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Zegers J, Peters M, Albada B. DNA G-quadruplex-stabilizing metal complexes as anticancer drugs. J Biol Inorg Chem 2023; 28:117-138. [PMID: 36456886 PMCID: PMC9981530 DOI: 10.1007/s00775-022-01973-0] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2022] [Accepted: 11/17/2022] [Indexed: 12/04/2022]
Abstract
Guanine quadruplexes (G4s) are important targets for cancer treatments as their stabilization has been associated with a reduction of telomere ends or a lower oncogene expression. Although less abundant than purely organic ligands, metal complexes have shown remarkable abilities to stabilize G4s, and a wide variety of techniques have been used to characterize the interaction between ligands and G4s. However, improper alignment between the large variety of experimental techniques and biological activities can lead to improper identification of top candidates, which hampers progress of this important class of G4 stabilizers. To address this, we first review the different techniques for their strengths and weaknesses to determine the interaction of the complexes with G4s, and provide a checklist to guide future developments towards comparable data. Then, we surveyed 74 metal-based ligands for G4s that have been characterized to the in vitro level. Of these complexes, we assessed which methods were used to characterize their G4-stabilizing capacity, their selectivity for G4s over double-stranded DNA (dsDNA), and how this correlated to bioactivity data. For the biological activity data, we compared activities of the G4-stabilizing metal complexes with that of cisplatin. Lastly, we formulated guidelines for future studies on G4-stabilizing metal complexes to further enable maturation of this field.
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Affiliation(s)
- Jaccoline Zegers
- grid.4818.50000 0001 0791 5666Laboratory of Organic Chemistry, Wageningen University and Research, Stippeneng 4, 6708 WE Wageningen, The Netherlands
| | - Maartje Peters
- grid.4818.50000 0001 0791 5666Laboratory of Organic Chemistry, Wageningen University and Research, Stippeneng 4, 6708 WE Wageningen, The Netherlands
| | - Bauke Albada
- Laboratory of Organic Chemistry, Wageningen University and Research, Stippeneng 4, 6708 WE, Wageningen, The Netherlands.
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2
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Miglietta G, Russo M, Capranico G. G-quadruplex-R-loop interactions and the mechanism of anticancer G-quadruplex binders. Nucleic Acids Res 2020; 48:11942-11957. [PMID: 33137181 PMCID: PMC7708042 DOI: 10.1093/nar/gkaa944] [Citation(s) in RCA: 75] [Impact Index Per Article: 18.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2020] [Revised: 10/05/2020] [Accepted: 10/08/2020] [Indexed: 12/17/2022] Open
Abstract
Genomic DNA and cellular RNAs can form a variety of non-B secondary structures, including G-quadruplex (G4) and R-loops. G4s are constituted by stacked guanine tetrads held together by Hoogsteen hydrogen bonds and can form at key regulatory sites of eukaryote genomes and transcripts, including gene promoters, untranslated exon regions and telomeres. R-loops are 3-stranded structures wherein the two strands of a DNA duplex are melted and one of them is annealed to an RNA. Specific G4 binders are intensively investigated to discover new effective anticancer drugs based on a common rationale, i.e.: the selective inhibition of oncogene expression or specific impairment of telomere maintenance. However, despite the high number of known G4 binders, such a selective molecular activity has not been fully established and several published data point to a different mode of action. We will review published data that address the close structural interplay between G4s and R-loops in vitro and in vivo, and how these interactions can have functional consequences in relation to G4 binder activity. We propose that R-loops can play a previously-underestimated role in G4 binder action, in relation to DNA damage induction, telomere maintenance, genome and epigenome instability and alterations of gene expression programs.
