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He Z, Wu J, Li W, Du Y, Lu L. Investigation of G-Quadruplex DNA-Mediated Charge Transport for Exploring DNA Oxidative Damage in Telomeres. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2024. [PMID: 39177475 DOI: 10.1021/acs.langmuir.4c01604] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/24/2024]
Abstract
The human telomeric DNA 3' single-stranded overhang comprises tandem repeats of the sequence d(TTAGGG), which can fold into the stable secondary structure G-quadruplex (G4) and is susceptible to oxidative damage due to the enrichment of G bases. 8-Oxoguanine (8-oxoG) formed in telomeric DNA destabilizes G4 secondary structures and then inhibits telomere functions such as the binding of G4 proteins and the regulation of the length of telomeres. In this work, we developed a G4-DNA self-assembled monolayer electrochemical sensing interface using copper-free click chemistry based on the reaction of dibenzocyclooctyl with azide, resulting in a high yield of DNA tethers with order and homogeneity surfaces, that is more suitable for G-quadruplex DNA charge transport (CT) research. At high DNA coverage density surfaces, G-quadruplex DNA is 4 times more conductive than double-stranded DNA owing to the well-stacked aromatic rings of G-quartets acting as good charge transfer channels. The effect of telomeric oxidative damage on G-quadruplex-mediated CT is investigated. The accommodation of 8-oxoG at G sites originally in the syn or anti conformation around the glycosyl bond in the nonsubstituted hTel G-quadruplex causes structural perturbation and a conformational shift, which disrupts the π-stack, affecting the charge transfer and attenuating the electrochemical signal. The current intensity was found to correlate with the amount of 8-oxodG, and the detection limit was estimated to be approximately one lesion in 286 DNA bases, which can be converted into 64.7 fmol on the basis of the total surface DNA coverage. The improved G4-DNA order and homogeneity sensing interface represent a major step forward in this regard, providing a reliable and controlled electrochemical platform for the accurate measurement and diagnosis of G4-DNA oxidative damage.
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Affiliation(s)
- Zhangjin He
- Key Laboratory of Beijing on Regional Air Pollution Control, Department of Environmental Science, Beijing University of Technology, Beijing 100124, P. R. China
| | - Jiening Wu
- Key Laboratory of Beijing on Regional Air Pollution Control, Department of Environmental Science, Beijing University of Technology, Beijing 100124, P. R. China
| | - Wei Li
- Key Laboratory of Beijing on Regional Air Pollution Control, Department of Environmental Science, Beijing University of Technology, Beijing 100124, P. R. China
| | - Yuying Du
- Key Laboratory of Beijing on Regional Air Pollution Control, Department of Environmental Science, Beijing University of Technology, Beijing 100124, P. R. China
| | - Liping Lu
- Key Laboratory of Beijing on Regional Air Pollution Control, Department of Environmental Science, Beijing University of Technology, Beijing 100124, P. R. China
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Hu W, Jing H, Fu W, Wang Z, Zhou J, Zhang N. Conversion to Trimolecular G-Quadruplex by Spontaneous Hoogsteen Pairing-Based Strand Displacement Reaction between Bimolecular G-Quadruplex and Double G-Rich Probes. J Am Chem Soc 2023; 145:18578-18590. [PMID: 37553999 DOI: 10.1021/jacs.3c05617] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/10/2023]
Abstract
Bimolecular or tetramolecular G-quadruplexes (GQs) are predominantly self-assembled by the same sequence-identical G-rich oligonucleotides and usually remain inert to the strand displacement reaction (SDR) with other short G-rich invading fragments of DNA or RNA. Appealingly, in this study, we demonstrate that a parallel homomeric bimolecular GQ target of Tub10 d(CAGGGAGGGT) as the starting reactant, although completely folded in K+ solution and sufficiently stable (melting temperature of 57.7 °C), can still spontaneously accept strand invasion by a pair of short G-rich invading probes of P1 d(TGGGA) near room temperature. The final SDR product is a novel parallel heteromeric trimolecular GQ (tri-GQ) of Tub10/2P1 reassembled between one Tub10 strand and two P1 strands. Here we present, to the best of our knowledge, the first NMR solution structure of such a discrete heteromeric tri-GQ and unveil a unique mode of two probes vs one target in mutual recognition among G-rich canonical DNA oligomers. As a model system, the short invading probe P1 can spontaneously trap G-rich target Tub10 from a Watson-Crick duplex completely hybridized between Tub10 and its fully complementary strand d(ACCCTCCCTG). The Tub10 sequence of d(CAGGGAGGGT) is a fragment from the G-rich promoter region of the human β2-tubulin gene. Our findings provide new insights into the Hoogsteen pairing-based SDR between a GQ target and double invading probes of short G-rich DNA fragments and are expected to grant access to increasingly complex architectures in GQ-based DNA nanotechnology.
