 1870:167211. [PMID: 38701957 DOI: 10.1016/j.bbadis.2024.167211] [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: 10/18/2023] [Revised: 04/11/2024] [Accepted: 04/24/2024] [Indexed: 05/06/2024]
Abstract
The interaction between glioma cells and astrocytes promotes the proliferation of gliomas. Micro-RNAs (miRNAs) carried by astrocyte exosomes (exos) may be involved in this process, but the mechanism remains unclear. The oligonucleotide AS1411, which consists of 26 bases and has a G-quadruplex structure, is an aptamer that targets nucleolin. In this study, we demonstrate exosome-miRNA-27a-mediated cross-activation between astrocytes and glioblastoma and show that AS1411 reduces astrocytes' pro-glioma activity. The enhanced affinity of AS1411 toward nucleolin is attributed to its G-quadruplex structure. After binding to nucleolin, AS1411 inhibits the entry of the NF-κB pathway transcription factor P65 into the nucleus, then downregulates the expression of miRNA-27a in astrocytes surrounding gliomas. Then, AS1411 downregulates astrocyte exosome-miRNA-27a and upregulates the expression of INPP4B, the target gene of miRNA-27a in gliomas, thereby inhibiting the PI3K/AKT pathway and inhibiting glioma proliferation. These results were verified in mouse orthotopic glioma xenografts and human glioma samples. In conclusion, the parallel structure of AS1411 allows it to bind to nucleolin and disrupt the exosome-miRNA-27a-mediated reciprocal activation loop between glioma cells and astrocytes. Our results may help in the development of a novel approach to therapeutic modulation of the glioma microenvironment.
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Affiliation(s)
- Xiaoming Sun
- School of Basic Medical Sciences, Hubei University of Medicine, Shiyan 442000, China; Biomedical Research Institute, Hubei University of Medicine, Shiyan 442000, China; Hubei Key Laboratory of Embryonic Stem Cell Research, Hubei University of Medicine, Shiyan 442000, China
| | - Wenzi Zhang
- School of Basic Medical Sciences, Hubei University of Medicine, Shiyan 442000, China; Biomedical Research Institute, Hubei University of Medicine, Shiyan 442000, China; Hubei Key Laboratory of Embryonic Stem Cell Research, Hubei University of Medicine, Shiyan 442000, China
| | - Changlong Gou
- Department of ultrasound medicine, Taihe Hospital, Hubei University of Medicine, Shiyan 442000, China
| | - Xinyu Wang
- School of Basic Medical Sciences, Hubei University of Medicine, Shiyan 442000, China; Biomedical Research Institute, Hubei University of Medicine, Shiyan 442000, China; Hubei Key Laboratory of Embryonic Stem Cell Research, Hubei University of Medicine, Shiyan 442000, China
| | - Xianhui Wang
- Biomedical Research Institute, Hubei University of Medicine, Shiyan 442000, China; Hubei Key Laboratory of Embryonic Stem Cell Research, Hubei University of Medicine, Shiyan 442000, China
| | - Xin Shao
- School of Basic Medical Sciences, Hubei University of Medicine, Shiyan 442000, China
| | - Xiao Chen
- Department of Pharmacology, School of Basic Medical Sciences, Wuhan University, Wuhan 430072, China.
| | - Zhuo Chen
- School of Basic Medical Sciences, Hubei University of Medicine, Shiyan 442000, China; Biomedical Research Institute, Hubei University of Medicine, Shiyan 442000, China; Hubei Key Laboratory of Embryonic Stem Cell Research, Hubei University of Medicine, Shiyan 442000, China.
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2
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Wang J, Tang Y, Zheng J, Xie Z, Zhou J, Wu Y. DNAzyme-based and smartphone-assisted colorimetric biosensor for ultrasensitive and highly selective detection of histamine in meats. Food Chem 2024; 435:137526. [PMID: 37742463 DOI: 10.1016/j.foodchem.2023.137526] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2023] [Revised: 08/27/2023] [Accepted: 09/16/2023] [Indexed: 09/26/2023]
Abstract
Herein, a colorimetric biosensor for histamine detection in meat is first established based on the enhancement of DNAzyme with peroxidase-mimic activity. Histamine can boost the generation of G-quadruplex sequences, and make them more easily bond with hemin to produce many DNAzyme molecules. In addition, histamine increases the affinity of DNAzyme to the substrate 3,3',5,5'-tetramethylbenzidine (TMB). Therefore, the obtained DNAzyme can catalyze H2O2 and dissolved oxygen to produce many reactive oxygen species (ROS), which cause the TMB molecule to lose two electrons and generate yellow products, exhibiting a clear absorption peak at 450 nm. The colorimetric biosensor has excellent sensitivity, and the detection limit is as low as 38 μg·L-1 for histamine. Moreover, the biosensor has high selectivity and anti-interference ability, and exhibits a good recovery rate in actual meats. The above results show that the strategy has potential for application in the detection of trace histamine in meats.
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Affiliation(s)
- Junjun Wang
- Guizhou Province Key Laboratory of Fermentation Engineering and Biopharmacy, School of Liquor and Food Engineering, Guizhou University, Guiyang 550025, China
| | - Yue Tang
- College of Life Sciences, Guizhou University, Guiyang 550025, China
| | - Jia Zheng
- Wuliangye Yibin Co., Ltd, Yibin 644000, Sichuan Province, China
| | - Zhengmin Xie
- Wuliangye Yibin Co., Ltd, Yibin 644000, Sichuan Province, China
| | - Jianli Zhou
- Guizhou Province Key Laboratory of Fermentation Engineering and Biopharmacy, School of Liquor and Food Engineering, Guizhou University, Guiyang 550025, China
| | - Yuangen Wu
- Guizhou Province Key Laboratory of Fermentation Engineering and Biopharmacy, School of Liquor and Food Engineering, Guizhou University, Guiyang 550025, China; College of Life Sciences, Guizhou University, Guiyang 550025, China.
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3
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Jana J, Vianney YM, Weisz K. Impact of loop length and duplex extensions on the design of hybrid-type G-quadruplexes. Chem Commun (Camb) 2024; 60:854-857. [PMID: 38131370 DOI: 10.1039/d3cc05625b] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2023]
Abstract
A G-rich core sequence G3-TCA-G3-T1,2-G3-T1,2-G3 can be designed to fold into a parallel or into two different (3+1) hybrid-type G-quadruplexes, among them an elusive topology with one lateral followed by two propeller loops. Favored folds can be rationalized based on the number of intervening thymidines and on additional complementary flanking sequences.
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Affiliation(s)
- Jagannath Jana
- Institut für Biochemie, Universität Greifswald, Felix-Hausdorff Str. 4, Greifswald D-17489, Germany.
| | - Yoanes Maria Vianney
- Institut für Biochemie, Universität Greifswald, Felix-Hausdorff Str. 4, Greifswald D-17489, Germany.
| | - Klaus Weisz
- Institut für Biochemie, Universität Greifswald, Felix-Hausdorff Str. 4, Greifswald D-17489, Germany.
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4
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Huang R, Feng Y, Gao Z, Ahmed A, Zhang W. The Epigenomic Features and Potential Functions of PEG- and PDS-Favorable DNA G-Quadruplexes in Rice. Int J Mol Sci 2024; 25:634. [PMID: 38203805 PMCID: PMC10779103 DOI: 10.3390/ijms25010634] [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: 11/29/2023] [Revised: 12/26/2023] [Accepted: 12/29/2023] [Indexed: 01/12/2024] Open
Abstract
A G-quadruplex (G4) is a typical non-B DNA structure and involved in various DNA-templated events in eukaryotic genomes. PEG and PDS chemicals have been widely applied for promoting the folding of in vivo or in vitro G4s. However, how PEG and PDS preferentially affect a subset of G4 formation genome-wide is still largely unknown. We here conducted a BG4-based IP-seq in vitro under K++PEG or K++PDS conditions in the rice genome. We found that PEG-favored IP-G4s+ have distinct sequence features, distinct genomic distributions and distinct associations with TEGs, non-TEGs and subtypes of TEs compared to PDS-favored ones. Strikingly, PEG-specific IP-G4s+ are associated with euchromatin with less enrichment levels of DNA methylation but with more enriched active histone marks, while PDS-specific IP-G4s+ are associated with heterochromatin with higher enrichment levels of DNA methylation and repressive marks. Moreover, we found that genes with PEG-specific IP-G4s+ are more expressed than those with PDS-specific IP-G4s+, suggesting that PEG/PDS-specific IP-G4s+ alone or coordinating with epigenetic marks are involved in the regulation of the differential expression of related genes, therefore functioning in distinct biological processes. Thus, our study provides new insights into differential impacts of PEG and PDS on G4 formation, thereby advancing our understanding of G4 biology.
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Affiliation(s)
| | | | | | | | - Wenli Zhang
- State Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, CIC-MCP, Nanjing Agricultural University, No.1 Weigang, Nanjing 210095, China; (R.H.); (Y.F.); (Z.G.); (A.A.)
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5
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Papp C, Mukundan VT, Jenjaroenpun P, Winnerdy FR, Ow GS, Phan AT, Kuznetsov VA. Stable bulged G-quadruplexes in the human genome: identification, experimental validation and functionalization. Nucleic Acids Res 2023; 51:4148-4177. [PMID: 37094040 DOI: 10.1093/nar/gkad252] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2022] [Revised: 03/23/2023] [Accepted: 04/19/2023] [Indexed: 04/26/2023] Open
Abstract
DNA sequence composition determines the topology and stability of G-quadruplexes (G4s). Bulged G-quadruplex structures (G4-Bs) are a subset of G4s characterized by 3D conformations with bulges. Current search algorithms fail to capture stable G4-B, making their genome-wide study infeasible. Here, we introduced a large family of computationally defined and experimentally verified potential G4-B forming sequences (pG4-BS). We found 478 263 pG4-BS regions that do not overlap 'canonical' G4-forming sequences in the human genome and are preferentially localized in transcription regulatory regions including R-loops and open chromatin. Over 90% of protein-coding genes contain pG4-BS in their promoter or gene body. We observed generally higher pG4-BS content in R-loops and their flanks, longer genes that are associated with brain tissue, immune and developmental processes. Also, the presence of pG4-BS on both template and non-template strands in promoters is associated with oncogenesis, cardiovascular disease and stemness. Our G4-BS models predicted G4-forming ability in vitro with 91.5% accuracy. Analysis of G4-seq and CUT&Tag data strongly supports the existence of G4-BS conformations genome-wide. We reconstructed a novel G4-B 3D structure located in the E2F8 promoter. This study defines a large family of G4-like sequences, offering new insights into the essential biological functions and potential future therapeutic uses of G4-B.
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Affiliation(s)
- Csaba Papp
- Department of Urology, Department of Biochemistry and Molecular Biology, SUNY Upstate Medical University, Syracuse, NY 13210, USA
| | - Vineeth T Mukundan
- School of Physical and Mathematical Sciences, Nanyang Technological University, Singapore 637371, Singapore
| | - Piroon Jenjaroenpun
- Division of Bioinformatics and Data Management for Research, Research Group and Research Network Division, Research Department, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, Thailand
- Bioinformatics Institute, A*STAR Biomedical Institutes, Singapore, Singapore
| | - Fernaldo Richtia Winnerdy
- School of Physical and Mathematical Sciences, Nanyang Technological University, Singapore 637371, Singapore
| | - Ghim Siong Ow
- Bioinformatics Institute, A*STAR Biomedical Institutes, Singapore, Singapore
| | - Anh Tuân Phan
- School of Physical and Mathematical Sciences, Nanyang Technological University, Singapore 637371, Singapore
- NTU Institute of Structural Biology, Nanyang Technological University, Singapore 636921, Singapore
| | - Vladimir A Kuznetsov
- Department of Urology, Department of Biochemistry and Molecular Biology, SUNY Upstate Medical University, Syracuse, NY 13210, USA
- Bioinformatics Institute, A*STAR Biomedical Institutes, Singapore, Singapore
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6
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Peng H, Dang L, Toghraie D. Molecular dynamics simulation of thermal characteristics of globulin protein dissolved in dilute salt solutions using equilibrium and non-equilibrium methods. J Therm Biol 2023; 113:103505. [PMID: 37055105 DOI: 10.1016/j.jtherbio.2023.103505] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2022] [Revised: 01/28/2023] [Accepted: 02/08/2023] [Indexed: 02/13/2023]
Abstract
The aggregation of 7S globulin protein (7SGP) in mature soybean (Glycine max) seeds is an extracellular matrix protein. This atomic compound can be detected in various food products. So, this protein structure's thermal properties (TP) can be important for various food industry products. Molecular Dynamics (MD) simulations describe the atomic arrangement of this protein and forecast TP of them in various initial conditions. The present computational work estimates the 7SGP thermal behavior (TB) by equilibrium (E) and non-equilibrium (NE) methods. In these two methods, the 7SGP is represented using DREIDING interatomic potential. MD outputs predicted 0.59 and 0.58 W/mK values for thermal conductivity (TC) of 7SGP at T0 = 300 K and P0 = 1 bar using E and NE methods. Furthermore, computational results represented that the pressure (P) and temperature (T) are significant factors for the TB of 7SGP. Numerically, TC of 7SGP reaches 0.68 W/mK, 0.52 W/mK by T/P increasing. MD results predicted the interaction energy (IE) between 7SGP and aqueous media could fluctuate between -110.64 and 161.53 kcal/mol by the change in T/P after t = 10 ns?These results should be supposed to design new methods for various food industry purposes, such as producing and processing edible oils.
