1
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Wang Z, Ferreira Rodrigues C, Jurt S, Domínguez-Martín A, Johannsen S, Sigel RKO. Elucidating the solution structure of the monomolecular BCL2 RNA G-quadruplex: a new robust NMR assignment approach. Chem Sci 2025:d5sc01416f. [PMID: 40181818 PMCID: PMC11962745 DOI: 10.1039/d5sc01416f] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2025] [Accepted: 03/26/2025] [Indexed: 04/05/2025] Open
Abstract
5' untranslated regions (UTRs) of mRNA commonly feature G-quadruplexes (G4s), crucial for translational regulation and promising as drug targets to modulate gene expression. While NMR spectroscopy is well-suited for studying these motifs' structure and dynamics, their guanine-rich nature complicates resonance assignment due to high signal overlap. Exploiting the inherent rigidity of G4 cores, we developed a universally applicable assignment strategy for uniformly isotopically enriched G4 structures, relying solely on through-bond correlations to establish the G-tetrads. Applying this approach, we resolved the solution structures of two triple mutants of the RNA G4 in the 5' UTR of the human BCL2 proto-oncogene, one of the first natural monomolecular RNA G4 structures available to date. Comparative analysis with other RNA and DNA G4s reveals their notably compact and well-defined cores. Moreover, the sugar pucker geometries of the tetrad guanines are far less stringent than previously assumed, adeptly accommodating specific structural features. This contrasts with the canonical base pairing in RNA and DNA, in which the sugar pucker dictates the type of the double-helical structure. The strategy presented provides a direct path to uncovering G4 structural intricacies, advancing our grasp of their biological roles, and paving the way for RNA-targeted therapeutics.
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Affiliation(s)
- Zenghui Wang
- Department of Chemistry, University of Zürich 8057 Zürich Switzerland
| | | | - Simon Jurt
- Department of Chemistry, University of Zürich 8057 Zürich Switzerland
| | - Alicia Domínguez-Martín
- Department of Inorganic Chemistry, Faculty of Pharmacy, University of Granada 18071 Granada Spain
| | - Silke Johannsen
- Department of Chemistry, University of Zürich 8057 Zürich Switzerland
| | - Roland K O Sigel
- Department of Chemistry, University of Zürich 8057 Zürich Switzerland
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2
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Chilton B, Roach RJ, Edwards PJB, Jameson GB, Hale TK, Filichev VV. Inverted strand polarity yields thermodynamically stable G-quadruplexes and prevents duplex formation within extended DNA. Chem Sci 2024:d3sc05432b. [PMID: 39246343 PMCID: PMC11376080 DOI: 10.1039/d3sc05432b] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2023] [Accepted: 08/26/2024] [Indexed: 09/10/2024] Open
Abstract
DNA G-quadruplexes (G4) formed in guanine-rich sequences play a key role in genome function and maintenance, interacting with multiple proteins. However, structural and functional studies of G4s within duplex DNA have been challenging because of the transient nature of G4s and thermodynamic preference of G-rich DNA to form duplexes with their complementary strand rather than G4s. To overcome these challenges, we have incorporated native nucleotides in G-rich sequences using commercially available inverted 3'-O-DMT-5'-O-phosphoramidites of native nucleosides, to give 3'-3' and 5'-5' linkages in the centre of the G-tract. Using circular dichroism and 1H nuclear magnetic resonance spectroscopies and native gel electrophoresis, we demonstrate that these polarity-inverted DNA sequences containing four telomeric repeats form G4s of parallel topology with one lateral or diagonal loop across the face of the quadruplex and two propeller loops across the edges of the quadruplex. These G4s were stable even in the presence of complementary C-rich DNA. As an example, G4 assemblies of inverted polarity were shown to bind to the hinge region of Heterochromatin Protein 1α (HP1α), a known G4-interacting domain. As such, internal polarity inversions in DNA provide a useful tool to control G4 topology while also disrupting the formation of other secondary structures, particularly the canonical duplex.
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Affiliation(s)
- Bruce Chilton
- School of Food Technology and Natural Sciences, Massey University Private Bag 11-222 Palmerston North 4442 New Zealand
| | - Ruby J Roach
- School of Food Technology and Natural Sciences, Massey University Private Bag 11-222 Palmerston North 4442 New Zealand
| | - Patrick J B Edwards
- School of Food Technology and Natural Sciences, Massey University Private Bag 11-222 Palmerston North 4442 New Zealand
| | - Geoffrey B Jameson
- School of Food Technology and Natural Sciences, Massey University Private Bag 11-222 Palmerston North 4442 New Zealand
| | - Tracy K Hale
- School of Food Technology and Natural Sciences, Massey University Private Bag 11-222 Palmerston North 4442 New Zealand
| | - Vyacheslav V Filichev
- School of Food Technology and Natural Sciences, Massey University Private Bag 11-222 Palmerston North 4442 New Zealand
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3
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De Rache A, Marquevielle J, Bouaziz S, Vialet B, Andreola ML, Mergny JL, Amrane S. Structure of a DNA G-quadruplex that Modulates SP1 Binding Sites Architecture in HIV-1 Promoter. J Mol Biol 2024; 436:168359. [PMID: 37952768 DOI: 10.1016/j.jmb.2023.168359] [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: 09/19/2023] [Revised: 11/02/2023] [Accepted: 11/03/2023] [Indexed: 11/14/2023]
Abstract
Nucleic acid sequences containing guanine tracts are able to form non-canonical DNA or RNA structures known as G-quadruplexes (or G4s). These structures, based on the stacking of G-tetrads, are involved in various biological processes such as gene expression regulation. Here, we investigated a G4 forming sequence, HIVpro2, derived from the HIV-1 promoter. This motif is located 60 nucleotides upstream of the proviral Transcription Starting Site (TSS) and overlaps with two SP1 transcription factor binding sites. Using NMR spectroscopy, we determined that HIVpro2 forms a hybrid type G4 structure with a core that is interrupted by a single nucleotide bulge. An additional reverse-Hoogsteen AT base pair is stacked on top of the tetrad. SP1 transcription factor is known to regulate transcription activity of many genes through the recognition of Guanine-rich duplex motifs. Here, the formation of HIVpro2 G4 may modulate SP1 binding sites architecture by competing with the formation of the canonical duplex structure. Such DNA structural switch potentially participates to the regulation of viral transcription and may also interfere with HIV-1 reactivation or viral latency.
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Affiliation(s)
- Aurore De Rache
- Université de Bordeaux, Bordeaux, France; ARNA Laboratory, INSERM U1212, CNRS UMR 5320, IECB, Bordeaux, France; Department of Chemistry, U. Namur, 61 rue de Bruxelles, B5000 Namur, Belgium
| | - Julien Marquevielle
- Université de Bordeaux, Bordeaux, France; ARNA Laboratory, INSERM U1212, CNRS UMR 5320, IECB, Bordeaux, France
| | | | - Brune Vialet
- Université de Bordeaux, Bordeaux, France; ARNA Laboratory, INSERM U1212, CNRS UMR 5320, IECB, Bordeaux, France
| | - Marie-Line Andreola
- Université de Bordeaux, Bordeaux, France; MFP Laboratory, UMR5234, CNRS, Bordeaux, France
| | - Jean-Louis Mergny
- Laboratoire d'Optique & Biosciences, École Polytechnique, CNRS, Inserm, Institut Polytechnique de Paris, 91120 Palaiseau, France
| | - Samir Amrane
- Université de Bordeaux, Bordeaux, France; ARNA Laboratory, INSERM U1212, CNRS UMR 5320, IECB, Bordeaux, France.
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4
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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: 1.5] [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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5
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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: 19] [Impact Index Per Article: 3.8] [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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6
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Wan C, Fu W, Jing H, Zhang N. NMR solution structure of an asymmetric intermolecular leaped V-shape G-quadruplex: selective recognition of the d(G2NG3NG4) sequence motif by a short linear G-rich DNA probe. Nucleic Acids Res 2019; 47:1544-1556. [PMID: 30445650 PMCID: PMC6379650 DOI: 10.1093/nar/gky1167] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2018] [Revised: 11/01/2018] [Accepted: 11/04/2018] [Indexed: 02/07/2023] Open
Abstract
Aside from classical loops among G-quadruplexes, the unique leaped V-shape scaffold spans over three G-tetrads, without any intervening residues. This scaffold enables a sharp reversal of two adjacent strand directions and simultaneously participates in forming the G-tetrad core. These features make this scaffold itself distinctive and thus an essentially more accessible target. As an alternative to the conventional antisense method using a complementary chain, forming an intermolecular G-quadruplex from two different oligomers, in which the longer one as the target is captured by a short G-rich fragment, could be helpful for recognizing G-rich sequences and structural motifs. However, such an intermolecular leaped V-shape G-quadruplex consisting of DNA oligomers of quite different lengths has not been evaluated. Here, we present the first nuclear magnetic resonance (NMR) study of an asymmetric intermolecular leaped V-shape G-quadruplex assembled between an Oxytricha nova telomeric sequence d(G2T4G4T4G4) and a single G-tract fragment d(TG4A). Furthermore, we explored the selectivity of this short fragment as a potential probe, examined the kinetic discrimination for probing a specific mutant, and proposed the key sequence motif d(G2NG3NG4) essential for building the leaped V-shape G-quadruplexes.
