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Wang J, Qiao J, Zheng W, Lian H. Study on the Interaction of a Peptide Targeting Specific G-Quadruplex Structures Based on Chromatographic Retention Behavior. Int J Mol Sci 2023; 24:ijms24021438. [PMID: 36674950 PMCID: PMC9866954 DOI: 10.3390/ijms24021438] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2022] [Revised: 01/01/2023] [Accepted: 01/09/2023] [Indexed: 01/12/2023] Open
Abstract
G-quadruplexes (G4s) are of vital biological significance and G4-specific ligands with conformational selectivity show great application potential in disease treatment and biosensing. RHAU, a RNA helicase associated with AU-rich element, exerts biological functions through the mediation of G4s and has been identified to be a G4 binder. Here, we investigated the interactions between the RHAU peptide and G4s with different secondary structures using size exclusion chromatography (SEC) in association with circular dichroism (CD), ultraviolet-visible (UV-Vis) absorption, and native polyacrylamide gel electrophoresis (Native-PAGE). Spectral results demonstrated that the RHAU peptide did not break the main structure of G4s, making it more reliable for G4 structural analysis. The RHAU peptide was found to display a structural selectivity for a preferential binding to parallel G4s as reflected by the distinct chromatographic retention behaviors. In addition, the RHAU peptide exhibited different interactions with intermolecular parallel G4s and intramolecular parallel G4s, providing a novel recognition approach to G4 structures. The findings of this study enriched the insight into the binding of RHAU to G4s with various conformations. It is noteworthy that SEC technology can be easy and reliable for elucidating G4-peptide interactions, especially for a multiple G4 coexisting system, which supplied an alternative strategy to screen novel specific ligands for G4s.
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Affiliation(s)
- Ju Wang
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry & Chemical Engineering and Center of Materials Analysis, Nanjing University, 163 Xianlin Avenue, Nanjing 210023, China
| | - Junqin Qiao
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry & Chemical Engineering and Center of Materials Analysis, Nanjing University, 163 Xianlin Avenue, Nanjing 210023, China
- Correspondence: (J.Q.); (H.L.)
| | - Weijuan Zheng
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, 163 Xianlin Avenue, Nanjing 210023, China
| | - Hongzhen Lian
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry & Chemical Engineering and Center of Materials Analysis, Nanjing University, 163 Xianlin Avenue, Nanjing 210023, China
- Correspondence: (J.Q.); (H.L.)
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2
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Tsao L, Shepardson-Fungairiño S, Murayama H, Cecere A, Wren E, Núñez M. Assessing the Potential for DNA Quadruplex Formation in the Predatory Bacterium Bdellovibrio bacteriovorus. Biochemistry 2022; 61:2073-2087. [PMID: 36193632 PMCID: PMC9536305 DOI: 10.1021/acs.biochem.2c00443] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2022] [Revised: 08/25/2022] [Indexed: 11/29/2022]
Abstract
During its life cycle, the predatory bacterium Bdellovibrio bacteriovorus switches between an attack and a growth phase, each of which is characterized by a distinct pattern of gene expression. Twenty-one potential G-quadruplex-forming sequences (PQFS) have been identified in the Bdellovibrio genome. These G-rich sequences are prevalent within open reading frames and nearly evenly distributed between the template and the coding strand, suggesting that they could play a role in gene expression and life cycle switching. Published transcriptomic data show that the genes nearest these sequences are not (de)activated together during the same phases of the life cycle. We explored the biophysical properties of three identified PQFS using circular dichroism (CD) spectroscopy and gel electrophoresis and demonstrated that all three sequences fold into stable unimolecular quadruplexes with distinct topologies. In the presence of their complementary strands, each forms an equilibrium mixture of duplex and quadruplex in which quadruplex formation is favored at higher temperatures. Once the quadruplexes are folded, they are slow to form a duplex when the complementary strand is added, with one sequence requiring the equivalent of many Bdellovibrio lifetimes to do so. Using a variety of cosolutes, we showed that molecular crowding mimicking cellular conditions stabilizes the quadruplex structures and induces structural transitions to the parallel topology regardless of the original topology. Taken together, these experiments suggest that Bdellovibrio PQFS are capable of forming quadruplexes in vivo and thereby playing a role in gene expression.
