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Postberg J, Tsytlonok M, Sparvoli D, Rhodes D, Lipps HJ. A telomerase-associated RecQ protein-like helicase resolves telomeric G-quadruplex structures during replication. Gene 2012; 497:147-54. [PMID: 22327026 PMCID: PMC3650557 DOI: 10.1016/j.gene.2012.01.068] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2011] [Revised: 01/18/2012] [Accepted: 01/25/2012] [Indexed: 11/30/2022]
Abstract
It is well established that G-quadruplex DNA structures form at ciliate telomeres and their formation throughout the cell-cycle by telomere-end-binding proteins (TEBPs) has been analyzed. During replication telomeric G-quadruplex structure has to be resolved to allow telomere replication by telomerase. It was shown that both phosphorylation of TEBPβ and binding of telomerase are prerequisites for this process, but probably not sufficient to unfold G-quadruplex structure in timely manner to allow replication to proceed. Here we describe a RecQ-like helicase required for unfolding of G-quadruplex structures in vivo. This helicase is highly reminiscent of human RecQ protein-like 4 helicase as well as other RecQ-like helicase found in various eukaryotes and E. coli. In situ analyses combined with specific silencing of either the telomerase or the helicase by RNAi and co-immunoprecipitation experiments demonstrate that this helicase is associated with telomerase during replication and becomes recruited to telomeres by this enzyme. In vitro assays showed that a nuclear extract prepared from cells in S-phase containing both the telomerase as well as the helicase resolves telomeric G-quadruplex structure. This finding can be incorporated into a mechanistic model about the replication of telomeric G-quadruplex structures during the cell cycle.
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Affiliation(s)
- Jan Postberg
- Centre for Biomedical Education and Research, Institute of Cell Biology, Witten, Germany
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52
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Abstract
G-quartets are square planar arrangements of four guanine bases, which can form extraordinarily stable stacks when present in nucleic acid sequences. Such G-quadruplex structures were long regarded as an in vitro phenomenon, but the widespread presence of suitable sequences in genomes and the identification of proteins that stabilize, modify or resolve these nucleic acid structures have provided circumstantial evidence for their physiological relevance. The therapeutic potential of small molecules that can stabilize or disrupt G-quadruplex structures has invigorated the field in recent years. Here we review some of the key observations that support biological functions for G-quadruplex DNA as well as the techniques and tools that have enabled researchers to probe these structures and their interactions with proteins and small molecules.
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Affiliation(s)
- Tracy M Bryan
- Children's Medical Research Institute, University of Sydney, 214 Hawkesbury Road, Westmead, Sydney, NSW 2145, Australia.
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53
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Hirsch ML, Fagan BM, Dumitru R, Bower JJ, Yadav S, Porteus MH, Pevny LH, Samulski RJ. Viral single-strand DNA induces p53-dependent apoptosis in human embryonic stem cells. PLoS One 2011; 6:e27520. [PMID: 22114676 PMCID: PMC3219675 DOI: 10.1371/journal.pone.0027520] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2011] [Accepted: 10/18/2011] [Indexed: 11/19/2022] Open
Abstract
Human embryonic stem cells (hESCs) are primed for rapid apoptosis following mild forms of genotoxic stress. A natural form of such cellular stress occurs in response to recombinant adeno-associated virus (rAAV) single-strand DNA genomes, which exploit the host DNA damage response for replication and genome persistence. Herein, we discovered a unique DNA damage response induced by rAAV transduction specific to pluripotent hESCs. Within hours following rAAV transduction, host DNA damage signaling was elicited as measured by increased gamma-H2AX, ser15-p53 phosphorylation, and subsequent p53-dependent transcriptional activation. Nucleotide incorporation assays demonstrated that rAAV transduced cells accumulated in early S-phase followed by the induction of apoptosis. This lethal signaling sequalae required p53 in a manner independent of transcriptional induction of Puma, Bax and Bcl-2 and was not evident in cells differentiated towards a neural lineage. Consistent with a lethal DNA damage response induced upon rAAV transduction of hESCs, empty AAV protein capsids demonstrated no toxicity. In contrast, DNA microinjections demonstrated that the minimal AAV origin of replication and, in particular, a 40 nucleotide G-rich tetrad repeat sequence, was sufficient for hESC apoptosis. Our data support a model in which rAAV transduction of hESCs induces a p53-dependent lethal response that is elicited by a telomeric sequence within the AAV origin of replication.