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Affiliation(s)
- Giulia Miglietta
- Department of Pharmacy and Biotechnology, Alma Mater Studiorum University of Bologna, via Selmi 3, 40126 Bologna, Italy
| | - Marco Russo
- Department of Pharmacy and Biotechnology, Alma Mater Studiorum University of Bologna, via Selmi 3, 40126 Bologna, Italy
| | - Giovanni Capranico
- Department of Pharmacy and Biotechnology, Alma Mater Studiorum University of Bologna, via Selmi 3, 40126 Bologna, Italy
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3
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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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4
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Zhou Y, Yu Y, Gao L, Fei Y, Ye T, Li Q, Zhou X, Gan N, Shao Y. Structuring polarity-inverted TBA to G-quadruplex for selective recognition of planarity of natural isoquinoline alkaloids. Analyst 2018; 143:4907-4914. [PMID: 30238092 DOI: 10.1039/c8an01561a] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
Efficient structuring of DNA by small molecules is very crucial in developing DNA-based novel switches with an ideal performance. In this work, we found that inverting only the polarity of the 3' terminal guanine of the thrombin-binding aptamer (3iTBA) totally eradicates the original TBA G-quadruplex (G4) structure in K+. The unstructured 3iTBA can be further refolded upon specifically interacting with small molecules of natural isoquinoline alkaloids (IAs) due to their fruitful binding patterns with variant nucleic acid structures. We identified that 3iTBA can serve as a topology selector for planar IAs. Nitidine (NIT), owing to the planar aromatic ring and coplanar substituents, is the most efficient to restructure the 3iTBA random coil toward the anti-parallel G4 conformation. However, common metal ions can't realize this structuring. The topology selector competency of 3iTBA toward IAs' planarity can be visualized using gold nanoparticles (AuNPs) as the chromogenic readout. Our work expands the G4 repertoire by exploring the polarity inversion regulation and provides a new approach to switch nucleic acid structures toward a small molecule structure-sensitive sensor.
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Affiliation(s)
- Yufeng Zhou
- Institute of Physical Chemistry, College of Chemistry and Life Sciences, Zhejiang Normal University, Jinhua 321004, Zhejiang, China.
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5
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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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6
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Transformation of a Thermostable G-Quadruplex Structure into DNA Duplex Driven by Reverse Gyrase. Molecules 2017; 22:molecules22112021. [PMID: 29165328 PMCID: PMC6150213 DOI: 10.3390/molecules22112021] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2017] [Revised: 11/14/2017] [Accepted: 11/17/2017] [Indexed: 11/27/2022] Open
Abstract
Reverse gyrase is a topoisomerase that can introduce positive supercoils to its substrate DNA. It is demonstrated in our studies that a highly thermal stable G-quadruplex structure in a mini-plasmid DNA was transformed into its duplex conformation after a treatment with reverse gyrase. The structural difference of the topoisomers were verified and analyzed by gel electrophoresis, atomic force microscopy examination, and endonuclease digestion assays. All evidence suggested that the overwinding structure of positive supercoil could provide a driven force to disintegrate G-quadruplex and reform duplex. The results of our studies could suggest that hyperthermophiles might use reverse gyrase to manipulate the disintegration of non-B DNA structures and safekeep their genomic information.
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Reilly SM, Morgan RK, Brooks TA, Wadkins RM. Effect of interior loop length on the thermal stability and pK(a) of i-motif DNA. Biochemistry 2015; 54:1364-70. [PMID: 25619229 DOI: 10.1021/bi5014722] [Citation(s) in RCA: 48] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
The four-stranded i-motif (iM) conformation of cytosine-rich DNA is important in a wide variety of biochemical systems ranging from its use in nanomaterials to a potential role in oncogene regulation. An iM is stabilized by acidic pH that allows hemiprotonated cytidines to form a C·C(+) base pair. Fundamental studies that aim to understand how the lengths of loops connecting the protonated C·C(+) pairs affect intramolecular iM physical properties are described here. We characterized both the thermal stability and the pK(a) of intramolecular iMs with differing loop lengths, in both dilute solutions and solutions containing molecular crowding agents. Our results showed that intramolecular iMs with longer central loops form at pHs and temperatures higher than those of iMs with longer outer loops. Our studies also showed that increases in thermal stability of iMs when molecular crowding agents are present are dependent on the loop that is lengthened. However, the increase in pK(a) for iMs when molecular crowding agents are present is insensitive to loop length. Importantly, we also determined the proton activity of solutions containing high concentrations of molecular crowding agents to ascertain whether the increase in pK(a) of an iM is caused by alteration of this activity in buffered solutions. We determined that crowding agents alone increase the apparent pK(a) of a number of small molecules as well as iMs but that increases to iM pK(a) were greater than that expected from a shift in proton activity.
