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Bali SD, Ahsan M, Revanasiddappa PD. Structural Insights into the Antiparallel G-Quadruplex in the Presence of K + and Mg 2+ Ions. J Phys Chem B 2023; 127:1499-1512. [PMID: 36757392 DOI: 10.1021/acs.jpcb.2c05128] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/10/2023]
Abstract
G-Quadruplex (GQ) is a secondary structural unit of DNA, formed at the telomere region of the chromosome with a high guanine content. It is reported that the GQs can hinder many biological processes. Thus, research thrives to explore the structural stability of GQs. Studies based on circular dichroism (CD) and nuclear magnetic resonance (NMR) experiments established the vital role of cations such as K+ and Mg2+ in the stability of antiparallel G-quadruplexes (AGQs). However, there is a need to understand how stability in AGQ is attained in the presence of cations. Here, we employed molecular dynamics (MD) simulations, steered MD (SMD) simulations, and QM/MM calculations to understand the biophysical and electronic bases of the stability imparted to AGQs via cation binding. Our results showed that Mg2+ prefers to bind in the plane with the guanine tetrad, whereas K+ binds in between the AGQ tetrads. Thus, three Mg2+ cations or two K+ ions are needed to stabilize an AGQ molecule, where each and every tetrad binds to Mg2+ more robustly with a higher binding affinity. SMD revealed that the traversal of K+ through the AGQ central channel required less force than that of Mg2+, illustrating the presence of more strong interactions between Mg2+ and AGQ tetrads compared to K+. The stabilization in the AGQ tetrads due to cation binding is reassessed by employing ab initio simulations. Mixed QM/MM calculations confirmed that Mg2+ binds strongly to AGQ compared to K+, and it induces higher interactions between the guanine tetrads. However, K+ binding to AGQ induces a higher stabilization energy than Mg2+ binding to AGQ tetrads. Despite the higher binding energy, Mg2+ binding imparts lower stabilization to AGQ due to its unfavorable fermionic quantum energy.
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Affiliation(s)
- Sindhu D Bali
- Department of Biotechnology, Siddaganga Institute of Technology, Tumakuru 572103, Karnataka, India
| | - Mohd Ahsan
- Department of Bioengineering, University of California Riverside, Riverside, California 92521-9800, United States
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2
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Wang X, Chu H, Xu X, Tian J, Wu Y, Xu W, Tian H, Zhu L. Rapid label-free colorimetric dual-functional aptasensor for β-lactoglobulin detection based on a rational tailoring strategy. Biosens Bioelectron 2022; 208:114223. [DOI: 10.1016/j.bios.2022.114223] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2021] [Revised: 02/20/2022] [Accepted: 03/24/2022] [Indexed: 11/02/2022]
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3
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Caterino M, Paeschke K. Action and function of helicases on RNA G-quadruplexes. Methods 2021; 204:110-125. [PMID: 34509630 PMCID: PMC9236196 DOI: 10.1016/j.ymeth.2021.09.003] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2021] [Revised: 08/02/2021] [Accepted: 09/07/2021] [Indexed: 12/12/2022] Open
Abstract
Methodological progresses and piling evidence prove the rG4 biology in vivo. rG4s step in virtually every aspect of RNA biology. Helicases unwinding of rG4s is a fine regulatory layer to the downstream processes and general cell homeostasis. The current knowledge is however limited to a few cell lines. The regulation of helicases themselves is delineating as a important question. Non-helicase rG4-processing proteins likely play a role.
The nucleic acid structure called G-quadruplex (G4) is currently discussed to function in nucleic acid-based mechanisms that influence several cellular processes. They can modulate the cellular machinery either positively or negatively, both at the DNA and RNA level. The majority of what we know about G4 biology comes from DNA G4 (dG4) research. RNA G4s (rG4), on the other hand, are gaining interest as researchers become more aware of their role in several aspects of cellular homeostasis. In either case, the correct regulation of G4 structures within cells is essential and demands specialized proteins able to resolve them. Small changes in the formation and unfolding of G4 structures can have severe consequences for the cells that could even stimulate genome instability, apoptosis or proliferation. Helicases are the most relevant negative G4 regulators, which prevent and unfold G4 formation within cells during different pathways. Yet, and despite their importance only a handful of rG4 unwinding helicases have been identified and characterized thus far. This review addresses the current knowledge on rG4s-processing helicases with a focus on methodological approaches. An example of a non-helicase rG4s-unwinding protein is also briefly described.
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Affiliation(s)
- Marco Caterino
- Department of Oncology, Hematology and Rheumatology, University Hospital Bonn, 53127 Bonn, Germany
| | - Katrin Paeschke
- Department of Oncology, Hematology and Rheumatology, University Hospital Bonn, 53127 Bonn, Germany.
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4
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Banerjee N, Panda S, Chatterjee S. Frontiers in G-Quadruplex Therapeutics in Cancer: Selection of Small Molecules, Peptides and Aptamers. Chem Biol Drug Des 2021; 99:1-31. [PMID: 34148284 DOI: 10.1111/cbdd.13910] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2021] [Revised: 05/27/2021] [Accepted: 06/07/2021] [Indexed: 11/28/2022]
Abstract
G-quadruplex, a unique secondary structure in nucleic acids found throughout human genome, elicited widespread interest in the field of therapeutic research. Being present in key regulatory regions of oncogenes, RNAs and telomere, G-quadruplex structure regulates transcription, translation, splicing etc. Changes in its structure and stability leads to differential expression of oncogenes causing cancer. Thus, targeting G-Quadruplex structures with small molecules/other biologics has shown elevated research interest. Covering previous reports, in this review we try to enlighten the facts on the structural diversity in G-quadruplex ligands aiming to provide newer insights to design first-in-class drugs for the next generation cancer treatment.
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Affiliation(s)
- Nilanjan Banerjee
- Department of Biophysics, Bose Institute, P-1/12 CIT Road, Scheme VIIM, Kankurgachi, Kolkata, 700054, India
| | - Suman Panda
- Department of Biophysics, Bose Institute, P-1/12 CIT Road, Scheme VIIM, Kankurgachi, Kolkata, 700054, India
| | - Subhrangsu Chatterjee
- Department of Biophysics, Bose Institute, P-1/12 CIT Road, Scheme VIIM, Kankurgachi, Kolkata, 700054, India
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5
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Devereux SJ, Poynton FE, Baptista FR, Gunnlaugsson T, Cardin CJ, Sazanovich IV, Towrie M, Kelly JM, Quinn SJ. Caught in the Loop: Binding of the [Ru(phen) 2 (dppz)] 2+ Light-Switch Compound to Quadruplex DNA in Solution Informed by Time-Resolved Infrared Spectroscopy. Chemistry 2020; 26:17103-17109. [PMID: 32725823 DOI: 10.1002/chem.202002165] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2020] [Indexed: 01/05/2023]
Abstract
Ultrafast time-resolved infrared (TRIR) is used to report on the binding site of the [Ru(phen)2 (dppz)]2+ "light-switch" complex with both bimolecular (Oxytricha nova telomere) and intramolecular (human telomere) guanine-quadruplex structures in both K+ and Na+ containing solutions. TRIR permits the simultaneous monitoring both of the "dark" and "bright" states of the complex and of the quadruplex nucleobase bases, the latter via a Stark effect induced by the excited state of the complex. These data are used to establish the contribution of guanine base stacking and loop interactions to the binding site of this biologically relevant DNA structure in solution. A particularly striking observation is the strong thymine signal observed for the Na+ form of the human telomere sequence, which is expected to be in the anti-parallel conformation.