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Affiliation(s)
- Matthew L. Hirsch
- Gene Therapy Center, University of North Carolina, Chapel Hill, North Carolina, United States of America
- * E-mail: (MLH); (RJS)
| | - B. Matthew Fagan
- Human Embryonic Stem Cell Core Facility, University of North Carolina, Chapel Hill, North Carolina, United States of America
| | - Raluca Dumitru
- Department of Cell and Developmental Biology, Neuroscience Center, University of North Carolina, Chapel Hill, North Carolina, United States of America
| | - Jacquelyn J. Bower
- Department of Pathology and Laboratory Medicine, University of North Carolina, Chapel Hill, North Carolina, United States of America
| | - Swati Yadav
- Gene Therapy Center, University of North Carolina, Chapel Hill, North Carolina, United States of America
| | - Matthew H. Porteus
- Department of Pediatrics-Cancer Biology, Stanford University, Palo Alto, California, United States of America
| | - Larysa H. Pevny
- Department of Genetics, University of North Carolina, Chapel Hill, North Carolina, United States of America
- Department of Cell and Developmental Biology, Neuroscience Center, University of North Carolina, Chapel Hill, North Carolina, United States of America
| | - R. Jude Samulski
- Gene Therapy Center, University of North Carolina, Chapel Hill, North Carolina, United States of America
- Department of Pharmacology, University of North Carolina, Chapel Hill, North Carolina, United States of America
- * E-mail: (MLH); (RJS)
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54
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Kaluzhny D, Ilyinsky N, Shchekotikhin A, Sinkevich Y, Tsvetkov PO, Tsvetkov V, Veselovsky A, Livshits M, Borisova O, Shtil A, Shchyolkina A. Disordering of human telomeric G-quadruplex with novel antiproliferative anthrathiophenedione. PLoS One 2011; 6:e27151. [PMID: 22102877 PMCID: PMC3216923 DOI: 10.1371/journal.pone.0027151] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2011] [Accepted: 10/11/2011] [Indexed: 11/18/2022] Open
Abstract
Linear heteroareneanthracenediones have been shown to interfere with DNA functions, thereby causing death of human tumor cells and their drug resistant counterparts. Here we report the interaction of our novel antiproliferative agent 4,11-bis[(2-{[acetimido]amino}ethyl)amino]anthra[2,3-b]thiophene-5,10-dione with telomeric DNA structures studied by isothermal titration calorimetry, circular dichroism and UV absorption spectroscopy. New compound demonstrated a high affinity (K(ass)∼10⁶ M⁻¹) for human telomeric antiparallel quadruplex d(TTAGGG)₄ and duplex d(TTAGGG)₄∶d(CCCTAA)₄. Importantly, a ∼100-fold higher affinity was determined for the ligand binding to an unordered oligonucleotide d(TTAGGG TTAGAG TTAGGG TTAGGG unable to form quadruplex structures. Moreover, in the presence of Na+ the compound caused dramatic conformational perturbation of the telomeric G-quadruplex, namely, almost complete disordering of G-quartets. Disorganization of a portion of G-quartets in the presence of K+ was also detected. Molecular dynamics simulations were performed to illustrate how the binding of one molecule of the ligand might disrupt the G-quartet adjacent to the diagonal loop of telomeric G-quadruplex. Our results provide evidence for a non-trivial mode of alteration of G-quadruplex structure by tentative antiproliferative drugs.
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Affiliation(s)
- Dmitry Kaluzhny
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, Russian Federation.
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55
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Abstract
G-quadruplex structures formed by DNA at the human telomeres are attractive anticancer targets. Human telomeric sequences can adopt a diverse range of intramolecular G-quadruplex conformations: a parallel-stranded conformation was observed in the crystalline state, while at least four other forms were seen in K(+) solution, raising the question of which conformation is favored in crowded cellular environment. Here, we report the first NMR structure of a human telomeric G-quadruplex in crowded solution. We show that four different G-quadruplex conformations are converted to a propeller-type parallel-stranded G-quadruplex in K(+)-containing crowded solution due to water depletion. This study also reveals the formation of a new higher-order G-quadruplex structure under molecular crowding conditions. Our molecular dynamics simulations of solvent distribution provide insights at molecular level on the formation of parallel-stranded G-quadruplex in environment depleted of water. These results regarding human telomeric DNA can be extended to oncogenic promoters and other genomic G-rich sequences.
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Affiliation(s)
- Brahim Heddi
- School of Physical and Mathematical Sciences, Nanyang Technological University, Singapore
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56
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Zhou W, Brand NJ, Ying L. G-quadruplexes-novel mediators of gene function. J Cardiovasc Transl Res 2011; 4:256-70. [PMID: 21302011 DOI: 10.1007/s12265-011-9258-2] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/28/2010] [Accepted: 01/24/2011] [Indexed: 11/30/2022]
Abstract
Since the famous double-helix model was proposed, chromosomal DNA has been regarded as a rigid molecule containing the genetic information of an organism. It is clear now that DNA can adopt many transient, complex structures that can perform different biological functions. The G4 DNA (also called DNA G-quadruplex or G-tetraplex), a four-stranded DNA structure composed of stacked G-tetrads (guanine tetrads), has attracted much attention during the past two decades due to its ability to adopt a variety of structures and its possible biological functions. This review gives a glimpse on the structural diversity and biophysical properties of these fascinating DNA structures. Common methods that are widely used in investigating biophysical properties and biological functions of G4 DNA are described briefly. Next, bioinformatics studies that indicate evidence of evolutionary selection and potential functions of G4 DNA are discussed. Finally, examples of various biological functions of different G4 DNA are given, and potential roles of G4 DNA in respect of cardiovascular science are discussed.
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Affiliation(s)
- Wenhua Zhou
- Molecular Medicine, National Heart and Lung Institute, Imperial College London, UK.
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57
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Xu H, Gao S, Yang Q, Pan D, Wang L, Fan C. Amplified fluorescent recognition of g-quadruplex folding with a cationic conjugated polymer and DNA intercalator. ACS APPLIED MATERIALS & INTERFACES 2010; 2:3211-3216. [PMID: 21028820 DOI: 10.1021/am1006854] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/30/2023]
Abstract
The single stranded DNA (ssDNA) with G-rich sequence can fold into G-quadruplex via intramolecular hydrogen-bonding interaction in the presence of ligand. This structure conversion can be specifically detected by a fluorescence method based on different interaction between SYBR Green I (SG) and various DNA structures. SG is proved to intercalate into G-quadruplex and results in high fluorescence intensity, which can be further amplified by 6-fold through fluorescence resonance energy transfer (FRET) from a water-soluble cationic conjugated polymer (CCP) to SG due to the high affinity of positively charged CCP to negatively charged rigid G-quadruplex, whereas it is not performed for ssDNA in the absence of K(+). As a result, the ssDNA/SG/CCP complex can be used to detect potassium ions with improved selectivity in a label-free and cost-effective manner.