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Affiliation(s)
- Samantha M Reilly
- Department of Chemistry and Biochemistry, University of Mississippi , University, Mississippi 38677, United States
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8
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Abstract
![]()
All biological processes take place
in highly crowded cellular
environments. However, the effect that molecular crowding agents have
on the folding and catalytic properties of RNA molecules remains largely
unknown. Here, we have combined single-molecule fluorescence resonance
energy transfer (smFRET) and bulk cleavage assays to determine the
effect of a molecular crowding agents on the folding and catalysis
of a model RNA enzyme, the hairpin ribozyme. Our single-molecule data
reveal that PEG favors the formation of the docked (active) structure
by increasing the docking rate constant with increasing PEG concentrations.
Furthermore, Mg2+ ion-induced folding in the presence of
PEG occurs at concentrations ∼7-fold lower than in the absence
of PEG, near the physiological range (∼1 mM). Lastly, bulk
cleavage assays in the presence of the crowding agent show that the
ribozyme’s activity increases while the heterogeneity decreases.
Our data is consistent with the idea that molecular crowding plays
an important role in the stabilization of ribozyme active conformations in vivo.
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Affiliation(s)
- Bishnu P Paudel
- Department of Medicine, Section of Virology, and Single Molecule Imaging Group, MRC-Clinical Sciences Centre, Imperial College London , Du Cane Road, London W12 0NN, U.K
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9
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Sugimoto N. Noncanonical structures and their thermodynamics of DNA and RNA under molecular crowding: beyond the Watson-Crick double helix. INTERNATIONAL REVIEW OF CELL AND MOLECULAR BIOLOGY 2014; 307:205-73. [PMID: 24380597 DOI: 10.1016/b978-0-12-800046-5.00008-4] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
How does molecular crowding affect the stability of nucleic acid structures inside cells? Water is the major solvent component in living cells, and the properties of water in the highly crowded media inside cells differ from that in buffered solution. As it is difficult to measure the thermodynamic behavior of nucleic acids in cells directly and quantitatively, we recently developed a cell-mimicking system using cosolutes as crowding reagents. The influences of molecular crowding on the structures and thermodynamics of various nucleic acid sequences have been reported. In this chapter, we discuss how the structures and thermodynamic properties of nucleic acids differ under various conditions such as highly crowded environments, compartment environments, and in the presence of ionic liquids, and the major determinants of the crowding effects on nucleic acids are discussed. The effects of molecular crowding on the activities of ribozymes and riboswitches on noncanonical structures of DNA- and RNA-like quadruplexes that play important roles in transcription and translation are also described.
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Affiliation(s)
- Naoki Sugimoto
- Frontier Institute for Biomolecular Engineering Research (FIBER) and Faculty of Frontiers of Innovative Research in Science and Technology (FIRST), Konan University, Kobe, Japan.