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Affiliation(s)
- Chanjuan Wan
- High Magnetic Field Laboratory, Chinese Academy of Sciences, Hefei 230031, China.,University of Science and Technology of China, Hefei 230026, China
| | - Wenqiang Fu
- High Magnetic Field Laboratory, Chinese Academy of Sciences, Hefei 230031, China.,University of Science and Technology of China, Hefei 230026, China
| | - Haitao Jing
- High Magnetic Field Laboratory, Chinese Academy of Sciences, Hefei 230031, China.,University of Science and Technology of China, Hefei 230026, China
| | - Na Zhang
- High Magnetic Field Laboratory, Chinese Academy of Sciences, Hefei 230031, China.,Key Laboratory of High Magnetic Field and Ion Beam Physical Biology, Hefei Institutes of Physical Science, Chinese Academy of Sciences, Hefei 230031, China.,Key Laboratory of Anhui Province for High Field Magnetic Resonance Imaging, Hefei 230031, China
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7
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Abou Assi H, El-Khoury R, González C, Damha MJ. 2'-Fluoroarabinonucleic acid modification traps G-quadruplex and i-motif structures in human telomeric DNA. Nucleic Acids Res 2017; 45:11535-11546. [PMID: 29036537 PMCID: PMC5714228 DOI: 10.1093/nar/gkx838] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2017] [Revised: 09/10/2017] [Accepted: 09/15/2017] [Indexed: 12/30/2022] Open
Abstract
Human telomeres and promoter regions of genes fulfill a significant role in cellular aging and cancer. These regions comprise of guanine and cytosine-rich repeats, which under certain conditions can fold into G-quadruplex (G4) and i-motif structures, respectively. Herein, we use UV, circular dichroism and NMR spectroscopy to study several human telomeric sequences and demonstrate that G4/i-motif-duplex interconversion kinetics are slowed down dramatically by 2'-β-fluorination and the presence of G4/i-motif-duplex junctions. NMR-monitored kinetic experiments on 1:1 mixtures of native and modified C- and G-rich human telomeric sequences reveal that strand hybridization kinetics are controlled by G4 or i-motif unfolding. Furthermore, we provide NMR evidence for the formation of a hybrid complex containing G4 and i-motif structures proximal to a duplex DNA segment at neutral pH. While the presence of i-motif and G4 folds may be mutually exclusive in promoter genome sequences, our results suggest that they may co-exist transiently as intermediates in telomeric sequences.
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Affiliation(s)
- Hala Abou Assi
- Department of Chemistry, McGill University, Montreal, QC H3A 0B8, Canada
| | - Roberto El-Khoury
- Department of Chemistry, McGill University, Montreal, QC H3A 0B8, Canada
| | - Carlos González
- Instituto de Química Física ‘Rocasolano’, CSIC, Serrano 119, 28006 Madrid, Spain
| | - Masad J. Damha
- Department of Chemistry, McGill University, Montreal, QC H3A 0B8, Canada
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8
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Antiparallel RNA G-quadruplex Formed by Human Telomere RNA Containing 8-Bromoguanosine. Sci Rep 2017; 7:6695. [PMID: 28751647 PMCID: PMC5532209 DOI: 10.1038/s41598-017-07050-w] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2017] [Accepted: 06/21/2017] [Indexed: 11/09/2022] Open
Abstract
In this study, by combining nuclear magnetic resonance (NMR), circular dichroism (CD), liquid chromatography-electrospray ionization-mass spectrometry (LC-ESI-MS), and gel electrophoresis, we report an unusual topological structure of the RNA G-quadruplex motif formed by human telomere RNA r(UAGGGU) containing 8-bromoguanosine. Results showed that the RNA sequence formed an antiparallel tetramolecular G-quadruplex, in which each pair of diagonal strands run in opposite directions. Furthermore, guanosines were observed both in syn- and anti-conformations. In addition, two of these G-quadruplex subunits were found to be stacking on top of each other, forming a dimeric RNA G-quadruplex. Our findings provide a new insight into the behavior of RNA G-quadruplex structures.
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9
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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: 3.5] [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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10
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Harkness RW, Mittermaier AK. G-quadruplex dynamics. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2017. [PMID: 28642152 DOI: 10.1016/j.bbapap.2017.06.012] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
G-quadruplexes (GQs) are four-stranded nucleic acid secondary structures formed by guanosine (G)-rich DNA and RNA sequences. It is becoming increasingly clear that cellular processes including gene expression and mRNA translation are regulated by GQs. GQ structures have been extensively characterized, however little attention to date has been paid to their conformational dynamics, despite the fact that many biological GQ sequences populate multiple structures of similar free energies, leading to an ensemble of exchanging conformations. The impact of these dynamics on biological function is currently not well understood. Recently, structural dynamics have been demonstrated to entropically stabilize GQ ensembles, potentially modulating gene expression. Transient, low-populated states in GQ ensembles may additionally regulate nucleic acid interactions and function. This review will underscore the interplay of GQ dynamics and biological function, focusing on several dynamic processes for biological GQs and the characterization of GQ dynamics by nuclear magnetic resonance (NMR) spectroscopy in conjunction with other biophysical techniques. This article is part of a Special Issue entitled: Biophysics in Canada, edited by Lewis Kay, John Baenziger, Albert Berghuis and Peter Tieleman.
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Affiliation(s)
- Robert W Harkness
- McGill University Department of Chemistry, 801 Sherbrooke St. W., Montreal, QC H3A 0B8, Canada
| | - Anthony K Mittermaier
- McGill University Department of Chemistry, 801 Sherbrooke St. W., Montreal, QC H3A 0B8, Canada.
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11
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Xiao CD, Ishizuka T, Zhu XQ, Li Y, Sugiyama H, Xu Y. Unusual Topological RNA Architecture with an Eight-Stranded Helical Fragment Containing A-, G-, and U-Tetrads. J Am Chem Soc 2017; 139:2565-2568. [DOI: 10.1021/jacs.6b12274] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Affiliation(s)
- Chao-Da Xiao
- Division
of Chemistry, Department of Medical Sciences, Faculty of Medicine, University of Miyazaki, 5200 Kihara, Kiyotake, Miyazaki 889-1692, Japan
| | - Takumi Ishizuka
- Division
of Chemistry, Department of Medical Sciences, Faculty of Medicine, University of Miyazaki, 5200 Kihara, Kiyotake, Miyazaki 889-1692, Japan
| | - Xiao-Qing Zhu
- Division
of Chemistry, Department of Medical Sciences, Faculty of Medicine, University of Miyazaki, 5200 Kihara, Kiyotake, Miyazaki 889-1692, Japan
| | - Yue Li
- Department
of Chemistry, Graduate School of Science, Kyoto University, Kitashirakawa-oiwakecho,
Sakyo-ku, Kyoto 606-8502, Japan
| | - Hiroshi Sugiyama
- Department
of Chemistry, Graduate School of Science, Kyoto University, Kitashirakawa-oiwakecho,
Sakyo-ku, Kyoto 606-8502, Japan
| | - Yan Xu
- Division
of Chemistry, Department of Medical Sciences, Faculty of Medicine, University of Miyazaki, 5200 Kihara, Kiyotake, Miyazaki 889-1692, Japan
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12
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De Nicola B, Lech CJ, Heddi B, Regmi S, Frasson I, Perrone R, Richter SN, Phan AT. Structure and possible function of a G-quadruplex in the long terminal repeat of the proviral HIV-1 genome. Nucleic Acids Res 2016; 44:6442-51. [PMID: 27298260 PMCID: PMC5291261 DOI: 10.1093/nar/gkw432] [Citation(s) in RCA: 70] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2015] [Revised: 05/04/2016] [Accepted: 05/06/2016] [Indexed: 02/07/2023] Open
Abstract
The long terminal repeat (LTR) of the proviral human immunodeficiency virus (HIV)-1 genome is integral to virus transcription and host cell infection. The guanine-rich U3 region within the LTR promoter, previously shown to form G-quadruplex structures, represents an attractive target to inhibit HIV transcription and replication. In this work, we report the structure of a biologically relevant G-quadruplex within the LTR promoter region of HIV-1. The guanine-rich sequence designated LTR-IV forms a well-defined structure in physiological cationic solution. The nuclear magnetic resonance (NMR) structure of this sequence reveals a parallel-stranded G-quadruplex containing a single-nucleotide thymine bulge, which participates in a conserved stacking interaction with a neighboring single-nucleotide adenine loop. Transcription analysis in a HIV-1 replication competent cell indicates that the LTR-IV region may act as a modulator of G-quadruplex formation in the LTR promoter. Consequently, the LTR-IV G-quadruplex structure presented within this work could represent a valuable target for the design of HIV therapeutics.