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Affiliation(s)
- Hui Xu
- School of Chemistry and Material Sciences, Ludong University, Yantai 264025, China
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58
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Nambiar M, Goldsmith G, Moorthy BT, Lieber MR, Joshi MV, Choudhary B, Hosur RV, Raghavan SC. Formation of a G-quadruplex at the BCL2 major breakpoint region of the t(14;18) translocation in follicular lymphoma. Nucleic Acids Res 2010; 39:936-48. [PMID: 20880994 PMCID: PMC3035451 DOI: 10.1093/nar/gkq824] [Citation(s) in RCA: 100] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
The t(14;18) translocation in follicular lymphoma is one of the most common chromosomal translocations. Most breaks on chromosome 18 are located at the 3′-UTR of the BCL2 gene and are mainly clustered in the major breakpoint region (MBR). Recently, we found that the BCL2 MBR has a non-B DNA character in genomic DNA. Here, we show that single-stranded DNA modeled from the template strand of the BCL2 MBR, forms secondary structures that migrate faster on native PAGE in the presence of potassium, due to the formation of intramolecular G-quadruplexes. Circular dichroism shows evidence for a parallel orientation for G-quadruplex structures in the template strand of the BCL2 MBR. Mutagenesis and the DMS modification assay confirm the presence of three guanine tetrads in the structure. 1H nuclear magnetic resonance studies further confirm the formation of an intramolecular G-quadruplex and a representative model has been built based on all of the experimental evidence. We also provide data consistent with the possible formation of a G-quadruplex structure at the BCL2 MBR within mammalian cells. In summary, these important features could contribute to the single-stranded character at the BCL2 MBR, thereby contributing to chromosomal fragility.
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Affiliation(s)
- Mridula Nambiar
- Department of Biochemistry, Indian Institute of Science, Bangalore-560 012, India
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59
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Wyatt HDM, West SC, Beattie TL. InTERTpreting telomerase structure and function. Nucleic Acids Res 2010; 38:5609-22. [PMID: 20460453 PMCID: PMC2943602 DOI: 10.1093/nar/gkq370] [Citation(s) in RCA: 123] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2010] [Revised: 04/20/2010] [Accepted: 04/26/2010] [Indexed: 12/15/2022] Open
Abstract
The Nobel Prize in Physiology or Medicine was recently awarded to Elizabeth Blackburn, Carol Greider and Jack Szostak for their pioneering studies on chromosome termini (telomeres) and their discovery of telomerase, the enzyme that synthesizes telomeres. Telomerase is a unique cellular reverse transcriptase that contains an integral RNA subunit, the telomerase RNA and a catalytic protein subunit, the telomerase reverse transcriptase (TERT), as well as several species-specific accessory proteins. Telomerase is essential for genome stability and is associated with a broad spectrum of human diseases including various forms of cancer, bone marrow failure and pulmonary fibrosis. A better understanding of telomerase structure and function will shed important insights into how this enzyme contributes to human disease. To this end, a series of high-resolution structural studies have provided critical information on TERT architecture and may ultimately elucidate novel targets for therapeutic intervention. In this review, we discuss the current knowledge of TERT structure and function, revealed through the detailed analysis of TERT from model organisms. To emphasize the physiological importance of telomeres and telomerase, we also present a general discussion of the human diseases associated with telomerase dysfunction.
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Affiliation(s)
- Haley D. M. Wyatt
- London Research Institute, Cancer Research UK, Clare Hall Laboratories, South Mimms, EN6 3LD, UK and Southern Alberta Cancer Research Institute and Departments of Biochemistry and Molecular Biology and Oncology, Calgary, Alberta, T2N 4N1, Canada
| | - Stephen C. West
- London Research Institute, Cancer Research UK, Clare Hall Laboratories, South Mimms, EN6 3LD, UK and Southern Alberta Cancer Research Institute and Departments of Biochemistry and Molecular Biology and Oncology, Calgary, Alberta, T2N 4N1, Canada
| | - Tara L. Beattie
- London Research Institute, Cancer Research UK, Clare Hall Laboratories, South Mimms, EN6 3LD, UK and Southern Alberta Cancer Research Institute and Departments of Biochemistry and Molecular Biology and Oncology, Calgary, Alberta, T2N 4N1, Canada
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60
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Abstract
The linear nature of eukaryotic chromosomes necessitates protection of their physical ends, the telomeres, because the DNA-repair machinery can misconstrue the ends as double-stranded DNA breaks. Thus, protection is crucial for avoiding an unwarranted DNA-damage response that could have catastrophic ramifications for the integrity and stability of the linear genome. In this Commentary, we attempt to define what is currently understood by the term ;telomere protection'. Delineating the defining boundaries of chromosome-end protection is important now more than ever, as it is becoming increasingly evident that, although unwanted DNA repair at telomeres must be avoided at all costs, the molecular players involved in recognition, signaling and repair of DNA damage might also serve to protect telomeres.
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Affiliation(s)
- Liana Oganesian
- The Salk Institute for Biological Studies, Molecular and Cellular Biology Department, La Jolla, CA 92037, USA
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61
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Murat P, Bonnet R, Van der Heyden A, Spinelli N, Labbé P, Monchaud D, Teulade-Fichou MP, Dumy P, Defrancq E. Template-assembled synthetic G-quadruplex (TASQ): a useful system for investigating the interactions of ligands with constrained quadruplex topologies. Chemistry 2010; 16:6106-14. [PMID: 20397247 DOI: 10.1002/chem.200903456] [Citation(s) in RCA: 52] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
A new biomolecular device for investigating the interactions of ligands with constrained DNA quadruplex topologies, using surface plasmon resonance (SPR), is reported. Biomolecular systems containing an intermolecular-like G-quadruplex motif 1 (parallel G-quadruplex conformation), an intramolecular G-quadruplex 2, and a duplex DNA 3 have been designed and developed. The method is based on the concept of template-assembled synthetic G-quadruplex (TASQ), whereby quadruplex DNA structures are assembled on a template that allows precise control of the parallel G-quadruplex conformation. Various known G-quadruplex ligands have been used to investigate the affinities of ligands for intermolecular 1 and intramolecular 2 DNA quadruplexes. As anticipated, ligands displaying a pi-stacking binding mode showed a higher binding affinity for intermolecular-like G-quadruplexes 1, whereas ligands with other binding modes (groove and/or loop binding) showed no significant difference in their binding affinities for the two quadruplexes 1 or 2. In addition, the present method has also provided information about the selectivity of ligands for G-quadruplex DNA over the duplex DNA. A numerical parameter, termed the G-quadruplex binding mode index (G4-BMI), has been introduced to express the difference in the affinities of ligands for intermolecular G-quadruplex 1 against intramolecular G-quadruplex 2. The G-quadruplex binding mode index (G4-BMI) of a ligand is defined as follows: G4-BMI=K(D)(intra)/K(D)(inter), where K(D)(intra) is the dissociation constant for intramolecular G-quadruplex 2 and K(D)(inter) is the dissociation constant for intermolecular G-quadruplex 1. In summary, the present work has demonstrated that the use of parallel-constrained quadruplex topology provides more precise information about the binding modes of ligands.