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Affiliation(s)
| | - Fergus E Poynton
- School of Chemistry, Trinity College Dublin, Dublin, 2, Ireland.,Trinity Biomedical Sciences Institute (TBSI), Trinity College Dublin, Dublin, 2, Ireland
| | | | - Thorfinnur Gunnlaugsson
- School of Chemistry, Trinity College Dublin, Dublin, 2, Ireland.,Trinity Biomedical Sciences Institute (TBSI), Trinity College Dublin, Dublin, 2, Ireland
| | - Christine J Cardin
- Department of Chemistry, University of Reading, Whiteknights, Reading, RG6 6AD, UK
| | | | - Michael Towrie
- Rutherford Appleton Laboratory, STFC, Harwell Campus, OX11 0FA, UK
| | - John M Kelly
- School of Chemistry, Trinity College Dublin, Dublin, 2, Ireland
| | - Susan J Quinn
- School of Chemistry, University College Dublin, Dublin, 4, Ireland
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6
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Kenny PJ, Kim M, Skariah G, Nielsen J, Lannom MC, Ceman S. The FMRP-MOV10 complex: a translational regulatory switch modulated by G-Quadruplexes. Nucleic Acids Res 2020; 48:862-878. [PMID: 31740951 PMCID: PMC7145700 DOI: 10.1093/nar/gkz1092] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2019] [Revised: 10/30/2019] [Accepted: 11/04/2019] [Indexed: 01/19/2023] Open
Abstract
The Fragile X Mental Retardation Protein (FMRP) is an RNA binding protein that regulates translation and is required for normal cognition. FMRP upregulates and downregulates the activity of microRNA (miRNA)-mediated silencing in the 3' UTR of a subset of mRNAs through its interaction with RNA helicase Moloney leukemia virus 10 (MOV10). This bi-functional role is modulated through RNA secondary structures known as G-Quadruplexes. We elucidated the mechanism of FMRP's role in suppressing Argonaute (AGO) family members' association with mRNAs by mapping the interacting domains of FMRP, MOV10 and AGO and then showed that the RGG box of FMRP protects a subset of co-bound mRNAs from AGO association. The N-terminus of MOV10 is required for this protection: its over-expression leads to increased levels of the endogenous proteins encoded by this co-bound subset of mRNAs. The N-terminus of MOV10 also leads to increased RGG box-dependent binding to the SC1 RNA G-Quadruplex and is required for outgrowth of neurites. Lastly, we showed that FMRP has a global role in miRNA-mediated translational regulation by recruiting AGO2 to a large subset of RNAs in mouse brain.
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Affiliation(s)
- Phillip J Kenny
- Cell and Developmental Biology, University of Illinois-Urbana Champaign, Urbana, IL 61801, USA
| | - Miri Kim
- Neuroscience Program, University of Illinois-Urbana Champaign, Urbana, IL 61801, USA
| | - Geena Skariah
- Neuroscience Program, University of Illinois-Urbana Champaign, Urbana, IL 61801, USA
| | - Joshua Nielsen
- Integrative Biology, University of Illinois-Urbana Champaign, Urbana, IL 61801, USA
| | - Monica C Lannom
- Cell and Developmental Biology, University of Illinois-Urbana Champaign, Urbana, IL 61801, USA
| | - Stephanie Ceman
- Cell and Developmental Biology, University of Illinois-Urbana Champaign, Urbana, IL 61801, USA
- Neuroscience Program, University of Illinois-Urbana Champaign, Urbana, IL 61801, USA
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7
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Abstract
The molecular scale pore structure, called nanopore, can be formed from protein ion channels by genetic engineering or fabricated on solid substrates using fashion nanotechnology. Target molecules in interaction with the functionalized lumen of nanopore, can produce characteristic changes in the pore conductance, which act as fingerprints, allowing us to identify single molecules and simultaneously quantify each target species in the mixture. Nanopore sensors have been created for tremendous biomedical detections, with targets ranging from metal ions, drug compounds and cellular second messengers, to proteins and DNAs. Recently, we have used the nanopore technique to dissect folding and unfolding mechanism of a single G-quadruplex DNA aptamer regulated by a variety of ions; we also created a portable and durable molecular device that integrated a protein pore sensor with a solidified lipid membrane for real-time detection.
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Affiliation(s)
- L Q Gu
- Biological Engineering and Dalton Cardiovascular Research Center, University of Missouri, Columbia, Missouri 65211, USA
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8
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Chen M, Lin W, Hong L, Ji N, Zhao H. The Development and Lifetime Stability Improvement of Guanosine-Based Supramolecular Hydrogels through Optimized Structure. BIOMED RESEARCH INTERNATIONAL 2019; 2019:6258248. [PMID: 31312660 PMCID: PMC6595390 DOI: 10.1155/2019/6258248] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/19/2019] [Revised: 04/12/2019] [Accepted: 04/24/2019] [Indexed: 02/05/2023]
Abstract
Guanosine is an important building block for supramolecular gels owing to the unique self-assembly property that results from the unique hydrogen bond acceptors and donor groups. Guanosine-derived supramolecular hydrogels have promise in the fields of drug delivery, targeted release, tissue engineering applications, etc. However, the property of poor longevity and the need for excess cations hinder the widespread applications of guanosine hydrogels. Although guanosine-derived supramolecular hydrogels have been reviewed previously by Dash et al., the structural framework of this review is different, as the modification of guanosine is described at the molecular level. In this review, we summarize the development and lifetime stability improvement of guanosine-based supramolecular hydrogels through optimized structure and elaborate on three aspects: sugar modification, base modification, and binary gels. Additionally, we introduce the concept and recent research progress of self-healing gels, providing inspiration for the development of guanosine-derived supramolecular hydrogels with longer lifespans, unique physicochemical properties, and biological activities.
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Affiliation(s)
- Miao Chen
- State Key Laboratory of Oral Diseases, National Clinical Research Center for Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu 610041, China
| | - Weimin Lin
- State Key Laboratory of Oral Diseases, National Clinical Research Center for Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu 610041, China
| | - Le Hong
- State Key Laboratory of Oral Diseases, National Clinical Research Center for Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu 610041, China
| | - Ning Ji
- State Key Laboratory of Oral Diseases, National Clinical Research Center for Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu 610041, China
| | - Hang Zhao
- State Key Laboratory of Oral Diseases, National Clinical Research Center for Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu 610041, China
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9
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Oprzeska-Zingrebe EA, Smiatek J. Preferential Binding of Urea to Single-Stranded DNA Structures: A Molecular Dynamics Study. Biophys J 2019; 114:1551-1562. [PMID: 29642026 DOI: 10.1016/j.bpj.2018.02.013] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2017] [Revised: 01/12/2018] [Accepted: 02/12/2018] [Indexed: 01/06/2023] Open
Abstract
In nature, a wide range of biological processes such as transcription termination and intermolecular binding depend on the formation of specific DNA secondary and tertiary structures. These structures can be both stabilized or destabilized by different cosolutes coexisting with nucleic acids in the cellular environment. In our molecular dynamics simulation study, we investigate the binding of urea at different concentrations to short 7-nucleotide single-stranded DNA structures in aqueous solution. The local concentration of urea around a native DNA hairpin in comparison to an unfolded DNA conformation is analyzed by a preferential binding model in light of the Kirkwood-Buff theory. All our findings indicate a pronounced accumulation of urea around DNA that is driven by a combination of electrostatic and dispersion interactions and accomplished by a significant replacement of hydrating water molecules. The outcomes of our study can be regarded as a first step into a deeper mechanistic understanding toward cosolute-induced effects on nucleotide structures in general.
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Affiliation(s)
| | - Jens Smiatek
- Institute for Computational Physics, University of Stuttgart, Stuttgart, Germany; Helmholtz Institute Münster: Ionics in Energy Storage, Forschungszentrum Jülich, Münster, Germany.
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10
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Saha P, Panda D, Dash J. The application of click chemistry for targeting quadruplex nucleic acids. Chem Commun (Camb) 2019; 55:731-750. [PMID: 30489575 DOI: 10.1039/c8cc07107a] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
The Cu(i)-catalyzed azide and alkyne 1,3-dipolar cycloaddition (CuAAC), commonly known as the "click reaction", has emerged as a powerful and versatile synthetic tool that finds a broad spectrum of applications in chemistry, biology and materials science. The efficiency, selectivity and versatility of the CuAAC reactions have enabled the preparation of vast arrays of triazole compounds with biological and pharmaceutical applications. In this feature article, we outline the applications and future prospects of click chemistry in the synthesis and development of small molecules that target G-quadruplex nucleic acids and show promising biological activities. Furthermore, this article highlights the template-assisted in situ click chemistry for developing G-quadruplex specific ligands and the use of click chemistry for enhancing drug specificity as well as designing imaging and sensor systems to elucidate the biological functions of G-quadruplex nucleic acids in live cells.