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Affiliation(s)
- Beatrice De Nicola
- School of Physical and Mathematical Sciences, Nanyang Technological University, Singapore Department of Molecular Medicine, University of Padua, Italy
| | - Christopher J Lech
- School of Physical and Mathematical Sciences, Nanyang Technological University, Singapore
| | - Brahim Heddi
- School of Physical and Mathematical Sciences, Nanyang Technological University, Singapore
| | - Sagar Regmi
- School of Physical and Mathematical Sciences, Nanyang Technological University, Singapore
| | - Ilaria Frasson
- Department of Molecular Medicine, University of Padua, Italy
| | - Rosalba Perrone
- Department of Molecular Medicine, University of Padua, Italy
| | - Sara N Richter
- Department of Molecular Medicine, University of Padua, Italy
| | - Anh Tuân Phan
- School of Physical and Mathematical Sciences, Nanyang Technological University, Singapore
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13
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Ganguly M, Bradsher C, Goodwin P, Petty JT. DNA-Directed Fluorescence Switching of Silver Clusters. THE JOURNAL OF PHYSICAL CHEMISTRY. C, NANOMATERIALS AND INTERFACES 2015; 119:27829-27837. [PMID: 30220954 PMCID: PMC6136663 DOI: 10.1021/acs.jpcc.5b08834] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/10/2023]
Abstract
Silver clusters with ≲30 atoms are molecules with diverse electronic spectra and wide-ranging emission intensities. Specific cluster chromophores form within DNA strands, and we consider a DNA scaffold that transforms a pair of silver clusters. This ~20-nucleotide strand has two components, a cluster domain (S1) that stabilizes silver clusters and a recognition site (S2) that hybridizes with complementary oligonucleotides (S2C). The single-stranded S1-S2 exclusively develops clusters with violet absorption and low emission. This conjugate hybridizes with S2C to form S1-S2:S2C, and the violet chromophore transforms to a fluorescent counterpart with λex ≈ 490 nm/λem ≈ 550 nm and with ~100-fold stronger emission. Our studies focus on both the S1 sequence and structure that direct this violet → blue-green cluster transformation. From the sequence perspective, C4X sequences with X = adenine, thymine, and/or guanine favor the blue-green cluster, and the specificity of the binding site depends on three factors: the number of C4X repeats, the identity of the X nucleobase, and the number of contiguous cytosines. A systematic series of oligonucleotides identified the optimal S1 sequence C4AC4T and discerned distinct roles for the adenine, thymine, and cytosines. From the structure perspective, two factors guide the conformation of the C4AC4T sequence: hybridization with the S2C complement and coordination by the cluster adduct. Spectroscopic and chromatographic studies show that the single-stranded C4AC4T is folded by its blue-green cluster adduct. We propose a structural model in which the two C4X motifs within C4AC4T are cross-linked by the encapsulated cluster. These studies suggest that the structures of the DNA host and the cluster adduct are interdependent.
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Affiliation(s)
- Mainak Ganguly
- Department of Chemistry, Furman University, Greenville, South Carolina 29613, United States
| | - Cara Bradsher
- Department of Chemistry, Furman University, Greenville, South Carolina 29613, United States
| | - Peter Goodwin
- Center for Integrated Nanotechnologies, Los Alamos National Laboratory, Los Alamos, New Mexico 87545, United States
| | - Jeffrey T. Petty
- Department of Chemistry, Furman University, Greenville, South Carolina 29613, United States
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14
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Cheong VV, Heddi B, Lech CJ, Phan AT. Xanthine and 8-oxoguanine in G-quadruplexes: formation of a G·G·X·O tetrad. Nucleic Acids Res 2015; 43:10506-14. [PMID: 26400177 PMCID: PMC4666386 DOI: 10.1093/nar/gkv826] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2015] [Accepted: 07/28/2015] [Indexed: 01/31/2023] Open
Abstract
G-quadruplexes are four-stranded structures built from stacked G-tetrads (G·G·G·G), which are planar cyclical assemblies of four guanine bases interacting through Hoogsteen hydrogen bonds. A G-quadruplex containing a single guanine analog substitution, such as 8-oxoguanine (O) or xanthine (X), would suffer from a loss of a Hoogsteen hydrogen bond within a G-tetrad and/or potential steric hindrance. We show that a proper arrangement of O and X bases can reestablish the hydrogen-bond pattern within a G·G·X·O tetrad. Rational incorporation of G·G·X·O tetrads in a (3+1) G-quadruplex demonstrated a similar folding topology and thermal stability to that of the unmodified G-quadruplex. pH titration conducted on X·O-modified G-quadruplexes indicated a protonation-deprotonation equilibrium of X with a pKa ∼6.7. The solution structure of a G-quadruplex containing a G·G·X·O tetrad was determined, displaying the same folding topology in both the protonated and deprotonated states. A G-quadruplex containing a deprotonated X·O pair was shown to exhibit a more electronegative groove compared to that of the unmodified one. These differences are likely to manifest in the electronic properties of G-quadruplexes and may have important implications for drug targeting and DNA-protein interactions.
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Affiliation(s)
- Vee Vee Cheong
- School of Physical and Mathematical Sciences, Nanyang Technological University, 637371 Singapore
| | - Brahim Heddi
- School of Physical and Mathematical Sciences, Nanyang Technological University, 637371 Singapore
| | - Christopher Jacques Lech
- School of Physical and Mathematical Sciences, Nanyang Technological University, 637371 Singapore
| | - Anh Tuân Phan
- School of Physical and Mathematical Sciences, Nanyang Technological University, 637371 Singapore
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15
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Lim KW, Jenjaroenpun P, Low ZJ, Khong ZJ, Ng YS, Kuznetsov VA, Phan AT. Duplex stem-loop-containing quadruplex motifs in the human genome: a combined genomic and structural study. Nucleic Acids Res 2015; 43:5630-46. [PMID: 25958397 PMCID: PMC4477648 DOI: 10.1093/nar/gkv355] [Citation(s) in RCA: 61] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2015] [Accepted: 04/02/2015] [Indexed: 12/12/2022] Open
Abstract
Duplex stem-loops and four-stranded G-quadruplexes have been implicated in (patho)biological processes. Overlap of stem-loop- and quadruplex-forming sequences could give rise to quadruplex-duplex hybrids (QDH), which combine features of both structural forms and could exhibit unique properties. Here, we present a combined genomic and structural study of stem-loop-containing quadruplex sequences (SLQS) in the human genome. Based on a maximum loop length of 20 nt, our survey identified 80 307 SLQS, embedded within 60 172 unique clusters. Our analysis suggested that these should cover close to half of total SLQS in the entire genome. Among these, 48 508 SLQS were strand-specifically located in genic/promoter regions, with the majority of genes displaying a low number of SLQS. Notably, genes containing abundant SLQS clusters were strongly associated with brain tissues. Enrichment analysis of SLQS-positive genes and mapping of SLQS onto transcriptional/mutagenesis hotspots and cancer-associated genes, provided a statistical framework supporting the biological involvements of SLQS. In vitro formation of diverse QDH by selective SLQS hits were successfully verified by nuclear magnetic resonance spectroscopy. Folding topologies of two SLQS were elucidated in detail. We also demonstrated that sequence changes at mutation/single-nucleotide polymorphism loci could affect the structural conformations adopted by SLQS. Thus, our predicted SLQS offer novel insights into the potential involvement of QDH in diverse (patho)biological processes and could represent novel regulatory signals.
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Affiliation(s)
- Kah Wai Lim
- School of Physical and Mathematical Sciences, Nanyang Technological University, 637371, Singapore School of Biological Sciences, Nanyang Technological University, 637551, Singapore
| | - Piroon Jenjaroenpun
- Department of Genome and Gene Expression Data Analysis, Bioinformatics Institute, 138671, Singapore
| | - Zhen Jie Low
- School of Physical and Mathematical Sciences, Nanyang Technological University, 637371, Singapore School of Biological Sciences, Nanyang Technological University, 637551, Singapore
| | - Zi Jian Khong
- School of Physical and Mathematical Sciences, Nanyang Technological University, 637371, Singapore
| | - Yi Siang Ng
- School of Physical and Mathematical Sciences, Nanyang Technological University, 637371, Singapore
| | | | - Anh Tuân Phan
- School of Physical and Mathematical Sciences, Nanyang Technological University, 637371, Singapore
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16
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Szulik MW, Voehler M, Stone MP. NMR analysis of base-pair opening kinetics in DNA. CURRENT PROTOCOLS IN NUCLEIC ACID CHEMISTRY 2014; 59:7.20.1-18. [PMID: 25501592 PMCID: PMC4274747 DOI: 10.1002/0471142700.nc0720s59] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
Base pairing in nucleic acids plays a crucial role in their structure and function. Differences in the base-pair opening and closing kinetics of individual double-stranded DNA sequences or between chemically modified base pairs provide insight into the recognition of these base pairs by DNA processing enzymes. This unit describes how to quantify the kinetics for localized base pairs by observing changes in the imino proton signals by nuclear magnetic resonance spectroscopy. The determination of all relevant parameters using state-of-the art techniques and NMR instrumentation, including cryoprobes, is discussed.
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Affiliation(s)
- Marta W Szulik
- Department of Chemistry and Center for Structural Biology, Vanderbilt University, Nashville, Tennesee; These authors contributed equally to this work
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17
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Sengar A, Heddi B, Phan AT. Formation of G-quadruplexes in poly-G sequences: structure of a propeller-type parallel-stranded G-quadruplex formed by a G₁₅ stretch. Biochemistry 2014; 53:7718-23. [PMID: 25375976 DOI: 10.1021/bi500990v] [Citation(s) in RCA: 58] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Poly-G sequences are found in different genomes including human and have the potential to form higher-order structures with various applications. Previously, long poly-G sequences were thought to lead to multiple possible ways of G-quadruplex folding, rendering their structural characterization challenging. Here we investigate the structure of G-quadruplexes formed by poly-G sequences d(TTG(n)T), where n = 12 to 19. Our data show the presence of multiple and/or higher-order G-quadruplex structures in most sequences. Strikingly, NMR spectra of the TTG₁₅T sequence containing a stretch of 15 continuous guanines are exceptionally well-resolved and indicate the formation of a well-defined G-quadruplex structure. The NMR solution structure of this sequence revealed a propeller-type parallel-stranded G-quadruplex containing three G-tetrad layers and three single-guanine propeller loops. The same structure can potentially form anywhere along a long G(n) stretch, making it unique for molecular recognition by other cellular molecules.