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Affiliation(s)
- Pierre Murat
- Département de Chimie Moléculaire, UMR CNRS 5250, Université Joseph Fourier, BP 53, 38041 Grenoble cedex 9, France
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62
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Paeschke K, McDonald KR, Zakian VA. Telomeres: structures in need of unwinding. FEBS Lett 2010; 584:3760-72. [PMID: 20637196 DOI: 10.1016/j.febslet.2010.07.007] [Citation(s) in RCA: 64] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2010] [Revised: 06/25/2010] [Accepted: 07/02/2010] [Indexed: 11/26/2022]
Abstract
Telomeres protect the ends of eukaryotic chromosomes from being recognized and processed as double strand breaks. In most organisms, telomeric DNA is highly repetitive with a high GC-content. Moreover, the G residues are concentrated in the strand running 3'-5' from the end of the chromosome towards its center. This G-rich strand is extended to form a 3' single-stranded tail that can form unusual secondary structures such as T-loops and G-quadruplex DNA. Both the duplex repeats and the single-stranded G-tail are assembled into stable protein-DNA complexes. The unique architecture, high GC content, and multi-protein association create particularly stable protein-DNA complexes that are a challenge for replication, recombination, and transcription. Helicases utilize the energy of nucleotide hydrolysis to unwind base paired nucleic acids and, in some cases, to displace proteins from them. The telomeric functions of helicases from the RecQ, Pifl, FANCJ, and DNA2 families are reviewed in this article. We summarize data showing that perturbation of their telomere activities can lead to telomere dysfunction and genome instability and in some cases human disease.
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Affiliation(s)
- Katrin Paeschke
- Department of Molecular Biology, Princeton University, Princeton, NJ 08544, USA
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63
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Taylor A, Taylor J, Watson GW, Boyd RJ. Electronic Energy Changes Associated with Guanine Quadruplex Formation: An Investigation at the Atomic Level. J Phys Chem B 2010; 114:9833-9. [DOI: 10.1021/jp912013k] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Alexis Taylor
- Department of Chemistry, Dalhousie University, Halifax, NS, Canada B3H 4J3, School of Chemistry, Trinity College, University of Dublin, Dublin 2, Ireland
| | - Justine Taylor
- Department of Chemistry, Dalhousie University, Halifax, NS, Canada B3H 4J3, School of Chemistry, Trinity College, University of Dublin, Dublin 2, Ireland
| | - Graeme W. Watson
- Department of Chemistry, Dalhousie University, Halifax, NS, Canada B3H 4J3, School of Chemistry, Trinity College, University of Dublin, Dublin 2, Ireland
| | - Russell J. Boyd
- Department of Chemistry, Dalhousie University, Halifax, NS, Canada B3H 4J3, School of Chemistry, Trinity College, University of Dublin, Dublin 2, Ireland
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64
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Lubitz I, Zikich D, Kotlyar A. Specific high-affinity binding of thiazole orange to triplex and G-quadruplex DNA. Biochemistry 2010; 49:3567-74. [PMID: 20329708 DOI: 10.1021/bi1000849] [Citation(s) in RCA: 134] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Interaction of Thiazole Orange (TO) with double-, triple-, and quadruple-stranded forms of DNA was studied. We have demonstrated by UV-vis absorption, circular dichroism (CD), and fluorescence spectroscopy that TO binds with much higher affinity to triplex and G-quadruplex DNA structures compared to double-stranded (ds) DNA. Complexes of the dye with DNA triplexes and G-quadruplexes are very stable and do not dissociate during chromatography and gel electrophoresis. TO binding to either triple- or quadruple-stranded DNA structures results in a >1000-fold increase in dye fluorescence. The fluorescence titration data showed that TO to triad and tetrad ratios, in tight complexes with the triplex and the G-quadruplex, are equal to 0.5 and 1, respectively. Preferential binding of TO to triplexes and G-quadruplexes enables selective detection of only these DNA forms in gels in the absence of free TO in electrophoresis running buffer. We have also demonstrated that incubation of U2OS cells with submicromolar concentrations of TO results in preferential staining of certain areas in the nucleus in contrast to DAPI which binds to dsDNA and efficiently stains regions that are unstained with TO. We suggest that TO staining may be useful for the detection of noncanonical structural motifs in genomic DNA.
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Affiliation(s)
- Irit Lubitz
- Department of Biochemistry, George S. Wise Faculty of Life Sciences, Tel Aviv University, Ramat Aviv, 69978 Israel
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65
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Min B, Collins K. Multiple mechanisms for elongation processivity within the reconstituted tetrahymena telomerase holoenzyme. J Biol Chem 2010; 285:16434-43. [PMID: 20363756 DOI: 10.1074/jbc.m110.119172] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
To maintain telomeres, telomerase evolved a unique biochemical activity: the use of a single-stranded RNA template for the synthesis of single-stranded DNA repeats. High repeat addition processivity (RAP) of the Tetrahymena telomerase holoenzyme requires association of the catalytic core with the telomere adaptor subcomplex (TASC) and an RPA1-related subunit (p82 or Teb1). Here, we used DNA binding and holoenzyme reconstitution assays to investigate the mechanism by which Teb1 and TASC confer high RAP. We show that TASC association with the recombinant telomerase catalytic core increases enzyme activity. Subsequent association of the Teb1 C-terminal domain with TASC confers the capacity for high RAP even though the Teb1 C-terminal domain does not provide a high-affinity DNA interaction site. Efficient RAP also requires suppression of nascent product folding mediated by the central Teb1 DNA-binding domains (DBDs). These sequence-specific high-affinity DBDs of Teb1 can be functionally substituted by the analogous DBDs of Tetrahymena Rpa1 to suppress nascent product folding but only if the Rpa1 high-affinity DBDs are physically tethered into holoenzyme context though the Teb1 C-terminal domain. Overall, our findings reveal multiple mechanisms and multiple surfaces of protein-DNA and protein-protein interaction that give rise to elongation processivity in the synthesis of a single-stranded nucleic acid product.