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Affiliation(s)
- Lucille
H. Tsao
- Department of Chemistry and
Program in Biochemistry, Wellesley College, Wellesley, Massachusetts 02481, United States
| | - Sally Shepardson-Fungairiño
- Department of Chemistry and
Program in Biochemistry, Wellesley College, Wellesley, Massachusetts 02481, United States
| | - Hikari Murayama
- Department of Chemistry and
Program in Biochemistry, Wellesley College, Wellesley, Massachusetts 02481, United States
| | - Amelia Cecere
- Department of Chemistry and
Program in Biochemistry, Wellesley College, Wellesley, Massachusetts 02481, United States
| | - Elizabeth Wren
- Department of Chemistry and
Program in Biochemistry, Wellesley College, Wellesley, Massachusetts 02481, United States
| | - Megan Núñez
- Department of Chemistry and
Program in Biochemistry, Wellesley College, Wellesley, Massachusetts 02481, United States
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3
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Bruni L, Manghi M, De Sanctis P, Zucchini C, Croci S. Validation of circular dichroic spectroscopy of synthetic oligonucleotide PS2.M for K + concentration measurements. EUROPEAN PHYSICAL JOURNAL PLUS 2022; 137:433. [PMID: 35411290 PMCID: PMC8988120 DOI: 10.1140/epjp/s13360-022-02581-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/29/2021] [Accepted: 03/03/2022] [Indexed: 06/14/2023]
Abstract
The single-stranded synthetic oligonucleotide PS2.M is known to provide a basis for developing sensors since it tends to fold into structures called G-quadruplexes (G4) having characteristic topology and orientation with probabilities that depend on the chemical environment. The presence and concentration of cation species are among the key factors that determine the outcome of such a process. PS2.M and other aptamers have been used in several applications in conjunction with various probes, such as hemin, at the cost of increased technical complexity and applicability limitations. We instead validated the application limits of Circular Dichroic spectroscopy (CD) as only measurement method to assay PS2.M asK + sensor in a variety of solutions having different chemical complexity. The tested solutions range from simple NaCl and KCl solutions to chemically complex solutions like DMEM-Dulbecco's Modified Eagle Medium-which is widely used in a biological laboratory. PS2.M was also evaluated in solutions of KHCO 3 and D-ribose (K:D-rib), an antioxidant potassium compound, to compare its response to the simple KCl solution case. Our findings show that, within specific concentration applicability ranges, CD spectra can estimate theK + concentration in the examined water solutions even at high Na + concentrations with respect toK + and in the presence of antioxidant molecules. Supplementary Information The online version supplementary material available at 10.1140/epjp/s13360-022-02581-2.
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Affiliation(s)
- Luca Bruni
- National Institute for Biostructures and Biosystems, Rome, Italy
| | - Massimo Manghi
- Department of Medicine and Surgery, University of Parma, Parma, Italy
| | - Paola De Sanctis
- Department of Experimental, Diagnostic and Specialty Medicine (DIMES), Unit of Histology, Embryology and Applied Biology, Università di Bologna, Bologna, Italy
| | - Cinzia Zucchini
- Department of Experimental, Diagnostic and Specialty Medicine (DIMES), Unit of Histology, Embryology and Applied Biology, Università di Bologna, Bologna, Italy
| | - Simonetta Croci
- National Institute for Biostructures and Biosystems, Rome, Italy
- Department of Medicine and Surgery, University of Parma, Parma, Italy
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4
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G-Quadruplex Structures in Bacteria: Biological Relevance and Potential as an Antimicrobial Target. J Bacteriol 2021; 203:e0057720. [PMID: 33649149 DOI: 10.1128/jb.00577-20] [Citation(s) in RCA: 36] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
DNA strands consisting of multiple runs of guanines can adopt a noncanonical, four-stranded DNA secondary structure known as G-quadruplex or G4 DNA. G4 DNA is thought to play an important role in transcriptional and translational regulation of genes, DNA replication, genome stability, and oncogene expression in eukaryotic genomes. In other organisms, including several bacterial pathogens and some plant species, the biological roles of G4 DNA and G4 RNA are starting to be explored. Recent investigations showed that G4 DNA and G4 RNA are generally conserved across plant species. In silico analyses of several bacterial genomes identified putative guanine-rich, G4 DNA-forming sequences in promoter regions. The sequences were particularly abundant in certain gene classes, suggesting that these highly diverse structures can be employed to regulate the expression of genes involved in secondary metabolite synthesis and signal transduction. Furthermore, in the pathogen Mycobacterium tuberculosis, the distribution of G4 motifs and their potential role in the regulation of gene transcription advocate for the use of G4 ligands to develop novel antitubercular therapies. In this review, we discuss the various roles of G4 structures in bacterial DNA and the application of G4 DNA as inhibitors or therapeutic agents to address bacterial pathogens.