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Affiliation(s)
- Puja Saha
- School of Chemical Sciences, Indian Association for the Cultivation of Science, Jadavpur, Kolkata-700032, India.
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11
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Zhang Y, Chen J, Ju H, Zhou J. Thermal denaturation profile: A straightforward signature to characterize parallel G-quadruplexes. Biochimie 2019; 157:22-25. [DOI: 10.1016/j.biochi.2018.10.018] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2018] [Accepted: 10/25/2018] [Indexed: 10/28/2022]
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12
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Raffa RB, Pergolizzi JV, Taylor R, Ossipov MH. Discovery of "folded DNA" structures in human cells: Potential drug targets. J Clin Pharm Ther 2018; 44:125-128. [PMID: 30144395 DOI: 10.1111/jcpt.12758] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2018] [Accepted: 08/01/2018] [Indexed: 12/14/2022]
Abstract
WHAT IS KNOWN AND OBJECTIVE The double-helical conformation of human DNA (hDNA) is so axiomatic that it is called the "canonical" form. Recently, though, intrastrand folds ("I-motifs" and "G-quadruplexes") have been identified in hDNA. These could be targets for novel drug discovery. COMMENT Any interruption of the canonical form of hDNA fundamentally impacts the normal progression of transduction and translation. In particular, the synthesis of receptors and cognate protein ligands would be affected, as well as their affinity for-and signal transduction of-pharmacotherapeutic agents. Recent studies have identified normally occurring, folded structures superimposed on the usual double-helix motif of hDNA. WHAT IS NEW AND CONCLUSION The newly identified "folded DNA" structures ("I-motifs" and "G-quadruplexes") could represent novel drug-discovery targets, most likely for cancer.
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Affiliation(s)
- Robert B Raffa
- University of Arizona College of Pharmacy, Tucson, Arizona.,Temple University School of Pharmacy, Philadelphia, Pennsylvania.,Neumentum, Inc., Palo Alto, California
| | - Joseph V Pergolizzi
- Neumentum, Inc., Palo Alto, California.,NEMA Research, Inc., Naples, Florida
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13
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Ding Y, Xie L, Zhang C, Xu W. Real-space evidence of the formation of the GCGC tetrad and its competition with the G-quartet on the Au(111) surface. Chem Commun (Camb) 2017; 53:9846-9849. [PMID: 28825090 DOI: 10.1039/c7cc05548j] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
From the interplay of high-resolution scanning tunneling microscopy (STM) imaging and density functional theory (DFT) calculations, we show the first real-space evidence of the formation of GCGC tetrad on an Au(111) surface, and further investigate its competition with the well-known G-quartet with the aid of NaCl under ultrahigh vacuum (UHV) conditions.
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Affiliation(s)
- Yuanqi Ding
- Interdisciplinary Materials Research Center, Tongji-Aarhus Joint Research Center for Nanostructures and Functional Nanomaterials, College of Materials Science and Engineering, Tongji University, Shanghai 201804, P. R. China.
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14
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Chariker JH, Miller DM, Rouchka EC. Computational Analysis of G-Quadruplex Forming Sequences across Chromosomes Reveals High Density Patterns Near the Terminal Ends. PLoS One 2016; 11:e0165101. [PMID: 27776185 PMCID: PMC5077116 DOI: 10.1371/journal.pone.0165101] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2016] [Accepted: 10/06/2016] [Indexed: 12/17/2022] Open
Abstract
G-quadruplex structures (G4) are found throughout the human genome and are known to play a regulatory role in a variety of molecular processes. Structurally, they have many configurations and can form from one or more DNA strands. At the gene level, they regulate gene expression and protein synthesis. In this paper, chromosomal-level patterns of distribution are analyzed on the human genome to identify high-level distribution patterns potentially related to global functional processes. Here we show unique high density banding patterns on individual chromosomes that are highly correlated, appearing in a mirror pattern, across forward and reverse DNA strands. The highest density of G4 sequences occurs within four megabases of one end of most chromosomes and contains G4 motifs that bind with zinc finger proteins. These findings suggest that G4 may play a role in global chromosomal processes such as those found in meiosis.
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Affiliation(s)
- Julia H. Chariker
- Department of Psychological and Brain Sciences, University of Louisville, Louisville, KY, United States of America
- Kentucky Biomedical Research Infrastructure Network Bioinformatics Core, University of Louisville, Louisville, KY, United States of America
| | - Donald M. Miller
- James Graham Brown Cancer Center, University of Louisville, Louisville, KY, United States of America
- Department of Medicine, University of Louisville, Louisville, KY, United States of America
| | - Eric C. Rouchka
- Kentucky Biomedical Research Infrastructure Network Bioinformatics Core, University of Louisville, Louisville, KY, United States of America
- Department of Computer Engineering and Computer Science, University of Louisville, Louisville KY, United States of America
- * E-mail:
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15
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RNA Secondary Structure Modulates FMRP's Bi-Functional Role in the MicroRNA Pathway. Int J Mol Sci 2016; 17:ijms17060985. [PMID: 27338369 PMCID: PMC4926514 DOI: 10.3390/ijms17060985] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2016] [Revised: 05/23/2016] [Accepted: 06/14/2016] [Indexed: 11/28/2022] Open
Abstract
MicroRNAs act by post-transcriptionally regulating the gene expression of 30%–60% of mammalian genomes. MicroRNAs are key regulators in all cellular processes, though the mechanism by which the cell activates or represses microRNA-mediated translational regulation is poorly understood. In this review, we discuss the RNA binding protein Fragile X Mental Retardation Protein (FMRP) and its role in microRNA-mediated translational regulation. Historically, FMRP is known to function as a translational suppressor. However, emerging data suggests that FMRP has both an agonistic and antagonistic role in regulating microRNA-mediated translational suppression. This bi-functional role is dependent on FMRP’s interaction with the RNA helicase Moloney leukemia virus 10 (MOV10), which modifies the structural landscape of bound mRNA, therefore facilitating or inhibiting its association with the RNA-Induced Silencing Complex.
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16
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Liu Y, Cheng D, Ge M, Lin W. The Truncated Human Telomeric Sequence forms a Hybrid-Type Intramolecular Mixed Parallel/antiparallel G-quadruplex Structure in K(+) Solution. Chem Biol Drug Des 2016; 88:122-8. [PMID: 26867976 DOI: 10.1111/cbdd.12740] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2015] [Revised: 11/03/2015] [Accepted: 01/16/2016] [Indexed: 12/24/2022]
Abstract
In 80-90% tumor cells, telomerase becomes active and stabilizes the length of telomeres. The formation and stabilization of G-quadruplexes formed from human telomeric sequences have been proved able to inhibit the activity of telomerase, thus human telomeric G-quadruplex structure has become a potential target for the development of cancer therapy. Hence, structure of G-quadruplex formed in K(+) solution has been an attractive hotspot for further studies. However, the exact structure of human telomeric G-quadruplex in K(+) is extremely controversial, this study provides information for the understanding of different G-quadruplexes. Here, we report that 22nt and 24nt human telomeric sequences form unimolecular hybrid-type mixed parallel/antiparallel G-quadruplex in K(+) solution elucidated utilizing Circular Dichroism, Differential Scanning Calorimetry, and gel electrophoresis. Moreover, individual configuration of these two sequences was speculated in this study. The detailed structure information of the G-quadruplex formed under physiologically relevant condition is necessary for structure-based rational drug design.