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7
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Chang-Gu B, Venkatesan S, Russell R. Kinetics measurements of G-quadruplex binding and unfolding by helicases. Methods 2022; 204:1-13. [PMID: 35483547 PMCID: PMC10034854 DOI: 10.1016/j.ymeth.2022.04.012] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2022] [Revised: 04/15/2022] [Accepted: 04/22/2022] [Indexed: 01/28/2023] Open
Abstract
G-quadruplex structures (G4s) form readily in DNA and RNA and play diverse roles in gene expression and other processes, and their inappropriate formation and stabilization are linked to human diseases. G4s are inherently long-lived, such that their timely unfolding depends on a suite of DNA and RNA helicase proteins. Biochemical analysis of G4 binding and unfolding by individual helicase proteins is important for establishing their levels of activity, affinity, and specificity for G4s, including individual G4s of varying sequence and structure. Here we describe a set of simple, accessible methods in which electrophoretic mobility shift assays (EMSA) are used to measure the kinetics of G4 binding, dissociation, and unfolding by helicase proteins. We focus on practical considerations and the pitfalls that are most likely to arise when these methods are used to study the activities of helicases on G4s.
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Affiliation(s)
- Bruce Chang-Gu
- Department of Molecular Biosciences, University of Texas at Austin, Austin TX 78712, United States
| | - Sneha Venkatesan
- Department of Molecular Biosciences, University of Texas at Austin, Austin TX 78712, United States
| | - Rick Russell
- Department of Molecular Biosciences, University of Texas at Austin, Austin TX 78712, United States.
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8
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Jana J, Vianney YM, Schröder N, Weisz K. Guiding the folding of G-quadruplexes through loop residue interactions. Nucleic Acids Res 2022; 50:7161-7175. [PMID: 35758626 PMCID: PMC9262619 DOI: 10.1093/nar/gkac549] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2022] [Revised: 05/25/2022] [Accepted: 06/14/2022] [Indexed: 12/24/2022] Open
Abstract
A G-rich sequence was designed to allow folding into either a stable parallel or hybrid-type topology. With the parent sequence featuring coexisting species, various related sequences with single and double mutations and with a shortened central propeller loop affected the topological equilibrium. Two simple modifications, likewise introduced separately to all sequences, were employed to lock folds into one of the topologies without noticeable structural alterations. The unique combination of sequence mutations, high-resolution NMR structural information, and the thermodynamic stability for both topological competitors identified critical loop residue interactions. In contrast to first loop residues, which are mostly disordered and exposed to solvent in both propeller and lateral loops bridging a narrow groove, the last loop residue in a lateral three-nucleotide loop is engaged in stabilizing stacking interactions. The propensity of single-nucleotide loops to favor all-parallel topologies by enforcing a propeller-like conformation of an additional longer loop is shown to result from their preference in linking two outer tetrads of the same tetrad polarity. Taken together, the present studies contribute to a better structural and thermodynamic understanding of delicate loop interactions in genomic and artificially designed quadruplexes, e.g. when employed as therapeutics or in other biotechnological applications.
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Affiliation(s)
- Jagannath Jana
- Institute of Biochemistry, Universität Greifswald, D-17489 Greifswald, Germany
| | | | - Nina Schröder
- Institute of Biochemistry, Universität Greifswald, D-17489 Greifswald, Germany
| | - Klaus Weisz
- To whom correspondence should be addressed. Tel: +49 3834 420 4426; Fax: +49 3834 420 4427;
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9
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Devi G, Winnerdy FR, Ang JCY, Lim KW, Phan AT. Four-Layered Intramolecular Parallel G-Quadruplex with Non-Nucleotide Loops: An Ultra-Stable Self-Folded DNA Nano-Scaffold. ACS NANO 2022; 16:533-540. [PMID: 34927423 DOI: 10.1021/acsnano.1c07630] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
A four-stranded scaffold of nucleic acids termed G-quadruplex (G4) has found growing applications in nano- and biotechnology. Propeller loops are a hallmark of the most stable intramolecular parallel-stranded G4s. To date, propeller loops have been observed to span only a maximum of three G-tetrad layers. Going beyond that would allow creation of more stable scaffolds useful for building robust nanodevices. Here we investigate the formation of propeller loops spanning more than three layers. We show that native nucleotide sequences are incompatible toward this goal, and we report on synthetic non-nucleotide linkers that form a propeller loop across four layers. With the established linkers, we constructed a four-layered intramolecular parallel-stranded G4, which exhibited ultrahigh thermal stability. Control on loop design would augment the toolbox toward engineering of G4-based nanoscaffolds for diverse applications.
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Affiliation(s)
- Gitali Devi
- School of Physical and Mathematical Sciences, Nanyang Technological University, Singapore 637371, Singapore
| | - Fernaldo Richtia Winnerdy
- School of Physical and Mathematical Sciences, Nanyang Technological University, Singapore 637371, Singapore
| | - Jason Cheng Yu Ang
- School of Physical and Mathematical Sciences, Nanyang Technological University, Singapore 637371, Singapore
| | - Kah Wai Lim
- School of Physical and Mathematical Sciences, Nanyang Technological University, Singapore 637371, Singapore
| | - Anh Tuân Phan
- School of Physical and Mathematical Sciences, Nanyang Technological University, Singapore 637371, Singapore
- NTU Institute of Structural Biology, Nanyang Technological University, Singapore 636921, Singapore
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10
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Grün JT, Schwalbe H. Folding dynamics of polymorphic G-quadruplex structures. Biopolymers 2021; 113:e23477. [PMID: 34664713 DOI: 10.1002/bip.23477] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2021] [Revised: 09/30/2021] [Accepted: 09/30/2021] [Indexed: 12/14/2022]
Abstract
G-quadruplexes (G4), found in numerous places within the human genome, are involved in essential processes of cell regulation. Chromosomal DNA G4s are involved for example, in replication and transcription as first steps of gene expression. Hence, they influence a plethora of downstream processes. G4s possess an intricate structure that differs from canonical B-form DNA. Identical DNA G4 sequences can adopt multiple long-lived conformations, a phenomenon known as G4 polymorphism. A detailed understanding of the molecular mechanisms that drive G4 folding is essential to understand their ambivalent regulatory roles. Disentangling the inherent dynamic and polymorphic nature of G4 structures thus is key to unravel their biological functions and make them amenable as molecular targets in novel therapeutic approaches. We here review recent experimental approaches to monitor G4 folding and discuss structural aspects for possible folding pathways. Substantial progress in the understanding of G4 folding within the recent years now allows drawing comprehensive models of the complex folding energy landscape of G4s that we herein evaluate based on computational and experimental evidence.
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Affiliation(s)
- J Tassilo Grün
- Department of Chemical and Biological Physics, Weizmann Institute of Science, Rehovot, Israel
| | - Harald Schwalbe
- Institute for Organic Chemistry and Chemical Biology, Johann Wolfgang Goethe-University, Frankfurt/M, Germany.,Center for Biomolecular Magnetic Resonance (BMRZ), Johann Wolfgang Goethe-University Frankfurt, Frankfurt/M, Germany
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11
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Jana J, Weisz K. Thermodynamic Stability of G-Quadruplexes: Impact of Sequence and Environment. Chembiochem 2021; 22:2848-2856. [PMID: 33844423 PMCID: PMC8518667 DOI: 10.1002/cbic.202100127] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2021] [Revised: 04/09/2021] [Indexed: 12/19/2022]
Abstract
G-quadruplexes have attracted growing interest in recent years due to their occurrence in vivo and their possible biological functions. In addition to being promising targets for drug design, these four-stranded nucleic acid structures have also been recognized as versatile tools for various technological applications. Whereas a large number of studies have yielded insight into their remarkable structural diversity, our current knowledge on G-quadruplex stabilities as a function of sequence and environmental factors only gradually emerges with an expanding collection of thermodynamic data. This minireview provides an overview of general rules that may be used to better evaluate quadruplex thermodynamic stabilities but also discusses present challenges in predicting most stable folds for a given sequence and environment.
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Affiliation(s)
- Jagannath Jana
- Institute of BiochemistryUniversität GreifswaldFelix-Hausdorff Str. 417489GreifswaldGermany
| | - Klaus Weisz
- Institute of BiochemistryUniversität GreifswaldFelix-Hausdorff Str. 417489GreifswaldGermany
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12
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Hossain KA, Jurkowski M, Czub J, Kogut M. Mechanism of recognition of parallel G-quadruplexes by DEAH/RHAU helicase DHX36 explored by molecular dynamics simulations. Comput Struct Biotechnol J 2021; 19:2526-2536. [PMID: 34025941 PMCID: PMC8114077 DOI: 10.1016/j.csbj.2021.04.039] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2021] [Revised: 04/14/2021] [Accepted: 04/16/2021] [Indexed: 02/07/2023] Open
Abstract
Because of high stability and slow unfolding rates of G-quadruplexes (G4), cells have evolved specialized helicases that disrupt these non-canonical DNA and RNA structures in an ATP-dependent manner. One example is DHX36, a DEAH-box helicase, which participates in gene expression and replication by recognizing and unwinding parallel G4s. Here, we studied the molecular basis for the high affinity and specificity of DHX36 for parallel-type G4s using all-atom molecular dynamics simulations. By computing binding free energies, we found that the two main G4-interacting subdomains of DHX36, DSM and OB, separately exhibit high G4 affinity but they act cooperatively to recognize two distinctive features of parallel G4s: the exposed planar face of a guanine tetrad and the unique backbone conformation of a continuous guanine tract, respectively. Our results also show that DSM-mediated interactions are the main contributor to the binding free energy and rely on making extensive van der Waals contacts between the GXXXG motifs and hydrophobic residues of DSM and a flat guanine plane. Accordingly, the sterically more accessible 5'-G-tetrad allows for more favorable van der Waals and hydrophobic interactions which leads to the preferential binding of DSM to the 5'-side. In contrast to DSM, OB binds to G4 mostly through polar interactions by flexibly adapting to the 5'-terminal guanine tract to form a number of strong hydrogen bonds with the backbone phosphate groups. We also identified a third DHX36/G4 interaction site formed by the flexible loop missing in the crystal structure.
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Affiliation(s)
- Kazi Amirul Hossain
- Department of Physical Chemistry, Gdansk University of Technology, ul. Narutowicza 11/12, 80-233 Gdansk, Poland
| | - Michal Jurkowski
- Department of Physical Chemistry, Gdansk University of Technology, ul. Narutowicza 11/12, 80-233 Gdansk, Poland
| | - Jacek Czub
- Department of Physical Chemistry, Gdansk University of Technology, ul. Narutowicza 11/12, 80-233 Gdansk, Poland
| | - Mateusz Kogut
- Institute of Physics, Polish Academy of Sciences, Al. Lotnikow 32/46, 02-668 Warsaw, Poland
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13
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Vianney YM, Purwanto MGM, Weisz K. G-Quadruplex Formation in a Putative Coding Region of White Spot Syndrome Virus: Structural and Thermodynamic Aspects. Chembiochem 2021; 22:1932-1935. [PMID: 33710715 PMCID: PMC8252560 DOI: 10.1002/cbic.202100064] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2021] [Revised: 03/04/2021] [Indexed: 01/05/2023]
Abstract
White spot disease (WSD) is one of the most devastating viral infections of crustaceans caused by the white spot syndrome virus (WSSV). A conserved sequence WSSV131 in the DNA genome of WSSV was found to fold into a polymorphic G‐quadruplex structure. Supported by two mutant sequences with single G→T substitutions in the third G4 tract of WSSV131, circular dichroism and NMR spectroscopic analyses demonstrate folding of the wild‐type sequence into a three‐tetrad parallel topology comprising three propeller loops with a major 1 : 3 : 1 and a minor 1 : 2 : 2 loop length arrangement. A thermodynamic analysis of quadruplex formation by differential scanning calorimetry (DSC) indicates a thermodynamically more stable 1 : 3 : 1 loop isomer. DSC also revealed the formation of additional highly stable multimeric species with populations depending on potassium ion concentration.