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10
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Nakano SI, Miyoshi D, Sugimoto N. Effects of molecular crowding on the structures, interactions, and functions of nucleic acids. Chem Rev 2013; 114:2733-58. [PMID: 24364729 DOI: 10.1021/cr400113m] [Citation(s) in RCA: 367] [Impact Index Per Article: 33.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Affiliation(s)
- Shu-ichi Nakano
- Department of Nanobiochemistry, Faculty of Frontiers of Innovative Research in Science and Technology (FIRST) and Frontier Institute for Biomolecular Engineering Research (FIBER), Konan University , 7-1-20 Minatojima-minamimachi, Chuo-ku, Kobe 650-0047, Japan
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11
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Belotserkovskii BP, Mirkin SM, Hanawalt PC. DNA sequences that interfere with transcription: implications for genome function and stability. Chem Rev 2013; 113:8620-37. [PMID: 23972098 DOI: 10.1021/cr400078y] [Citation(s) in RCA: 83] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
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12
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Buscaglia R, Miller MC, Dean WL, Gray RD, Lane AN, Trent JO, Chaires JB. Polyethylene glycol binding alters human telomere G-quadruplex structure by conformational selection. Nucleic Acids Res 2013; 41:7934-46. [PMID: 23804761 PMCID: PMC3763525 DOI: 10.1093/nar/gkt440] [Citation(s) in RCA: 108] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Abstract
Polyethylene glycols (PEGs) are widely used to perturb the conformations of nucleic acids, including G-quadruplexes. The mechanism by which PEG alters G-quadruplex conformation is poorly understood. We describe here studies designed to determine how PEG and other co-solutes affect the conformation of the human telomeric quadruplex. Osmotic stress studies using acetonitrile and ethylene glycol show that conversion of the ‘hybrid’ conformation to an all-parallel ‘propeller’ conformation is accompanied by the release of about 17 water molecules per quadruplex and is energetically unfavorable in pure aqueous solutions. Sedimentation velocity experiments show that the propeller form is hydrodynamically larger than hybrid forms, ruling out a crowding mechanism for the conversion by PEG. PEGs do not alter water activity sufficiently to perturb quadruplex hydration by osmotic stress. PEG titration experiments are most consistent with a conformational selection mechanism in which PEG binds more strongly to the propeller conformation, and binding is coupled to the conformational transition between forms. Molecular dynamics simulations show that PEG binding to the propeller form is sterically feasible and energetically favorable. We conclude that PEG does not act by crowding and is a poor mimic of the intranuclear environment, keeping open the question of the physiologically relevant quadruplex conformation.
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Affiliation(s)
- Robert Buscaglia
- James Graham Brown Cancer Center, University of Louisville, 505 S. Hancock, Louisville, KY, 40202
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13
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Lv B, Li D, Zhang H, Lee JY, Li T. DNA gyrase-driven generation of a G-quadruplex from plasmid DNA. Chem Commun (Camb) 2013; 49:8317-9. [DOI: 10.1039/c3cc44675a] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
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14
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Zhou J, Bourdoncle A, Rosu F, Gabelica V, Mergny JL. Tri-G-Quadruplex: Controlled Assembly of a G-Quadruplex Structure from Three G-Rich Strands. Angew Chem Int Ed Engl 2012. [DOI: 10.1002/ange.201205390] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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15
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Zhou J, Bourdoncle A, Rosu F, Gabelica V, Mergny JL. Tri-G-quadruplex: controlled assembly of a G-quadruplex structure from three G-rich strands. Angew Chem Int Ed Engl 2012; 51:11002-5. [PMID: 23038222 DOI: 10.1002/anie.201205390] [Citation(s) in RCA: 55] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2012] [Indexed: 12/17/2022]
Abstract
In my (DNA) dreams: A tri-G-quadruplex was constructed from three strands (T1-T3) of DNA using duplex formation to guide the G-rich tracts into close proximity with the addition of Li(+) ions (see scheme). The defined G-quadruplex structure was formed upon addition of Na(+) ions and characterized by gel electrophoresis and spectroscopy.