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Affiliation(s)
- Yuxia Liu
- Center for Thorium Molten Salt Reactor System, Shanghai Institute of Applied Physics, Chinese Academy of Sciences, 2019 Jialuo Road, Shanghai, 201800, China
| | - Dengfeng Cheng
- Department of Nuclear Medicine, Zhongshan Hospital, Fudan University, 180 Fenglin Road, Shanghai, 200032, China.,Shanghai Institute of Medical Imaging, 180 Fenglin Road, Shanghai, 200032, China
| | - Min Ge
- Center for Thorium Molten Salt Reactor System, Shanghai Institute of Applied Physics, Chinese Academy of Sciences, 2019 Jialuo Road, Shanghai, 201800, China
| | - Weizhen Lin
- Center for Thorium Molten Salt Reactor System, Shanghai Institute of Applied Physics, Chinese Academy of Sciences, 2019 Jialuo Road, Shanghai, 201800, China
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17
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Rodríguez-Vázquez N, Fuertes A, Amorín M, Granja JR. Bioinspired Artificial Sodium and Potassium Ion Channels. Met Ions Life Sci 2016; 16:485-556. [DOI: 10.1007/978-3-319-21756-7_14] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
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18
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Bailey LJ, Bianchi J, Hégarat N, Hochegger H, Doherty AJ. PrimPol-deficient cells exhibit a pronounced G2 checkpoint response following UV damage. Cell Cycle 2015; 15:908-18. [PMID: 26694751 PMCID: PMC4889237 DOI: 10.1080/15384101.2015.1128597] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2015] [Revised: 11/26/2015] [Accepted: 11/27/2015] [Indexed: 12/04/2022] Open
Abstract
PrimPol is a recently identified member of the archaeo-eukaryote primase (AEP) family of primase-polymerases. It has been shown that this mitochondrial and nuclear localized enzyme plays roles in the maintenance of both unperturbed replication fork progression and in the bypass of lesions after DNA damage. Here, we utilized an avian (DT40) knockout cell line to further study the consequences of loss of PrimPol (PrimPol(-/-)) on the downstream maintenance of cells after UV damage. We report that PrimPol(-/-) cells are more sensitive to UV-C irradiation in colony survival assays than Pol η-deficient cells. Although this increased UV sensitivity is not evident in cell viability assays, we show that this discrepancy is due to an enhanced checkpoint arrest after UV-C damage in the absence of PrimPol. PrimPol(-/-) arrested cells become stalled in G2, where they are protected from UV-induced cell death. Despite lacking an enzyme required for the bypass and maintenance of replication fork progression in the presence of UV damage, we show that PrimPol(-/-) cells actually have an advantage in the presence of a Chk1 inhibitor due to their slow progression through S-phase.
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Affiliation(s)
- Laura J Bailey
- a Genome Damage and Stability Centre, School of Life Sciences, University of Sussex , Brighton , UK
| | - Julie Bianchi
- a Genome Damage and Stability Centre, School of Life Sciences, University of Sussex , Brighton , UK
- b Present address: Department of Oncology-Pathology, Cancer Center Karolinska, Karolinska Institutet , Stockholm , Sweden
| | - Nadia Hégarat
- a Genome Damage and Stability Centre, School of Life Sciences, University of Sussex , Brighton , UK
| | - Helfrid Hochegger
- a Genome Damage and Stability Centre, School of Life Sciences, University of Sussex , Brighton , UK
| | - Aidan J Doherty
- a Genome Damage and Stability Centre, School of Life Sciences, University of Sussex , Brighton , UK
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19
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20
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Combination of conjugated polyelectrolytes and biomolecules: A new optical platform for highly sensitive and selective chemo- and biosensors. Macromol Res 2014. [DOI: 10.1007/s13233-014-2080-3] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
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21
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Shen Q, Zhou L, Yuan Y, Huang Y, Xiang B, Chen C, Nie Z, Yao S. Intra-molecular G-quadruplex structure generated by DNA-templated click chemistry: “Turn-on” fluorescent probe for copper ions. Biosens Bioelectron 2014; 55:187-94. [DOI: 10.1016/j.bios.2013.12.019] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2013] [Revised: 12/05/2013] [Accepted: 12/06/2013] [Indexed: 01/30/2023]
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22
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Huang Y, Mrázek J. Assessing diversity of DNA structure-related sequence features in prokaryotic genomes. DNA Res 2014; 21:285-97. [PMID: 24408877 PMCID: PMC4060949 DOI: 10.1093/dnares/dst057] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023] Open
Abstract
Prokaryotic genomes are diverse in terms of their nucleotide and oligonucleotide composition as well as presence of various sequence features that can affect physical properties of the DNA molecule. We present a survey of local sequence patterns which have a potential to promote non-canonical DNA conformations (i.e. different from standard B-DNA double helix) and interpret the results in terms of relationships with organisms' habitats, phylogenetic classifications, and other characteristics. Our present work differs from earlier similar surveys not only by investigating a wider range of sequence patterns in a large number of genomes but also by using a more realistic null model to assess significant deviations. Our results show that simple sequence repeats and Z-DNA-promoting patterns are generally suppressed in prokaryotic genomes, whereas palindromes and inverted repeats are over-represented. Representation of patterns that promote Z-DNA and intrinsic DNA curvature increases with increasing optimal growth temperature (OGT), and decreases with increasing oxygen requirement. Additionally, representations of close direct repeats, palindromes and inverted repeats exhibit clear negative trends with increasing OGT. The observed relationships with environmental characteristics, particularly OGT, suggest possible evolutionary scenarios of structural adaptation of DNA to particular environmental niches.
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Affiliation(s)
- Yongjie Huang
- Institute of Bioinformatics, University of Georgia, Athens, GA 30602, USA
| | - Jan Mrázek
- Institute of Bioinformatics, University of Georgia, Athens, GA 30602, USA Department of Microbiology, University of Georgia, Athens, GA 30602, USA
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23
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Sugimoto N. Noncanonical structures and their thermodynamics of DNA and RNA under molecular crowding: beyond the Watson-Crick double helix. INTERNATIONAL REVIEW OF CELL AND MOLECULAR BIOLOGY 2014; 307:205-73. [PMID: 24380597 DOI: 10.1016/b978-0-12-800046-5.00008-4] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
How does molecular crowding affect the stability of nucleic acid structures inside cells? Water is the major solvent component in living cells, and the properties of water in the highly crowded media inside cells differ from that in buffered solution. As it is difficult to measure the thermodynamic behavior of nucleic acids in cells directly and quantitatively, we recently developed a cell-mimicking system using cosolutes as crowding reagents. The influences of molecular crowding on the structures and thermodynamics of various nucleic acid sequences have been reported. In this chapter, we discuss how the structures and thermodynamic properties of nucleic acids differ under various conditions such as highly crowded environments, compartment environments, and in the presence of ionic liquids, and the major determinants of the crowding effects on nucleic acids are discussed. The effects of molecular crowding on the activities of ribozymes and riboswitches on noncanonical structures of DNA- and RNA-like quadruplexes that play important roles in transcription and translation are also described.
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Affiliation(s)
- Naoki Sugimoto
- Frontier Institute for Biomolecular Engineering Research (FIBER) and Faculty of Frontiers of Innovative Research in Science and Technology (FIRST), Konan University, Kobe, Japan.
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24
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Henderson A, Wu Y, Huang YC, Chavez EA, Platt J, Johnson FB, Brosh RM, Sen D, Lansdorp PM. Detection of G-quadruplex DNA in mammalian cells. Nucleic Acids Res 2013; 42:860-9. [PMID: 24163102 PMCID: PMC3902944 DOI: 10.1093/nar/gkt957] [Citation(s) in RCA: 360] [Impact Index Per Article: 32.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
It has been proposed that guanine-rich DNA forms four-stranded structures in vivo called G-quadruplexes or G4 DNA. G4 DNA has been implicated in several biological processes, but tools to study G4 DNA structures in cells are limited. Here we report the development of novel murine monoclonal antibodies specific for different G4 DNA structures. We show that one of these antibodies designated 1H6 exhibits strong nuclear staining in most human and murine cells. Staining intensity increased on treatment of cells with agents that stabilize G4 DNA and, strikingly, cells deficient in FANCJ, a G4 DNA-specific helicase, showed stronger nuclear staining than controls. Our data strongly support the existence of G4 DNA structures in mammalian cells and indicate that the abundance of such structures is increased in the absence of FANCJ. We conclude that monoclonal antibody 1H6 is a valuable tool for further studies on the role of G4 DNA in cell and molecular biology.