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Affiliation(s)
- Yoanes Maria Vianney
- Institute of Biochemistry, Universität Greifswald, Felix-Hausdorff Str. 4, 17489, Greifswald, Germany
| | | | - Klaus Weisz
- Institute of Biochemistry, Universität Greifswald, Felix-Hausdorff Str. 4, 17489, Greifswald, Germany
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14
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Responses of DNA Mismatch Repair Proteins to a Stable G-Quadruplex Embedded into a DNA Duplex Structure. Int J Mol Sci 2020; 21:ijms21228773. [PMID: 33233554 PMCID: PMC7699706 DOI: 10.3390/ijms21228773] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2020] [Revised: 11/16/2020] [Accepted: 11/18/2020] [Indexed: 12/26/2022] Open
Abstract
DNA mismatch repair (MMR) plays a crucial role in the maintenance of genomic stability. The main MMR protein, MutS, was recently shown to recognize the G-quadruplex (G4) DNA structures, which, along with regulatory functions, have a negative impact on genome integrity. Here, we studied the effect of G4 on the DNA-binding activity of MutS from Rhodobacter sphaeroides (methyl-independent MMR) in comparison with MutS from Escherichia coli (methyl-directed MMR) and evaluated the influence of a G4 on the functioning of other proteins involved in the initial steps of MMR. For this purpose, a new DNA construct was designed containing a biologically relevant intramolecular stable G4 structure flanked by double-stranded regions with the set of DNA sites required for MMR initiation. The secondary structure of this model was examined using NMR spectroscopy, chemical probing, fluorescent indicators, circular dichroism, and UV spectroscopy. The results unambiguously showed that the d(GGGT)4 motif, when embedded in a double-stranded context, adopts a G4 structure of a parallel topology. Despite strong binding affinities of MutS and MutL for a G4, the latter is not recognized by E. coli MMR as a signal for repair, but does not prevent MMR processing when a G4 and G/T mismatch are in close proximity.
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15
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Cheng Y, Zhang Y, Gong Z, Zhang X, Li Y, Shi X, Pei Y, You H. High Mechanical Stability and Slow Unfolding Rates Are Prevalent in Parallel-Stranded DNA G-Quadruplexes. J Phys Chem Lett 2020; 11:7966-7971. [PMID: 32885976 DOI: 10.1021/acs.jpclett.0c02229] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Guanine-rich repeat sequences are known to adopt diverse G-quadruplex (G4) topologies. Determining the unfolding rates of individual G4 species is challenging due to the coexistence of multiple G4 conformations in a solution. Here, using single-molecule magnetic tweezers, we systematically measured the unfolding force distributions of 4 oncogene promoter G4s, 12 model sequences with two 1-nucleotide (nt) thymine loops that predominantly adopt parallel-stranded G4 structures, and 6 sequences forming multiple G4 structures. All parallel-stranded G4s reveal an unfolding force peak at 40-60 pN, which is associated with extremely slow unfolding rates on the order of 10-5-10-7 s-1. In contrast, nonparallel G4s and partially folded intermediate states reveal an unfolding force peak <40 pN. These results suggest a strong correlation between the parallel-stranded G4s folding topology and the slow unfolding rates and provide important insights into the mechanism that govern the stability and the transition kinetics of G4s.
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Affiliation(s)
- Yuanlei Cheng
- School of Pharmacy, Tongji Medical College, Huazhong University of Science and Technology, 430030 Wuhan, China
| | - Yashuo Zhang
- School of Pharmacy, Tongji Medical College, Huazhong University of Science and Technology, 430030 Wuhan, China
| | - Zhou Gong
- CAS Key Laboratory of Magnetic Resonance in Biological Systems, State Key Laboratory of Magnetic Resonance and Atomic Molecular Physics, National Center for Magnetic Resonance at Wuhan, Wuhan Institute of Physics and Mathematics of the Chinese Academy of Sciences, 430071 Wuhan, China
| | - Xinghua Zhang
- College of Life Sciences, the Institute for Advanced Studies, State Key Laboratory of Virology, Hubei Key Laboratory of Cell Homeostasis, Wuhan University, 430072 Wuhan, China
| | - Yutong Li
- School of Pharmacy, Tongji Medical College, Huazhong University of Science and Technology, 430030 Wuhan, China
| | - Xiangqian Shi
- School of Pharmacy, Tongji Medical College, Huazhong University of Science and Technology, 430030 Wuhan, China
| | - Yufeng Pei
- School of Pharmacy, Tongji Medical College, Huazhong University of Science and Technology, 430030 Wuhan, China
| | - Huijuan You
- School of Pharmacy, Tongji Medical College, Huazhong University of Science and Technology, 430030 Wuhan, China
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16
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Chalikian TV, Liu L, Macgregor RB. Duplex-tetraplex equilibria in guanine- and cytosine-rich DNA. Biophys Chem 2020; 267:106473. [PMID: 33031980 DOI: 10.1016/j.bpc.2020.106473] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2020] [Accepted: 09/03/2020] [Indexed: 02/07/2023]
Abstract
Noncanonical four-stranded DNA structures, including G-quadruplexes and i-motifs, have been discovered in the cell and are implicated in a variety of genomic regulatory functions. The tendency of a specific guanine- and cytosine-rich region of genomic DNA to adopt a four-stranded conformation depends on its ability to overcome the constraints of duplex base-pairing by undergoing consecutive duplex-to-coil and coil-to-tetraplex transitions. The latter ability is determined by the balance between the free energies of participating ordered and disordered structures. In this review, we present an overview of the literature on the stability of G-quadruplex and i-motif structures and discuss the extent of duplex-tetraplex competition as a function of the sequence context of the DNA and environmental conditions including temperature, pH, salt, molecular crowding, and the presence of G-quadruplex-binding ligands. We outline how the results of in vitro studies can be expanded to understanding duplex-tetraplex equilibria in vivo.
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Affiliation(s)
- Tigran V Chalikian
- Department of Pharmaceutical Sciences, Leslie Dan Faculty of Pharmacy, University of Toronto, 144 College Street, Toronto, Ontario M5S 3M2, Canada.
| | - Lutan Liu
- Department of Pharmaceutical Sciences, Leslie Dan Faculty of Pharmacy, University of Toronto, 144 College Street, Toronto, Ontario M5S 3M2, Canada
| | - Robert B Macgregor
- Department of Pharmaceutical Sciences, Leslie Dan Faculty of Pharmacy, University of Toronto, 144 College Street, Toronto, Ontario M5S 3M2, Canada
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17
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Smirnov IP, Kolganova NA, Surzhikov SA, Grechishnikova IV, Novikov RA, Timofeev EN. Folding topology, structural polymorphism, and dimerization of intramolecular DNA G-quadruplexes with inverted polarity strands and non-natural loops. Int J Biol Macromol 2020; 162:1972-1981. [PMID: 32800956 DOI: 10.1016/j.ijbiomac.2020.08.097] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2020] [Revised: 08/09/2020] [Accepted: 08/10/2020] [Indexed: 01/27/2023]
Abstract
Synthetically modified DNA G-quadruplexes (GQs) have great potential in the development of designer molecules for a wide range of applications. Identification of the role of various structural elements in the folding and final topology of artificial GQs is necessary to predict their secondary structure. We report here the results of spectroscopic and electrophoretic studies of GQ scaffolds formed by G-rich sequences comprising four G3-tracts of different polarity connected by either a single-nucleotide thymine loop or a non-natural tetraethyleneglycol loop. Depending on G-strand polarities, loop arrangement and the presence of extra 5'-base G-rich oligonucleotides form monomeric, dimeric, or multimeric species of different topologies. In most cases, oligonucleotides were able to fold into stable parallel or hybrid GQs. However, certain specific arrangements of loops and G-tracts resulted in a diverse mixture of low stable structures. Comparative analysis of topology, stability, and structural heterogeneity of different G-rich sequences suggests the important role of loop type and arrangement, G3-tract polarities, and the presence of 5'-capping residues in the outcome of the folding process. The results also imply that the formation of anti-parallel G-hairpin intermediates is a key event in major favourable folding pathways.
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Affiliation(s)
- Igor P Smirnov
- Federal Research and Clinical Center of Physical-Chemical Medicine, Moscow 119435, Russia
| | - Natalia A Kolganova
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, 119991 Moscow, Russia
| | - Sergei A Surzhikov
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, 119991 Moscow, Russia
| | - Irina V Grechishnikova
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, 119991 Moscow, Russia
| | - Roman A Novikov
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, 119991 Moscow, Russia; Zelinsky Institute of Organic Chemistry, Russian Academy of Sciences, 119991, Moscow, Russia
| | - Edward N Timofeev
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, 119991 Moscow, Russia.
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18
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Reina C, Cavalieri V. Epigenetic Modulation of Chromatin States and Gene Expression by G-Quadruplex Structures. Int J Mol Sci 2020; 21:E4172. [PMID: 32545267 PMCID: PMC7312119 DOI: 10.3390/ijms21114172] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2020] [Revised: 06/07/2020] [Accepted: 06/10/2020] [Indexed: 02/07/2023] Open
Abstract
G-quadruplexes are four-stranded helical nucleic acid structures formed by guanine-rich sequences. A considerable number of studies have revealed that these noncanonical structural motifs are widespread throughout the genome and transcriptome of numerous organisms, including humans. In particular, G-quadruplexes occupy strategic locations in genomic DNA and both coding and noncoding RNA molecules, being involved in many essential cellular and organismal functions. In this review, we first outline the fundamental structural features of G-quadruplexes and then focus on the concept that these DNA and RNA structures convey a distinctive layer of epigenetic information that is critical for the complex regulation, either positive or negative, of biological activities in different contexts. In this framework, we summarize and discuss the proposed mechanisms underlying the functions of G-quadruplexes and their interacting factors. Furthermore, we give special emphasis to the interplay between G-quadruplex formation/disruption and other epigenetic marks, including biochemical modifications of DNA bases and histones, nucleosome positioning, and three-dimensional organization of chromatin. Finally, epigenetic roles of RNA G-quadruplexes in post-transcriptional regulation of gene expression are also discussed. Undoubtedly, the issues addressed in this review take on particular importance in the field of comparative epigenetics, as well as in translational research.
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Affiliation(s)
- Chiara Reina
- Department of Health Promotion, Mother and Child Care, Internal Medicine and Medical Specialties (PROMISE), University of Palermo, 90127 Palermo, Italy;
| | - Vincenzo Cavalieri
- Department of Biological, Chemical and Pharmaceutical Sciences and Technologies (STEBICEF), University of Palermo, 90128 Palermo, Italy
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19
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Maity A, Winnerdy FR, Chang WD, Chen G, Phan AT. Intra-locked G-quadruplex structures formed by irregular DNA G-rich motifs. Nucleic Acids Res 2020; 48:3315-3327. [PMID: 32100003 PMCID: PMC7102960 DOI: 10.1093/nar/gkaa008] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2019] [Revised: 12/30/2019] [Accepted: 02/24/2020] [Indexed: 12/14/2022] Open
Abstract
G-rich DNA sequences with tracts of three or more continuous guanines (G≥3) are known to have high propensity to adopt stable G-quadruplex (G4) structures. Bioinformatic analyses suggest high prevalence of G-rich sequences with short G-tracts (G≤2) in the human genome. However, due to limited structural studies, the folding principles of such sequences remain largely unexplored and hence poorly understood. Here, we present the solution NMR structure of a sequence named AT26 consisting of irregularly spaced G2 tracts and two isolated single guanines. The structure is a four-layered G4 featuring two bi-layered blocks, locked between themselves in an unprecedented fashion making it a stable scaffold. In addition to edgewise and propeller-type loops, AT26 also harbors two V-shaped loops: a 2-nt V-shaped loop spanning two G-tetrad layers and a 0-nt V-shaped loop spanning three G-tetrad layers, which are named as VS- and VR-loop respectively, based on their distinct structural features. The intra-lock motif can be a basis for extending the G-tetrad core and a very stable intra-locked G4 can be formed by a sequence with G-tracts of various lengths including several G2 tracts. Findings from this study will aid in understanding the folding of G4 topologies from sequences containing irregularly spaced multiple short G-tracts.