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Affiliation(s)
- Wenxuan Hu
- High Magnetic Field Laboratory, Hefei Institutes of Physical Science, Chinese Academy of Sciences, Hefei 230031, China
- University of Science and Technology of China, Hefei 230026, China
| | - Haitao Jing
- High Magnetic Field Laboratory, Hefei Institutes of Physical Science, Chinese Academy of Sciences, Hefei 230031, China
| | - Wenqiang Fu
- High Magnetic Field Laboratory, Hefei Institutes of Physical Science, Chinese Academy of Sciences, Hefei 230031, China
| | - Zengrong Wang
- High Magnetic Field Laboratory, Hefei Institutes of Physical Science, Chinese Academy of Sciences, Hefei 230031, China
- University of Science and Technology of China, Hefei 230026, China
| | - Jiang Zhou
- Analytical Instrumentation Center, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China
| | - Na Zhang
- High Magnetic Field Laboratory, 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
- High Magnetic Field Laboratory of Anhui Province, 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
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3
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Yang N, Wang Y, Wang X, Zhang F, Xiao Y, Yan B, Zhang T, Liu X, Li Y. Label-Free Detection of DNA Supramolecular Structure Formation by Surface-Enhanced Raman Spectroscopy. J Phys Chem Lett 2022; 13:6208-6214. [PMID: 35770782 DOI: 10.1021/acs.jpclett.2c01461] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
The precise self-assembly of DNA molecules can be used to create nanoprecision supramolecular materials. However, the lack of methods to characterize such supramolecular materials limits their development. Surface-enhanced Raman spectroscopy (SERS) is widely used to detect the secondary structure of simple DNA molecules, but its application in the revealing of complex DNA supramolecular information remains challenging. Herein, we proposed a modified SERS-based platform able to provide structural information on DNA supramolecular materials. The silver nanoparticle-enhanced substrate uses acetonitrile as an internal standard and modifier, and calcium ions are used as an aggregating agent to induce the formation of stable "hotspots" of silver nanoparticles, where the base planes in DNA supramolecules are perpendicular to the surface of the substrate, obtaining enhanced Raman signals of base ring in both single-stranded DNA and DNA supramolecules for the first time. The structure of DNA supramolecules was efficiently characterized using this technique, showing the great application potential of this technique in the structural analysis of nucleic acids and their ligands.
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Affiliation(s)
- Ni Yang
- School of Chemistry and Chemical Engineering, Guizhou University, No. 2708, South Section of Huaxi Avenue, Guiyang City 550025, Guizhou Province, P. R. China
| | - Yunpeng Wang
- Department of Pharmaceutical Analysis and Analytical Chemistry (Research Center for Innovative Technology of Pharmaceutical Analysis), College of Pharmacy, Harbin Medical University, 157 Baojian Road, Harbin 150081, Heilongjiang Province, P. R. China
| | - Xiaotong Wang
- Department of Pharmaceutical Analysis and Analytical Chemistry (Research Center for Innovative Technology of Pharmaceutical Analysis), College of Pharmacy, Harbin Medical University, 157 Baojian Road, Harbin 150081, Heilongjiang Province, P. R. China
| | - Fenghai Zhang
- School of Chemistry and Chemical Engineering, Guizhou University, No. 2708, South Section of Huaxi Avenue, Guiyang City 550025, Guizhou Province, P. R. China
| | - Yanlong Xiao
- The Second Hospital of Jilin University, Jilin University, Changchun 130041, P. R. China
| | - Bingdi Yan
- The Second Hospital of Jilin University, Jilin University, Changchun 130041, P. R. China
| | - Ting Zhang
- Department of Pharmaceutical Analysis and Analytical Chemistry (Research Center for Innovative Technology of Pharmaceutical Analysis), College of Pharmacy, Harbin Medical University, 157 Baojian Road, Harbin 150081, Heilongjiang Province, P. R. China
| | - Xin Liu
- Department of Pharmaceutical Analysis and Analytical Chemistry (Research Center for Innovative Technology of Pharmaceutical Analysis), College of Pharmacy, Harbin Medical University, 157 Baojian Road, Harbin 150081, Heilongjiang Province, P. R. China
| | - Yang Li
- School of Chemistry and Chemical Engineering, Guizhou University, No. 2708, South Section of Huaxi Avenue, Guiyang City 550025, Guizhou Province, P. R. China