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Affiliation(s)
- Anjali Sengar
- School of Physical and Mathematical Sciences, Nanyang Technological University , Singapore 637371, Singapore
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18
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Petty JT, Nicholson D, Sergev OO, Graham SK. Near-infrared silver cluster optically signaling oligonucleotide hybridization and assembling two DNA hosts. Anal Chem 2014; 86:9220-8. [PMID: 25157472 PMCID: PMC4165452 DOI: 10.1021/ac502192w] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2014] [Accepted: 08/26/2014] [Indexed: 12/11/2022]
Abstract
Silver clusters with ~10 atoms form within DNA strands, and the conjugates are chemical sensors. The DNA host hybridizes with short oligonucleotides, and the cluster moieties optically respond to these analytes. Our studies focus on how the cluster adducts perturb the structure of their DNA hosts. Our sensor is comprised of an oligonucleotide with two components: a 5'-cluster domain that complexes silver clusters and a 3'-recognition site that hybridizes with a target oligonucleotide. The single-stranded sensor encapsulates an ~11 silver atom cluster with violet absorption at 400 nm and with minimal emission. The recognition site hybridizes with complementary oligonucleotides, and the violet cluster converts to an emissive near-infrared cluster with absorption at 730 nm. Our key finding is that the near-infrared cluster coordinates two of its hybridized hosts. The resulting tertiary structure was investigated using intermolecular and intramolecular variants of the same dimer. The intermolecular dimer assembles in concentrated (~5 μM) DNA solutions. Strand stoichiometries and orientations were chromatographically determined using thymine-modified complements that increase the overall conjugate size. The intramolecular dimer develops within a DNA scaffold that is founded on three linked duplexes. The high local cluster concentrations and relative strand arrangements again favor the antiparallel dimer for the near-infrared cluster. When the two monomeric DNA/violet cluster conjugates transform to one dimeric DNA/near-infrared conjugate, the DNA strands accumulate silver. We propose that these correlated changes in DNA structure and silver stoichiometry underlie the violet to near-infrared cluster transformation.
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Affiliation(s)
| | - David
A. Nicholson
- Department of Chemistry, Furman
University, Greenville, South Carolina 29613, United States
| | - Orlin O. Sergev
- Department of Chemistry, Furman
University, Greenville, South Carolina 29613, United States
| | - Stuart K. Graham
- Department of Chemistry, Furman
University, Greenville, South Carolina 29613, United States
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19
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Adrian M, Ang DJ, Lech CJ, Heddi B, Nicolas A, Phan AT. Structure and conformational dynamics of a stacked dimeric G-quadruplex formed by the human CEB1 minisatellite. J Am Chem Soc 2014; 136:6297-305. [PMID: 24742225 DOI: 10.1021/ja4125274] [Citation(s) in RCA: 57] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
CEB1 is a highly polymorphic human minisatellite. In yeast, the size variation of CEB1 tandem arrays has been associated with the capacity of the motif to form G-quadruplexes. Here we report on the NMR solution structure of a G-quadruplex formed by the CEB1 DNA G-rich fragment d(AGGGGGGAGGGAGGGTGG), harboring several G-tracts including one with six continuous guanines. This sequence forms a dimeric G-quadruplex involving the stacking of two subunits, each being a unique snapback parallel-stranded scaffold with three G-tetrad layers, three double-chain-reversal loops, and a V-shaped loop. The two subunits are stacked at their 5'-end tetrads, and multiple stacking rotamers may be present due to a high symmetry at the stacking interface. There is a conformational exchange in the millisecond time scale involving a swapping motion between two bases of the six-guanine tract. Our results not only add to the understanding of how the G-quadruplex formation in human minisatellite leads to genetic instability but also address the fundamental questions regarding stacking of G-quadruplexes and how a long continuous G-tract participates in the structure and conformational dynamics of G-quadruplexes.
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Affiliation(s)
- Michael Adrian
- School of Physical and Mathematical Sciences, Nanyang Technological University , Singapore 637371, Singapore
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20
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Martadinata H, Phan AT. Formation of a stacked dimeric G-quadruplex containing bulges by the 5'-terminal region of human telomerase RNA (hTERC). Biochemistry 2014; 53:1595-600. [PMID: 24601523 DOI: 10.1021/bi4015727] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
We investigate the structure formed by the first 18-nt of the 5'-terminal region of the human telomerase RNA (hTERC or hTR) using gel electrophoresis and UV, CD, and NMR spectroscopy. Our data suggest that this 18-nt sequence, r(GGGUUGCGGAGGGUGGGC), can form a stacked dimeric G-quadruplex in potassium solution. The two subunits, each being a three-layer parallel-stranded G-quadruplex with a cytosine bulge, are stacked at their 5'-end. The formation of this stacked dimeric G-quadruplex containing bulges could be biologically relevant for the dimerization and other interactions of the active human telomerase.
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Affiliation(s)
- Herry Martadinata
- School of Physical and Mathematical Sciences, Nanyang Technological University , Singapore 637371
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21
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Li Z, Lech CJ, Phan AT. Sugar-modified G-quadruplexes: effects of LNA-, 2'F-RNA- and 2'F-ANA-guanosine chemistries on G-quadruplex structure and stability. Nucleic Acids Res 2013; 42:4068-79. [PMID: 24371274 PMCID: PMC3973314 DOI: 10.1093/nar/gkt1312] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
G-quadruplex-forming oligonucleotides containing modified nucleotide chemistries have demonstrated promising pharmaceutical potential. In this work, we systematically investigate the effects of sugar-modified guanosines on the structure and stability of a (4+0) parallel and a (3+1) hybrid G-quadruplex using over 60 modified sequences containing a single-position substitution of 2′-O-4′-C-methylene-guanosine (LNAG), 2′-deoxy-2′-fluoro-riboguanosine (FG) or 2′-deoxy-2′-fluoro-arabinoguanosine (FANAG). Our results are summarized in two parts: (I) Generally, LNAG substitutions into ‘anti’ position guanines within a guanine-tetrad lead to a more stable G-quadruplex, while substitutions into ‘syn’ positions disrupt the native G-quadruplex conformation. However, some interesting exceptions to this trend are observed. We discover that a LNAG modification upstream of a short propeller loop hinders G-quadruplex formation. (II) A single substitution of either FG or FANAG into a ‘syn’ position is powerful enough to perturb the (3+1) G-quadruplex. Substitution of either FG or FANAG into any ‘anti’ position is well tolerated in the two G-quadruplex scaffolds. FANAG substitutions to ‘anti’ positions are better tolerated than their FG counterparts. In both scaffolds, FANAG substitutions to the central tetrad layer are observed to be the most stabilizing. The observations reported herein on the effects of LNAG, FG and FANAG modifications on G-quadruplex structure and stability will enable the future design of pharmaceutically relevant oligonucleotides.
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Affiliation(s)
- Zhe Li
- School of Physical and Mathematical Sciences, Nanyang Technological University, Singapore 637371
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22
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D'Atri V, Borbone N, Amato J, Gabelica V, D'Errico S, Piccialli G, Mayol L, Oliviero G. DNA-based nanostructures: The effect of the base sequence on octamer formation from d(XGGYGGT) tetramolecular G-quadruplexes. Biochimie 2013; 99:119-28. [PMID: 24316277 DOI: 10.1016/j.biochi.2013.11.020] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2013] [Accepted: 11/22/2013] [Indexed: 11/28/2022]
Abstract
In a previous work we have demonstrated that the DNA sequence CGGTGGT folds into a higher order G-quadruplex structure (2Q), obtained by the 5'-5' stacking of two unusual G(:C):G(:C):G(:C):G(:C) planar octads belonging to two identical tetra-stranded parallel quadruplexes, when annealed in the presence of ammonium or potassium ions. In the present paper, we discuss the role played by the title nucleosides X and Y (where X and Y stand for A, C, G, or T) on the formation and stability of 2Q structures formed by the XGGYGGT oligodeoxynucleotides. We found that the above mentioned dimerization pathway is not peculiar to the CGGTGGT sequence, but is possible for all the remaining CGGYGGT sequences (with Y = A, C, or G). Furthermore, we have found that the TGGAGGT sequence, despite the absence of the 5'-ending C, is also capable of forming a 2Q-like higher order quadruplex by using a slightly different dimerization interface, as characterized by NMR spectroscopy. To the best of our knowledge, this is the first characterization of a quadruplex multimer formed by an oligodeoxynucleotide presenting a thymine at its 5'-end. Examples of such structures were observed previously only in crystals and in the presence of non-physiological cations. Our results expand the repertoire of DNA quadruplex nanostructures of chosen length and add further complexity to the structural polymorphism of G-rich DNA sequences.