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Affiliation(s)
- Arijit Maity
- School of Physical and Mathematical Sciences, Nanyang Technological University, Singapore 637371, Singapore
| | - Fernaldo Richtia Winnerdy
- School of Physical and Mathematical Sciences, Nanyang Technological University, Singapore 637371, Singapore
| | - Weili Denyse Chang
- School of Biological Sciences, Nanyang Technological University, Singapore 637551, Singapore
| | - Gang Chen
- School of Physical and Mathematical Sciences, Nanyang Technological University, Singapore 637371, Singapore
| | - Anh Tuân Phan
- School of Physical and Mathematical Sciences, Nanyang Technological University, Singapore 637371, Singapore.,NTU Institute of Structural Biology, Nanyang Technological University, Singapore 636921, Singapore
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20
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Effects of Length and Loop Composition on Structural Diversity and Similarity of (G 3TG 3N mG 3TG 3) G-Quadruplexes. Molecules 2020; 25:molecules25081779. [PMID: 32294984 PMCID: PMC7221631 DOI: 10.3390/molecules25081779] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2020] [Revised: 04/09/2020] [Accepted: 04/09/2020] [Indexed: 11/17/2022] Open
Abstract
A G-rich sequence containing three loops to connect four G-tracts with each ≥2 guanines can possibly form G-quadruplex structures. Given that all G-quadruplex structures comprise the stacking of G-quartets, the loop sequence plays a major role on their folding topology and thermal stability. Here circular dichroism, NMR, and PAGE are used to study the effect of loop length and base composition in the middle loop, and a single base difference in loop 1 and 3 on G-quadruplex formation of (G3HG3NmG3HG3) sequences with and without flanking nucleotides, where H is T, A, or C and N is T, A, C, or G. In addition, melting curve for G-quadruplex unfolding was used to provide relatively thermal stability of G-quadruplex structure after the addition of K+ overnight. We further studied the effects of K+ concentration on their stability and found structural changes in several sequences. Such (G3HG3NmG3HG3) configuration can be found in a number of native DNA sequences. The study of structural diversity and similarity from these sequences may allow us to establish the correlation between model sequences and native sequences. Moreover, several sequences upon interaction with a G-quadruplex ligand, BMVC, show similar spectral change, implying that structural similarity is crucial for drug development.
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21
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Liu J, Feng W, Zhang W. A single-molecule study reveals novel rod-like structures formed by a thrombin aptamer repeat sequence. NANOSCALE 2020; 12:4159-4166. [PMID: 32022812 DOI: 10.1039/c9nr09054a] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Thrombin aptamers (TBAs) have attracted much attention due to their various applications. The structures and properties of long ssDNA chains with multiple TBA repeat sequences are interesting and distinct from those of their monomers. Due to the complexity of the sample system, it is quite difficult to reveal the structure of such a long-chain ssDNA using traditional methods. In this work, we investigated the repeated ssDNA by using single-molecule magnetic tweezers and AFM imaging. To do that we developed the polymerase change-rolling circle amplification (PC-RCA) synthetic method and prepared two-end modified repeated ssDNA. The rod-like G4 structures formed by intramolecular stacking of the repeat sequence were for the first time identified. This novel structure is different from those higher-order quadruplex structures formed by G-tetrads or loop-mediated interactions. It is also quite interesting to find that the increase of the TBA copy number can unitize the diversity of TBA conformation to the best-fit binding structure for thrombin. The methodology developed in this work can be used for studying other repeat sequences in the genome, such as telomeric DNA as well as interactions of ssDNA with the binding molecule.
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Affiliation(s)
- Jianyu Liu
- State Key Laboratory of Supramolecular Structure and Materials, College of Chemistry, Jilin University, Changchun 130012, People's Republic of China.
| | - Wei Feng
- Institute of Atomic and Molecular Physics, Jilin University, Changchun 130012, People's Republic of China
| | - Wenke Zhang
- State Key Laboratory of Supramolecular Structure and Materials, College of Chemistry, Jilin University, Changchun 130012, People's Republic of China.
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22
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Parekh VJ, Niccum BA, Shah R, Rivera MA, Novak MJ, Geinguenaud F, Wien F, Arluison V, Sinden RR. Role of Hfq in Genome Evolution: Instability of G-Quadruplex Sequences in E. coli. Microorganisms 2019; 8:microorganisms8010028. [PMID: 31877879 PMCID: PMC7023247 DOI: 10.3390/microorganisms8010028] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2019] [Revised: 12/16/2019] [Accepted: 12/17/2019] [Indexed: 11/16/2022] Open
Abstract
Certain G-rich DNA repeats can form quadruplex in bacterial chromatin that can present blocks to DNA replication and, if not properly resolved, may lead to mutations. To understand the participation of quadruplex DNA in genomic instability in Escherichia coli (E. coli), mutation rates were measured for quadruplex-forming DNA repeats, including (G3T)4, (G3T)8, and a RET oncogene sequence, cloned as the template or nontemplate strand. We evidence that these alternative structures strongly influence mutagenesis rates. Precisely, our results suggest that G-quadruplexes form in E. coli cells, especially during transcription when the G-rich strand can be displaced by R-loop formation. Structure formation may then facilitate replication misalignment, presumably associated with replication fork blockage, promoting genomic instability. Furthermore, our results also evidence that the nucleoid-associated protein Hfq is involved in the genetic instability associated with these sequences. Hfq binds and stabilizes G-quadruplex structure in vitro and likely in cells. Collectively, our results thus implicate quadruplexes structures and Hfq nucleoid protein in the potential for genetic change that may drive evolution or alterations of bacterial gene expression.
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Affiliation(s)
- Virali J. Parekh
- Laboratory of DNA Structure and Mutagenesis, Department of Chemistry and Applied Biological Sciences, South Dakota School of Mines and Technology, Rapid City, SD 57701, USA;
| | - Brittany A. Niccum
- Department of Mathematics, Florida Institute of Technology, Melbourne, FL 32901, USA;
| | - Rachna Shah
- Department of Biological Sciences, Florida Institute of Technology, Melbourne, FL 32901, USA; (R.S.); (M.A.R.)
| | - Marisa A. Rivera
- Department of Biological Sciences, Florida Institute of Technology, Melbourne, FL 32901, USA; (R.S.); (M.A.R.)
| | - Mark J. Novak
- Department of Chemistry and Applied Biological Sciences, South Dakota School of Mines and Technology; Rapid City, SD 57701, USA;
| | - Frederic Geinguenaud
- Plateforme CNanoMat & Inserm U1148, Laboratory for Vascular Translational Science, UFR SMBH, Université Paris 13, Sorbonne Paris Cité, F-93017 Bobigny, France;
| | - Frank Wien
- Synchrotron SOLEIL, 91192 Gif-sur-Yvette, France;
| | - Véronique Arluison
- Laboratoire Léon Brillouin LLB, CEA, CNRS UMR12, Université Paris Saclay, CEA Saclay, 91191 Gif-sur-Yvette, France
- Université de Paris, UFR Sciences du vivant, 35 rue Hélène Brion, 75205 Paris cedex, France
- Correspondence: (V.A.); (R.R.S.); Tel.: +1-605-394-1678 (R.R.S.)
| | - Richard R. Sinden
- Laboratory of DNA Structure and Mutagenesis, Department of Chemistry and Applied Biological Sciences, South Dakota School of Mines and Technology, Rapid City, SD 57701, USA;
- Correspondence: (V.A.); (R.R.S.); Tel.: +1-605-394-1678 (R.R.S.)
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23
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Cheng M, Cheng Y, Hao J, Jia G, Zhou J, Mergny JL, Li C. Loop permutation affects the topology and stability of G-quadruplexes. Nucleic Acids Res 2019; 46:9264-9275. [PMID: 30184167 PMCID: PMC6182180 DOI: 10.1093/nar/gky757] [Citation(s) in RCA: 50] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2018] [Accepted: 08/21/2018] [Indexed: 12/14/2022] Open
Abstract
G-quadruplexes are unusual DNA and RNA secondary structures ubiquitous in a variety of organisms including vertebrates, plants, viruses and bacteria. The folding topology and stability of intramolecular G-quadruplexes are determined to a large extent by their loops. Loop permutation is defined as swapping two or three of these regions so that intramolecular G-quadruplexes only differ in the sequential order of their loops. Over the past two decades, both length and base composition of loops have been studied extensively, but a systematic study on the effect of loop permutation has been missing. In the present work, 99 sequences from 21 groups with different loop permutations were tested. To our surprise, both conformation and thermal stability are greatly dependent on loop permutation. Loop permutation actually matters as much as loop length and base composition on G-quadruplex folding, with effects on Tm as high as 17°C. Sequences containing a longer central loop have a high propensity to adopt a stable non-parallel topology. Conversely, sequences containing a short central loop tend to form a parallel topology of lower stability. In addition, over half of interrogated sequences were found in the genomes of diverse organisms, implicating their potential regulatory roles in the genome or as therapeutic targets. This study illustrates the structural roles of loops in G-quadruplex folding and should help to establish rules to predict the folding pattern and stability of G-quadruplexes.
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Affiliation(s)
- Mingpan Cheng
- State Key Laboratory of Catalysis, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China.,University of Chinese Academy of Sciences, No. 19A Yuquan Road, Beijing 100049, China
| | - Yu Cheng
- State Key Laboratory of Catalysis, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China.,University of Chinese Academy of Sciences, No. 19A Yuquan Road, Beijing 100049, China
| | - Jingya Hao
- State Key Laboratory of Catalysis, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China.,University of Chinese Academy of Sciences, No. 19A Yuquan Road, Beijing 100049, China
| | - Guoqing Jia
- State Key Laboratory of Catalysis, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China
| | - Jun Zhou
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, China
| | - Jean-Louis Mergny
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, China.,ARNA Laboratory, Inserm U1212, CNRS UMR5320, IECB, Université de Bordeaux, Pessac 33607, France.,Institute of Biophysics of the CAS, v.v.i., Královopolská 135, 612 65 Brno, Czech Republic
| | - Can Li
- State Key Laboratory of Catalysis, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China
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24
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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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25
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Effects of Central Loop Length and Metal Ions on the Thermal Stability of G-Quadruplexes. Molecules 2019; 24:molecules24101863. [PMID: 31096553 PMCID: PMC6571788 DOI: 10.3390/molecules24101863] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2019] [Revised: 05/04/2019] [Accepted: 05/07/2019] [Indexed: 01/03/2023] Open
Abstract
The central loop of G-quadruplex molecular beacons is a key element to sense target DNA or RNA sequences. In this study, circular dichroism spectroscopy (CD), thermal difference spectrum (TDS), non-denatured non-denaturing gel electrophoresis, and thermal stability analysis were used to investigate the effect of the central loop length on G-quadruplex features. Two series of G-quadruplexes, AG3TTAG3-(TTA)n-G3TTAG3T (n = 1–8) (named TTA series) and AG3TTTG3-(TTA)n-G3TTTG3T (n = 1–8) (named TTT series) were examined in K+ and Na+ solutions, respectively. CD and TDS spectral data indicated that TTA series adopted an antiparallel G-quadruplex structure in Na+ solution and a hybrid G-quadruplex structure in K+ solution respectively. TTT series exhibited a hybrid G-quadruplex structure in both Na+ and K+ solutions. UV melting curves indicated that the stability of G-quadruplex in both series was reduced by the elongation of central loop. Thermal stability analysis concluded that the G-quadruplex destabilization with long central loop is an entropy-driven process due to more flexible and longer central loops.
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26
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Marzano M, Falanga AP, D'Errico S, Pinto B, Roviello GN, Piccialli G, Oliviero G, Borbone N. New G-Quadruplex-Forming Oligodeoxynucleotides Incorporating a Bifunctional Double-Ended Linker (DEL): Effects of DEL Size and ODNs Orientation on the Topology, Stability, and Molecularity of DEL-G-Quadruplexes. Molecules 2019; 24:molecules24030654. [PMID: 30759875 PMCID: PMC6384581 DOI: 10.3390/molecules24030654] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2019] [Revised: 02/04/2019] [Accepted: 02/06/2019] [Indexed: 01/13/2023] Open
Abstract
G-quadruplexes (G4s) are unusual secondary structures of DNA occurring in guanosine-rich oligodeoxynucleotide (ODN) strands that are extensively studied for their relevance to the biological processes in which they are involved. In this study, we report the synthesis of a new kind of G4-forming molecule named double-ended-linker ODN (DEL-ODN), in which two TG₄T strands are attached to the two ends of symmetric, non-nucleotide linkers. Four DEL-ODNs differing for the incorporation of either a short or long linker and the directionality of the TG₄T strands were synthesized, and their ability to form G4 structures and/or multimeric species was investigated by PAGE, HPLC⁻size-exclusion chromatography (HPLC⁻SEC), circular dichroism (CD), and NMR studies in comparison with the previously reported monomeric tetra-ended-linker (TEL) analogues and with the corresponding tetramolecular species (TG₄T)₄. The structural characterization of DEL-ODNs confirmed the formation of stable, bimolecular DEL-G4s for all DEL-ODNs, as well as of additional DEL-G4 multimers with higher molecular weights, thus suggesting a way towards the obtainment of thermally stable DNA nanostructures based on reticulated DEL-G4s.