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Affiliation(s)
- Bosun Min
- Department of Molecular and Cell Biology, University of California, Berkeley, California 94720-3200, USA
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66
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Yeast telomerase subunit Est1p has guanine quadruplex-promoting activity that is required for telomere elongation. Nat Struct Mol Biol 2010; 17:202-9. [PMID: 20098422 DOI: 10.1038/nsmb.1760] [Citation(s) in RCA: 54] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2009] [Accepted: 11/04/2009] [Indexed: 11/08/2022]
Abstract
Telomeres are eukaryotic protein-DNA complexes found at the ends of linear chromosomes that are essential for maintaining genome integrity and are implicated in cellular aging and cancer. The guanine (G)-rich strand of telomeric DNA, usually elongated by the telomerase reverse transcriptase, can form a higher-order structure known as a G-quadruplex in vitro and in vivo. Several factors that promote or resolve G-quadruplexes have been identified, but the functional importance of these structures for telomere maintenance is not well understood. Here we show that the yeast telomerase subunit Est1p, known to be involved in telomerase recruitment to telomeres, can convert single-stranded telomeric G-rich DNA into a G-quadruplex structure in vitro in a Mg(2+)-dependent manner. Cells carrying Est1p mutants deficient in G-quadruplex formation in vitro showed gradual telomere shortening and cellular senescence, indicating a positive regulatory role for G-quadruplex in the maintenance of telomere length.
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67
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Moon IK, Jarstfer MB. Preparation of G-quartet structures and detection by native gel electrophoresis. Methods Mol Biol 2010; 608:51-63. [PMID: 20012415 DOI: 10.1007/978-1-59745-363-9_4] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/28/2023]
Abstract
Mounting evidence supporting the existence of DNA structures containing G-quartets in vivo makes these unique and diverse nucleic acid structures an important research subject, and future investigations aimed at elucidating their biological significance are expected. The purification and characterization of G-quartet structures can be challenging because their inherent structural diversity, complexity, and stability are sensitive to an array of variables. The stability of G-quartet structures depends on many factors including number of DNA strands involved in G-quartet formation, the identity of the stabilizing cation(s), the number and sequence context of the guanosines involved in stacking, the presence of single-stranded overhangs, the intervening loop size, and the identity of nucleosides in the loop. Here we detail current methods used in G-quartet preparation and their purification and characterization by native gel electrophoresis.
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Affiliation(s)
- Ian K Moon
- Division of Medicinal Chemistry and Natural Products, School of Pharmacy, University of North Carolina, Chapel Hill, NC, USA
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68
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Abstract
G-quartets are square planar arrangements of four guanine bases, which can form extraordinarily stable stacks when present in nucleic acid sequences. Such G-quadruplex structures were long regarded as an in vitro phenomenon, but the widespread presence of suitable sequences in genomes and the identification of proteins that stabilize, modify, or resolve these nucleic acid structures have provided circumstantial evidence for their physiological relevance. The therapeutic potential of small molecules that can stabilize or disrupt G-quadruplex structures has invigorated the field in recent years. Here we review some of the key observations that support biological functions for G-quadruplex DNA as well as the techniques and tools that have enabled researchers to probe these structures and their interactions with proteins and small molecules.
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Affiliation(s)
- Tracy M Bryan
- Children's Medical Research Institute and the University of Sydney, Sydney, Australia
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69
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Jain AK, Reddy VV, Paul A, K. M, Bhattacharya S. Synthesis and Evaluation of a Novel Class of G-Quadruplex-Stabilizing Small Molecules Based on the 1,3-Phenylene-Bis(piperazinyl benzimidazole) System. Biochemistry 2009; 48:10693-704. [DOI: 10.1021/bi9003815] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Akash K. Jain
- Department of Organic Chemistry, Indian Institute of Science, Bangalore 560012, India
| | - Vishnu Vardhan Reddy
- Department of Biochemistry, Indian Institute of Science, Bangalore 560012, India
| | - Ananya Paul
- Department of Organic Chemistry, Indian Institute of Science, Bangalore 560012, India
| | - Muniyappa K.
- Department of Biochemistry, Indian Institute of Science, Bangalore 560012, India
| | - Santanu Bhattacharya
- Department of Organic Chemistry, Indian Institute of Science, Bangalore 560012, India
- Chemical Biology Unit, Jawaharlal Nehru Centre for Advanced Scientific Research, Bangalore 560012, India
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70
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Arora A, Maiti S. Stability and molecular recognition of quadruplexes with different loop length in the absence and presence of molecular crowding agents. J Phys Chem B 2009; 113:8784-92. [PMID: 19480441 DOI: 10.1021/jp809486g] [Citation(s) in RCA: 54] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
G-quadruplexes are known to be potential targets for therapeutic intervention, thus resulting in development of various quadruplex interacting ligands. However, until now, no systemic study has been performed to understand molecular recognition of quadruplex in the presence of molecular crowding agents mimicking cellular conditions. The stability and molecular recognition of quadruplex can be influenced by loop length. Herein, we attempted to study the interaction of 5,10,15,20-tetrakis(1-methyl-4-pyridyl)-21H,23H-porphine (TMPyP4), a well-known G-quadruplex binding ligand with various DNA quadruplexes differing in total loop length and loop arrangement in both the absence and presence of molecular crowding agents. Results obtained from CD studies revealed that longer loops favor mixed and antiparallel conformation in both the absence and presence of 30% ethylene glycol. UV thermal melting studies revealed that the stability and formation of quadruplex increases in the presence of 30% ethylene glycol. Moreover, the binding of TMPyP4 molecule to both of the binding sites in different quadruplexes with total loop length varying from 3 to 9 remains unchanged in both the absence and presence of 30% ethylene glycol. The binding affinity (K(a)) of TMPyP4 was found to be decreased approximately by 1 order for the quadruplex sequences with total loop length varying from 11 to 15 in the presence of molecular crowding agents.