- Department of Pharmaceutical Analysis and Analytical Chemistry (Research Center for Innovative Technology of Pharmaceutical Analysis), College of Pharmacy, Harbin Medical University, 157 Baojian Road, Harbin 150081, Heilongjiang Province, P. R. China
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Romanucci V, Oliva R, Petraccone L, Claes S, Schols D, Zarrelli A, Di Fabio G. Synthesis of new riboflavin modified ODNs: Effect of riboflavin moiety on the G-quadruplex arrangement and stability. Bioorg Chem 2020; 104:104213. [PMID: 32919132 DOI: 10.1016/j.bioorg.2020.104213] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2020] [Revised: 07/31/2020] [Accepted: 08/24/2020] [Indexed: 10/23/2022]
Abstract
In the panorama of modified G-quadruplexes (G4s) with interesting proprieties, here, it has been reported the synthesis of new modified d(TGGGAG) sequences forming G-quadruplexes, with the insertion of a riboflavin unit (Rf, vitamin B2). Exploiting the flavin similarity with the hydrogen bond pattern of guanine and aiming at mimic a typical nucleoside scaffold, the synthesis of the riboflavin building block 3 it has been efficiently carried out. The effect of insertion of riboflavin mimic nucleoside on the G-quadruplex properties has been here, for the first time investigated. A biophysical characterization of Rf-modified sequences (A-D) has been carried out by circular dichroism (CD), fluorescence spectroscopy, differential scanning calorimetry (DSC) and native gel electrophoresis. CD and electrophoresis data have suggested that Rf-modified sequences are able to form parallel tetramolecular G4 structures similar to that of the unmodified sequence. Analysis of the DSC thermograms has revealed that all modified G-quadruplexes have a higher thermal stability compared with the natural sequence, particularly the stabilisation is higher when the Rf residue is introduced at the 3'-end. Further, DSC analysis has revealed that the Rf residues introduced at the 3'-end are able to form additional stabilising interactions, energetically almost comparable to the enthalpic contribution of a G-tetrad. Fluorescence measurement are consistent with this result showing that the Rf residues introduced at 3'-end are able to form stacking interactions with the adjacent bases within the G-quadruplex structure. The whole of data suggested that the introduction of Rf unit can stabilize G-quadruplex structures and can be a promising candidate for future theranostic applications.
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Affiliation(s)
- Valeria Romanucci
- Department of Chemical Sciences, University of Napoli Federico II, Complesso di Monte Sant'Angelo, Via Cintia 4, I-80126 Napoli, Italy.
| | - Rosario Oliva
- Department of Chemical Sciences, University of Napoli Federico II, Complesso di Monte Sant'Angelo, Via Cintia 4, I-80126 Napoli, Italy; Physical Chemistry I - Biophysical Chemistry, TU Dortmund University, Otto-Hahn Strasse 4a, D-44227 Dortmund, Germany
| | - Luigi Petraccone
- Department of Chemical Sciences, University of Napoli Federico II, Complesso di Monte Sant'Angelo, Via Cintia 4, I-80126 Napoli, Italy
| | - Sandra Claes
- Department of Microbiology, Immunology and Transplantation, Rega Institute, KU Leuven, Herestraat 49, 3000 Leuven, Belgium
| | - Dominique Schols
- Department of Microbiology, Immunology and Transplantation, Rega Institute, KU Leuven, Herestraat 49, 3000 Leuven, Belgium
| | - Armando Zarrelli
- Department of Chemical Sciences, University of Napoli Federico II, Complesso di Monte Sant'Angelo, Via Cintia 4, I-80126 Napoli, Italy
| | - Giovanni Di Fabio
- Department of Chemical Sciences, University of Napoli Federico II, Complesso di Monte Sant'Angelo, Via Cintia 4, I-80126 Napoli, Italy.
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Rauser V, Weinhold E. Quantitative Formation of Monomeric G-Quadruplex DNA from Multimeric Structures of c-Myc Promoter Sequence. Chembiochem 2020; 21:2445-2448. [PMID: 32267052 PMCID: PMC7496815 DOI: 10.1002/cbic.202000159] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2020] [Revised: 04/07/2020] [Indexed: 12/02/2022]
Abstract
G‐Quadruplex (G4)‐forming DNA sequences have a tendency to form stable multimeric structures. This can be problematic for studies with synthetic oligodeoxynucleotides. Herein, we describe a method that quantitatively converts multimeric intermolecular structures of the Pu27 sequence from the c‐myc promoter into the desired monomeric G4 by alkaline treatment and refolding.