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Affiliation(s)
- Maria Marzano
- Dipartimento di Farmacia, Università degli Studi di Napoli Federico II, via Domenico Montesano 49, 80131 Napoli, Italy.
| | - Andrea Patrizia Falanga
- Dipartimento di Farmacia, Università degli Studi di Napoli Federico II, via Domenico Montesano 49, 80131 Napoli, Italy.
| | - Stefano D'Errico
- Dipartimento di Farmacia, Università degli Studi di Napoli Federico II, via Domenico Montesano 49, 80131 Napoli, Italy.
| | - Brunella Pinto
- Dipartimento di Chimica, Università degli Studi di Milano, via Camillo Golgi 19, 20133 Milano, Italy.
| | | | - Gennaro Piccialli
- Dipartimento di Farmacia, Università degli Studi di Napoli Federico II, via Domenico Montesano 49, 80131 Napoli, Italy.
| | - Giorgia Oliviero
- Dipartimento di Medicina Molecolare e Biotecnologie Mediche, Università degli Studi di Napoli Federico II, via Sergio Pansini 5, 80131 Napoli, Italy.
| | - Nicola Borbone
- Dipartimento di Farmacia, Università degli Studi di Napoli Federico II, via Domenico Montesano 49, 80131 Napoli, Italy.
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27
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Al-Zeer MA, Kurreck J. Deciphering the Enigmatic Biological Functions of RNA Guanine-Quadruplex Motifs in Human Cells. Biochemistry 2018; 58:305-311. [PMID: 30350579 DOI: 10.1021/acs.biochem.8b00904] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Guanine-rich sequences in nucleic acids can form noncanonical structures known as guanine quadruplexes (G-quadruplexes), which constitute a not yet fully elucidated layer of regulatory function for central cellular processes. RNA G-quadruplexes have been shown to be involved in the modulation of translation, the regulation of (alternative) splicing, and the subcellular transport of mRNAs, among other processes. However, in living cells, an equilibrium between the formation of G-quadruplex structures and their unwinding by RNA helicases is likely. The extent to which G-rich sequences adopt G-quadruplex structures in living eukaryotic cells is currently a matter of debate. Multiple lines of evidence confirm the intracellular formation of G-quadruplex structures, such as their detection by immunochemical approaches, fluorogenic probes, and in vivo nuclear magnetic resonance. However, intracellular chemical probing suggests most if not all are in an unfolded state. It is therefore tempting to speculate that some G-quadruplex structures are only temporarily formed when they are required to contribute to the fine-tuning of the processes mentioned above. Future research should focus on the analysis of G-quadruplex formation under physiological conditions, which will allow the re-evaluation of the biological function of G-quadruplex motifs in regulatory processes in their natural environment and at physiological expression levels. This will help in the elucidation of their significance in the regulation of central processes in molecular biology and the exploitation of their potential as therapeutic targets.
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Affiliation(s)
- Munir A Al-Zeer
- Institute of Biotechnology, Department of Applied Biochemistry , Technische Universität Berlin , 13355 Berlin , Germany
| | - Jens Kurreck
- Institute of Biotechnology, Department of Applied Biochemistry , Technische Universität Berlin , 13355 Berlin , Germany
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28
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Wang L, Wang QM, Wang YR, Xi XG, Hou XM. DNA-unwinding activity of Saccharomyces cerevisiae Pif1 is modulated by thermal stability, folding conformation, and loop lengths of G-quadruplex DNA. J Biol Chem 2018; 293:18504-18513. [PMID: 30305390 DOI: 10.1074/jbc.ra118.005071] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2018] [Revised: 10/04/2018] [Indexed: 12/23/2022] Open
Abstract
G-quadruplexes (G4s) are four-stranded DNA structures formed by Hoogsteen base pairing between stacked sets of four guanines. Pif1 helicase plays critical roles in suppressing genomic instability in the yeast Saccharomyces cerevisiae by resolving G4s. However, the structural properties of G4s in S. cerevisiae and the substrate preference of Pif1 for different G4s remain unknown. Here, using CD spectroscopy and 83 G4 motifs from S. cerevisiae ranging in length from 30 to 60 nucleotides, we first show that G4 structures can be formed with a broad range of loop sizes in vitro and that a parallel conformation is favored. Using single-molecule FRET analysis, we then systematically addressed Pif1-mediated unwinding of various G4s and found that Pif1 is sensitive to G4 stability. Moreover, Pif1 preferentially unfolded antiparallel G4s rather than parallel G4s having similar stability. Furthermore, our results indicate that most G4 structures in S. cerevisiae sequences have long loops and can be efficiently unfolded by Pif1 because of their low stability. However, we also found that G4 structures with short loops can be barely unfolded. This study highlights the formidable capability of Pif1 to resolve the majority of G4s in S. cerevisiae sequences, narrows the fractions of G4s that may be challenging for genomic stability, and provides a framework for understanding the influence of different G4s on genomic stability via their processing by Pif1.
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Affiliation(s)
- Lei Wang
- From the State Key Laboratory of Crop Stress Biology for Arid Areas and College of Life Sciences, Northwest A&F University, Yangling, Shaanxi 712100, China and
| | - Qing-Man Wang
- From the State Key Laboratory of Crop Stress Biology for Arid Areas and College of Life Sciences, Northwest A&F University, Yangling, Shaanxi 712100, China and
| | - Yi-Ran Wang
- From the State Key Laboratory of Crop Stress Biology for Arid Areas and College of Life Sciences, Northwest A&F University, Yangling, Shaanxi 712100, China and
| | - Xu-Guang Xi
- From the State Key Laboratory of Crop Stress Biology for Arid Areas and College of Life Sciences, Northwest A&F University, Yangling, Shaanxi 712100, China and.,Laboratoire de Biologie et Pharmacologie Appliquée, Ecole Normale Supérieure de Cachan, CNRS, 61 Avenue du Président Wilson, 94235 Cachan, France
| | - Xi-Miao Hou
- From the State Key Laboratory of Crop Stress Biology for Arid Areas and College of Life Sciences, Northwest A&F University, Yangling, Shaanxi 712100, China and
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29
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Havrila M, Stadlbauer P, Kührová P, Banáš P, Mergny JL, Otyepka M, Šponer J. Structural dynamics of propeller loop: towards folding of RNA G-quadruplex. Nucleic Acids Res 2018; 46:8754-8771. [PMID: 30165550 PMCID: PMC6158699 DOI: 10.1093/nar/gky712] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2018] [Revised: 07/03/2018] [Accepted: 07/27/2018] [Indexed: 02/04/2023] Open
Abstract
We have carried out an extended set of standard and enhanced-sampling MD simulations (for a cumulative simulation time of 620 μs) with the aim to study folding landscapes of the rGGGUUAGGG and rGGGAGGG parallel G-hairpins (PH) with propeller loop. We identify folding and unfolding pathways of the PH, which is bridged with the unfolded state via an ensemble of cross-like structures (CS) possessing mutually tilted or perpendicular G-strands interacting via guanine-guanine H-bonding. The oligonucleotides reach the PH conformation from the unfolded state via a conformational diffusion through the folding landscape, i.e. as a series of rearrangements of the H-bond interactions starting from compacted anti-parallel hairpin-like structures. Although isolated PHs do not appear to be thermodynamically stable we suggest that CS and PH-types of structures are sufficiently populated during RNA guanine quadruplex (GQ) folding within the context of complete GQ-forming sequences. These structures may participate in compact coil-like ensembles that involve all four G-strands and already some bound ions. Such ensembles can then rearrange into the fully folded parallel GQs via conformational diffusion. We propose that the basic atomistic folding mechanism of propeller loops suggested in this work may be common for their formation in RNA and DNA GQs.
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Affiliation(s)
- Marek Havrila
- Institute of Biophysics of the Czech Academy of Sciences, Královopolská 135, 612 65 Brno, Czech Republic
| | - Petr Stadlbauer
- Institute of Biophysics of the Czech Academy of Sciences, Královopolská 135, 612 65 Brno, Czech Republic
- Regional Centre of Advanced Technologies and Materials, Department of Physical Chemistry, Faculty of Science, Palacký University, 17. listopadu 12, 77146 Olomouc, Czech Republic
| | - Petra Kührová
- Regional Centre of Advanced Technologies and Materials, Department of Physical Chemistry, Faculty of Science, Palacký University, 17. listopadu 12, 77146 Olomouc, Czech Republic
| | - Pavel Banáš
- Regional Centre of Advanced Technologies and Materials, Department of Physical Chemistry, Faculty of Science, Palacký University, 17. listopadu 12, 77146 Olomouc, Czech Republic
| | - Jean-Louis Mergny
- Institute of Biophysics of the Czech Academy of Sciences, Královopolská 135, 612 65 Brno, Czech Republic
- Université de Bordeaux, INSERM U1212, CNRS UMR 5320, ARNA Laboratory, IECB, Pessac, France
| | - Michal Otyepka
- Institute of Biophysics of the Czech Academy of Sciences, Královopolská 135, 612 65 Brno, Czech Republic
- Regional Centre of Advanced Technologies and Materials, Department of Physical Chemistry, Faculty of Science, Palacký University, 17. listopadu 12, 77146 Olomouc, Czech Republic
| | - Jiří Šponer
- Institute of Biophysics of the Czech Academy of Sciences, Královopolská 135, 612 65 Brno, Czech Republic
- Regional Centre of Advanced Technologies and Materials, Department of Physical Chemistry, Faculty of Science, Palacký University, 17. listopadu 12, 77146 Olomouc, Czech Republic
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30
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Kumar M, Kaushik M, Kukreti S. A topological transition from bimolecular quadruplex to G-triplex/tri-G-quadruplex exhibited by truncated double repeats of human telomere. EUROPEAN BIOPHYSICS JOURNAL: EBJ 2018; 47:903-915. [PMID: 29934676 DOI: 10.1007/s00249-018-1312-4] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/01/2017] [Revised: 04/11/2018] [Accepted: 05/21/2018] [Indexed: 12/12/2022]
Abstract
Human telomeric G-rich sequences can fold back into various conformations depending upon the salt (Na+ or K+) at physiological pH. On the basis of results obtained by native PAGE electrophoresis, circular dichroism, and UV-melting experiments, we report here that truncated sequences of human telomere (d-GGGTTAGGG; GM9, d-AGGGTTAGGG; GM10, d-TAGGGTTAGGG; GM11) adopt a varied range of quadruplex conformations as a function of the cation present. By correlating CD and gel electrophoresis experiments; it was concluded that the GM9 oligonucleotide can self-associate to form a tetramer quadruplex (antiparallel; AP) in Na+ solution and a mixture of G-triplex (AP) or tri-G-quadruplex (parallel; P) along with a tetramer G-quadruplex structure (AP) in K+. The GM10 oligonucleotide formed a bimolecular G-quadruplex in both Na+ and K+ solutions, while GM11 associated to form a bimolecular G-quadruplex (AP) structure in Na+ solution and a mixture of bimolecular G-quadruplex (AP) and bimolecular G-quadruplex (P) along with parallel G-triplex or antiparallel tri-G-quadruplex in K+. All the UV-melting profiles, thermal difference spectra, and CD melting curves suggested the formation of a variety of G-quadruplex conformations by the DNA sequences studied in Na+ and K+ ions. Hypothetical models for different conformations adopted by these DNA molecules have also been proposed, which may further enhance our knowledge about the divergent topologies of guanine quadruplexes.
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Affiliation(s)
- Mohan Kumar
- Nucleic Acid Research Laboratory, Department of Chemistry, University of Delhi, Delhi, India
| | - Mahima Kaushik
- Nucleic Acid Research Laboratory, Department of Chemistry, University of Delhi, Delhi, India.,Cluster Innovation Centre, University of Delhi, Delhi, India
| | - Shrikant Kukreti
- Nucleic Acid Research Laboratory, Department of Chemistry, University of Delhi, Delhi, India.