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5
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Møller Sønderskov S, Hyldgaard Klausen L, Amland Skaanvik S, Han X, Dong M. In situ Surface Charge Density Visualization of Self-assembled DNA Nanostructures after Ion Exchange. Chemphyschem 2020; 21:1474-1482. [PMID: 32330354 PMCID: PMC7891384 DOI: 10.1002/cphc.201901168] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2019] [Revised: 04/14/2020] [Indexed: 12/30/2022]
Abstract
The charge density of DNA is a key parameter in strand hybridization and for the interactions occurring between DNA and molecules in biological systems. Due to the intricate structure of DNA, visualization of the surface charge density of DNA nanostructures under physiological conditions was not previously possible. Here, we perform a simultaneous analysis of the topography and surface charge density of DNA nanostructures using atomic force microscopy and scanning ion conductance microscopy. The effect of in situ ion exchange using various alkali metal ions is tested with respect to the adsorption of DNA origami onto mica, and a quantitative study of surface charge density reveals ion exchange phenomena in mica as a key parameter in DNA adsorption. This is important for structure-function studies of DNA nanostructures. The research provides an efficient approach to study surface charge density of DNA origami nanostructures and other biological molecules at a single molecule level.
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Affiliation(s)
| | - Lasse Hyldgaard Klausen
- Interdisciplinary Nanoscience Center (iNANO)Aarhus University, Denmark
- Department of ChemistryStanford University333 Campus DriveStanfordCA 94305USA
| | | | - Xiaojun Han
- State Key Laboratory of Urban Water Resource and EnvironmentSchool of Chemistry and Chemical EngineeringHarbin Institute of Technology, China
| | - Mingdong Dong
- Interdisciplinary Nanoscience Center (iNANO)Aarhus University, Denmark
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6
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Xie X, Zuffo M, Teulade-Fichou MP, Granzhan A. Identification of optimal fluorescent probes for G-quadruplex nucleic acids through systematic exploration of mono- and distyryl dye libraries. Beilstein J Org Chem 2019; 15:1872-1889. [PMID: 31467609 PMCID: PMC6693400 DOI: 10.3762/bjoc.15.183] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2019] [Accepted: 07/23/2019] [Indexed: 12/20/2022] Open
Abstract
A library of 52 distyryl and 9 mono-styryl cationic dyes was synthesized and investigated with respect to their optical properties, propensity to aggregation in aqueous medium, and capacity to serve as fluorescence “light-up” probes for G-quadruplex (G4) DNA and RNA structures. Among the 61 compounds, 57 dyes showed preferential enhancement of fluorescence intensity in the presence of one or another G4-DNA or RNA structure, while no dye displayed preferential response to double-stranded DNA or single-stranded RNA analytes employed at equivalent nucleotide concentration. Thus, preferential fluorimetric response towards G4 structures appears to be a common feature of mono- and distyryl dyes, including long-known mono-styryl dyes used as mitochondrial probes or protein stains. However, the magnitude of the G4-induced “light-up” effect varies drastically, as a function of both the molecular structure of the dyes and the nature or topology of G4 analytes. Although our results do not allow to formulate comprehensive structure–properties relationships, we identified several structural motifs, such as indole- or pyrrole-substituted distyryl dyes, as well as simple mono-stryryl dyes such as DASPMI [2-(4-(dimethylamino)styryl)-1-methylpyridinium iodide] or its 4-isomer, as optimal fluorescent light-up probes characterized by high fluorimetric response (I/I0 of up to 550-fold), excellent selectivity with respect to double-stranded DNA or single-stranded RNA controls, high quantum yield in the presence of G4 analytes (up to 0.32), large Stokes shift (up to 150 nm) and, in certain cases, structural selectivity with respect to one or another G4 folding topology. These dyes can be considered as promising G4-responsive sensors for in vitro or imaging applications. As a possible application, we implemented a simple two-dye fluorimetric assay allowing rapid topological classification of G4-DNA structures.