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Affiliation(s)
- Valentina D'Atri
- Dipartimento di Farmacia, Università di Napoli Federico II, Via D. Montesano 49, 80131 Napoli, Italy
| | - Nicola Borbone
- Dipartimento di Farmacia, Università di Napoli Federico II, Via D. Montesano 49, 80131 Napoli, Italy.
| | - Jussara Amato
- Dipartimento di Farmacia, Università di Napoli Federico II, Via D. Montesano 49, 80131 Napoli, Italy
| | - Valérie Gabelica
- Univ. Bordeaux, IECB, ARNA Laboratory, F-33600 Pessac, France; INSERM, U869, ARNA laboratory, F-33000 Bordeaux, France
| | - Stefano D'Errico
- Dipartimento di Farmacia, Università di Napoli Federico II, Via D. Montesano 49, 80131 Napoli, Italy
| | - Gennaro Piccialli
- Dipartimento di Farmacia, Università di Napoli Federico II, Via D. Montesano 49, 80131 Napoli, Italy
| | - Luciano Mayol
- Dipartimento di Farmacia, Università di Napoli Federico II, Via D. Montesano 49, 80131 Napoli, Italy
| | - Giorgia Oliviero
- Dipartimento di Farmacia, Università di Napoli Federico II, Via D. Montesano 49, 80131 Napoli, Italy
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23
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Petty JT, Sergev OO, Nicholson DA, Goodwin PM, Giri B, McMullan DR. A silver cluster-DNA equilibrium. Anal Chem 2013; 85:9868-76. [PMID: 24032398 PMCID: PMC4532306 DOI: 10.1021/ac4028559] [Citation(s) in RCA: 46] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
DNA encapsulates silver clusters, and these hybrid nanomaterials form molecular sensors. We discuss a silver cluster-oligonucleotide sensor with four characteristics. First, a specific reporting cluster forms within a single-stranded DNA. This template uses the 5' cluster domain CCCCAACTCCTT with different 3' recognition sites for complementary oligonucleotides. The modular composite strand exclusively forms a cluster with λmax = 400 nm and with low emission. Conjugates were chromatographically purified, and their elemental analysis measured a cluster adduct with ∼11 silver atoms. Second, hybridization transforms the cluster. Size exclusion chromatography shows that the 3' recognition sites of the single-stranded conjugates hybridize with their complements. This secondary structural change both shifts cluster absorption from 400 to 490 nm and develops emission at 550 nm. Third, cluster size remains intact. Like their violet predecessors, purified blue-green clusters have ∼11 silver atoms. Cluster integrity is further supported by extracting the complement from the blue-green conjugate and reversing the spectral changes. Fourth, the cluster transformation is an equilibrium. Complementary strands generate an isosbestic point and thus directly link single-stranded hosts for the violet cluster and their hybridized analogs for the blue-green cluster. This equilibrium shifts with temperature. A van't Hoff analysis shows that longer and more stable duplexes favor the blue-green cluster. However, hybridized cluster hosts are less stable than their native DNA counterparts, and stability further degrades when short complements expose nucleobases within S1-S2. Duplex instability suggests that unpaired nucleobases coordinate the violet cluster and favor the single-stranded sensor. A balance between innate hybridization and exogenous folding highlights a distinct feature of silver clusters for sensing: they are both chromophoric reporters and ligands that modulate analyte-sensor interactions.
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Affiliation(s)
- Jeffrey T. Petty
- Department of Chemistry, Furman University, Greenville, SC 29613
| | - Orlin O. Sergev
- Department of Chemistry, Furman University, Greenville, SC 29613
| | | | | | - Banabihari Giri
- Department of Chemistry, Furman University, Greenville, SC 29613
| | - D. Ryan McMullan
- Department of Chemistry, Furman University, Greenville, SC 29613
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24
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Lim KW, Ng VCM, Martín-Pintado N, Heddi B, Phan AT. Structure of the human telomere in Na+ solution: an antiparallel (2+2) G-quadruplex scaffold reveals additional diversity. Nucleic Acids Res 2013; 41:10556-62. [PMID: 23999095 PMCID: PMC3905899 DOI: 10.1093/nar/gkt771] [Citation(s) in RCA: 110] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023] Open
Abstract
Single-stranded DNA overhangs at the ends of human telomeric repeats are capable of adopting four-stranded G-quadruplex structures, which could serve as potential anticancer targets. Out of the five reported intramolecular human telomeric G-quadruplex structures, four were formed in the presence of K+ ions and only one in the presence of Na+ ions, leading often to a perception that this structural polymorphism occurs exclusively in the presence of K+ but not Na+. Here we present the structure of a new antiparallel (2+2) G-quadruplex formed by a derivative of a 27-nt human telomeric sequence in Na+ solution, which comprises a novel core arrangement distinct from the known topologies. This structure complements the previously elucidated basket-type human telomeric G-quadruplex to serve as reference structures in Na+-containing environment. These structures, together with the coexistence of other conformations in Na+ solution as observed by nuclear magnetic resonance spectroscopy, establish the polymorphic nature of human telomeric repeats beyond the influence of K+ ions.
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Affiliation(s)
- Kah Wai Lim
- School of Physical and Mathematical Sciences, Nanyang Technological University, 637371 Singapore, School of Biological Sciences, Nanyang Technological University, 637551 Singapore and Instituto de Química Física Rocasolano, CSIC, 28006 Madrid, Spain
| | - Veronica Chinn Min Ng
- School of Physical and Mathematical Sciences, Nanyang Technological University, 637371 Singapore, School of Biological Sciences, Nanyang Technological University, 637551 Singapore and Instituto de Química Física Rocasolano, CSIC, 28006 Madrid, Spain
| | - Nerea Martín-Pintado
- School of Physical and Mathematical Sciences, Nanyang Technological University, 637371 Singapore, School of Biological Sciences, Nanyang Technological University, 637551 Singapore and Instituto de Química Física Rocasolano, CSIC, 28006 Madrid, Spain
| | - Brahim Heddi
- School of Physical and Mathematical Sciences, Nanyang Technological University, 637371 Singapore, School of Biological Sciences, Nanyang Technological University, 637551 Singapore and Instituto de Química Física Rocasolano, CSIC, 28006 Madrid, Spain
| | - Anh Tuân Phan
- School of Physical and Mathematical Sciences, Nanyang Technological University, 637371 Singapore, School of Biological Sciences, Nanyang Technological University, 637551 Singapore and Instituto de Química Física Rocasolano, CSIC, 28006 Madrid, Spain
- *To whom correspondence should be addressed. Tel: +65 6514 1915; Fax: +65 6795 7981;
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25
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Chung WJ, Heddi B, Tera M, Iida K, Nagasawa K, Phan AT. Solution Structure of an Intramolecular (3 + 1) Human Telomeric G-Quadruplex Bound to a Telomestatin Derivative. J Am Chem Soc 2013; 135:13495-501. [DOI: 10.1021/ja405843r] [Citation(s) in RCA: 137] [Impact Index Per Article: 11.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Affiliation(s)
- Wan Jun Chung
- School of Physical and Mathematical
Sciences, Nanyang Technological University, Singapore
| | - Brahim Heddi
- School of Physical and Mathematical
Sciences, Nanyang Technological University, Singapore
| | - Masayuki Tera
- Department
of Biotechnology and Life Science, Faculty of Technology, Tokyo University of Agriculture and Technology, Japan
- Bioorganic Research Institute, Suntory Foundation for Life Science, Japan
| | - Keisuke Iida
- Department
of Biotechnology and Life Science, Faculty of Technology, Tokyo University of Agriculture and Technology, Japan
| | - Kazuo Nagasawa
- Department
of Biotechnology and Life Science, Faculty of Technology, Tokyo University of Agriculture and Technology, Japan
| | - Anh Tuân Phan
- School of Physical and Mathematical
Sciences, Nanyang Technological University, Singapore
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26
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Zhou J, Amrane S, Korkut DN, Bourdoncle A, He HZ, Ma DL, Mergny JL. Combination of i-Motif and G-Quadruplex Structures within the Same Strand: Formation and Application. Angew Chem Int Ed Engl 2013. [DOI: 10.1002/ange.201301278] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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27
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Zhou J, Amrane S, Korkut DN, Bourdoncle A, He HZ, Ma DL, Mergny JL. Combination of i-motif and G-quadruplex structures within the same strand: formation and application. Angew Chem Int Ed Engl 2013; 52:7742-6. [PMID: 23775868 DOI: 10.1002/anie.201301278] [Citation(s) in RCA: 61] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2013] [Revised: 05/06/2013] [Indexed: 12/11/2022]
Abstract
Peaceful coexistence: A double quadruplex composed of an i-motif and a G-quadruplex was constructed within one oligonucleotide strand (see picture). The defined double-quadruplex structure can serve as a NOTIF logic gate on the basis of the fluorescence of crystal violet.
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Affiliation(s)
- Jun Zhou
- Université de Bordeaux, ARNA Laboratory, 33000 Bordeaux, France
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28
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Martadinata H, Phan AT. Structure of human telomeric RNA (TERRA): stacking of two G-quadruplex blocks in K(+) solution. Biochemistry 2013; 52:2176-83. [PMID: 23445442 DOI: 10.1021/bi301606u] [Citation(s) in RCA: 76] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Abstract
Telomeric repeat-containing RNAs (TERRA) are transcription products of the telomeres. Human TERRA sequences containing UUAGGG repeats can form parallel-stranded G-quadruplexes. The stacking interaction of such structures was shown to be important for ligand targeting and higher-order arrangement of G-quadruplexes in long TERRA sequences. Here we report on the first high-resolution structure of a stacked G-quadruplex formed by the 10-nucleotide human TERRA sequence r(GGGUUAGGGU) in potassium solution. This structure comprises two dimeric three-layer parallel-stranded G-quadruplex blocks, which stack on each other at their 5'-ends. The adenine in each UUA loop is nearly coplanar with the 5'-end G-tetrad forming an A·(G·G·G·G)·A hexad, thereby increasing the stacking contacts between the two blocks. Interestingly, this stacking and loop conformation is different from all structures previously reported for the free human TERRA but resembles the structure previously determined for a complex between a human TERRA sequence and an acridine ligand. This stacking conformation is a potential target for drugs that recognize or induce the stacking interface.