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31
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Sekibo DAT, Fox KR. The effects of DNA supercoiling on G-quadruplex formation. Nucleic Acids Res 2017; 45:12069-12079. [PMID: 29036619 PMCID: PMC5716088 DOI: 10.1093/nar/gkx856] [Citation(s) in RCA: 36] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2017] [Accepted: 09/13/2017] [Indexed: 01/06/2023] Open
Abstract
Guanine-rich DNAs can fold into four-stranded structures that contain stacks of G-quartets. Bioinformatics studies have revealed that G-rich sequences with the potential to adopt these structures are unevenly distributed throughout genomes, and are especially found in gene promoter regions. With the exception of the single-stranded telomeric DNA, all genomic G-rich sequences will always be present along with their C-rich complements, and quadruplex formation will be in competition with the corresponding Watson–Crick duplex. Quadruplex formation must therefore first require local dissociation (melting) of the duplex strands. Since negative supercoiling is known to facilitate the formation of alternative DNA structures, we have investigated G-quadruplex formation within negatively supercoiled DNA plasmids. Plasmids containing multiple copies of (G3T)n and (G3T4)n repeats, were probed with dimethylsulphate, potassium permanganate and S1 nuclease. While dimethylsulphate footprinting revealed some evidence for G-quadruplex formation in (G3T)n sequences, this was not affected by supercoiling, and permanganate failed to detect exposed thymines in the loop regions. (G3T4)n sequences were not protected from DMS and showed no reaction with permanganate. Similarly, both S1 nuclease and 2D gel electrophoresis of DNA topoisomers did not detect any supercoil-dependent structural transitions. These results suggest that negative supercoiling alone is not sufficient to drive G-quadruplex formation.
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Affiliation(s)
- Doreen A T Sekibo
- Biological Sciences, Life Sciences Building 85, University of Southampton, Southampton SO17 1BJ, UK
| | - Keith R Fox
- Biological Sciences, Life Sciences Building 85, University of Southampton, Southampton SO17 1BJ, UK
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32
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Yangyuoru PM, Bradburn DA, Liu Z, Xiao TS, Russell R. The G-quadruplex (G4) resolvase DHX36 efficiently and specifically disrupts DNA G4s via a translocation-based helicase mechanism. J Biol Chem 2017; 293:1924-1932. [PMID: 29269411 DOI: 10.1074/jbc.m117.815076] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2017] [Revised: 12/18/2017] [Indexed: 12/22/2022] Open
Abstract
Single-stranded DNA (ssDNA) and RNA regions that include at least four closely spaced runs of three or more consecutive guanosines strongly tend to fold into stable G-quadruplexes (G4s). G4s play key roles as DNA regulatory sites and as kinetic traps that can inhibit biological processes, but how G4s are regulated in cells remains largely unknown. Here, we developed a kinetic framework for G4 disruption by DEAH-box helicase 36 (DHX36), the dominant G4 resolvase in human cells. Using tetramolecular DNA and RNA G4s with four to six G-quartets, we found that DHX36-mediated disruption is highly efficient, with rates that depend on G4 length under saturating conditions (kcat) but not under subsaturating conditions (kcat/Km ). These results suggest that a step during G4 disruption limits the kcat value and that DHX36 binding limits kcat/Km Similar results were obtained for unimolecular DNA G4s. DHX36 activity depended on a 3' ssDNA extension and was blocked by a polyethylene glycol linker, indicating that DHX36 loads onto the extension and translocates 3'-5' toward the G4. DHX36 unwound dsDNA poorly compared with G4s of comparable intrinsic lifetime. Interestingly, we observed that DHX36 has striking 3'-extension sequence preferences that differ for G4 disruption and dsDNA unwinding, most likely arising from differences in the rate-limiting step for the two activities. Our results indicate that DHX36 disrupts G4s with a conventional helicase mechanism that is tuned for great efficiency and specificity for G4s. The dependence of DHX36 on the 3'-extension sequence suggests that the extent of formation of genomic G4s may not track directly with G4 stability.
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Affiliation(s)
- Philip M Yangyuoru
- From the Department of Molecular Biosciences and the Institute for Cellular and Molecular Biology, University of Texas at Austin, Austin, Texas 78712 and
| | - Devin A Bradburn
- From the Department of Molecular Biosciences and the Institute for Cellular and Molecular Biology, University of Texas at Austin, Austin, Texas 78712 and
| | - Zhonghua Liu
- the Department of Pathology, Case Western Reserve University, Cleveland, Ohio 44106
| | - Tsan Sam Xiao
- the Department of Pathology, Case Western Reserve University, Cleveland, Ohio 44106
| | - Rick Russell
- From the Department of Molecular Biosciences and the Institute for Cellular and Molecular Biology, University of Texas at Austin, Austin, Texas 78712 and
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33
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Serikawa T, Spanos C, von Hacht A, Budisa N, Rappsilber J, Kurreck J. Comprehensive identification of proteins binding to RNA G-quadruplex motifs in the 5' UTR of tumor-associated mRNAs. Biochimie 2017; 144:169-184. [PMID: 29129743 DOI: 10.1016/j.biochi.2017.11.003] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2017] [Accepted: 11/06/2017] [Indexed: 12/31/2022]
Abstract
G-quadruplex structures in the 5' UTR of mRNAs are widely considered to suppress translation without affecting transcription. The current study describes the comprehensive analysis of proteins binding to four different G-quadruplex motifs located in mRNAs of the cancer-related genes Bcl-2, NRAS, MMP16, and ARPC2. Following metabolic labeling (Stable Isotope Labeling with Amino acids in Cell culture, SILAC) of proteins in the human cell line HEK293, G-quadruplex binding proteins were enriched by pull-down assays and identified by LC-orbitrap mass spectrometry. We found different patterns of interactions for the G-quadruplex motifs under investigation. While the G-quadruplexes in the mRNAs of NRAS and MMP16 specifically interacted with a small number of proteins, the Bcl-2 and ARPC2 G-quadruplexes exhibited a broad range of proteinaceous interaction partners with 99 and 82 candidate proteins identified in at least two replicates, respectively. The use of a control composed of samples from all G-quadruplex-forming sequences and their mutated controls ensured that the identified proteins are specific for RNA G-quadruplex structures and are not general RNA-binding proteins. Independent validation experiments based on pull-down assays and Western blotting confirmed the MS data. Among the interaction partners were many proteins known to bind to RNA, including multiple heterogenous nuclear ribonucleoproteins (hnRNPs). Several of the candidate proteins are likely to reflect stalling of the ribosome by RNA G-quadruplex structures. Interestingly, additional proteins were identified that have not previously been described to interact with RNA. Gene ontology analysis of the candidate proteins revealed that many interaction partners are known to be tumor related. The majority of the identified RNA G-quadruplex interacting proteins are thought to be involved in post-transcriptional processes, particularly in splicing. These findings indicate that protein-G-quadruplex interactions are not only important for the fine-tuning of translation but are also relevant to the regulation of mRNA maturation and may play an important role in tumor biology. Proteomic data are available via ProteomeXchange with identifier PXD005761.
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Affiliation(s)
- Tatsuo Serikawa
- Department of Applied Biochemistry, Institute of Biotechnology, TIB 4/3-2, Technische Universität Berlin, Gustav-Meyer-Allee 25, 13355, Berlin, Germany
| | - Christos Spanos
- Wellcome Trust Centre for Cell Biology, Institute of Cell Biology, School of Biological Sciences, University of Edinburgh, Edinburgh, EH9 3BF, UK
| | - Annekathrin von Hacht
- Department of Applied Biochemistry, Institute of Biotechnology, TIB 4/3-2, Technische Universität Berlin, Gustav-Meyer-Allee 25, 13355, Berlin, Germany
| | - Nediljko Budisa
- Department of Biocatalysis, Institute of Chemistry, L 1, Technische Universität Berlin, Müller-Breslau-Straße 10, 10623, Berlin, Germany
| | - Juri Rappsilber
- Wellcome Trust Centre for Cell Biology, Institute of Cell Biology, School of Biological Sciences, University of Edinburgh, Edinburgh, EH9 3BF, UK; Department of Bioanalytics, Institute of Biotechnology, TIB 4/4-3, Technische Universität Berlin, Gustav-Meyer-Allee 25, 13355, Berlin, Germany
| | - Jens Kurreck
- Department of Applied Biochemistry, Institute of Biotechnology, TIB 4/3-2, Technische Universität Berlin, Gustav-Meyer-Allee 25, 13355, Berlin, Germany.
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34
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Sagi J. In What Ways Do Synthetic Nucleotides and Natural Base Lesions Alter the Structural Stability of G-Quadruplex Nucleic Acids? J Nucleic Acids 2017; 2017:1641845. [PMID: 29181193 PMCID: PMC5664352 DOI: 10.1155/2017/1641845] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2017] [Accepted: 08/15/2017] [Indexed: 01/03/2023] Open
Abstract
Synthetic analogs of natural nucleotides have long been utilized for structural studies of canonical and noncanonical nucleic acids, including the extensively investigated polymorphic G-quadruplexes (GQs). Dependence on the sequence and nucleotide modifications of the folding landscape of GQs has been reviewed by several recent studies. Here, an overview is compiled on the thermodynamic stability of the modified GQ folds and on how the stereochemical preferences of more than 70 synthetic and natural derivatives of nucleotides substituting for natural ones determine the stability as well as the conformation. Groups of nucleotide analogs only stabilize or only destabilize the GQ, while the majority of analogs alter the GQ stability in both ways. This depends on the preferred syn or anti N-glycosidic linkage of the modified building blocks, the position of substitution, and the folding architecture of the native GQ. Natural base lesions and epigenetic modifications of GQs explored so far also stabilize or destabilize the GQ assemblies. Learning the effect of synthetic nucleotide analogs on the stability of GQs can assist in engineering a required stable GQ topology, and exploring the in vitro action of the single and clustered natural base damage on GQ architectures may provide indications for the cellular events.
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Affiliation(s)
- Janos Sagi
- Rimstone Laboratory, RLI, Carlsbad, CA 92010, USA
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35
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Piazza A, Cui X, Adrian M, Samazan F, Heddi B, Phan AT, Nicolas AG. Non-Canonical G-quadruplexes cause the hCEB1 minisatellite instability in Saccharomyces cerevisiae. eLife 2017; 6. [PMID: 28661396 PMCID: PMC5491262 DOI: 10.7554/elife.26884] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2017] [Accepted: 05/25/2017] [Indexed: 11/13/2022] Open
Abstract
G-quadruplexes (G4) are polymorphic four-stranded structures formed by certain G-rich nucleic acids in vitro, but the sequence and structural features dictating their formation and function in vivo remains uncertain. Here we report a structure-function analysis of the complex hCEB1 G4-forming sequence. We isolated four G4 conformations in vitro, all of which bear unusual structural features: Form 1 bears a V-shaped loop and a snapback guanine; Form 2 contains a terminal G-triad; Form 3 bears a zero-nucleotide loop; and Form 4 is a zero-nucleotide loop monomer or an interlocked dimer. In vivo, Form 1 and Form 2 differently account for 2/3rd of the genomic instability of hCEB1 in two G4-stabilizing conditions. Form 3 and an unidentified form contribute to the remaining instability, while Form 4 has no detectable effect. This work underscores the structural polymorphisms originated from a single highly G-rich sequence and demonstrates the existence of non-canonical G4s in cells, thus broadening the definition of G4-forming sequences. DOI:http://dx.doi.org/10.7554/eLife.26884.001 Molecules of DNA encode the information needed to build cells and keep them alive. DNA is made of two strands that contain several different chemical groups known as bases arranged in different orders, like letters and words in a phrase. Generally, two DNA strands wrap around each other to make a three dimensional structure known as a double helix. However, in certain circumstances, some sequences of DNA bases can adopt alternative structures. For example, DNA sequences that contain lots of a base known as guanine may sometimes form structures called G-quadruplexes in which sets of four guanines come together. G-quadruplexes are involved in many processes in cells including regulating the activity of genes, but they can also interfere with the process that replicates the DNA at each generation. This causes the cell’s genetic information to be modified, which can damage the cell and can promote cancer. However, it is difficult to predict which DNA sequences are susceptible to form G-quadruplexes and what consequence their folding might have on the biological processes happening in cells. Recent computational and biophysical studies have shown that G-quadruplexes can form a larger variety of structures than previously known. Piazza et al. studied how some of these new “non-canonical” structures form in yeast cells and how they may interfere with DNA copying. The experiments show that a single guanine-rich DNA sequence can form several types of non-canonical G-quadruplex structures in yeast cells. This includes structures that do not have complete sets of guanines at their center or are missing loops that connect the bases to one another. Further experiments demonstrate that the threat posed by these G-quadruplexes is linked to the length of their connecting loops and how well their three-dimensional structures withstand heat. The findings of Piazza et al. identify a set of DNA sequences that are capable of forming G-quadruplexes that harm the cell. The next challenge will be to develop specific molecules that can stabilize the structures of G-quadruplexes. In the future, this avenue of research may aid the development of new treatments for cancer that target specific DNA structures. DOI:http://dx.doi.org/10.7554/eLife.26884.002
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Affiliation(s)
- Aurèle Piazza
- Institut Curie, CNRS UMR3244, PSL Research University, Paris, France
| | - Xiaojie Cui
- Institut Curie, CNRS UMR3244, PSL Research University, Paris, France
| | - Michael Adrian
- School of Physical and Mathematical Sciences, Nanyang Technological University, , Singapore
| | - Frédéric Samazan
- Institut Curie, CNRS UMR3244, PSL Research University, Paris, France
| | - Brahim Heddi
- School of Physical and Mathematical Sciences, Nanyang Technological University, , Singapore
| | - Anh-Tuan Phan
- School of Physical and Mathematical Sciences, Nanyang Technological University, , Singapore
| | - Alain G Nicolas
- Institut Curie, CNRS UMR3244, PSL Research University, Paris, France
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36
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Oliviero G, D'Errico S, Pinto B, Nici F, Dardano P, Rea I, De Stefano L, Mayol L, Piccialli G, Borbone N. Self-Assembly of G-Rich Oligonucleotides Incorporating a 3'-3' Inversion of Polarity Site: A New Route Towards G-Wire DNA Nanostructures. ChemistryOpen 2017; 6:599-605. [PMID: 28794955 PMCID: PMC5542749 DOI: 10.1002/open.201700024] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2017] [Indexed: 01/20/2023] Open
Abstract
Obtaining DNA nanostructures with potential applications in drug discovery, diagnostics, and electronics in a simple and affordable way represents one of the hottest topics in nanotechnological and medical sciences. Herein, we report a novel strategy to obtain structurally homogeneous DNA G-wire nanostructures of known length, starting from the short unmodified G-rich oligonucleotide d(5'-CGGT-3'-3'-GGC-5') (1) incorporating a 3'-3' inversion of polarity site. The reported approach allowed us to obtain long G-wire assemblies through 5'-5' π-π stacking interactions in between the tetramolecular G-quadruplex building blocks that form when 1 is annealed in the presence of potassium ions. Our results expand the repertoire of synthetic methodologies to obtain new tailored DNA G-wire nanostructures.