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Affiliation(s)
- Jun Zhou
- Univ. Bordeaux, ARNA Laboratory, F-33000 Bordeaux, France
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16
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Miyoshi D, Fujimoto T, Sugimoto N. Molecular Crowding and Hydration Regulating of G-Quadruplex Formation. Top Curr Chem (Cham) 2012; 330:87-110. [DOI: 10.1007/128_2012_335] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
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17
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Pramanik S, Nagatoishi S, Sugimoto N. DNA tetraplex structure formation from human telomeric repeat motif (TTAGGG):(CCCTAA) in nanocavity water pools of reverse micelles. Chem Commun (Camb) 2012; 48:4815-7. [PMID: 22456442 DOI: 10.1039/c2cc30622k] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
In an equimolar ratio the human telomeric oligonucleotides d[AGGG(TTAGGG)(3)] and d[(CCCTAA)(3)CCCT] formed mixed structures of duplex and tetraplex in bis(2-ethylhexyl)sulfosuccinate reverse micelles; only the duplex was observed in aqueous buffer. This finding suggests that heterogeneous confined media in the cell nucleus might induce a significant fraction of the telomeric region of genomic DNA to adopt non-canonical tetraplex structure.
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Affiliation(s)
- Smritimoy Pramanik
- Frontier Institute for Biomolecular Engineering Research (FIBER), Konan University, 7-1-20 Minatojima-minamimachi, Kobe 650-0047, Japan
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18
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Petraccone L, Pagano B, Giancola C. Studying the effect of crowding and dehydration on DNA G-quadruplexes. Methods 2012; 57:76-83. [PMID: 22406490 DOI: 10.1016/j.ymeth.2012.02.011] [Citation(s) in RCA: 47] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2012] [Revised: 02/20/2012] [Accepted: 02/21/2012] [Indexed: 01/01/2023] Open
Abstract
Intracellular environment is crowded with biomolecules that occupy a significant fraction (up to 40%) of the cellular volume, with a total concentration in the range 300-400mg/ml. Recently, the effect of crowding/dehydrating agents on the DNA G-quadruplexes has become a subject of an increasing interest. Crowding and/or dehydrating agents have been used to simulate how G-quadruplexes behave under cell-mimicking conditions characterized by a large excluded volume and a lower water activity. Indeed, the presence of both steric crowding and a lower water activity can affect G-quadruplex stability, their folding/unfolding kinetics, as well as their binding processes with proteins or small ligands. Many of these effects can be explored experimentally by measuring the dependence of the conformational stability, isomerisation kinetics and equilibria on the concentration of cosolutes which do not interact with the molecules (G-quadruplexes) under investigation. Spectroscopic methodologies, like circular dichroism, UV and fluorescence, have been widely employed to study G-quadruplexes in dilute solution. Here we focus on some aspects that need to be taken into account when employing such techniques in the presence of large amount of a cosolute. Additionally, we discuss possible problems/artifacts that arise in setting experiments in presence of these commonly employed cosolutes and in interpreting the results.
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Affiliation(s)
- Luigi Petraccone
- Dipartimento di Scienze Chimiche, Università degli Studi di Napoli "Federico II", Via Cintia, I-80126 Napoli, Italy
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19
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Petraccone L, Malafronte A, Amato J, Giancola C. G-Quadruplexes from Human Telomeric DNA: How Many Conformations in PEG Containing Solutions? J Phys Chem B 2012; 116:2294-305. [DOI: 10.1021/jp209170v] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Affiliation(s)
- Luigi Petraccone
- Dipartimento di Chimica “P.
Corradini”, Via Cintia, Università “Federico II” di Napoli, 80126, Naples, Italy
| | - Anna Malafronte
- Dipartimento di Chimica “P.
Corradini”, Via Cintia, Università “Federico II” di Napoli, 80126, Naples, Italy
| | - Jussara Amato
- Dipartimento di Chimica delle
Sostanze Naturali, Via D. Montesano 49, Università “Federico II” di Napoli, 80131, Naples,
Italy
| | - Concetta Giancola
- Dipartimento di Chimica “P.