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Affiliation(s)
- Amit Arora
- Institute of Genomics and Integrative Biology, CSIR, Delhi, India
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71
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Sekaran VG, Soares J, Jarstfer MB. Structures of telomerase subunits provide functional insights. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2009; 1804:1190-201. [PMID: 19665593 DOI: 10.1016/j.bbapap.2009.07.019] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/05/2009] [Revised: 07/09/2009] [Accepted: 07/28/2009] [Indexed: 01/14/2023]
Abstract
BACKGROUND Telomerase continues to generate substantial attention both because of its pivotal roles in cellular proliferation and aging and because of its unusual structure and mechanism. By replenishing telomeric DNA lost during the cell cycle, telomerase overcomes one of the many hurdles facing cellular immortalization. Functionally, telomerase is a reverse transcriptase, and it shares structural and mechanistic features with this class of nucleotide polymerases. Telomerase is a very unusual reverse transcriptase because it remains stably associated with its template and because it reverse transcribes multiple copies of its template onto a single primer in one reaction cycle. SCOPE OF REVIEW Here, we review recent findings that illuminate our understanding of telomerase. Even though the specific emphasis is on structure and mechanism, we also highlight new insights into the roles of telomerase in human biology. GENERAL SIGNIFICANCE Recent advances in the structural biology of telomerase, including high resolution structures of the catalytic subunit of a beetle telomerase and two domains of a ciliate telomerase catalytic subunit, provide new perspectives into telomerase biochemistry and reveal new puzzles.
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Affiliation(s)
- Vijay G Sekaran
- Division of Medicinal Chemistry and Natural Products, Eshelman School of Pharmacy, The University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, USA
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72
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Keene FR, Smith JA, Collins JG. Metal complexes as structure-selective binding agents for nucleic acids. Coord Chem Rev 2009. [DOI: 10.1016/j.ccr.2009.01.004] [Citation(s) in RCA: 167] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
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73
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Lipps HJ, Rhodes D. G-quadruplex structures: in vivo evidence and function. Trends Cell Biol 2009; 19:414-22. [PMID: 19589679 DOI: 10.1016/j.tcb.2009.05.002] [Citation(s) in RCA: 666] [Impact Index Per Article: 41.6] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2009] [Revised: 05/14/2009] [Accepted: 05/18/2009] [Indexed: 10/20/2022]
Abstract
Although many biochemical and structural studies have demonstrated that DNA sequences containing runs of adjacent guanines spontaneously fold into G-quadruplex DNA structures in vitro, only recently has evidence started to accumulate for their presence and function in vivo. Genome-wide analyses have revealed that functional genomic regions from highly divergent organisms are enriched in DNA sequences with G-quadruplex-forming potential, suggesting that G-quadruplexes could provide a nucleic-acid-based mechanism for regulating telomere maintenance, as well as transcription, replication and translation. Here, we review recent studies aimed at uncovering the in vivo presence and function of G-quadruplexes in genomes and RNA, with a particular focus on telomeric G-quadruplexes and how their formation and resolution is regulated to permit telomere synthesis.
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Affiliation(s)
- Hans J Lipps
- Institute of Cell Biology, University Witten/Herdecke, Stockumer Str. 10, 58448 Witten, Germany
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74
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Herbert BS, Huppert JL, Johnson FB, Lane AN, Phan AT. Meeting report: second international meeting on quadruplex DNA. Biochimie 2009; 91:1059-65. [PMID: 19555734 DOI: 10.1016/j.biochi.2009.06.011] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2009] [Accepted: 06/15/2009] [Indexed: 01/27/2023]
Abstract
A two and a half day meeting on G-quadruplexes was held in Louisville, KY, USA (April 18-21, 2009). A specific goal of this conference was to promote discussion on the biology of G-quadruplexes. In practice this was represented in four main ways, namely in biophysics, bio/nanotechnology, therapeutics, and what might be termed "intrinsic biology". Research into the basic biophysical and structural properties of G-quadruplexes continues to be important for understanding biology, and for optimizing aptamers for therapeutic and bio/technological purposes. The meeting comprised two Keynote lectures, twenty-three invited talks, and forty-two posters covering various aspects of these topics using a wide variety of technologies.
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Affiliation(s)
- Brittney-Shea Herbert
- Dept of Medical and Molecular Genetics, Indiana University Melvin and Bren Simon Cancer Center, Indiana University Center for Regenerative Biology and Medicine, Indiana University School of Medicine, IB 242 Indianapolis, IN 46202, USA.