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Affiliation(s)
- Herry Martadinata
- School of Physical and Mathematical Sciences, Nanyang Technological University, Singapore
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29
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Petty JT, Giri B, Miller IC, Nicholson DA, Sergev OO, Banks TM, Story SP. Silver clusters as both chromophoric reporters and DNA ligands. Anal Chem 2013; 85:2183-90. [PMID: 23330780 DOI: 10.1021/ac303531y] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Molecular silver clusters conjugated with DNA act as analyte sensors. Our studies evaluate a type of cluster-laden DNA strand whose structure and silver stoichiometry change with hybridization. The sensor strand integrates two functions: the 3' region binds target DNA strands through base recognition while the 5' sequence C(3)AC(3)AC(3)TC(3)A favors formation of a near-infrared absorbing and emitting cluster. This precursor form exclusively harbors an ∼11 silver atom cluster that absorbs at 400 nm and that condenses its single-stranded host. The 3' recognition site associates with a complementary target strand, thereby effecting a 330 nm red-shift in cluster absorption and a background-limited recovery of cluster emission at 790 nm. One factor underlying these changes is sensor unfolding and aggregation. Variations in salt and oligonucleotide concentrations control cluster development by influencing DNA association. Structural studies using fluorescence anisotropy, fluorescence correlation spectroscopy, and size exclusion chromatography show that the sensor-cluster conjugate opens and subsequently dimerizes with hybridization. A second factor contributing to the spectral and photophysical changes is cluster transformation. Empirical silver stoichiometries are preserved through hybridization, so hybridized, dimeric near-infrared conjugates host twice the amount of silver in relation to their violet absorbing predecessors. These DNA structure and net silver stoichiometry alterations provide insight into how DNA-silver conjugates recognize analytes.
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Affiliation(s)
- Jeffrey T Petty
- Department of Chemistry, Furman University, Greenville, South Carolina 29613, United States.
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30
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Adrian M, Heddi B, Phan AT. NMR spectroscopy of G-quadruplexes. Methods 2012; 57:11-24. [DOI: 10.1016/j.ymeth.2012.05.003] [Citation(s) in RCA: 184] [Impact Index Per Article: 14.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2012] [Revised: 05/15/2012] [Accepted: 05/16/2012] [Indexed: 12/24/2022] Open
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31
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Amrane S, Adrian M, Heddi B, Serero A, Nicolas A, Mergny JL, Phan AT. Formation of Pearl-Necklace Monomorphic G-Quadruplexes in the Human CEB25 Minisatellite. J Am Chem Soc 2012; 134:5807-16. [DOI: 10.1021/ja208993r] [Citation(s) in RCA: 77] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Samir Amrane
- School of
Physical and Mathematical
Sciences, Nanyang Technological University, 637371 Singapore
- University of Bordeaux, European
Institute of Chemistry
and Biology, INSERM U869, 33600 Pessac, France
| | - Michael Adrian
- School of
Physical and Mathematical
Sciences, Nanyang Technological University, 637371 Singapore
| | - Brahim Heddi
- School of
Physical and Mathematical
Sciences, Nanyang Technological University, 637371 Singapore
| | - Alexandre Serero
- Institut
Curie, Centre de Recherche,
UMR3244 CNRS, Université Pierre et Marie Curie, 75248 Paris, France
| | - Alain Nicolas
- Institut
Curie, Centre de Recherche,
UMR3244 CNRS, Université Pierre et Marie Curie, 75248 Paris, France
| | - Jean-Louis Mergny
- University of Bordeaux, European
Institute of Chemistry
and Biology, INSERM U869, 33600 Pessac, France
| | - Anh Tuân Phan
- School of
Physical and Mathematical
Sciences, Nanyang Technological University, 637371 Singapore
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32
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Lech CJ, Cheow Lim JK, Wen Lim JM, Amrane S, Heddi B, Phan AT. Effects of site-specific guanine C8-modifications on an intramolecular DNA G-quadruplex. Biophys J 2012; 101:1987-98. [PMID: 22004753 DOI: 10.1016/j.bpj.2011.08.049] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2011] [Revised: 08/15/2011] [Accepted: 08/19/2011] [Indexed: 10/16/2022] Open
Abstract
Understanding the fundamentals of G-quadruplex formation is important both for targeting G-quadruplexes formed by natural sequences and for engineering new G-quadruplexes with desired properties. Using a combination of experimental and computational techniques, we have investigated the effects of site-specific substitution of a guanine with C8-modified guanine derivatives, including 8-bromo-guanine, 8-O-methyl-guanine, 8-amino-guanine, and 8-oxo-guanine, within a well-defined (3 + 1) human telomeric G-quadruplex platform. The effects of substitutions on the stability of the G-quadruplex were found to depend on the type and position of the modification among different guanines in the structure. An interesting modification-dependent NMR chemical-shift effect was observed across basepairing within a guanine tetrad. This effect was reproduced by ab initio quantum mechanical computations, which showed that the observed variation in imino proton chemical shift is largely influenced by changes in hydrogen-bond geometry within the guanine tetrad.
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33
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Petty JT, Story SP, Juarez S, Votto SS, Herbst AG, Degtyareva NN, Sengupta B. Optical sensing by transforming chromophoric silver clusters in DNA nanoreactors. Anal Chem 2012; 84:356-64. [PMID: 22098274 PMCID: PMC4532300 DOI: 10.1021/ac202697d] [Citation(s) in RCA: 49] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Bifunctional DNA oligonucleotides serve as templates for chromophoric silver clusters and as recognition sites for target DNA strands, and communication between these two components is the basis of an oligonucleotide sensor. Few-atom silver clusters exhibit distinct electronic spectra spanning the visible and near-infrared region, and they are selectively synthesized by varying the base sequence of the DNA template. In these studies, a 16-base cluster template is adjoined with a 12-base sequence complementary to the target analyte, and hybridization induces structural changes in the composite sensor that direct the conversion between two spectrally and stoichiometrically distinct clusters. Without its complement, the sensor strand selectively harbors ~7 Ag atoms that absorb at 400 nm and fold the DNA host. Upon association of the target with its recognition site, the sensor strand opens to expose the cluster template that has the binding site for ~11 Ag atoms, and absorption at 720 nm with relatively strong emission develops in lieu of the violet absorption. Variations in the length and composition of the recognition site and the cluster template indicate that these types of dual-component sensors provide a general platform for near-infrared-based detection of oligonucleotides in challenging biological environments.
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Affiliation(s)
- Jeffrey T Petty
- Department of Chemistry, Furman University, Greenville, South Carolina 29163, USA.
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34
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Dao NT, Haselsberger R, Michel-Beyerle ME, Phan AT. Following G-quadruplex formation by its intrinsic fluorescence. FEBS Lett 2011; 585:3969-77. [PMID: 22079665 DOI: 10.1016/j.febslet.2011.11.004] [Citation(s) in RCA: 54] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2011] [Revised: 10/23/2011] [Accepted: 11/01/2011] [Indexed: 12/11/2022]
Abstract
We characterized and compared the fluorescence properties of various well-defined G-quadruplex structures. The increase of intrinsic fluorescence of G-rich DNA sequences when they form G-quadruplexes can be used to monitor the folding and unfolding of G-quadruplexes as a function of cations and temperature. The temperature-dependent fluorescence spectra of different G-quadruplexes also exhibit characteristic patterns. Thus, the stability and possibly also the structure of G-quadruplexes can be characterized and distinguished by their intrinsic fluorescence spectra.
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Affiliation(s)
- Nguyen Thuan Dao
- Division of Physics and Applied Physics, School of Physical and Mathematical Sciences, Nanyang Technological University, Singapore
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35
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Do NQ, Lim KW, Teo MH, Heddi B, Phan AT. Stacking of G-quadruplexes: NMR structure of a G-rich oligonucleotide with potential anti-HIV and anticancer activity. Nucleic Acids Res 2011; 39:9448-57. [PMID: 21840903 PMCID: PMC3241632 DOI: 10.1093/nar/gkr539] [Citation(s) in RCA: 148] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Abstract
G-rich oligonucleotides T30695 (or T30923), with the sequence of (GGGT)4, and T40214, with the sequence of (GGGC)4, have been reported to exhibit anti-HIV and anticancer activity. Here we report on the structure of a dimeric G-quadruplex adopted by a derivative of these sequences in K+ solution. It comprises two identical propeller-type parallel-stranded G-quadruplex subunits each containing three G-tetrad layers that are stacked via the 5′-5′ interface. We demonstrated control over the stacking of the two monomeric subunits by sequence modifications. Our analysis of possible structures at the stacking interface provides a general principle for stacking of G-quadruplexes, which could have implications for the assembly and recognition of higher-order G-quadruplex structures.
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Affiliation(s)
- Ngoc Quang Do
- School of Physical and Mathematical Sciences and School of Biological Sciences, Nanyang Technological University, Singapore
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36
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Petty JT, Sengupta B, Story SP, Degtyareva NN. DNA sensing by amplifying the number of near-infrared emitting, oligonucleotide-encapsulated silver clusters. Anal Chem 2011; 83:5957-64. [PMID: 21702495 PMCID: PMC4201625 DOI: 10.1021/ac201321m] [Citation(s) in RCA: 66] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
A bifunctional oligonucleotide integrates in situ synthesis of a fluorogenic silver cluster with recognition of a target DNA sequence. With the template C(3)AC(3)AC(3)GC(3)A, a complex forms with 10 silver atoms that possesses electronic transitions in the near-infrared and that is detected at nanomolar concentrations using diode laser excitation. Pendant to this cluster encoding region, the recognition component binds a target DNA strand through hybridization, and decoupling of these two regions of the composite sensor renders a modular sensor for specific oligonucleotides. A target is detected using a quencher strand that bridges the cluster template and recognition components and disturbs cluster binding, as indicated by static quenching. Competitive displacement of the quencher by the target strand restores the favored cluster environment, and our key finding is that this exchange enhances emission through a proportional increase in the number of emissive clusters. DNA detection is also accomplished in serum-containing buffers by taking advantage of the high brightness of this fluorophore and the inherently low endogenous background in the near-infrared spectral region. Cluster stability in this biological environment is enhanced by supplementing the solutions with Ag(+).