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Affiliation(s)
- Valerie Rauser
- Institute of Organic Chemistry, RWTH Aachen University, Landoltweg 1, 52074, Aachen, Germany
| | - Elmar Weinhold
- Institute of Organic Chemistry, RWTH Aachen University, Landoltweg 1, 52074, Aachen, Germany
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Sjakste T, Leonova E, Petrovs R, Trapina I, Röder MS, Sjakste N. Tight DNA-protein complexes isolated from barley seedlings are rich in potential guanine quadruplex sequences. PeerJ 2020; 8:e8569. [PMID: 32110488 PMCID: PMC7034378 DOI: 10.7717/peerj.8569] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2019] [Accepted: 01/15/2020] [Indexed: 11/20/2022] Open
Abstract
Background The concept of chromatin domains attached to the nuclear matrix is being revisited, with nucleus described as a set of topologically associating domains. The significance of the tightly bound to DNA proteins (TBP), a protein group that remains attached to DNA after its deproteinization should be also revisited, as the existence of these interactions is in good agreement with the concept of the topologically associating domain. The work aimed to characterize the DNA component of TBP isolated from barley seedlings. Methods The tight DNA-protein complexes from the first leaves, coleoptiles, and roots of barley seedlings were isolated by purification with chromatography on nitrocellulose or exhaustive digestion of DNA with DNase I. Cloning and transformation were performed using pMOSBBlue Blunt Ended Cloning Kit. Inserts were amplified by PCR, and sequencing was performed on the MegaBace 1000 Sequencing System. The BLAST search was performed using sequence databases at NCBI, CR-EST, and TREP and Ensembl Plants databases. Comparison to MAR/SAR sequences was performed using http://smartdb.bioinf.med.uni-goettingen.de/cgi-bin/SMARtDB/smar.cgi database. The prediction of G quadruplexes (GQ) was performed with the aid of R-studio library pqsfinder. CD spectra were recorded on a Chirascan CS/3D spectrometer. Results Although the barley genome is AT-rich (43% of GC pairs), most DNA fragments associated with TBP were GC-rich (up to 70% in some fractions). Both fractionation procedures yielded a high proportion of CT-motif sequences presented predominantly by the 16-bp CC(TCTCCC)2 TC fragment present in clones derived from the TBP-bound DNA and absent in free DNA. BLAST analysis revealed alignment with different barley repeats. Some clones, however, aligned with both nuclear and chloroplast structural genes. Alignments with MAR/SAR motifs were very few. The analysis produced by the pqsfinder program revealed numerous potential quadruplex-forming sites in the TBP-bound sequences. A set of oligonucleotides containing sites of possible GQs were designed and ordered. Three of them represented the minus strand of the CT-repeat. Two were derived from sequences of two clones of nitrocellulose retained fraction from leaves and contained GC-rich motifs different from the CT motif. Circular dichroism spectroscopy revealed profound changes in spectra when oligonucleotides were incubated with 100 mM KCl. There was either an increase of positive band in the area of 260 nm or the formation of a positive band at 290 nm. In the former case, changes are typical for parallel G-quadruplexes and, in the latter, 3 + 1 structures. Discussion The G-quadruplexes anchor proteins are probably involved in the maintenance of the topologically associated domain structure.
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Affiliation(s)
- Tatjana Sjakste
- Genomics and Bioinformatics Group, Institute of Biology, University of Latvia, Riga, Latvia
| | - Elina Leonova
- Faculty of Medicine, University of Latvia, Riga, Latvia
| | | | - Ilva Trapina
- Genomics and Bioinformatics Group, Institute of Biology, University of Latvia, Riga, Latvia
| | - Marion S Röder
- Leibniz Institute for Plant Genetics and Crop Research, Gatersleben, Germany
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Lightfoot HL, Hagen T, Tatum NJ, Hall J. The diverse structural landscape of quadruplexes. FEBS Lett 2019; 593:2083-2102. [PMID: 31325371 DOI: 10.1002/1873-3468.13547] [Citation(s) in RCA: 88] [Impact Index Per Article: 17.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2019] [Revised: 07/09/2019] [Accepted: 07/15/2019] [Indexed: 12/15/2022]
Abstract
G-quadruplexes are secondary structures formed in G-rich sequences in DNA and RNA. Considerable research over the past three decades has led to in-depth insight into these unusual structures in DNA. Since the more recent exploration into RNA G-quadruplexes, such structures have demonstrated their in cellulo existence, function and roles in pathology. In comparison to Watson-Crick-based secondary structures, most G-quadruplexes display highly redundant structural characteristics. However, numerous reports of G-quadruplex motifs/structures with unique features (e.g. bulges, long loops, vacancy) have recently surfaced, expanding the repertoire of G-quadruplex scaffolds. This review addresses G-quadruplex formation and structure, including recent reports of non-canonical G-quadruplex structures. Improved methods of detection will likely further expand this collection of novel structures and ultimately change the face of quadruplex-RNA targeting as a therapeutic strategy.