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Affiliation(s)
- Alexander Henderson
- Terry Fox Laboratory, British Columbia Cancer Agency, Vancouver, BC V5Z 1L3, Canada, Laboratory of Molecular Gerontology, National Institute on Aging, National Institutes of Health, NIH Biomedical Research Center, Baltimore, MD 21224, USA, Department of Chemistry, Simon Fraser University, Burnaby, BC V5A 1S6, Canada, Department of Pathology and Laboratory Medicine, University of Pennsylvania, Philadelphia, PA 19104-6100, USA, Division of Hematology, Department of Medicine, University of British Columbia, Vancouver, BC V6T 1Z4, Canada and European Research Institute for the Biology of Ageing, University of Groningen, University Medical Centre Groningen, A. Deusinglaan 1, NL-9713 AV Groningen, The Netherlands
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25
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Zhang C, Liu HH, Zheng KW, Hao YH, Tan Z. DNA G-quadruplex formation in response to remote downstream transcription activity: long-range sensing and signal transducing in DNA double helix. Nucleic Acids Res 2013; 41:7144-52. [PMID: 23716646 PMCID: PMC3737545 DOI: 10.1093/nar/gkt443] [Citation(s) in RCA: 52] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
G-quadruplexes, four-stranded structures formed by Guanine-rich nucleic acids, are implicated in many physiological and pathological processes. G-quadruplex-forming sequences are abundant in genomic DNA, and G-quadruplexes have recently been shown to exist in the genome of mammalian cells. However, how G-quadruplexes are formed in the genomes remains largely unclear. Here, we show that G-quadruplex formation can be remotely induced by downstream transcription events that are thousands of base pairs away. The induced G-quadruplexes alter protein recognition and cause transcription termination at the local region. These results suggest that a G-quadruplex-forming sequence can serve as a sensor or receiver to sense remote DNA tracking activity in response to the propagation of mechanical torsion in a DNA double helix. We propose that the G-quadruplex formation may provide a mean for long-range sensing and communication between distal genomic locations to coordinate regulatory transactions in genomic DNA.
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Affiliation(s)
- Chao Zhang
- State Key Laboratory of Biomembrane and Membrane Biotechnology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, PR China
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26
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Inui Y, Shiro M, Fukuzumi S, Kojima T. Quartet formation of a guanine derivative with an isopropyl group: crystal structures of “naked” G-quartets and thermodynamics of G-quartet formation. Org Biomol Chem 2013; 11:758-64. [DOI: 10.1039/c2ob26877a] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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27
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Wang SR, Zhang D, Luo FL, Liu L, Weng XC, Huang J, Li GR, Zhang XL, Zhou X. Some cationic porphyrins: synthesis, stabilization of G-quadruplexes, and down-regulation of c-myc in Hep G2 cells. J PORPHYR PHTHALOCYA 2012. [DOI: 10.1142/s1088424609001121] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
The stabilization of G-quadruplex DNA represents an attractive strategy for the design and development of novel antitumor drugs. In the present work, we have designed and synthesized nine cationic porphyrins, each with four side arms at their meso positions. The interactions of these porphyrins with both human telomeric DNA and NHE III1 G-quadruplexes were measured by various DNA binding assays, including polymerase stop assay, circular dichroism (CD) and CD melting assay. We then proceeded to investigate their effects on the expression of c-myc oncogene in the Hep G2 cell line. The experimental results indicate that these porphyrins are capable of effectively inducing or stabilizing both human telomeric and NHE III1 G-quadruplexes in the presence or absence of metal ions. Furthermore, we have discovered that porphyrins with a stronger stabilizing effect on c-myc G-quadruplexes lead to more pronounced down-regulation of the c-myc oncogene in the Hep G2 cell line.
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Affiliation(s)
- Shao R. Wang
- College of Chemistry and Molecular Sciences, Wuhan University, Hubei, Wuhan 430072, P.R. China
| | - Dan Zhang
- College of Chemistry and Molecular Sciences, Wuhan University, Hubei, Wuhan 430072, P.R. China
| | - Feng L. Luo
- State Key Laboratory of Virology, Department of Immunology, Hubei Province Key Laboratory of Allergy and Immunology, Wuhan University School of Medicine, Wuhan 430071, P.R. China
| | - Lin Liu
- College of Chemistry and Molecular Sciences, Wuhan University, Hubei, Wuhan 430072, P.R. China
| | - Xiao C. Weng
- College of Chemistry and Molecular Sciences, Wuhan University, Hubei, Wuhan 430072, P.R. China
| | - Jing Huang
- College of Chemistry and Molecular Sciences, Wuhan University, Hubei, Wuhan 430072, P.R. China
| | - Guo R. Li
- College of Chemistry and Molecular Sciences, Wuhan University, Hubei, Wuhan 430072, P.R. China
| | - Xiao L. Zhang
- State Key Laboratory of Virology, Department of Immunology, Hubei Province Key Laboratory of Allergy and Immunology, Wuhan University School of Medicine, Wuhan 430071, P.R. China
| | - Xiang Zhou
- College of Chemistry and Molecular Sciences, Wuhan University, Hubei, Wuhan 430072, P.R. China
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28
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Pramanik S, Nagatoishi S, Sugimoto N. DNA tetraplex structure formation from human telomeric repeat motif (TTAGGG):(CCCTAA) in nanocavity water pools of reverse micelles. Chem Commun (Camb) 2012; 48:4815-7. [PMID: 22456442 DOI: 10.1039/c2cc30622k] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
In an equimolar ratio the human telomeric oligonucleotides d[AGGG(TTAGGG)(3)] and d[(CCCTAA)(3)CCCT] formed mixed structures of duplex and tetraplex in bis(2-ethylhexyl)sulfosuccinate reverse micelles; only the duplex was observed in aqueous buffer. This finding suggests that heterogeneous confined media in the cell nucleus might induce a significant fraction of the telomeric region of genomic DNA to adopt non-canonical tetraplex structure.
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Affiliation(s)
- Smritimoy Pramanik
- Frontier Institute for Biomolecular Engineering Research (FIBER), Konan University, 7-1-20 Minatojima-minamimachi, Kobe 650-0047, Japan
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29
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Yaku H, Fujimoto T, Murashima T, Miyoshi D, Sugimoto N. Phthalocyanines: a new class of G-quadruplex-ligands with many potential applications. Chem Commun (Camb) 2012; 48:6203-16. [DOI: 10.1039/c2cc31037f] [Citation(s) in RCA: 97] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
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30
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Schlachter C, Lisdat F, Frohme M, Erdmann VA, Konthur Z, Lehrach H, Glökler J. Pushing the detection limits: the evanescent field in surface plasmon resonance and analyte-induced folding observation of long human telomeric repeats. Biosens Bioelectron 2011; 31:571-4. [PMID: 22152989 DOI: 10.1016/j.bios.2011.11.003] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2011] [Revised: 11/02/2011] [Accepted: 11/03/2011] [Indexed: 12/17/2022]
Abstract
Conventional analysis of molecular interactions by surface plasmon resonance is achieved by the observation of optical density changes due to analyte binding to the ligand on the surface. Low molecular weight interaction partners are normally not detected. However, if a macromolecule such as DNA can extend beyond the evanescent field and analyte interaction results in a large-scale contraction, then the refractive index changes due to the increasing amount of macromolecules close to the surface. In our proof-of-principle experiment we could observe the direct folding of long, human telomeric repeats induced by the small analyte potassium using surface plasmon resonance spectroscopy. This work demonstrates the feasibility of new evanescent field-based biosensors that can specifically observe small molecule interactions.