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Affiliation(s)
- Xiao Xie
- CNRS UMR9187, INSERM U1196, Institut Curie, Université Paris Sud, Université Paris Saclay, Bât. 110, Centre universitaire Paris Sud, F-91405 Orsay, France
| | - Michela Zuffo
- CNRS UMR9187, INSERM U1196, Institut Curie, Université Paris Sud, Université Paris Saclay, Bât. 110, Centre universitaire Paris Sud, F-91405 Orsay, France
| | - Marie-Paule Teulade-Fichou
- CNRS UMR9187, INSERM U1196, Institut Curie, Université Paris Sud, Université Paris Saclay, Bât. 110, Centre universitaire Paris Sud, F-91405 Orsay, France
| | - Anton Granzhan
- CNRS UMR9187, INSERM U1196, Institut Curie, Université Paris Sud, Université Paris Saclay, Bât. 110, Centre universitaire Paris Sud, F-91405 Orsay, France
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7
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Bulged and Canonical G-Quadruplex Conformations Determine NDPK Binding Specificity. Molecules 2019; 24:molecules24101988. [PMID: 31126138 PMCID: PMC6572678 DOI: 10.3390/molecules24101988] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2019] [Revised: 05/20/2019] [Accepted: 05/22/2019] [Indexed: 11/17/2022] Open
Abstract
Guanine-rich DNA strands can adopt tertiary structures known as G-quadruplexes (G4s) that form when Hoogsteen base-paired guanines assemble as planar stacks, stabilized by a central cation like K+. In this study, we investigated the conformational heterogeneity of a G-rich sequence from the 5′ untranslated region of the Zea mayshexokinase4 gene. This sequence adopted an extensively polymorphic G-quadruplex, including non-canonical bulged G-quadruplex folds that co-existed in solution. The nature of this polymorphism depended, in part, on the incorporation of different sets of adjacent guanines into a quadruplex core, which permitted the formation of the different conformations. Additionally, we showed that the maize homolog of the human nucleoside diphosphate kinase (NDPK) NM23-H2 protein—ZmNDPK1—specifically recognizes and promotes formation of a subset of these conformations. Heteromorphic G-quadruplexes play a role in microorganisms’ ability to evade the host immune system, so we also discuss how the underlying properties that determine heterogeneity of this sequence could apply to microorganism G4s.
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8
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Zuffo M, Xie X, Granzhan A. Strength in Numbers: Development of a Fluorescence Sensor Array for Secondary Structures of DNA. Chemistry 2019; 25:1812-1818. [DOI: 10.1002/chem.201805422] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2018] [Indexed: 12/16/2022]
Affiliation(s)
- Michela Zuffo
- CNRS UMR9187; INSERM U1196; Institut Curie; PSL Research University; 91405 Orsay France
- CNRS UMR9187; INSERM U1196; Université Paris Sud; Université Paris Saclay; 91405 Orsay France
| | - Xiao Xie
- CNRS UMR9187; INSERM U1196; Institut Curie; PSL Research University; 91405 Orsay France
- CNRS UMR9187; INSERM U1196; Université Paris Sud; Université Paris Saclay; 91405 Orsay France
| | - Anton Granzhan
- CNRS UMR9187; INSERM U1196; Institut Curie; PSL Research University; 91405 Orsay France
- CNRS UMR9187; INSERM U1196; Université Paris Sud; Université Paris Saclay; 91405 Orsay France
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9
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Donohue MP, Szalai VA. Distance measurements between paramagnetic ligands bound to parallel stranded guanine quadruplexes. Phys Chem Chem Phys 2018; 18:15447-55. [PMID: 27218217 DOI: 10.1039/c6cp01121g] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Aside from a double helix, deoxyribonucleic acid (DNA) folds into non-canonical structures, one of which is the guanine quadruplex. Cationic porphyrins bind guanine quadruplexes, but the effects of ligand binding on the structure of guanine quadruplexes with more than four contiguous guanine quartets remains to be fully elucidated. Double electron-electron resonance (DEER) spectroscopy conducted at 9.5 GHz (X-band) using broadband, shaped inversion pulses was used to measure the distances between cationic copper porphyrins bound to model parallel-stranded guanine quadruplexes with increasing numbers of guanine quartets. A single Gaussian component was found to best model the time domain datasets, characteristic of a 2 : 1 binding stoichiometry between the porphyrins and each quadruplex. The measured Cu(2+)-Cu(2+) distances were found to be linearly proportional with the number of guanines. Rather unexpectedly, the ligand end-stacking distance was found to monotonically decreases the overall quadruplex length was extended, suggesting a conformational change in the quadruplex secondary structure dependent upon the number of successive guanine quartets.
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Affiliation(s)
- M P Donohue
- Center for Nanoscale Science and Technology, National Institute of Standards and Technology, Gaithersburg, MD 20899, USA. and Maryland NanoCenter, University of Maryland, College Park, MD 20742, USA
| | - V A Szalai
- Center for Nanoscale Science and Technology, National Institute of Standards and Technology, Gaithersburg, MD 20899, USA.
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10
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Engelhard DM, Meyer A, Berndhäuser A, Schiemann O, Clever GH. Di-copper(ii) DNA G-quadruplexes as EPR distance rulers. Chem Commun (Camb) 2018; 54:7455-7458. [DOI: 10.1039/c8cc04053b] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Paramagnetic Cu(ii) complexes, immobilized via four-point-attachment to both ends of G-quadruplexes, serve as EPR-based distance rulers for studying DNA structure.