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Affiliation(s)
- Jeffrey T Petty
- Department of Chemistry, Furman University, Greenville, South Carolina 29613, United States.
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37
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Mukundan VT, Do NQ, Phan AT. HIV-1 integrase inhibitor T30177 forms a stacked dimeric G-quadruplex structure containing bulges. Nucleic Acids Res 2011; 39:8984-91. [PMID: 21771859 PMCID: PMC3203613 DOI: 10.1093/nar/gkr540] [Citation(s) in RCA: 82] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023] Open
Abstract
T30177 is a G-rich oligonucleotide with the sequence (GTGGTGGGTGGGTGGGT) which inhibits the HIV-1 integrase activity at nanomolar concentrations. Here we show that this DNA sequence forms in K(+) solution a dimeric G-quadruplex structure comprising a total of six G-tetrad layers through the stacking of two propeller-type parallel-stranded G-quadruplex subunits at their 5'-end. All twelve guanines in the sequence participate in the G-tetrad formation, despite the interruption in the first G-tract by a thymine, which forms a bulge between two adjacent G-tetrads. In this work, we also propose a simple analytical approach to stoichiometry determination using concentration-dependent melting curves.
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Affiliation(s)
- Vineeth Thachappilly Mukundan
- School of Physical and Mathematical Sciences and School of Biological Sciences, Nanyang Technological University, Singapore
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38
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Martadinata H, Heddi B, Lim KW, Phan AT. Structure of Long Human Telomeric RNA (TERRA): G-Quadruplexes Formed by Four and Eight UUAGGG Repeats Are Stable Building Blocks. Biochemistry 2011; 50:6455-61. [DOI: 10.1021/bi200569f] [Citation(s) in RCA: 62] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Herry Martadinata
- School of Physical and Mathematical Sciences and ‡School of Biological Sciences, Nanyang Technological University, Singapore
| | - Brahim Heddi
- School of Physical and Mathematical Sciences and ‡School of Biological Sciences, Nanyang Technological University, Singapore
| | - Kah Wai Lim
- School of Physical and Mathematical Sciences and ‡School of Biological Sciences, Nanyang Technological University, Singapore
| | - Anh Tuân Phan
- School of Physical and Mathematical Sciences and ‡School of Biological Sciences, Nanyang Technological University, Singapore
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39
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Abstract
G-quadruplex structures formed by DNA at the human telomeres are attractive anticancer targets. Human telomeric sequences can adopt a diverse range of intramolecular G-quadruplex conformations: a parallel-stranded conformation was observed in the crystalline state, while at least four other forms were seen in K(+) solution, raising the question of which conformation is favored in crowded cellular environment. Here, we report the first NMR structure of a human telomeric G-quadruplex in crowded solution. We show that four different G-quadruplex conformations are converted to a propeller-type parallel-stranded G-quadruplex in K(+)-containing crowded solution due to water depletion. This study also reveals the formation of a new higher-order G-quadruplex structure under molecular crowding conditions. Our molecular dynamics simulations of solvent distribution provide insights at molecular level on the formation of parallel-stranded G-quadruplex in environment depleted of water. These results regarding human telomeric DNA can be extended to oncogenic promoters and other genomic G-rich sequences.
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Affiliation(s)
- Brahim Heddi
- School of Physical and Mathematical Sciences, Nanyang Technological University, Singapore
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40
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Pedersen EB, Nielsen JT, Nielsen C, Filichev VV. Enhanced anti-HIV-1 activity of G-quadruplexes comprising locked nucleic acids and intercalating nucleic acids. Nucleic Acids Res 2011; 39:2470-81. [PMID: 21062811 PMCID: PMC3064782 DOI: 10.1093/nar/gkq1133] [Citation(s) in RCA: 58] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2010] [Revised: 10/21/2010] [Accepted: 10/22/2010] [Indexed: 01/23/2023] Open
Abstract
Two G-quadruplex forming sequences, 5'-TGGGAG and the 17-mer sequence T30177, which exhibit anti-HIV-1 activity on cell lines, were modified using either locked nucleic acids (LNA) or via insertions of (R)-1-O-(pyren-1-ylmethyl)glycerol (intercalating nucleic acid, INA) or (R)-1-O-[4-(1-pyrenylethynyl)phenylmethyl]glycerol (twisted intercalating nucleic acid, TINA). Incorporation of LNA or INA/TINA monomers provide as much as 8-fold improvement of anti-HIV-1 activity. We demonstrate for the first time a detailed analysis of the effect the incorporation of INA/TINA monomers in quadruplex forming oligonucleotides (QFOs) and the effect of LNA monomers in the context of biologically active QFOs. In addition, recent literature reports and our own studies on the gel retardation of the phosphodiester analogue of T30177 led to the conclusion that this sequence forms a parallel, dimeric G-quadruplex. Introduction of the 5'-phosphate inhibits dimerisation of this G-quadruplex as a result of negative charge-charge repulsion. Contrary to that, we found that attachment of the 5'-O-DMT-group produced a more active 17-mer sequence that showed signs of aggregation-forming multimeric G-quadruplex species in solution. Many of the antiviral QFOs in the present study formed more thermally stable G-quadruplexes and also high-order G-quadruplex structures which might be responsible for the increased antiviral activity observed.
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Affiliation(s)
- Erik B. Pedersen
- Nucleic Acid Center, Department of Physics and Chemistry, University of Southern Denmark, 5230 Odense, Department of Virology, Retrovirus Laboratory, State Serum Institute, 2300 Copenhagen, Denmark and Institute of Fundamental Sciences, Massey University, Palmerston North, Private Bag 11-222, New Zealand
| | - Jakob T. Nielsen
- Nucleic Acid Center, Department of Physics and Chemistry, University of Southern Denmark, 5230 Odense, Department of Virology, Retrovirus Laboratory, State Serum Institute, 2300 Copenhagen, Denmark and Institute of Fundamental Sciences, Massey University, Palmerston North, Private Bag 11-222, New Zealand
| | - Claus Nielsen
- Nucleic Acid Center, Department of Physics and Chemistry, University of Southern Denmark, 5230 Odense, Department of Virology, Retrovirus Laboratory, State Serum Institute, 2300 Copenhagen, Denmark and Institute of Fundamental Sciences, Massey University, Palmerston North, Private Bag 11-222, New Zealand
| | - Vyacheslav V. Filichev
- Nucleic Acid Center, Department of Physics and Chemistry, University of Southern Denmark, 5230 Odense, Department of Virology, Retrovirus Laboratory, State Serum Institute, 2300 Copenhagen, Denmark and Institute of Fundamental Sciences, Massey University, Palmerston North, Private Bag 11-222, New Zealand
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41
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Lim KW, Lacroix L, Yue DJE, Lim JKC, Lim JMW, Phan AT. Coexistence of two distinct G-quadruplex conformations in the hTERT promoter. J Am Chem Soc 2010; 132:12331-42. [PMID: 20704263 DOI: 10.1021/ja101252n] [Citation(s) in RCA: 120] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The catalytic subunit of human telomerase, hTERT, actively elongates the 3' end of the telomere in most cancer cells. The hTERT promoter, which contains many guanine-rich stretches on the same DNA strand, exhibits an exceptional potential for G-quadruplex formation. Here we show that one particular G-rich sequence in this region coexists in two G-quadruplex conformations in potassium solution: a (3 + 1) and a parallel-stranded G-quadruplexes. We present the NMR solution structures of both conformations, each comprising several robust structural elements, among which include the (3 + 1) and all-parallel G-tetrad cores, single-residue double-chain-reversal loops, and a capping A.T base pair. A combination of NMR and CD techniques, complemented with sequence modifications and variations of experimental condition, allowed us to better understand the coexistence of the two G-quadruplex conformations in equilibrium and how different structural elements conspire to favor a particular form.
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Affiliation(s)
- Kah Wai Lim
- School of Physical and Mathematical Sciences, Nanyang Technological University, Singapore
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42
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Basundra R, Kumar A, Amrane S, Verma A, Phan AT, Chowdhury S. A novel G-quadruplex motif modulates promoter activity of human thymidine kinase 1. FEBS J 2010; 277:4254-64. [DOI: 10.1111/j.1742-4658.2010.07814.x] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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43
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Xu Y, Ishizuka T, Kimura T, Komiyama M. A U-tetrad stabilizes human telomeric RNA G-quadruplex structure. J Am Chem Soc 2010; 132:7231-3. [PMID: 20459096 DOI: 10.1021/ja909708a] [Citation(s) in RCA: 49] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Telomeric repeat-containing RNA is a new noncoding RNA molecule recently discovered in mammalian cells. Here we report the structural features of human telomere RNA r(UAGGGU) in the presence of K(+) and Na(+). We demonstrated for the first time that a novel U-tetrad is formed at the 3' end of a parallel human telomeric RNA G-quadruplex. The U-tetrad dramatically stabilizes human telomeric RNA G-quadruplex structure, leading to an increase in melting temperature (T(m)) of 29 degrees C. The U-tetrad-stabilized telomeric RNA G-quadruplex structure adds considerably to our understanding of the diversity of RNA G-quadruplex architectures. It shows that the structure of base "quartets" is important in RNA assembly. The structural information will be invaluable for understanding the function of human telomere RNA.
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Affiliation(s)
- Yan Xu
- Research Center for Advanced Science and Technology, The University of Tokyo, 4-6-1 Komaba, Meguro-ku, Tokyo 153-8904, Japan.