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Affiliation(s)
- Constanze Schlachter
- Department of Vertebrate Genomics, Max Planck Institute for Molecular Genetics, Ihnestrasse 63-73, 14195 Berlin, Germany
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31
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Prislan I, Khutsishvili I, Marky LA. Interaction of minor groove ligands with G-quadruplexes: thermodynamic contributions of the number of quartets, T-U substitutions, and conformation. Biochimie 2011; 93:1341-50. [PMID: 21684318 DOI: 10.1016/j.biochi.2011.06.001] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2011] [Accepted: 06/01/2011] [Indexed: 10/18/2022]
Abstract
In the presence of specific metal ions, DNA oligonucleotides containing guanine repeat sequences can adopt G-quadruplex structures. In this work, we used a combination of spectroscopic and calorimetric techniques to investigate the conformation and unfolding thermodynamics of the K(+)-form of five G-quadruplexes with sequences: d(G(2)T(2)G(2)TGTG(2)T(2)G(2)), G2, d(G(3)T(2)G(3)TGTG(3)T(2)G(3)), G3, their analogs where T is replaced with U, G2-U and G3-U, and r(G(2)U(2)G(2)UGUG(2)U(2)G(2)), rG2. These G-quadruplexes show CD spectra characteristic of the "chair" conformation (G2 and G2-U), or "basket" conformation (rG2); or a mixture of these two conformers (G3 and G3-U). Thermodynamic profiles show that the favorable folding of each G-quadruplex results from the typical compensation of a favorable enthalpy and unfavorable entropy contributions. G-quadruplex stability increase in the following order (in ΔG°(20)): rG2 (-1.3 kcal/mol) < G2 < G2-U <G3-U (chair) < G3 (chair) <G3-U (basket) < G3 (basket) (-8.6 kcal/mol), due to favorable enthalpy contribution from the stacking of G-quartets. We used ITC to determine thermodynamic binding profiles for the interaction of the minor groove ligands, netropsin and distamycin, with each G-quadruplex. Both ligands bind with high exothermic enthalpies (~ -10.8 kcal/mol), 1:1 stoichiometries, and weak affinities (~8 × 10(4) M(-1)). The similarity of the binding thermodynamic profiles, together with the absence of induced Cotton effects, indicates a surface or outside binding mode. We speculate that the top and bottom surfaces of the G-quadruplex comprise the potential MGBL binding sites, where the ligand lies on the surface forming van der Waals interactions with the guanines of the G-quartets and loop nucleotides.
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Affiliation(s)
- Iztok Prislan
- Department of Pharmaceutical Sciences, University of Nebraska Medical Center, 986025 Nebraska Medical Center, Omaha, NE 68198-6025, USA
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32
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Giri B, Smaldino PJ, Thys RG, Creacy SD, Routh ED, Hantgan RR, Lattmann S, Nagamine Y, Akman SA, Vaughn JP. G4 resolvase 1 tightly binds and unwinds unimolecular G4-DNA. Nucleic Acids Res 2011; 39:7161-78. [PMID: 21586581 PMCID: PMC3167620 DOI: 10.1093/nar/gkr234] [Citation(s) in RCA: 72] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023] Open
Abstract
It has been previously shown that the DHX36 gene product, G4R1/RHAU, tightly binds tetramolecular G4-DNA with high affinity and resolves these structures into single strands. Here, we test the ability of G4R1/RHAU to bind and unwind unimolecular G4-DNA. Gel mobility shift assays were used to measure the binding affinity of G4R1/RHAU for unimolecular G4-DNA-formed sequences from the Zic1 gene and the c-Myc promoter. Extremely tight binding produced apparent K(d)'s of 6, 3 and 4 pM for two Zic1 G4-DNAs and a c-Myc G4-DNA, respectively. The low enzyme concentrations required for measuring these K(d)'s limit the precision of their determination to upper boundary estimates. Similar tight binding was not observed in control non-G4 forming DNA sequences or in single-stranded DNA having guanine-rich runs capable of forming tetramolecular G4-DNA. Using a peptide nucleic acid (PNA) trap assay, we show that G4R1/RHAU catalyzes unwinding of unimolecular Zic1 G4-DNA into an unstructured state capable of hybridizing to a complementary PNA. Binding was independent of adenosine triphosphate (ATP), but the PNA trap assay showed that unwinding of G4-DNA was ATP dependent. Competition studies indicated that unimolecular Zic1 and c-Myc G4-DNA structures inhibit G4R1/RHAU-catalyzed resolution of tetramolecular G4-DNA. This report provides evidence that G4R1/RHAU tightly binds and unwinds unimolecular G4-DNA structures.
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Affiliation(s)
- Banabihari Giri
- Department of Cancer Biology and the Comprehensive Cancer Center of Wake Forest University School of Medicine, Winston-Salem, USA
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33
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Sissi C, Gatto B, Palumbo M. The evolving world of protein-G-quadruplex recognition: a medicinal chemist's perspective. Biochimie 2011; 93:1219-30. [PMID: 21549174 PMCID: PMC7126356 DOI: 10.1016/j.biochi.2011.04.018] [Citation(s) in RCA: 80] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2011] [Accepted: 04/20/2011] [Indexed: 01/02/2023]
Abstract
The physiological and pharmacological role of nucleic acids structures folded into the non canonical G-quadruplex conformation have recently emerged. Their activities are targeted at vital cellular processes including telomere maintenance, regulation of transcription and processing of the pre-messenger or telomeric RNA. In addition, severe conditions like cancer, fragile X syndrome, Bloom syndrome, Werner syndrome and Fanconi anemia J are related to genomic defects that involve G-quadruplex forming sequences. In this connection G-quadruplex recognition and processing by nucleic acid directed proteins and enzymes represents a key event to activate or deactivate physiological or pathological pathways. In this review we examine protein-G-quadruplex recognition in physiologically significant conditions and discuss how to possibly exploit the interactions' selectivity for targeted therapeutic intervention.
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Affiliation(s)
- Claudia Sissi
- Department of Pharmaceutical Sciences, University of Padova, Via Marzolo 5, Padua, Italy
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34
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Xu Y. Chemistry in human telomere biology: structure, function and targeting of telomere DNA/RNA. Chem Soc Rev 2011; 40:2719-40. [DOI: 10.1039/c0cs00134a] [Citation(s) in RCA: 249] [Impact Index Per Article: 19.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
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35
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Rother IB, Willermann M, Lippert B. Molecular Architecture with Nucleobases, Metal Ions and Water Molecules: Mixed Adenine, Hypoxanthine Quartet Containing trans -(NH 3 ) 2 Pt II and Ag + and Harboring a Water Hexamer in Its Chair Conformation. Supramol Chem 2010. [DOI: 10.1080/10610270290026095] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
Affiliation(s)
- Irene B. Rother
- a Fachbereich Chemie , Universität Dortmund , Dortmund , D-44221 , Germany
| | - Michael Willermann
- a Fachbereich Chemie , Universität Dortmund , Dortmund , D-44221 , Germany
| | - Bernhard Lippert
- a Fachbereich Chemie , Universität Dortmund , Dortmund , D-44221 , Germany
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36
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Woiczikowski PB, Kubař T, Gutiérrez R, Cuniberti G, Elstner M. Structural stability versus conformational sampling in biomolecular systems: Why is the charge transfer efficiency in G4-DNA better than in double-stranded DNA? J Chem Phys 2010; 133:035103. [DOI: 10.1063/1.3460132] [Citation(s) in RCA: 51] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023] Open
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37
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Toward a full structural characterization of G-quadruplex DNA in aqueous solution: Molecular dynamics simulations of four G-quadruplex molecules. ACTA ACUST UNITED AC 2010. [DOI: 10.1016/j.theochem.2010.04.035] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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38
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Affiliation(s)
- Francisco Boán
- Departamento de Bioquímica e Bioloxía Molecular, Facultade de Bioloxía-CIBUS, Universidade de Santiago de Compostela, 15782 Santiago, Galicia, Spain
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39
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Abstract
Molecular-scale pore structures, called nanopores, can be assembled by protein ion channels through genetic engineering or be artificially fabricated on solid substrates using fashion nanotechnology. When target molecules interact with the functionalized lumen of a nanopore, they characteristically block the ion pathway. The resulting conductance changes allow for identification of single molecules and quantification of target species in the mixture. In this review, we first overview nanopore-based sensory techniques that have been created for the detection of myriad biomedical targets, from metal ions, drug compounds, and cellular second messengers to proteins and DNA. Then we introduce our recent discoveries in nanopore single molecule detection: (1) using the protein nanopore to study folding/unfolding of the G-quadruplex aptamer; (2) creating a portable and durable biochip that is integrated with a single-protein pore sensor (this chip is compared with recently developed protein pore sensors based on stabilized bilayers on glass nanopore membranes and droplet interface bilayer); and (3) creating a glass nanopore-terminated probe for single-molecule DNA detection, chiral enantiomer discrimination, and identification of the bioterrorist agent ricin with an aptamer-encoded nanopore.