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Affiliation(s)
- David M. Engelhard
- Depart. of Chemistry and Chemical Biology
- TU Dortmund University
- Dortmund
- Germany
| | - Andreas Meyer
- Institute for Physical and Theoretical Chemistry
- Wegelerstr. 12
- Rheinische Friedrich-Wilhelms-Universität Bonn
- Bonn
- Germany
| | - Andreas Berndhäuser
- Institute for Physical and Theoretical Chemistry
- Wegelerstr. 12
- Rheinische Friedrich-Wilhelms-Universität Bonn
- Bonn
- Germany
| | - Olav Schiemann
- Institute for Physical and Theoretical Chemistry
- Wegelerstr. 12
- Rheinische Friedrich-Wilhelms-Universität Bonn
- Bonn
- Germany
| | - Guido H. Clever
- Depart. of Chemistry and Chemical Biology
- TU Dortmund University
- Dortmund
- Germany
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11
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Albanese CM, Suttapitugsakul S, Perati S, McGown LB. A genome-inspired, reverse selection approach to aptamer discovery. Talanta 2017; 177:150-156. [PMID: 29108569 DOI: 10.1016/j.talanta.2017.08.093] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2017] [Revised: 08/08/2017] [Accepted: 08/29/2017] [Indexed: 11/29/2022]
Abstract
Limitations of Systematic Evolution of Ligands by Exponential Enrichment (SELEX) and related methods that depend upon combinatorial oligonucleotide libraries have hindered progress in this area. Our laboratory has introduced a new approach to aptamer discovery that uses oligonucleotides with sequences drawn from the human genome to capture proteins from biological samples. Specifically, we have focused on capture of proteins in nuclear extracts from human cell lines using G-quadruplex (G4) forming genomic sequences. Previous studies identified capture of several proteins both in vitro and in live cells by the Pu28-mer sequence from the ERBB2 promoter region. Here we provide a more comprehensive study of protein capture from BT474 and MCF7 human breast cancer cells using G4-forming sequences from the CMYC, RB, VEGF and ERBB2 human oncogene promoter regions. Mass spectrometric analysis and Western blot analysis of protein capture at oligonucleotide-modified surfaces revealed capture of nucleolin by all three of the oligonucleotides in BT474 and MCF7 cells, and also of ribosomal protein L19 (RPL19) in BT474 cells. Chromatin immunoprecipitation (ChIP) analysis confirmed the interaction of nucleolin with all three promoter sequences in MCF7 cells and with RB in BT474 cells. ChIP also revealed interactions of RPL19 with CMYC in BT474 cells and of both RPL19 and ribosomal protein L14 (RPL14) with ERBB2 in BT474 cells. These results offer the basis for development of new aptamers based on the G4 sequences from the CMYC, RB, VEGF, and ERBB2 promoters toward proteins including nucleolin, RPL19 and RPL14. These interactions also may have biological and therapeutic significance.
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Affiliation(s)
- Christina M Albanese
- Department of Chemistry and Chemical Biology, Rensselaer Polytechnic Institute, 110 8th Street, Troy, NY 12180, USA
| | - Suttipong Suttapitugsakul
- Department of Chemistry and Chemical Biology, Rensselaer Polytechnic Institute, 110 8th Street, Troy, NY 12180, USA
| | - Shruthi Perati
- Department of Chemistry and Chemical Biology, Rensselaer Polytechnic Institute, 110 8th Street, Troy, NY 12180, USA
| | - Linda B McGown
- Department of Chemistry and Chemical Biology, Rensselaer Polytechnic Institute, 110 8th Street, Troy, NY 12180, USA.
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12
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Waller ZAE, Pinchbeck BJ, Buguth BS, Meadows TG, Richardson DJ, Gates AJ. Control of bacterial nitrate assimilation by stabilization of G-quadruplex DNA. Chem Commun (Camb) 2016; 52:13511-13514. [PMID: 27805200 PMCID: PMC5123632 DOI: 10.1039/c6cc06057a] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
Here we present a chemical-biology study in the model soil bacterium Paracoccus denitrificans, where we show ligand-specific control of nitrate assimilation. Stabilization of a G-quadruplex in the promoter region of the nas genes, encoding the assimilatory nitrate/nitrite reductase system, is achieved using known quadruplex ligands and results in attenuation of gene transcription.
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Affiliation(s)
- Zoë A E Waller
- School of Pharmacy, University of East Anglia, Norwich Research Park, NR4 7TJ, UK.