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Affiliation(s)
- Giorgia Oliviero
- Department of Molecular Medicine and Medical Biotechnologies Via S. Pansini 5 80131 Napoli Italy
| | - Stefano D'Errico
- Department of Pharmacy Università degli Studi di Napoli Federico II Via D. Montesano 49 80131 Napoli Italy
| | - Brunella Pinto
- Department of Pharmacy Università degli Studi di Napoli Federico II Via D. Montesano 49 80131 Napoli Italy
| | - Fabrizia Nici
- Department of Pharmacy Università degli Studi di Napoli Federico II Via D. Montesano 49 80131 Napoli Italy
| | - Principia Dardano
- Institute for Microelectronics and Microsystems Consiglio Nazionale delle Ricerche Via P. Castellino 111 80131 Napoli Italy
| | - Ilaria Rea
- Institute for Microelectronics and Microsystems Consiglio Nazionale delle Ricerche Via P. Castellino 111 80131 Napoli Italy
| | - Luca De Stefano
- Institute for Microelectronics and Microsystems Consiglio Nazionale delle Ricerche Via P. Castellino 111 80131 Napoli Italy
| | - Luciano Mayol
- Department of Pharmacy Università degli Studi di Napoli Federico II Via D. Montesano 49 80131 Napoli Italy
| | - Gennaro Piccialli
- Department of Pharmacy Università degli Studi di Napoli Federico II Via D. Montesano 49 80131 Napoli Italy
| | - Nicola Borbone
- Department of Pharmacy Università degli Studi di Napoli Federico II Via D. Montesano 49 80131 Napoli Italy
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37
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Kankia B, Gvarjaladze D, Rabe A, Lomidze L, Metreveli N, Musier-Forsyth K. Stable Domain Assembly of a Monomolecular DNA Quadruplex: Implications for DNA-Based Nanoswitches. Biophys J 2017; 110:2169-75. [PMID: 27224482 PMCID: PMC4880955 DOI: 10.1016/j.bpj.2016.04.031] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2016] [Revised: 04/16/2016] [Accepted: 04/25/2016] [Indexed: 12/31/2022] Open
Abstract
In the presence of K+ ions, the 5′-GGGTGGGTGGGTGGG-3′ (G3T) sequence folds into a monomolecular quadruplex with unusually high thermal stability and unique optical properties. In this study we report that although single G3T molecules unfold and fold rapidly with overlapping melting and refolding curves, G3T multimers (G3T units covalently attached to each other) demonstrate highly reproducible hysteretic behavior. We demonstrate that this behavior necessitates full-length tandem G3T monomers directly conjugated to each other. Any modification of the tandem sequences eliminates the hysteresis. The experimentally measured kinetic parameters and equilibrium transition profiles suggest a highly specific two-state transition in which the folding and unfolding of the first G3T monomer is rate-limiting for both annealing and melting processes. The highly reproducible hysteretic behavior of G3T multimers has the potential to be used in the design of heat-stimulated DNA switches or transistors.
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Affiliation(s)
- Besik Kankia
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, Ohio; Institute of Biophysics, Ilia State University, Tbilisi, Republic of Georgia.
| | - David Gvarjaladze
- Institute of Biophysics, Ilia State University, Tbilisi, Republic of Georgia
| | - Adam Rabe
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, Ohio
| | - Levan Lomidze
- Institute of Biophysics, Ilia State University, Tbilisi, Republic of Georgia
| | - Nunu Metreveli
- Institute of Biophysics, Ilia State University, Tbilisi, Republic of Georgia
| | - Karin Musier-Forsyth
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, Ohio
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Relations between the loop transposition of DNA G-quadruplex and the catalytic function of DNAzyme. Biochim Biophys Acta Gen Subj 2017; 1861:1913-1920. [PMID: 28533132 DOI: 10.1016/j.bbagen.2017.05.016] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2017] [Revised: 04/26/2017] [Accepted: 05/18/2017] [Indexed: 01/11/2023]
Abstract
The structures of DNA G-quadruplexes are essential for their functions in vivo and in vitro. Our present study revealed that sequential order of the three G-quadruplex loops, that is, loop transposition, could be a critical factor to determinate the G-quadruplex conformation and consequently improved the catalytic function of G-quadruplex based DNAzyme. In the presence of 100mM K+, loop transposition induced one of the G-quadruplex isomers which shared identical loops but differed in the sequential order of loops into a hybrid topology while the others into predominately parallel topologies. 1D NMR spectroscopy and mutation analysis suggested that the hydrogen bonding from loops residues with nucleotides in flanking sequences may be responsible for the stabilization of the different conformations. A well-known DNAzyme consisting of G-quadruplex and hemin (Ferriprotoporphyrin IX chloride) was chosen to test the catalytic function. We found that the loop transposition could enhance the reaction rate obviously by increasing the hemin binding affinity to G-quadruplex. These findings disclose the relations between the loop transposition, G-quadruplex conformation and catalytic function of DNAzyme.
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Šponer J, Bussi G, Stadlbauer P, Kührová P, Banáš P, Islam B, Haider S, Neidle S, Otyepka M. Folding of guanine quadruplex molecules-funnel-like mechanism or kinetic partitioning? An overview from MD simulation studies. Biochim Biophys Acta Gen Subj 2016; 1861:1246-1263. [PMID: 27979677 DOI: 10.1016/j.bbagen.2016.12.008] [Citation(s) in RCA: 74] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2016] [Revised: 12/04/2016] [Accepted: 12/11/2016] [Indexed: 01/18/2023]
Abstract
BACKGROUND Guanine quadruplexes (GQs) play vital roles in many cellular processes and are of much interest as drug targets. In contrast to the availability of many structural studies, there is still limited knowledge on GQ folding. SCOPE OF REVIEW We review recent molecular dynamics (MD) simulation studies of the folding of GQs, with an emphasis paid to the human telomeric DNA GQ. We explain the basic principles and limitations of all types of MD methods used to study unfolding and folding in a way accessible to non-specialists. We discuss the potential role of G-hairpin, G-triplex and alternative GQ intermediates in the folding process. We argue that, in general, folding of GQs is fundamentally different from funneled folding of small fast-folding proteins, and can be best described by a kinetic partitioning (KP) mechanism. KP is a competition between at least two (but often many) well-separated and structurally different conformational ensembles. MAJOR CONCLUSIONS The KP mechanism is the only plausible way to explain experiments reporting long time-scales of GQ folding and the existence of long-lived sub-states. A significant part of the natural partitioning of the free energy landscape of GQs comes from the ability of the GQ-forming sequences to populate a large number of syn-anti patterns in their G-tracts. The extreme complexity of the KP of GQs typically prevents an appropriate description of the folding landscape using just a few order parameters or collective variables. GENERAL SIGNIFICANCE We reconcile available computational and experimental studies of GQ folding and formulate basic principles characterizing GQ folding landscapes. 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)
- Jiří Šponer
- Institute of Biophysics, Academy of Sciences of the Czech Republic, Kralovopolska 135, 612 65 Brno, Czech Republic; Regional Centre of Advanced Technologies and Materials, Department of Physical Chemistry, Faculty of Science, Palacky University Olomouc, 17. listopadu 12, 771 46 Olomouc, Czech Republic.
| | - Giovanni Bussi
- Scuola Internazionale Superiore di Studi Avanzati, Via Bonomea 265, 34136 Trieste, Italy
| | - Petr Stadlbauer
- Institute of Biophysics, Academy of Sciences of the Czech Republic, Kralovopolska 135, 612 65 Brno, Czech Republic; Regional Centre of Advanced Technologies and Materials, Department of Physical Chemistry, Faculty of Science, Palacky University Olomouc, 17. listopadu 12, 771 46 Olomouc, Czech Republic
| | - Petra Kührová
- Regional Centre of Advanced Technologies and Materials, Department of Physical Chemistry, Faculty of Science, Palacky University Olomouc, 17. listopadu 12, 771 46 Olomouc, Czech Republic
| | - Pavel Banáš
- Regional Centre of Advanced Technologies and Materials, Department of Physical Chemistry, Faculty of Science, Palacky University Olomouc, 17. listopadu 12, 771 46 Olomouc, Czech Republic
| | - Barira Islam
- Institute of Biophysics, Academy of Sciences of the Czech Republic, Kralovopolska 135, 612 65 Brno, Czech Republic
| | - Shozeb Haider
- UCL School of Pharmacy, 29-39 Brunswick Square, London WC1N 1AX, UK
| | - Stephen Neidle
- UCL School of Pharmacy, 29-39 Brunswick Square, London WC1N 1AX, UK
| | - Michal Otyepka
- Regional Centre of Advanced Technologies and Materials, Department of Physical Chemistry, Faculty of Science, Palacky University Olomouc, 17. listopadu 12, 771 46 Olomouc, Czech Republic
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40
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Integrating Deoxyribozymes into Colorimetric Sensing Platforms. SENSORS 2016; 16:s16122061. [PMID: 27918487 PMCID: PMC5191042 DOI: 10.3390/s16122061] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/01/2016] [Revised: 11/30/2016] [Accepted: 11/30/2016] [Indexed: 01/05/2023]
Abstract
Biosensors are analytical devices that have found a variety of applications in medical diagnostics, food quality control, environmental monitoring and biodefense. In recent years, functional nucleic acids, such as aptamers and nucleic acid enzymes, have shown great potential in biosensor development due to their excellent ability in target recognition and catalysis. Deoxyribozymes (or DNAzymes) are single-stranded DNA molecules with catalytic activity and can be isolated to recognize a wide range of analytes through the process of in vitro selection. By using various signal transduction mechanisms, DNAzymes can be engineered into fluorescent, colorimetric, electrochemical and chemiluminescent biosensors. Among them, colorimetric sensors represent an attractive option as the signal can be easily detected by the naked eye. This reduces reliance on complex and expensive equipment. In this review, we will discuss the recent progress in the development of colorimetric biosensors that make use of DNAzymes and the prospect of employing these sensors in a range of chemical and biological applications.
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41
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Bhattacharyya D, Mirihana Arachchilage G, Basu S. Metal Cations in G-Quadruplex Folding and Stability. Front Chem 2016; 4:38. [PMID: 27668212 PMCID: PMC5016522 DOI: 10.3389/fchem.2016.00038] [Citation(s) in RCA: 377] [Impact Index Per Article: 47.1] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2016] [Accepted: 08/25/2016] [Indexed: 12/23/2022] Open
Abstract
This review is focused on the structural and physicochemical aspects of metal cation coordination to G-Quadruplexes (GQ) and their effects on GQ stability and conformation. G-quadruplex structures are non-canonical secondary structures formed by both DNA and RNA. G-quadruplexes regulate a wide range of important biochemical processes. Besides the sequence requirements, the coordination of monovalent cations in the GQ is essential for its formation and determines the stability and polymorphism of GQ structures. The nature, location, and dynamics of the cation coordination and their impact on the overall GQ stability are dependent on several factors such as the ionic radii, hydration energy, and the bonding strength to the O6 of guanines. The intracellular monovalent cation concentration and the localized ion concentrations determine the formation of GQs and can potentially dictate their regulatory roles. A wide range of biochemical and biophysical studies on an array of GQ enabling sequences have generated at a minimum the knowledge base that allows us to often predict the stability of GQs in the presence of the physiologically relevant metal ions, however, prediction of conformation of such GQs is still out of the realm.