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Affiliation(s)
- Li-Qun Gu
- Biological Engineering and Dalton Cardiovascular Research Center, University of Missouri, 134 Research Park, Columbia, Missouri 65211, USA.
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40
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Barros P, Boán F, Blanco MG, Gómez-Márquez J. Effect of monovalent cations and G-quadruplex structures on the outcome of intramolecular homologous recombination. FEBS J 2009; 276:2983-93. [DOI: 10.1111/j.1742-4658.2009.07013.x] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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41
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Xu Y, Suzuki Y, Komiyama M. Click chemistry for the identification of G-quadruplex structures: discovery of a DNA-RNA G-quadruplex. Angew Chem Int Ed Engl 2009; 48:3281-4. [PMID: 19334028 DOI: 10.1002/anie.200806306] [Citation(s) in RCA: 63] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
A trap that closes with a "click": The copper-catalyzed azide-alkyne cycloaddition can occur in different G-quadruplex structures (see scheme). The species trapped by the click reaction can then be separated and analyzed. By using this approach, a DNA-RNA hybrid-type G-quadruplex structure formed by human telomeric DNA and RNA sequences was detected.
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Affiliation(s)
- Yan Xu
- Research Center for Advanced Science and Technology, The University of Tokyo, Komaba, Meguro-ku, Tokyo 153-8904, Japan.
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42
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Xu Y, Suzuki Y, Komiyama M. Click Chemistry for the Identification of G-Quadruplex Structures: Discovery of a DNA-RNA G-Quadruplex. Angew Chem Int Ed Engl 2009. [DOI: 10.1002/ange.200806306] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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43
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Rubtsova MP, Skvortsov DA, Petruseva IO, Lavrik OI, Spirin PV, Prasolov VS, Kisseljov FL, Dontsova OA. Replication protein A modulates the activity of human telomerase in vitro. BIOCHEMISTRY (MOSCOW) 2009; 74:92-6. [PMID: 19232055 DOI: 10.1134/s0006297909010143] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
Our aim was to investigate how replication protein A (RPA) in a wide range of concentration can regulate the activity of human telomerase. We used an in vitro system based on human cell extracts with or without RPA. It has been shown that removal of RPA leads to loss of telomerase activity and addition of RPA restores telomerase activity and at the same time promotes telomerase processivity. However, high excess of RPA inhibited telomerase processivity and caused the synthesis of relatively short DNA fragments (about 50-100 nucleotides). We assume that, together with other telomere-binding proteins, RPA may take part in activation of telomere overhang elongation by telomerase at a certain stage of a cell cycle as well as in regulation of telomere length.
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Affiliation(s)
- M P Rubtsova
- Chemical Faculty, Lomonosov Moscow State University, Moscow, 119899, Russia
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Nishino K, Inoue E, Takada S, Abe T, Akita M, Yoshimura A, Tada S, Kobayashi M, Yamamoto KI, Seki M, Enomoto T. A novel role for Rad17 in homologous recombination. Genes Genet Syst 2009; 83:427-31. [PMID: 19168994 DOI: 10.1266/ggs.83.427] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
Replication checkpoint protein Rad17 senses DNA lesions during DNA replication and halts progression of replication fork. The cells derived from Bloom syndrome individuals show some defects in DNA replication. In order to investigate the functional relationship between the replication checkpoint protein Rad17 and BLM, which is the product of the causative gene of Bloom syndrome, we generated BLM/RAD17 double knockout (blm/rad17) cells using chicken DT40 cells. The blm/rad17 cells showed exaggerated growth defects as determined by analysis of their growth curves and plating efficiency compared to those of either of the single gene mutants. These defects seem to be due to an increase in DNA lesions that cause spontaneous cell death, suggesting that Rad17 and BLM execute different functions in the progression of replication forks. We also demonstrate that targeting integration was dramatically compromised by a lack of Rad17. In addition, the elevated frequency of sister chromatid exchange (SCE) due to homologous recombination in BLM knockout (blm) cells was greatly reduced by disruption of the RAD17 gene. Thus, in addition to its role in the replication checkpoint, Rad17 appears to play a role in homologous recombination.
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Affiliation(s)
- Katsuaki Nishino
- Molecular Cell Biology Laboratory, Graduate School of Pharmaceutical Sciences, Tohoku University, Sendai, Japan
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Zhang JL, Fu Y, Zheng L, Li W, Li H, Sun Q, Xiao Y, Geng F. Natural isoflavones regulate the quadruplex-duplex competition in human telomeric DNA. Nucleic Acids Res 2009; 37:2471-82. [PMID: 19261597 PMCID: PMC2677859 DOI: 10.1093/nar/gkp055] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023] Open
Abstract
Effects of natural isoflavones on the structural competition of human telomeric G-quadruplex d[AG(3)(T(2)AG(3))(3)] and its related Watson-Crick duplex d[AG(3)(T(2)AG(3))(3)-(C(3)TA(2))(3)C(3)T] are investigated by using circular dichroism (CD), ESI-MS, fluorescence quenching measurement, CD stopped-flow kinetic experiment, UV spectroscopy and molecular modeling methods. It is intriguing to find out that isoflavones can stabilize the G-quadruplex structure but destabilize its corresponding Watson-Crick duplex and this discriminated interaction is intensified by molecular crowding environments. Kinetic experiments indicate that the dissociation rate of quadruplex (k(obs290 nm)) is decreased by 40.3% at the daidzin/DNA molar ratio of 1.0 in K(+), whereas in Na(+) the observed rate constant is reduced by about 12.0%. Furthermore, glycosidic daidzin significantly induces a structural transition of the polymorphic G-quadruplex into the antiparallel conformation in K(+). This is the first report on the recognition of isoflavones with conformational polymorphism of G-quadruplex, which suggests that natural isoflavone constituents potentially exhibit distinct regulation on the structural competition of quadruplex versus duplex in human telomeric DNA.
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Affiliation(s)
- Jin-li Zhang
- Key Laboratory of Systems Bioengineering, Ministry of Education, School of Chemical Engineering & Technology, Tianjin University, Tianjin 300072, China
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Mani P, Yadav VK, Das SK, Chowdhury S. Genome-wide analyses of recombination prone regions predict role of DNA structural motif in recombination. PLoS One 2009; 4:e4399. [PMID: 19198658 PMCID: PMC2635932 DOI: 10.1371/journal.pone.0004399] [Citation(s) in RCA: 64] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2008] [Accepted: 12/17/2008] [Indexed: 11/18/2022] Open
Abstract
HapMap findings reveal surprisingly asymmetric distribution of recombinogenic regions. Short recombinogenic regions (hotspots) are interspersed between large relatively non-recombinogenic regions. This raises the interesting possibility of DNA sequence and/or other cis- elements as determinants of recombination. We hypothesized the involvement of non-canonical sequences that can result in local non-B DNA structures and tested this using the G-quadruplex DNA as a model. G-quadruplex or G4 DNA is a unique form of four-stranded non-B DNA structure that engages certain G-rich sequences, presence of such motifs has been noted within telomeres. In support of this hypothesis, genome-wide computational analyses presented here reveal enrichment of potential G4 (PG4) DNA forming sequences within 25618 human hotspots relative to 9290 coldspots (p<0.0001). Furthermore, co-occurrence of PG4 DNA within several short sequence elements that are associated with recombinogenic regions was found to be significantly more than randomly expected. Interestingly, analyses of more than 50 DNA binding factors revealed that co-occurrence of PG4 DNA with target DNA binding sites of transcription factors c-Rel, NF-kappa B (p50 and p65) and Evi-1 was significantly enriched in recombination-prone regions. These observations support involvement of G4 DNA in recombination, predicting a functional model that is consistent with duplex-strand separation induced by formation of G4 motifs in supercoiled DNA and/or when assisted by other cellular factors.