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Affiliation(s)
- Helen L Lightfoot
- Department of Chemistry and Applied Biosciences, Institute of Pharmaceutical Sciences, ETH Zurich, Switzerland
| | - Timo Hagen
- Department of Chemistry and Applied Biosciences, Institute of Pharmaceutical Sciences, ETH Zurich, Switzerland
| | - Natalie J Tatum
- Newcastle Cancer Centre, Northern Institute for Cancer Research, Medical School, Newcastle University, Newcastle upon Tyne, UK
| | - Jonathan Hall
- Department of Chemistry and Applied Biosciences, Institute of Pharmaceutical Sciences, ETH Zurich, Switzerland
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Conserved G-Quadruplexes Regulate the Immediate Early Promoters of Human Alphaherpesviruses. Molecules 2019; 24:molecules24132375. [PMID: 31252527 PMCID: PMC6651000 DOI: 10.3390/molecules24132375] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2019] [Revised: 06/24/2019] [Accepted: 06/26/2019] [Indexed: 01/15/2023] Open
Abstract
Human Alphaherpesviruses comprise three members, herpes simplex virus (HSV) 1 and 2 and varicella zoster virus (VZV). These viruses are characterized by a lytic cycle in epithelial cells and latency in the nervous system, with lifelong infections that may periodically reactivate and lead to serious complications, especially in immunocompromised patients. The mechanisms that regulate viral transcription have not been fully elucidated, but the master role of the immediate early (IE) genes has been established. G-quadruplexes are non-canonical nucleic-acid structures that control transcription, replication, and recombination in many organisms including viruses and that represent attractive antiviral targets. In this work, we investigate the presence, conservation, folding and activity of G-quadruplexes in the IE promoters of the Alphaherpesviruses. Our analysis shows that all IE promoters in the genome of HSV-1, HSV-2 and VZV contain fully conserved G-quadruplex forming sequences. These comprise sequences with long loops and bulges, and thus deviating from the classic G-quadruplex motifs. Moreover, their location is both on the leading and lagging strand and in some instances they contain exuberant G-tracts. Biophysical and biological analysis proved that all sequences actually fold into G-quadruplex under physiological conditions and can be further stabilized by the G-quadruplex ligand BRACO-19, with subsequent impairment of viral IE gene transcription in cells. These results help shed light on the control of viral transcription and indicate new viral targets to design drugs that impair the early steps of Alphaherpesviruses. In addition, they validate the significance of G-quadruplexes in the general regulation of viral cycles.
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Su Y, Fujii H, Burakova EA, Chelobanov BP, Fujii M, Stetsenko DA, Filichev VV. Neutral and Negatively Charged Phosphate Modifications Altering Thermal Stability, Kinetics of Formation and Monovalent Ion Dependence of DNA G-Quadruplexes. Chem Asian J 2019; 14:1212-1220. [PMID: 30600926 DOI: 10.1002/asia.201801757] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2018] [Revised: 12/22/2018] [Indexed: 12/18/2022]
Abstract
The effect of phosphate group modifications on formation and properties of G-quadruplexes (G4s) has not been investigated in detail. Here, we evaluated the structural, thermodynamic and kinetic properties of the parallel G-quadruplexes formed by oligodeoxynucleotides d(G4 T), d(TG4 T) and d(TG5 T), in which all phosphates were replaced with N-methanesulfonyl (mesyl) phosphoramidate or phosphoryl guanidine groups resulting in either negatively charged or neutral DNA sequences, respectively. We established that all modified sequences were able to form G-quadruplexes of parallel topology; however, the presence of modifications led to a decrease in thermal stability relative to unmodified G4s. In contrast to negatively charged G4s, assembly of neutral G4 DNA species was faster in the presence of sodium ions than potassium ions, and was independent of the salt concentration used. Formation of mixed G4s composed of both native and neutral G-rich strands has been detected using native gel electrophoresis, size-exclusion chromatography and ESI-MS. In summary, our results indicate that the phosphate modifications studied are compatible with G-quadruplex formation, which could be used for the design of biologically active compounds.
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Affiliation(s)
- Yongdong Su
- Institute of Fundamental Sciences, Massey University, Private Bag 11-222, 4442, Palmerston North, New Zealand
| | - Hirofumi Fujii
- Department of Biological and Environmental Chemistry, School of Humanity Oriented Science and Technology, Kindai University, Fukuoka, Iizuka, Japan
| | - Ekaterina A Burakova
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia
| | - Boris P Chelobanov
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia.,Novosibirsk State University, Novosibirsk, Russia
| | - Masayuki Fujii
- Department of Biological and Environmental Chemistry, School of Humanity Oriented Science and Technology, Kindai University, Fukuoka, Iizuka, Japan
| | - Dmitry A Stetsenko
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia.,Novosibirsk State University, Novosibirsk, Russia
| | - Vyacheslav V Filichev
- Institute of Fundamental Sciences, Massey University, Private Bag 11-222, 4442, Palmerston North, New Zealand
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Filitcheva J, Edwards PJB, Norris GE, Filichev VV. α-2′-Deoxyguanosine can switch DNA G-quadruplex topologies from antiparallel to parallel. Org Biomol Chem 2019; 17:4031-4042. [DOI: 10.1039/c9ob00360f] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
α-2′-Deoxyguanosine (α-dG) converts antiparallel, dimeric G-quadruplex DNA into a parallel, tetramolecular complex.