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Affiliation(s)
| | | | - Soumitra Basu
- Department of Chemistry and Biochemistry, Kent State UniversityKent, OH, USA
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42
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Accurate high-throughput identification of parallel G-quadruplex topology by a new tetraaryl-substituted imidazole. Biosens Bioelectron 2016; 83:77-84. [DOI: 10.1016/j.bios.2016.04.029] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2016] [Revised: 03/15/2016] [Accepted: 04/11/2016] [Indexed: 11/21/2022]
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43
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Sheu SY, Huang CH, Zhou JK, Yang DY. Relative stability of G-quadruplex structures: Interactions between the human Bcl2 promoter region and derivatives of carbazole and diphenylamine. Biopolymers 2016; 101:1038-50. [PMID: 24723333 DOI: 10.1002/bip.22497] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2013] [Revised: 04/07/2014] [Accepted: 04/07/2014] [Indexed: 01/24/2023]
Abstract
The bcl2 promoter region forms a G-quadruplex structure, which is a crucial target for anticancer drug development. In this study, we provide theoretical predictions of the stability of different G-quadruplex folds of the 23-mer bcl2 promoter region and G-quadruplex ligand. We take into account the whole G-quadruplex structure, including bound-cations and solvent effects, in order to compute the ligand binding free energy using molecular dynamics simulation. Two series of the carbazole and diphenylamine derivatives are used to screen for the most potent drug in terms of stabilization. The energy analysis identifies the predominant energy components affecting the stability of the various different G-quadruplex folds. The energy associated with the stability of the G-quadruplex-K(+) structures obtained displays good correlation with experimental Tm measurements. We found that loop orientation has an intrinsic influence on G-quadruplex stability and that the basket structure is the most stable. Furthermore, parallel loops are the most effective drug binding site. Our studies also demonstrate that rigidity and planarity are the key structural elements of a drug that stabilizes the G-quadruplex structure. BMVC-4 is the most potential G-quadruplex ligand. This approach demonstrates significant promise and should benefit drug design.
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Affiliation(s)
- Sheh-Yi Sheu
- Department of Life Sciences and Institute of Genome Sciences, National Yang-Ming University, Taipei, 112, Taiwan; Institute of Biomedical informatics, National Yang-Ming University, Taipei, 112, Taiwan
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44
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Gao S, Cao Y, Yan Y, Guo X. Sequence Effect on the Topology of 3 + 1 Interlocked Bimolecular DNA G-Quadruplexes. Biochemistry 2016; 55:2694-703. [PMID: 27027538 DOI: 10.1021/acs.biochem.5b01190] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Abstract
Electrospray ionization mass spectrometry (ESI-MS) combined with fluorescence, circular dichroism, UV spectrophotometer, and native polyacrylamide gel electrophoresis techniques are used to study structural features of interlocked dimers formed by DNA sequence 93del (GGGGTGGGAGGAGGGT) and its derivatives. Herein, we demonstrate that the interlocked dimers can be distinguished from stacked dimers formed by sequences T30923 (GGGTGGGTGGGTGGGT) and T30177 (GTGGTGGGTGGGTGGGT). In addition, loop length, the base at 5'-end, and the isolation of T and TT to the first 4G tract do significantly influence the formation and topologies of interlocked dimers. Furthermore, our results suggest that the 4G tract and the 2G tract in various locations in the 93del derivative sequence can form interlocked structure. This work not only provides new insight into the assembly of 3 + 1 interlocked DNA conformations but also demonstrates that ESI-MS combined with other analytical methods is rapid and useful for DNA structural studies.
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Affiliation(s)
- Shang Gao
- College of Chemistry, Jilin University , Changchun, China 130012
| | - Yanwei Cao
- College of Chemistry, Jilin University , Changchun, China 130012
| | - Yuting Yan
- College of Chemistry, Jilin University , Changchun, China 130012
| | - Xinhua Guo
- College of Chemistry, Jilin University , Changchun, China 130012
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45
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Fujii T, Sugimoto N. Loop nucleotides impact the stability of intrastrand i-motif structures at neutral pH. Phys Chem Chem Phys 2016; 17:16719-22. [PMID: 26058487 DOI: 10.1039/c5cp02794b] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
The stability of i-motif structures at neutral pH is of interest due to the potential of these structures to impact gene expression. A systematic investigation of loop sequence and length revealed that certain loop nucleobases stabilize i-motif quadruplexes.
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Affiliation(s)
- Taiga Fujii
- Frontier Institute for Biomolecular Engineering Research (FIBER), Konan University, 8-9-1 Minatojima-minamimachi, Chuo-ku, Kobe 650-0047, Japan.
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46
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Wu T, Zhang C, Wang Z, Ren H, Kang Y, Du Y. Tuning the sensing range of potassium ions by changing the loop size of G-quadruplex sensors. NEW J CHEM 2016. [DOI: 10.1039/c6nj02136k] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Fluorescence spectroscopy and thermodynamics were combined for the study of the loop size effect of G-quadruplex sensors in the K+ sensing range.
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Affiliation(s)
- Ting Wu
- School of Chemistry and Molecular Engineering
- East China University of Science and Technology
- Shanghai 200237
- China
| | - Chuanjing Zhang
- School of Chemistry and Molecular Engineering
- East China University of Science and Technology
- Shanghai 200237
- China
| | - Zhenping Wang
- School of Chemistry and Molecular Engineering
- East China University of Science and Technology
- Shanghai 200237
- China
| | - Hongxin Ren
- School of Chemistry and Molecular Engineering
- East China University of Science and Technology
- Shanghai 200237
- China
| | - Yan Kang
- School of Chemistry and Molecular Engineering
- East China University of Science and Technology
- Shanghai 200237
- China
| | - Yiping Du
- School of Chemistry and Molecular Engineering
- East China University of Science and Technology
- Shanghai 200237
- China
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47
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Largy E, Mergny JL, Gabelica V. Role of Alkali Metal Ions in G-Quadruplex Nucleic Acid Structure and Stability. Met Ions Life Sci 2016; 16:203-58. [PMID: 26860303 DOI: 10.1007/978-3-319-21756-7_7] [Citation(s) in RCA: 105] [Impact Index Per Article: 13.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
G-quadruplexes are guanine-rich nucleic acids that fold by forming successive quartets of guanines (the G-tetrads), stabilized by intra-quartet hydrogen bonds, inter-quartet stacking, and cation coordination. This specific although highly polymorphic type of secondary structure deviates significantly from the classical B-DNA duplex. G-quadruplexes are detectable in human cells and are strongly suspected to be involved in a number of biological processes at the DNA and RNA levels. The vast structural polymorphism exhibited by G-quadruplexes, together with their putative biological relevance, makes them attractive therapeutic targets compared to canonical duplex DNA. This chapter focuses on the essential and specific coordination of alkali metal cations by G-quadruplex nucleic acids, and most notably on studies highlighting cation-dependent dissimilarities in their stability, structure, formation, and interconversion. Section 1 surveys G-quadruplex structures and their interactions with alkali metal ions while Section 2 presents analytical methods used to study G-quadruplexes. The influence of alkali cations on the stability, structure, and kinetics of formation of G-quadruplex structures of quadruplexes will be discussed in Sections 3 and 4. Section 5 focuses on the cation-induced interconversion of G-quadruplex structures. In Sections 3 to 5, we will particularly emphasize the comparisons between cations, most often K(+) and Na(+) because of their prevalence in the literature and in cells.
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Affiliation(s)
- Eric Largy
- ARNA Laboratory, Université Bordeaux, IECB, 2, rue Robert Escarpit, F-33600, Pessac, France.,ARNA Laboratory, INSERM, U869, F-33000, Bordeaux, France
| | - Jean-Louis Mergny
- ARNA Laboratory, Université Bordeaux, IECB, 2, rue Robert Escarpit, F-33600, Pessac, France. .,ARNA Laboratory, INSERM, U869, F-33000, Bordeaux, France.
| | - Valérie Gabelica
- ARNA Laboratory, Université Bordeaux, IECB, 2, rue Robert Escarpit, F-33600, Pessac, France. .,ARNA Laboratory, INSERM, U869, F-33000, Bordeaux, France.
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48
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Stadlbauer P, Kührová P, Banáš P, Koča J, Bussi G, Trantírek L, Otyepka M, Šponer J. Hairpins participating in folding of human telomeric sequence quadruplexes studied by standard and T-REMD simulations. Nucleic Acids Res 2015; 43:9626-44. [PMID: 26433223 PMCID: PMC4787745 DOI: 10.1093/nar/gkv994] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2015] [Accepted: 09/22/2015] [Indexed: 11/13/2022] Open
Abstract
DNA G-hairpins are potential key structures participating in folding of human telomeric guanine quadruplexes (GQ). We examined their properties by standard MD simulations starting from the folded state and long T-REMD starting from the unfolded state, accumulating ∼130 μs of atomistic simulations. Antiparallel G-hairpins should spontaneously form in all stages of the folding to support lateral and diagonal loops, with sub-μs scale rearrangements between them. We found no clear predisposition for direct folding into specific GQ topologies with specific syn/anti patterns. Our key prediction stemming from the T-REMD is that an ideal unfolded ensemble of the full GQ sequence populates all 4096 syn/anti combinations of its four G-stretches. The simulations can propose idealized folding pathways but we explain that such few-state pathways may be misleading. In the context of the available experimental data, the simulations strongly suggest that the GQ folding could be best understood by the kinetic partitioning mechanism with a set of deep competing minima on the folding landscape, with only a small fraction of molecules directly folding to the native fold. The landscape should further include non-specific collapse processes where the molecules move via diffusion and consecutive random rare transitions, which could, e.g. structure the propeller loops.
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Affiliation(s)
- Petr Stadlbauer
- Institute of Biophysics, Academy of Sciences of the Czech Republic, Královopolská 135, 612 65 Brno, Czech Republic
| | - Petra Kührová
- Regional Centre of Advanced Technologies and Materials, Department of Physical Chemistry, Faculty of Science, Palacký University, tř. 17 listopadu 12, 771 46 Olomouc, Czech Republic
| | - Pavel Banáš
- Regional Centre of Advanced Technologies and Materials, Department of Physical Chemistry, Faculty of Science, Palacký University, tř. 17 listopadu 12, 771 46 Olomouc, Czech Republic
| | - Jaroslav Koča
- CEITEC - Central European Institute of Technology, Masaryk University, Campus Bohunice, Kamenice 5, 625 00 Brno, Czech Republic National Center for Biomolecular Research, Faculty of Science, Masaryk University, Campus Bohunice, Kamenice 5, 625 00 Brno, Czech Republic
| | - Giovanni Bussi
- Scuola Internazionale Superiore di Studi Avanzati, Via Bonomea 265, 34136 Trieste, Italy
| | - Lukáš Trantírek
- CEITEC - Central European Institute of Technology, Masaryk University, Campus Bohunice, Kamenice 5, 625 00 Brno, Czech Republic
| | - Michal Otyepka
- Regional Centre of Advanced Technologies and Materials, Department of Physical Chemistry, Faculty of Science, Palacký University, tř. 17 listopadu 12, 771 46 Olomouc, Czech Republic
| | - Jiří Šponer
- Institute of Biophysics, Academy of Sciences of the Czech Republic, Královopolská 135, 612 65 Brno, Czech Republic CEITEC - Central European Institute of Technology, Masaryk University, Campus Bohunice, Kamenice 5, 625 00 Brno, Czech Republic
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49
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Gao W, Zhang L, Liang RP, Qiu JD. Metal-Ion-Triggered Exonuclease III Activity for the Construction of DNA Colorimetric Logic Gates. Chemistry 2015; 21:15272-9. [DOI: 10.1002/chem.201502122] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2015] [Indexed: 01/05/2023]
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50
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Ogloblina AM, Bannikova VA, Khristich AN, Oretskaya TS, Yakubovskaya MG, Dolinnaya NG. Parallel G-quadruplexes formed by guanine-rich microsatellite repeats inhibit human topoisomerase I. BIOCHEMISTRY (MOSCOW) 2015; 80:1026-38. [DOI: 10.1134/s0006297915080088] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
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