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75
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Zambre VP, Murumkar PR, Giridhar R, Yadav MR. Structural Investigations of Acridine Derivatives by CoMFA and CoMSIA Reveal Novel Insight into Their Structures toward DNA G-Quadruplex Mediated Telomerase Inhibition and Offer a Highly Predictive 3D-Model for Substituted Acridines. J Chem Inf Model 2009; 49:1298-311. [DOI: 10.1021/ci900036w] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Vishal P. Zambre
- Pharmacy Department, Faculty of Technology and Engineering, Kalabhavan, The M.S. University of Baroda, Vadodara - 390001, Gujarat, India
| | - Prashant R. Murumkar
- Pharmacy Department, Faculty of Technology and Engineering, Kalabhavan, The M.S. University of Baroda, Vadodara - 390001, Gujarat, India
| | - Rajani Giridhar
- Pharmacy Department, Faculty of Technology and Engineering, Kalabhavan, The M.S. University of Baroda, Vadodara - 390001, Gujarat, India
| | - Mange Ram Yadav
- Pharmacy Department, Faculty of Technology and Engineering, Kalabhavan, The M.S. University of Baroda, Vadodara - 390001, Gujarat, India
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76
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Wu Y, Brosh RM. FANCJ helicase operates in the Fanconi Anemia DNA repair pathway and the response to replicational stress. Curr Mol Med 2009; 9:470-82. [PMID: 19519404 PMCID: PMC2763586 DOI: 10.2174/156652409788167159] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Fanconi anemia (FA) is an autosomal recessive disorder characterized by multiple congenital anomalies, progressive bone marrow failure, and high cancer risk. Cells from FA patients exhibit spontaneous chromosomal instability and hypersensitivity to DNA interstrand cross-linking (ICL) agents. Although the precise mechanistic details of the FA/BRCA pathway of ICL-repair are not well understood, progress has been made in the identification of the FA proteins that are required for the pathway. Among the 13 FA complementation groups from which all the FA genes have been cloned, only a few of the FA proteins are predicted to have direct roles in DNA metabolism. One of the more recently identified FA proteins, shown to be responsible for complementation of the FA complementation group J, is the BRCA1 Associated C-terminal Helicase (BACH1, designated FANCJ), originally identified as a protein associated with breast cancer. FANCJ has been proposed to function downstream of FANCD2 monoubiquitination, a critical event in the FA pathway. Evidence supports a role for FANCJ in a homologous recombination (HR) pathway of double strand break (DSB) repair. In this review, we will summarize the current knowledge in terms of FANCJ functions through its enzymatic activities and protein interactions. The molecular roles of FANCJ in DNA repair and the response to replicational stress will be discussed.
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Affiliation(s)
- Yuliang Wu
- Laboratory of Molecular Gerontology, National Institute on Aging, NIH, 5600 Nathan Shock Drive, Baltimore, MD 21224, USA
| | - Robert M. Brosh
- Laboratory of Molecular Gerontology, National Institute on Aging, NIH, 5600 Nathan Shock Drive, Baltimore, MD 21224, USA
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77
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Fu YT, Keppler BR, Soares J, Jarstfer MB. BRACO19 analog dimers with improved inhibition of telomerase and hPot 1. Bioorg Med Chem 2009; 17:2030-7. [DOI: 10.1016/j.bmc.2009.01.015] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2008] [Revised: 01/08/2009] [Accepted: 01/09/2009] [Indexed: 12/20/2022]
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78
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Pedroso IM, Hayward W, Fletcher TM. The effect of the TRF2 N-terminal and TRFH regions on telomeric G-quadruplex structures. Nucleic Acids Res 2009; 37:1541-54. [PMID: 19139067 PMCID: PMC2655686 DOI: 10.1093/nar/gkn1081] [Citation(s) in RCA: 42] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
The sequence of human telomeric DNA consists of tandem repeats of 5′-d(TTAGGG)-3′. This guanine-rich DNA can form G-quadruplex secondary structures which may affect telomere maintenance. A current model for telomere protection by the telomere-binding protein, TRF2, involves the formation of a t-loop which is stabilized by a strand invasion-like reaction. This type of reaction may be affected by G-quadruplex structures. We analyzed the influence of the arginine-rich, TRF2 N-terminus (TRF2B), as well as this region plus the TRFH domain of TRF2 (TRF2BH), on the structure of G-quadruplexes. Circular dichroism results suggest that oligonucleotides with 4, 7 and 8 5′-d(TTAGGG)-3′ repeats form hybrid structures, a mix of parallel/antiparallel strand orientation, in K+. TRF2B stimulated the formation of parallel-stranded structures and, in some cases, intermolecular structures. TRF2BH also stimulated intermolecular but not parallel-stranded structures. Only full-length TRF2 and TRF2BH stimulated uptake of a telomeric single-stranded oligonucleotide into a plasmid containing telomeric DNA in the presence of K+. The results in this study suggest that G-quadruplex formation inhibits oligonucleotide uptake into the plasmid, but the inhibition can be overcome by TRF2. This study is the first analysis of the effects of TRF2 domains on G-quadruplex structures and has implications for the role of G-quadruplexes and TRF2 in the formation of t-loops.
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Affiliation(s)
- Ilene M Pedroso
- Department of Biochemistry and Molecular Biology, University of Miami Miller School of Medicine, Miami, FL 33101-6129, USA
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79
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Tao Ng MT, Li X, Wang Y, Zhou T, Yang Z, Foo HY, Li T. Site-Specific Cleavage of G-quadruplexes Formed by Oxytricha Telometric Repeats. Aust J Chem 2009. [DOI: 10.1071/ch09061] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
We demonstrate that certain G-quadruplex structures formed by Oxytricha telomeric repeats possess DNA-cleavage ability. Further studies verify that this cleavage activity is both site-specific and G-quadruplex-dependent.
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80
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Nagata T, Takada Y, Ono A, Nagata K, Konishi Y, Nukina T, Ono M, Matsugami A, Furukawa A, Fujimoto N, Fukuda H, Nakagama H, Katahira M. Elucidation of the mode of interaction in the UP1-telomerase RNA-telomeric DNA ternary complex which serves to recruit telomerase to telomeric DNA and to enhance the telomerase activity. Nucleic Acids Res 2008; 36:6816-24. [PMID: 18953025 PMCID: PMC2588520 DOI: 10.1093/nar/gkn767] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
We found that UP1, a proteolytic product of heterogeneous nuclear ribonucleoprotein A1 (hnRNP A1), both enhances and represses the telomerase activity. The formation of the UP1–telomerase RNA–telomeric DNA ternary complex was revealed by a gel retardation experiment. The interactions in the ternary and binary complexes were elucidated by NMR. UP1 has two nucleic acid-binding domains, BD1 and BD2. In the UP1–telomerase RNA binary complex, both BD1 and BD2 interact with telomerase RNA. Interestingly, when telomeric DNA was added to the binary complex, telomeric DNA bound to BD1 in place of telomerase RNA. Thus, BD1 basically binds to telomeric DNA, while BD2 mainly binds to telomerase RNA, which resulted in the formation of the ternary complex. Here, UP1 bridges telomerase and telomeric DNA. It is supposed that UP1/hnRNP A1 serves to recruit telomerase to telomeric DNA through the formation of the ternary complex. A model has been proposed for how hnRNP A1/UP1 contributes to enhancement of the telomerase activity through recruitment and unfolding of the quadruplex of telomeric DNA.