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Affiliation(s)
- Jana Filitcheva
- School of Fundamental Sciences
- Massey University
- Palmerston North
- New Zealand
| | | | - Gillian E. Norris
- School of Fundamental Sciences
- Massey University
- Palmerston North
- New Zealand
- Maurice Wilkins Centre for Molecular Biodiscovery
| | - Vyacheslav V. Filichev
- School of Fundamental Sciences
- Massey University
- Palmerston North
- New Zealand
- Maurice Wilkins Centre for Molecular Biodiscovery
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Bose K, Lech CJ, Heddi B, Phan AT. High-resolution AFM structure of DNA G-wires in aqueous solution. Nat Commun 2018; 9:1959. [PMID: 29773796 PMCID: PMC5958085 DOI: 10.1038/s41467-018-04016-y] [Citation(s) in RCA: 45] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2017] [Accepted: 03/27/2018] [Indexed: 11/22/2022] Open
Abstract
We investigate the self-assembly of short pieces of the Tetrahymena telomeric DNA sequence d[G4T2G4] in physiologically relevant aqueous solution using atomic force microscopy (AFM). Wire-like structures (G-wires) of 3.0 nm height with well-defined surface periodic features were observed. Analysis of high-resolution AFM images allowed their classification based on the periodicity of these features. A major species is identified with periodic features of 4.3 nm displaying left-handed ridges or zigzag features on the molecular surface. A minor species shows primarily left-handed periodic features of 2.2 nm. In addition to 4.3 and 2.2 nm ridges, background features with periodicity of 0.9 nm are also observed. Using molecular modeling and simulation, we identify a molecular structure that can explain both the periodicity and handedness of the major G-wire species. Our results demonstrate the potential structural diversity of G-wire formation and provide valuable insight into the structure of higher-order intermolecular G-quadruplexes. Our results also demonstrate how AFM can be combined with simulation to gain insight into biomolecular structure. DNA and RNA G-quadruplexes can stack to form higher-order structures called G-wires. Here the authors report high-resolution AFM images of higher-order DNA G-quadruplexes in aqueous solution that could impact the design of G-wire based nanodevices and the understanding of G-wires in biology.
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Affiliation(s)
- Krishnashish Bose
- Division of Physics and Applied Physics, School of Physical and Mathematical Sciences, Nanyang Technological University, Singapore, 637371, Singapore
| | - Christopher J Lech
- Division of Physics and Applied Physics, School of Physical and Mathematical Sciences, Nanyang Technological University, Singapore, 637371, Singapore
| | - Brahim Heddi
- Division of Physics and Applied Physics, School of Physical and Mathematical Sciences, Nanyang Technological University, Singapore, 637371, Singapore.,Laboratoire de Biologie et de Pharmacologie Appliquée, CNRS, Ecole Normale Supérieure, Paris-Saclay, France
| | - Anh Tuân Phan
- Division of Physics and Applied Physics, School of Physical and Mathematical Sciences, Nanyang Technological University, Singapore, 637371, Singapore.
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Zhou J, Amrane S, Rosu F, Salgado GF, Bian Y, Tateishi-Karimata H, Largy E, Korkut DN, Bourdoncle A, Miyoshi D, Zhang J, Ju H, Wang W, Sugimoto N, Gabelica V, Mergny JL. Unexpected Position-Dependent Effects of Ribose G-Quartets in G-Quadruplexes. J Am Chem Soc 2017; 139:7768-7779. [PMID: 28523907 DOI: 10.1021/jacs.7b00648] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
To understand the role of ribose G-quartets and how they affect the properties of G-quadruplex structures, we studied three systems in which one, two, three, or four deoxyribose G-quartets were substituted with ribose G-quartets. These systems were a parallel DNA intramolecular G-quadruplex, d(TTGGGTGGGTTGGGTGGGTT), and two tetramolecular G-quadruplexes, d(TGGGT) and d(TGGGGT). Thermal denaturation experiments revealed that ribose G-quartets have position-dependent and cumulative effects on G-quadruplex stability. An unexpected destabilization was observed when rG quartets were presented at the 5'-end of the G stack. This observation challenges the general belief that RNA residues stabilize G-quadruplexes. Furthermore, in contrast to past proposals, hydration is not the main factor determining the stability of our RNA/DNA chimeric G-quadruplexes. Interestingly, the presence of rG residues in a central G-quartet facilitated the formation of additional tetramolecular G-quadruplex topologies showing positive circular dichroism signals at 295 nm. 2D NMR analysis of the tetramolecular TGgGGT (lowercase letter indicates ribose) indicates that Gs in the 5'-most G-quartet adopt the syn conformation. These analyses highlight several new aspects of the role of ribose G-quartets on G-quadruplex structure and stability, and demonstrate that the positions of ribose residues are critical for tuning G-quadruplex properties.