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44
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Jin Y, Li H, Liu P. Label-free electrochemical selection of G-quadruplex-binding ligands based on structure switching. Biosens Bioelectron 2010; 25:2669-74. [DOI: 10.1016/j.bios.2010.04.043] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2010] [Revised: 04/23/2010] [Accepted: 04/27/2010] [Indexed: 11/26/2022]
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45
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Wang L, Liu X, Yang Q, Fan Q, Song S, Fan C, Huang W. A colorimetric strategy based on a water-soluble conjugated polymer for sensing pH-driven conformational conversion of DNA i-motif structure. Biosens Bioelectron 2010; 25:1838-42. [DOI: 10.1016/j.bios.2009.12.016] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2009] [Accepted: 12/14/2009] [Indexed: 10/20/2022]
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46
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Hu L, Lim KW, Bouaziz S, Phan AT. Giardia telomeric sequence d(TAGGG)4 forms two intramolecular G-quadruplexes in K+ solution: effect of loop length and sequence on the folding topology. J Am Chem Soc 2010; 131:16824-31. [PMID: 19874015 DOI: 10.1021/ja905611c] [Citation(s) in RCA: 55] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Recently, it has been shown that in K(+) solution the human telomeric sequence d[TAGGG(TTAGGG)(3)] forms a (3 + 1) intramolecular G-quadruplex, while the Bombyx mori telomeric sequence d[TAGG(TTAGG)(3)], which differs from the human counterpart only by one G deletion in each repeat, forms a chair-type intramolecular G-quadruplex, indicating an effect of G-tract length on the folding topology of G-quadruplexes. To explore the effect of loop length and sequence on the folding topology of G-quadruplexes, here we examine the structure of the four-repeat Giardia telomeric sequence d[TAGGG(TAGGG)(3)], which differs from the human counterpart only by one T deletion within the non-G linker in each repeat. We show by NMR that this sequence forms two different intramolecular G-quadruplexes in K(+) solution. The first one is a novel basket-type antiparallel-stranded G-quadruplex containing two G-tetrads, a G x (A-G) triad, and two A x T base pairs; the three loops are consecutively edgewise-diagonal-edgewise. The second one is a propeller-type parallel-stranded G-quadruplex involving three G-tetrads; the three loops are all double-chain-reversal. Recurrence of several structural elements in the observed structures suggests a "cut and paste" principle for the design and prediction of G-quadruplex topologies, for which different elements could be extracted from one G-quadruplex and inserted into another.
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Affiliation(s)
- Lanying Hu
- Division of Physics and Applied Physics, School of Physical and Mathematical Sciences, Nanyang Technological University, 21 Nanyang Link, Singapore 637371
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47
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Bruylants G, Boccongelli M, Snoussi K, Bartik K. Comparison of the thermodynamics and base-pair dynamics of a full LNA:DNA duplex and of the isosequential DNA:DNA duplex. Biochemistry 2009; 48:8473-82. [PMID: 19670874 DOI: 10.1021/bi900615z] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
Locked nucleic acids (LNA), conformationally restricted nucleotide analogues, are known to enhance pairing stability and selectivity toward complementary strands. With the aim to contribute to a better understanding of the origin of these effects, the structure, thermal stability, hybridization thermodynamics, and base-pair dynamics of a full-LNA:DNA heteroduplex and of its isosequential DNA:DNA homoduplex were monitored and compared. CD measurements highlight differences in the duplex structures: the homoduplex and heteroduplex present B-type and A-type helical conformations, respectively. The pairing of the hybrid duplex is characterized, at all temperatures monitored (between 15 and 37 degrees C), by a larger stability constant but a less favorable enthalpic term. A major contribution to this thermodynamic profile emanates from the presence of a hairpin structure in the LNA single strand which contributes favorably to the entropy of interaction but leads to an enthalpy penalty upon duplex formation. The base-pair opening dynamics of both systems was monitored by NMR spectroscopy via imino protons exchange measurements. The measurements highlight that hybrid G-C base-pairs present a longer base-pair lifetime and higher stability than natural G-C base-pairs, but that an LNA substitution in an A-T base-pair does not have a favorable effect on the stability. The thermodynamic and dynamic data confirm a more favorable stacking of the bases in the hybrid duplex. This study emphasizes the complementarities between dynamic and thermodynamical studies for the elucidation of the relevant factors in binding events.
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Affiliation(s)
- Gilles Bruylants
- Molecular and Biomolecular Engineering, Service Matières et Matériaux, CP165/64, Université Libre de Bruxelles, 50 Avenue F.D. Roosevelt, 1050 Bruxelles, Belgium
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48
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Lim KW, Alberti P, Guédin A, Lacroix L, Riou JF, Royle NJ, Mergny JL, Phan AT. Sequence variant (CTAGGG)n in the human telomere favors a G-quadruplex structure containing a G.C.G.C tetrad. Nucleic Acids Res 2009; 37:6239-48. [PMID: 19692585 PMCID: PMC2764449 DOI: 10.1093/nar/gkp630] [Citation(s) in RCA: 110] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023] Open
Abstract
Short contiguous arrays of variant CTAGGG repeats in the human telomere are unstable in the male germline and somatic cells, suggesting formation of unusual structures by this repeat type. Here, we report on the structure of an intramolecular G-quadruplex formed by DNA sequences containing four human telomeric variant CTAGGG repeats in potassium solution. Our results reveal a new robust antiparallel G-quadruplex fold involving two G-tetrads sandwiched between a G.C base pair and a G.C.G.C tetrad, which could represent a new platform for drug design targeted to human telomeric DNA.
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Affiliation(s)
- Kah Wai Lim
- Division of Physics and Applied Physics, School of Physical and Mathematical Sciences, Nanyang Technological University, Singapore
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Martadinata H, Phan AT. Structure of propeller-type parallel-stranded RNA G-quadruplexes, formed by human telomeric RNA sequences in K+ solution. J Am Chem Soc 2009; 131:2570-8. [PMID: 19183046 DOI: 10.1021/ja806592z] [Citation(s) in RCA: 181] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Very recent studies showed that mammalian telomeres were transcribed into telomeric-repeat-containing RNAs and suggested that these RNA molecules were biologically important. Here we report on a structural study of RNA G-quadruplexes formed by human telomeric RNA sequences in K(+) solution. Our data indicated that these sequences formed propeller-type parallel-stranded RNA G-quadruplexes. We have determined the NMR-based solution structure of a dimeric propeller-type RNA G-quadruplex formed by the 12-nt human telomeric RNA sequence r(UAGGGUUAGGGU). We also observed the stacking of two such propeller-type G-quadruplex blocks for the 10-nt human telomeric RNA sequence r(GGGUUAGGGU) and a higher-order G-quadruplex structure for the 9-nt human telomeric RNA sequence r(GGGUUAGGG). Based on these findings we proposed how higher-order structures might be formed by long telomeric RNA.
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Affiliation(s)
- Herry Martadinata
- Division of Physics and Applied Physics, School of Physical and Mathematical Sciences, Nanyang Technological University, Singapore 637371
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Lim KW, Amrane S, Bouaziz S, Xu W, Mu Y, Patel DJ, Luu KN, Phan AT. Structure of the human telomere in K+ solution: a stable basket-type G-quadruplex with only two G-tetrad layers. J Am Chem Soc 2009; 131:4301-9. [PMID: 19271707 PMCID: PMC2662591 DOI: 10.1021/ja807503g] [Citation(s) in RCA: 395] [Impact Index Per Article: 24.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Previously, it has been reported that human telomeric DNA sequences could adopt in different experimental conditions four different intramolecular G-quadruplexes each involving three G-tetrad layers, namely, Na(+) solution antiparallel-stranded basket form, K(+) crystal parallel-stranded propeller form, K(+) solution (3 + 1) Form 1, and K(+) solution (3 + 1) Form 2. Here we present a new intramolecular G-quadruplex adopted by a four-repeat human telomeric sequence in K(+) solution (Form 3). This structure is a basket-type G-quadruplex with only two G-tetrad layers: loops are successively edgewise, diagonal, and edgewise; glycosidic conformations of guanines are syn x syn x anti x anti around each tetrad. Each strand of the core has both a parallel and an antiparallel adjacent strands; there are one narrow, one wide, and two medium grooves. Despite the presence of only two G-tetrads in the core, this structure is more stable than the three-G-tetrad intramolecular G-quadruplexes previously observed for human telomeric sequences in K(+) solution. Detailed structural elucidation of Form 3 revealed extensive base pairing and stacking in the loops capping both ends of the G-tetrad core, which might explain the high stability of the structure. This novel structure highlights the conformational heterogeneity of human telomeric DNA. It establishes a new folding principle for G-quadruplexes and suggests new loop sequences and structures for targeting in human telomeric DNA.
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Affiliation(s)
- Kah Wai Lim
- School of Physical and Mathematical Sciences, Nanyang Technological University, Singapore
| | - Samir Amrane
- School of Physical and Mathematical Sciences, Nanyang Technological University, Singapore
| | - Serge Bouaziz
- Unité de Pharmacologie Chimique et Génétique, INSERM U640 — CNRS UMR 8151, Université Paris Descartes, France
| | - Weixin Xu
- School of Biological Sciences, Nanyang Technological University, Singapore
| | - Yuguang Mu
- School of Biological Sciences, Nanyang Technological University, Singapore
| | - Dinshaw J. Patel
- Structural Biology Program, Memorial Sloan-Kettering Cancer Center, New York, USA
| | - Kim Ngoc Luu
- Structural Biology Program, Memorial Sloan-Kettering Cancer Center, New York, USA
| | - Anh Tuân Phan
- School of Physical and Mathematical Sciences, Nanyang Technological University, Singapore
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