Corradini”, Via Cintia, Università “Federico II” di Napoli, 80126, Naples, Italy
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20
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Influence of pH, temperature and the cationic porphyrin TMPyP4 on the stability of the i-motif formed by the 5′-(C3TA2)4-3′ sequence of the human telomere. Int J Biol Macromol 2011; 49:729-36. [DOI: 10.1016/j.ijbiomac.2011.07.004] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2011] [Revised: 07/04/2011] [Accepted: 07/05/2011] [Indexed: 12/11/2022]
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21
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Lane AN. The stability of intramolecular DNA G-quadruplexes compared with other macromolecules. Biochimie 2011; 94:277-86. [PMID: 21854828 DOI: 10.1016/j.biochi.2011.08.004] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2011] [Accepted: 08/04/2011] [Indexed: 11/19/2022]
Abstract
DNA quadruplexes are often conceived as very stable structures. However, most of the free energy of stabilization derives from specific ion binding via inner sphere coordination of the GO6 of the guanine residues comprising the basic quartet. When compared with other nucleic acid structures such as DNA or RNA duplexes and hairpins, or proteins of the same number of atoms, metal-coordinated intramolecular quadruplexes are found to be of comparable or lower thermodynamic stability under similar solution conditions. Furthermore, intramolecular quadruplexes are actually less stable kinetically, than DNA duplexes or hairpins of the same size. Although the literature is incomplete, it is clear that polyelectrolyte ion effects, the influence of solvation and steric crowding on stability are qualitatively different between intramolecular quadruplexes and DNA duplexes. For example, decreasing water activity destabilizes DNA duplexes, whereas quadruplexes are stabilized. The variety of folded conformations accessible to a single sequence further implies strong sensitivity of the conformational ensemble to the solution conditions, compared with DNA duplexes or small single domain proteins. These considerations may have relevance to the conditions prevailing inside cell nuclei and therefore the structures that potentially might form in vivo.
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Affiliation(s)
- Andrew N Lane
- JG Brown Cancer Center, University of Louisville, 505 S. Hancock St., Louisville, KY 40202, USA.
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22
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Petraccone L, Fotticchia I, Cummaro A, Pagano B, Ginnari-Satriani L, Haider S, Randazzo A, Novellino E, Neidle S, Giancola C. The triazatruxene derivative azatrux binds to the parallel form of the human telomeric G-quadruplex under molecular crowding conditions: Biophysical and molecular modeling studies. Biochimie 2011; 93:1318-27. [DOI: 10.1016/j.biochi.2011.05.017] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2011] [Accepted: 05/19/2011] [Indexed: 12/24/2022]
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Hänsel R, Löhr F, Foldynová-Trantírková S, Bamberg E, Trantírek L, Dötsch V. The parallel G-quadruplex structure of vertebrate telomeric repeat sequences is not the preferred folding topology under physiological conditions. Nucleic Acids Res 2011; 39:5768-75. [PMID: 21450807 PMCID: PMC3141269 DOI: 10.1093/nar/gkr174] [Citation(s) in RCA: 128] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
G-quadruplex topologies of telomeric repeat sequences from vertebrates were investigated in the presence of molecular crowding (MC) mimetics, namely polyethylene glycol 200 (PEG), Ficoll 70 as well as Xenopus laevis egg extract by CD and NMR spectroscopy and native PAGE. Here, we show that the conformational behavior of the telomeric repeats in X. laevis egg extract or in Ficoll is notably different from that observed in the presence of PEG. While the behavior of the telomeric repeat in X. laevis egg extract or in Ficoll resembles results obtained under dilute conditions, PEG promotes the formation of high-order parallel topologies. Our data suggest that PEG should not be used as a MC mimetic.
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Affiliation(s)
- Robert Hänsel
- Institute of Biophysical Chemistry and Center for Biomolecular Magnetic Resonance, Goethe University, Max-von-Laue Str. 9, 60438 Frankfurt/Main, Germany
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Zhou J, Wei C, Jia G, Wang X, Feng Z, Li C. Formation and stabilization of G-quadruplex in nanosized water pools. Chem Commun (Camb) 2010; 46:1700-2. [PMID: 20177621 DOI: 10.1039/b925000j] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
We demonstrate here that G-quadruplex structure can form and exhibits strong stability in nanosized water pools, providing new insight into investigating G-quadruplexes in the cellular environment.
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Affiliation(s)
- Jun Zhou
- State Key Laboratory of Catalysis, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China
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