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Affiliation(s)
- Jun Zhou
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry & Chemical Engineering, Nanjing University , Nanjing 210023, China.,Université de Bordeaux , INSERM U1212, CNRS UMR 5320, ARNA Laboratory, IECB, F-33600 Pessac, France
| | - Samir Amrane
- Université de Bordeaux , INSERM U1212, CNRS UMR 5320, ARNA Laboratory, IECB, F-33600 Pessac, France
| | - Frédéric Rosu
- Université de Bordeaux , CNRS UMS 3033, INSERM US001, IECB, F-33600 Pessac, France
| | - Gilmar F Salgado
- Université de Bordeaux , INSERM U1212, CNRS UMR 5320, ARNA Laboratory, IECB, F-33600 Pessac, France
| | - Yunqiang Bian
- Shandong Provincial Key Laboratory of Functional Macromolecular Biophysics, Institute of Biophysics, Dezhou University , Dezhou 253023, China
| | - Hisae Tateishi-Karimata
- Frontier Institute for Biomolecular Engineering Research (FIBER) and Graduate School of Frontiers of Innovative Research in Science and Technology (FIRST), Konan University , 7-1-20 Minatojima-minamimachi, Chuo-ku, Kobe 650-0047, Japan
| | - Eric Largy
- Université de Bordeaux , INSERM U1212, CNRS UMR 5320, ARNA Laboratory, IECB, F-33600 Pessac, France
| | - Dursun Nizam Korkut
- Université de Bordeaux , INSERM U1212, CNRS UMR 5320, ARNA Laboratory, IECB, F-33600 Pessac, France
| | - Anne Bourdoncle
- Université de Bordeaux , INSERM U1212, CNRS UMR 5320, ARNA Laboratory, IECB, F-33600 Pessac, France
| | - Daisuke Miyoshi
- Frontier Institute for Biomolecular Engineering Research (FIBER) and Graduate School of Frontiers of Innovative Research in Science and Technology (FIRST), Konan University , 7-1-20 Minatojima-minamimachi, Chuo-ku, Kobe 650-0047, Japan
| | - Jian Zhang
- Collaborative Innovation Center of Advanced Microstructures and Department of Physics, Nanjing University , Nanjing 210093, China
| | - Huangxian Ju
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry & Chemical Engineering, Nanjing University , Nanjing 210023, China
| | - Wei Wang
- Collaborative Innovation Center of Advanced Microstructures and Department of Physics, Nanjing University , Nanjing 210093, China
| | - Naoki Sugimoto
- Frontier Institute for Biomolecular Engineering Research (FIBER) and Graduate School of Frontiers of Innovative Research in Science and Technology (FIRST), Konan University , 7-1-20 Minatojima-minamimachi, Chuo-ku, Kobe 650-0047, Japan
| | - Valérie Gabelica
- Université de Bordeaux , INSERM U1212, CNRS UMR 5320, ARNA Laboratory, IECB, F-33600 Pessac, France
| | - Jean-Louis Mergny
- Université de Bordeaux , INSERM U1212, CNRS UMR 5320, ARNA Laboratory, IECB, F-33600 Pessac, France.,Institute of Biophysics of the CAS , v.v.i., Královopolská 135, 612 65 Brno, Czech Republic
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13
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Vialet B, Gissot A, Delzor R, Barthélémy P. Controlling G-quadruplex formation via lipid modification of oligonucleotide sequences. Chem Commun (Camb) 2017; 53:11560-11563. [DOI: 10.1039/c7cc05693a] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
G-quadruplexes (G4) represent attractive supramolecular scaffolds.
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Affiliation(s)
- Brune Vialet
- Univ. Bordeaux
- ARNA Laboratory
- F-33000 Bordeaux
- France
- INSERM
| | - Arnaud Gissot
- Univ. Bordeaux
- ARNA Laboratory
- F-33000 Bordeaux
- France
- INSERM
| | - Romain Delzor
- Univ. Bordeaux
- ARNA Laboratory
- F-33000 Bordeaux
- France
- INSERM
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14
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Goblirsch BR, Kalb EM, Marsh TC. Interfacial Au nanoparticle decoration of a disulfide modified G-wire. Biochim Biophys Acta Gen Subj 2016; 1861:1471-1476. [PMID: 27989638 DOI: 10.1016/j.bbagen.2016.12.010] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2016] [Revised: 11/17/2016] [Accepted: 12/14/2016] [Indexed: 10/20/2022]
Abstract
BACKGROUND The guanine-rich oligonucleotide (GRO), dGGGGTTGGGG (G4T2G4), has the capacity to form a linear supramolecular polymer known as a G-wire. Individual nucleotides of the component GROs can be functionally modified to serve as site-specific attachment points in the G-wire while not interfering with its self-assembling properties. An amine linker modification to an internal thymine base of the GRO, denoted G4TT*G4, serves as a chemically versatile attachment site. METHODS In this work, addition of an alkyl disulfide to G4TT*G4 produces the GRO G4TTdG4 enabling binding to gold nanoparticles via place exchange chemistry. G-wires assembled by combining G4T2G4 and G4TTdG4 were stably maintained in an aqueous environment. Disulfide modified G-wires (DS_G-wire) were then covered with dodecanethiol capped gold nanoparticles in an organic solvent via an interfacial place exchange reaction. Tapping Mode AFM and TEM were used to image G-wires decorated with gold nanoparticles. The specificity of the interfacial place exchange reaction was measured using a fluorometric dye displacement from the gold nanoparticles. RESULTS The results show that a two component DS_G-wire with an amphipathic tether readily self-assemble as shown by PAGE and TM-AFM. The amphipathic disulfide moiety of DS_G-wires facilitates place exchange chemistry with alkylthiol protected Au nanoparticles across an aqueous-organic interface. CONCLUSION Interfacial place exchange is an effective strategy for decorating DS_G-wires with Au nanoparticles. GENERAL SIGNIFICANCE The use of modified G-wire self-assembly combined with a high degree of nanoparticle binding specificity presents another strategy for the use of G-wires as a rigid one-dimensional molecular scaffold with potential applications in nanoscale device construction. This article is part of a Special Issue entitled "G-quadruplex" Guest Editor: Dr. Concetta Giancola and Dr. Daniela Montesarchio.