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13
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Yang L, Qing Z, Liu C, Tang Q, Li J, Yang S, Zheng J, Yang R, Tan W. Direct Fluorescent Detection of Blood Potassium by Ion-Selective Formation of Intermolecular G-Quadruplex and Ligand Binding. Anal Chem 2016; 88:9285-92. [PMID: 27558922 DOI: 10.1021/acs.analchem.6b02667] [Citation(s) in RCA: 55] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
G-quadruplex analogues have been widely used as molecular tools for detection of potassium ion (K(+)). However, interference from a higher concentration of sodium ion (Na(+)), enzymatic degradation of the oligonucleotide, and background absorption and fluorescence of blood samples have all limited the use of G-quadruplex for direct detection of K(+) in blood samples. Here, we reported, for the first time, an intermolecular G-quadruplex-based assay capable of direct fluorescent detection of blood K(+). Increased stringency of intermolecular G-quadruplex formation based on our screened G-rich oligonucleotide (5'-TGAGGGA GGGG-3') provided the necessary selectivity for K(+) against Na(+) at physiological ion level. To increase long-term stability of oligonucleotide in blood, the screened oligonucleotide was modified with an inverted thymine nucleotide whose 3'-terminus was connected to the 3'-terminus of the upstream nucleotide, acting as a blocking group to greatly improve antinuclease stability. Lastly, to avoid interference from background absorption and autofluorescence of blood, a G-quadruplex-binding, two-photon-excited ligand, EBMVC-B, was synthesized and chosen as the fluorescence reporter. Thus, based on selective K(+) ion-induced formation of intermolecular G-quadruplex and EBMVC-B binding, this approach could linearly respond to K(+) from 0.5 to 10 mM, which matches quite well with the physiologically relevant concentration of blood K(+). Moreover, the system was highly selective for K(+) against other metal ions, including Na(+), Ca(2+), Mg(2+), Zn(2+) common in blood. The practical application was demonstrated by direct detection of K(+) from real blood samples by two-photon fluorescence technology. To the best of our knowledge, this is the first attempt to exploit molecular G-quadruplex-based fluorescent sensing for direct assay of blood target. As such, we expect that it will promote the design and practical application of similar DNA-based sensors in complex real systems.
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Affiliation(s)
- Le Yang
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Molecular Science and Biomedicine Laboratory, Hunan University , Changsha 410082, P. R. China
| | - Zhihe Qing
- School of Chemistry and Biological Engineering, Changsha University of Science and Technology , Changsha 410004, P. R. China
| | - Changhui Liu
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Molecular Science and Biomedicine Laboratory, Hunan University , Changsha 410082, P. R. China
| | - Qiao Tang
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Molecular Science and Biomedicine Laboratory, Hunan University , Changsha 410082, P. R. China
| | - Jishan Li
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Molecular Science and Biomedicine Laboratory, Hunan University , Changsha 410082, P. R. China
| | - Sheng Yang
- School of Chemistry and Biological Engineering, Changsha University of Science and Technology , Changsha 410004, P. R. China
| | - Jing Zheng
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Molecular Science and Biomedicine Laboratory, Hunan University , Changsha 410082, P. R. China
| | - Ronghua Yang
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Molecular Science and Biomedicine Laboratory, Hunan University , Changsha 410082, P. R. China.,School of Chemistry and Biological Engineering, Changsha University of Science and Technology , Changsha 410004, P. R. China
| | - Weihong Tan
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Molecular Science and Biomedicine Laboratory, Hunan University , Changsha 410082, P. R. China
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14
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Gao Y, Wu S, Ye X. The effects of monovalent metal ions on the conformation of human telomere DNA using analytical ultracentrifugation. SOFT MATTER 2016; 12:5959-5967. [PMID: 27329676 DOI: 10.1039/c6sm01010e] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
A human telomere DNA segment (HT-DNA) can fold into a G-quadruplex in the presence of some monovalent cations. These cations can interact with the phosphate groups of the DNA segment and/or with the O6 oxygen atom of guanines, which are called non-specific interactions and specific interactions, respectively. However, until now how these two interactions affect the structure of HT-DNA has not been well understood. In this study, a combination of analytical ultracentrifugation (AUC) and circular dichroism (CD) was used to explore the effects of these two interactions on the structure of a 22-mer single-stranded DNA with a sequence of 5'-AGGG(TTAGGG)3-3'. The results showed that the standard sedimentation coefficient (s20,w) of HT-DNA starts to increase when the concentration of potassium ions (CK(+)) is higher than 10.0 µM due to the formation of a G-quadruplex through specific interactions. Whereas, for a control DNA, a higher CK(+) value of 1.0 mM was needed for increasing s20,w due to non-specific interactions. Moreover, potassium ions could promote the formation of the G-quadruplex much more easily than lithium, sodium and cesium ions, presumably due to its appropriate size in the dehydrated state and easier dehydration. The molar mass of DNA at different cation concentrations was nearly a constant and close to the theoretical value of the molar mass of monomeric HT-DNA, indicating that what we observed is the structural change of individual DNA chains.