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Affiliation(s)
- Prithvi Mani
- G. N. Ramachandran Knowledge Centre for Genome Informatics, Institute of Genomics and Integrative Biology, CSIR, Delhi, India
| | - Vinod Kumar Yadav
- G. N. Ramachandran Knowledge Centre for Genome Informatics, Institute of Genomics and Integrative Biology, CSIR, Delhi, India
| | - Swapan Kumar Das
- Functional Genomics Unit, Institute of Genomics and Integrative Biology, CSIR, Delhi, India
| | - Shantanu Chowdhury
- G. N. Ramachandran Knowledge Centre for Genome Informatics, Institute of Genomics and Integrative Biology, CSIR, Delhi, India
- Proteomics and Structural Biology Unit, Institute of Genomics and Integrative Biology, CSIR, Delhi, India
- * E-mail:
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Henn A, Joachimi A, Gonçalves DPN, Monchaud D, Teulade-Fichou MP, Sanders JKM, Hartig JS. Inhibition of dicing of guanosine-rich shRNAs by quadruplex-binding compounds. Chembiochem 2009; 9:2722-9. [PMID: 18924215 DOI: 10.1002/cbic.200800271] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
RNA interference is triggered by small hairpin precursors that are processed by the endonuclease dicer to yield active species such as siRNAs and miRNAs. To regulate the RNAi-mediated suppression of gene expression, we imagined a strategy that relies on the sequence-specific inhibition of shRNA precursor processing by immediate RNA-small molecule interactions. Here, we present a first step in this direction by augmenting shRNAs with guanosine-rich sequences that are prone to fold into four-stranded structures. The addition of small molecules that selectively bind to such quadruplex sequences should allow for the specific inhibition of dicing of shRNAs that contain suitable G-rich elements. In an attempt to find compounds that protect against dicer processing, we have examined the effects of quadruplex-binding compounds on the dicer processing of shRNAs containing G-quadruplexes. Although a variety of small molecules that are known to bind to quadruplexes inhibited in vitro dicing of shRNAs, only two substance classes, namely certain porphyrazines and bisquinolinium compounds, showed selective inhibition of G-rich shRNAs compared to control sequences lacking guanine-rich elements. The G-rich shRNAs displayed a potent knockdown of gene expression in mammalian cell culture, but the effect was not influenced by addition of the respective quadruplex-binding compounds.
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Affiliation(s)
- Anja Henn
- Department of Chemistry and Konstanz Research School of Chemical Biology (KoRS-CB), University of Konstanz, Universitätsstrasse 10, 78457 Konstanz, Germany
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Shim JW, Tan Q, Gu LQ. Single-molecule detection of folding and unfolding of the G-quadruplex aptamer in a nanopore nanocavity. Nucleic Acids Res 2009; 37:972-82. [PMID: 19112078 PMCID: PMC2647319 DOI: 10.1093/nar/gkn968] [Citation(s) in RCA: 108] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2008] [Revised: 11/12/2008] [Accepted: 11/16/2008] [Indexed: 11/12/2022] Open
Abstract
Guanine-rich nucleic acids can form G-quadruplexes that are important in gene regulation, biosensor design and nano-structure construction. In this article, we report on the development of a nanopore encapsulating single-molecule method for exploring how cations regulate the folding and unfolding of the G-quadruplex formed by the thrombin-binding aptamer (TBA, GGTTGGTGTGGTTGG). The signature blocks in the nanopore revealed that the G-quadruplex formation is cation-selective. The selectivity sequence is K(+) > NH(4)(+) approximately Ba(2+) > Cs(+) approximately Na(+) > Li(+), and G-quadruplex was not detected in Mg(2+) and Ca(2+). Ba(2+) can form a long-lived G-quadruplex with TBA. However, the capability is affected by the cation-DNA interaction. The cation-selective formation of the G-quadruplex is correlated with the G-quadruplex volume, which varies with cation species. The high formation capability of the K(+)-induced G-quadruplex is contributed largely by the slow unfolding reaction. Although the Na(+)- and Li(+)-quadruplexes feature similar equilibrium properties, they undergo radically different pathways. The Na(+)-quadruplex folds and unfolds most rapidly, while the Li(+)-quadruplex performs both reactions at the slowest rates. Understanding these ion-regulated properties of oligonucleotides is beneficial for constructing fine-tuned biosensors and nano-structures. The methodology in this work can be used for studying other quadruplexes and protein-aptamer interactions.
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Affiliation(s)
| | | | - Li-Qun Gu
- Department of Biological Engineering, Dalton Cardiovascular Research Center, University of Missouri, Columbia, MO, USA
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Creacy SD, Routh ED, Iwamoto F, Nagamine Y, Akman SA, Vaughn JP. G4 resolvase 1 binds both DNA and RNA tetramolecular quadruplex with high affinity and is the major source of tetramolecular quadruplex G4-DNA and G4-RNA resolving activity in HeLa cell lysates. J Biol Chem 2008; 283:34626-34. [PMID: 18842585 DOI: 10.1074/jbc.m806277200] [Citation(s) in RCA: 147] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Quadruplex structures that result from stacking of guanine quartets in nucleic acids possess such thermodynamic stability that their resolution in vivo is likely to require specific recognition by specialized enzymes. We previously identified the major tetramolecular quadruplex DNA resolving activity in HeLa cell lysates as the gene product of DHX36 (Vaughn, J. P., Creacy, S. D., Routh, E. D., Joyner-Butt, C., Jenkins, G. S., Pauli, S., Nagamine, Y., and Akman, S. A. (2005) J. Biol Chem. 280, 38117-38120), naming the enzyme G4 Resolvase 1 (G4R1). G4R1 is also known as RHAU, an RNA helicase associated with the AU-rich sequence of mRNAs. We now show that G4R1/RHAU binds to and resolves tetramolecular RNA quadruplex as well as tetramolecular DNA quadruplex structures. The apparent K(d) values of G4R1/RHAU for tetramolecular RNA quadruplex and tetramolecular DNA quadruplex were exceptionally low: 39 +/- 6 and 77 +/- 6 Pm, respectively, as measured by gel mobility shift assay. In competition studies tetramolecular RNA quadruplex structures inhibited tetramolecular DNA quadruplex structure resolution by G4R1/RHAU more efficiently than tetramolecular DNA quadruplex structures inhibited tetramolecular RNA quadruplex structure resolution. Down-regulation of G4R1/RHAU in HeLa T-REx cells by doxycycline-inducible short hairpin RNA caused an 8-fold loss of RNA and DNA tetramolecular quadruplex resolution, consistent with G4R1/RHAU representing the major tetramolecular quadruplex helicase activity for both RNA and DNA structures in HeLa cells. This study demonstrates for the first time the RNA quadruplex resolving enzymatic activity associated with G4R1/RHAU and its exceptional binding affinity, suggesting a potential novel role for G4R1/RHAU in targeting in vivo RNA quadruplex structures.
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Affiliation(s)
- Steven D Creacy
- Department of Cancer Biology and the Comprehensive Cancer Center, Wake Forest University School of Medicine, Winston-Salem, North Carolina 27157, USA
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