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Affiliation(s)
- Brandon R Goblirsch
- Department of Chemistry, University of St. Thomas, 2115 Summit Avenue, St. Paul, MN 55105, USA.
| | - Evan M Kalb
- Department of Chemistry, University of St. Thomas, 2115 Summit Avenue, St. Paul, MN 55105, USA.
| | - Thomas C Marsh
- Department of Chemistry, University of St. Thomas, 2115 Summit Avenue, St. Paul, MN 55105, USA.
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15
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Functional Hallmarks of a Catalytic DNA that Makes Lariat RNA. Chemistry 2015; 22:3720-8. [DOI: 10.1002/chem.201503238] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2015] [Indexed: 12/25/2022]
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16
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Cao Y, Qin Y, Bruist M, Gao S, Wang B, Wang H, Guo X. Formation and Dissociation of the Interstrand i-Motif by the Sequences d(XnC 4Y m) Monitored with Electrospray Ionization Mass Spectrometry. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2015; 26:994-1003. [PMID: 25862186 DOI: 10.1007/s13361-015-1093-2] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/04/2014] [Revised: 02/05/2015] [Accepted: 02/06/2015] [Indexed: 06/04/2023]
Abstract
Formation and dissociation of the interstrand i-motifs by DNA with the sequence d(X(n)C(4)Y(m)) (X and Y represent thymine, adenine, or guanine, and n, m range from 0 to 2) are studied with electrospray ionization mass spectrometry (ESI-MS), circular dichroism (CD), and UV spectrophotometry. The ion complexes detected in the gas phase and the melting temperatures (Tm) obtained in solution show that a non-C base residue located at 5' end favors formation of the four-stranded structures, with T > A > G for imparting stability. Comparatively, no rule is found when a non-C base is located at the 3' end. Detection of penta- and hexa-stranded ions indicates the formation of i-motifs with more than four strands. In addition, the i-motifs seen in our mass spectra are accompanied by single-, double-, and triple-stranded ions, and the trimeric ions were always less abundant during annealing and heat-induced dissociation process of the DNA strands in solution (pH = 4.5). This provides a direct evidence of a strand-by-strand formation and dissociation pathway of the interstrand i-motif and formation of the triple strands is the rate-limiting step. In contrast, the trimeric ions are abundant when the tetramolecular ions are subjected to collision-induced dissociation (CID) in the gas phase, suggesting different dissociation behaviors of the interstrand i-motif in the gas phase and in solution. Furthermore, hysteretic UV absorption melting and cooling curves reveal an irreversible dissociation and association kinetic process of the interstrand i-motif in solution.
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Affiliation(s)
- Yanwei Cao
- College of Chemistry, Jilin University, Changchun, 130012, People's Republic of China
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17
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Doluca O, Withers JM, Loo TS, Edwards PJB, González C, Filichev VV. Interdependence of pyrene interactions and tetramolecular G4-DNA assembly. Org Biomol Chem 2015; 13:3742-8. [DOI: 10.1039/c4ob02499k] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Our results demonstrate the expanded capabilities of G-quadruplex DNAs for directed chromophore arrangements and show new perspectives in the design of G-quadruplexes governed by non-guanine moieties.
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Affiliation(s)
- Osman Doluca
- College of Sciences
- Institute of Fundamental Sciences
- Massey University
- 4442 Palmerston North
- New Zealand
| | - Jamie M. Withers
- College of Sciences
- Institute of Fundamental Sciences
- Massey University
- 4442 Palmerston North
- New Zealand
| | - Trevor S. Loo
- College of Sciences
- Institute of Fundamental Sciences
- Massey University
- 4442 Palmerston North
- New Zealand
| | - Patrick J. B. Edwards
- College of Sciences
- Institute of Fundamental Sciences
- Massey University
- 4442 Palmerston North
- New Zealand
| | | | - Vyacheslav V. Filichev
- College of Sciences
- Institute of Fundamental Sciences
- Massey University
- 4442 Palmerston North
- New Zealand
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18
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Nucleic Acids Nanotechnology. Methods 2014; 67:103-4. [DOI: 10.1016/j.ymeth.2014.04.018] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
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