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Affiliation(s)
- Yating Gao
- Hefei National Laboratory for Physical Sciences at the Microscale, Department of Chemical Physics, University of Science and Technology of China, Hefei, Anhui 230026, China.
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Largy E, Mergny JL, Gabelica V. Role of Alkali Metal Ions in G-Quadruplex Nucleic Acid Structure and Stability. Met Ions Life Sci 2016; 16:203-58. [PMID: 26860303 DOI: 10.1007/978-3-319-21756-7_7] [Citation(s) in RCA: 105] [Impact Index Per Article: 13.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
G-quadruplexes are guanine-rich nucleic acids that fold by forming successive quartets of guanines (the G-tetrads), stabilized by intra-quartet hydrogen bonds, inter-quartet stacking, and cation coordination. This specific although highly polymorphic type of secondary structure deviates significantly from the classical B-DNA duplex. G-quadruplexes are detectable in human cells and are strongly suspected to be involved in a number of biological processes at the DNA and RNA levels. The vast structural polymorphism exhibited by G-quadruplexes, together with their putative biological relevance, makes them attractive therapeutic targets compared to canonical duplex DNA. This chapter focuses on the essential and specific coordination of alkali metal cations by G-quadruplex nucleic acids, and most notably on studies highlighting cation-dependent dissimilarities in their stability, structure, formation, and interconversion. Section 1 surveys G-quadruplex structures and their interactions with alkali metal ions while Section 2 presents analytical methods used to study G-quadruplexes. The influence of alkali cations on the stability, structure, and kinetics of formation of G-quadruplex structures of quadruplexes will be discussed in Sections 3 and 4. Section 5 focuses on the cation-induced interconversion of G-quadruplex structures. In Sections 3 to 5, we will particularly emphasize the comparisons between cations, most often K(+) and Na(+) because of their prevalence in the literature and in cells.
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Affiliation(s)
- Eric Largy
- ARNA Laboratory, Université Bordeaux, IECB, 2, rue Robert Escarpit, F-33600, Pessac, France.,ARNA Laboratory, INSERM, U869, F-33000, Bordeaux, France
| | - Jean-Louis Mergny
- ARNA Laboratory, Université Bordeaux, IECB, 2, rue Robert Escarpit, F-33600, Pessac, France. .,ARNA Laboratory, INSERM, U869, F-33000, Bordeaux, France.
| | - Valérie Gabelica
- ARNA Laboratory, Université Bordeaux, IECB, 2, rue Robert Escarpit, F-33600, Pessac, France. .,ARNA Laboratory, INSERM, U869, F-33000, Bordeaux, France.
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16
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Topoisomerase IB of Deinococcus radiodurans resolves guanine quadruplex DNA structures in vitro. J Biosci 2015; 40:833-43. [DOI: 10.1007/s12038-015-9571-z] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
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17
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Merkle T, Sinn M, Hartig JS. Interactions between Flavins and Quadruplex Nucleic Acids. Chembiochem 2015; 16:2437-40. [PMID: 26426822 DOI: 10.1002/cbic.201500463] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2015] [Indexed: 12/12/2022]
Abstract
Quadruplex nucleic acids are widespread in genomes. They influence processes such as transcription, translation, replication, recombination, and the regulation of gene expression. Several synthetic ligands have been demonstrated to target quadruplex nucleic acids. However, only very few metabolites have been reported to interact with quadruplexes. In principle, an intracellular metabolite that selectively binds to four-stranded sequences could modulate quadruplex formation, stability, and thus functions in a riboswitch (or deoxyriboswitch) manner. Here we report quadruplex interactions with flavin derivatives such as FMN and FAD. The affinities were highest with parallel quadruplexes, with low (14-20 μm) dissociation constants. Taking into account combined intracellular flavin concentrations of 243 μm in E. coli, the observed interactions in principle open up the possibility of flavin levels affecting gene expression and other processes by modulating quadruplex formation.
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Affiliation(s)
- Tobias Merkle
- Department of Chemistry and Research School Chemical Biology, University of Konstanz, Universitätsstrasse 10, P. O. Box: 630, 78457, Konstanz, Germany
| | - Malte Sinn
- Department of Chemistry and Research School Chemical Biology, University of Konstanz, Universitätsstrasse 10, P. O. Box: 630, 78457, Konstanz, Germany
| | - Jörg S Hartig
- Department of Chemistry and Research School Chemical Biology, University of Konstanz, Universitätsstrasse 10, P. O. Box: 630, 78457, Konstanz, Germany.
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18
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Wojciechowski F, Groß A, Holder IT, Knörr L, Drescher M, Hartig JS. Pulsed EPR spectroscopy distance measurements of DNA internally labelled with Gd(3+)-DOTA. Chem Commun (Camb) 2015; 51:13850-3. [PMID: 26236790 DOI: 10.1039/c5cc04234h] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Gd(3+) is increasingly used in EPR spectroscopy due to its increased intracellular stability and signal-to-noise ratios. Here we present the incorporation of Gd(3+)-DOTA into internal positions in DNA. Distance measurements via pulsed Electron Paramagnetic Resonance (EPR) spectroscopy in vitro and in cellula proved enhanced stability and efficiency compared to nitroxide labels.
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Affiliation(s)
- Filip Wojciechowski
- Department of Chemistry, University of Konstanz, Universitätsstr. 10, Konstanz, Germany.
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19
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Holder IT, Hartig JS. A matter of location: influence of G-quadruplexes on Escherichia coli gene expression. ACTA ACUST UNITED AC 2015; 21:1511-21. [PMID: 25459072 DOI: 10.1016/j.chembiol.2014.09.014] [Citation(s) in RCA: 53] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2014] [Revised: 08/13/2014] [Accepted: 09/17/2014] [Indexed: 01/01/2023]
Abstract
We provide important insights into secondary-structure-mediated regulation of gene expression in Escherichia coli. In a comprehensive survey, we show that the strand orientation and the exact position of a G-quadruplex sequence strongly influence its effect on transcription and translation. We generated a series of reporter gene constructs that contained systematically varied positions of quadruplexes and respective control sequences inserted into several positions within the promoter, 50-UTR, and 30-UTR regions. G-rich sequences at specific locations in the promoter and also in proximity to the ribosome-binding site (RBS) showed pronounced inhibitory effects. Additionally, we rationally designed a system where quadruplex formation showed a gene-activating behavior. Moreover, we characterized quadruplexes in proximity to the RBS that occur naturally in E. coli genes, demonstrating that some of these quadruplexes exert significant modulation of gene expression. Taken together, our data show strong position-dependent effects of quadruplex secondary structures on bacterial gene expression.
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Largy E, Mergny JL. Shape matters: size-exclusion HPLC for the study of nucleic acid structural polymorphism. Nucleic Acids Res 2014; 42:e149. [PMID: 25143531 PMCID: PMC4231728 DOI: 10.1093/nar/gku751] [Citation(s) in RCA: 54] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
In recent years, an increasing number of reports have been focused on the structure and biological role of non-canonical nucleic acid secondary structures. Many of these studies involve the use of oligonucleotides that can often adopt a variety of structures depending on the experimental conditions, and hence change the outcome of an assay. The knowledge of the structure(s) formed by oligonucleotides is thus critical to correctly interpret the results, and gain insight into the biological role of these particular sequences. Herein we demonstrate that size-exclusion HPLC (SE-HPLC) is a simple yet surprisingly powerful tool to quickly and effortlessly assess the secondary structure(s) formed by oligonucleotides. For the first time, an extensive calibration and validation of the use of SE-HPLC to confidently detect the presence of different species displaying various structure and/or molecularity, involving >110 oligonucleotides forming a variety of secondary structures (antiparallel, parallel, A-tract bent and mismatched duplexes, triplexes, G-quadruplexes and i-motifs, RNA stem loops), is performed. Moreover, we introduce simple metrics that allow the use of SE-HPLC without the need for a tedious calibration work. We show that the remarkable versatility of the method allows to quickly establish the influence of a number of experimental parameters on nucleic acid structuration and to operate on a wide range of oligonucleotide concentrations. Case studies are provided to clearly illustrate the all-terrain capabilities of SE-HPLC for oligonucleotide secondary structure analysis. Finally, this manuscript features a number of important observations contributing to a better understanding of nucleic acid structural polymorphism.
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Affiliation(s)
- Eric Largy
- ARNA Laboratory, University of Bordeaux, Bordeaux 33000, France INSERM, U869, IECB, Pessac 33600, France
| | - Jean-Louis Mergny
- ARNA Laboratory, University of Bordeaux, Bordeaux 33000, France INSERM, U869, IECB, Pessac 33600, France
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