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Affiliation(s)
- Takashi Nagata
- Supramolecular Biology, International Graduate School of Arts and Sciences, Yokohama City University, Yokohama, Japan
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81
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Lane AN, Chaires JB, Gray RD, Trent JO. Stability and kinetics of G-quadruplex structures. Nucleic Acids Res 2008; 36:5482-515. [PMID: 18718931 PMCID: PMC2553573 DOI: 10.1093/nar/gkn517] [Citation(s) in RCA: 587] [Impact Index Per Article: 34.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2008] [Revised: 07/26/2008] [Accepted: 07/29/2008] [Indexed: 12/30/2022] Open
Abstract
In this review, we give an overview of recent literature on the structure and stability of unimolecular G-rich quadruplex structures that are relevant to drug design and for in vivo function. The unifying theme in this review is energetics. The thermodynamic stability of quadruplexes has not been studied in the same detail as DNA and RNA duplexes, and there are important differences in the balance of forces between these classes of folded oligonucleotides. We provide an overview of the principles of stability and where available the experimental data that report on these principles. Significant gaps in the literature have been identified, that should be filled by a systematic study of well-defined quadruplexes not only to provide the basic understanding of stability both for design purposes, but also as it relates to in vivo occurrence of quadruplexes. Techniques that are commonly applied to the determination of the structure, stability and folding are discussed in terms of information content and limitations. Quadruplex structures fold and unfold comparatively slowly, and DNA unwinding events associated with transcription and replication may be operating far from equilibrium. The kinetics of formation and resolution of quadruplexes, and methodologies are discussed in the context of stability and their possible biological occurrence.
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Affiliation(s)
- Andrew N Lane
- Structural Biology Program, JG Brown Cancer Center, University of Louisville, KY 40202, USA.
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82
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Telomerase recruitment by the telomere end binding protein-β facilitates G-quadruplex DNA unfolding in ciliates. Nat Struct Mol Biol 2008; 15:598-604. [DOI: 10.1038/nsmb.1422] [Citation(s) in RCA: 113] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2007] [Accepted: 03/21/2008] [Indexed: 11/08/2022]
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83
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FANCJ helicase defective in Fanconia anemia and breast cancer unwinds G-quadruplex DNA to defend genomic stability. Mol Cell Biol 2008; 28:4116-28. [PMID: 18426915 DOI: 10.1128/mcb.02210-07] [Citation(s) in RCA: 334] [Impact Index Per Article: 19.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023] Open
Abstract
FANCJ mutations are associated with breast cancer and genetically linked to the bone marrow disease Fanconi anemia (FA). The genomic instability of FA-J mutant cells suggests that FANCJ helicase functions in the replicational stress response. A putative helicase with sequence similarity to FANCJ in Caenorhabditis elegans (DOG-1) and mouse (RTEL) is required for poly(G) tract maintenance, suggesting its involvement in the resolution of alternate DNA structures that impede replication. Under physiological conditions, guanine-rich sequences spontaneously assemble into four-stranded structures (G quadruplexes [G4]) that influence genomic stability. FANCJ unwound G4 DNA substrates in an ATPase-dependent manner. FANCJ G4 unwinding is specific since another superfamily 2 helicase, RECQ1, failed to unwind all G4 substrates tested under conditions in which the helicase unwound duplex DNA. Replication protein A stimulated FANCJ G4 unwinding, whereas the mismatch repair complex MSH2/MSH6 inhibited this activity. FANCJ-depleted cells treated with the G4-interactive compound telomestatin displayed impaired proliferation and elevated levels of apoptosis and DNA damage compared to small interfering RNA control cells, suggesting that G4 DNA is a physiological substrate of FANCJ. Although the FA pathway has been classically described in terms of interstrand cross-link (ICL) repair, the cellular defects associated with FANCJ mutation extend beyond the reduced ability to repair ICLs and involve other types of DNA structural roadblocks to replication.
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84
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Bryan TM, Jarstfer MB. Interrogation of G-quadruplex–protein interactions. Methods 2007; 43:332-9. [DOI: 10.1016/j.ymeth.2007.05.001] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2007] [Accepted: 05/01/2007] [Indexed: 10/22/2022] Open
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85
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De Cian A, Cristofari G, Reichenbach P, De Lemos E, Monchaud D, Teulade-Fichou MP, Shin-ya K, Lacroix L, Lingner J, Mergny JL. Reevaluation of telomerase inhibition by quadruplex ligands and their mechanisms of action. Proc Natl Acad Sci U S A 2007; 104:17347-52. [PMID: 17954919 PMCID: PMC2077259 DOI: 10.1073/pnas.0707365104] [Citation(s) in RCA: 229] [Impact Index Per Article: 12.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2007] [Indexed: 11/18/2022] Open
Abstract
Quadruplex ligands are often considered as telomerase inhibitors. Given the fact that some of these molecules are present in the clinical setting, it is important to establish the validity of this assertion. To analyze the effects of these compounds, we used a direct assay with telomerase-enriched extracts. The comparison of potent ligands from various chemical families revealed important differences in terms of effects on telomerase initiation and processivity. Although most quadruplex ligands may lock a quadruplex-prone sequence into a quadruplex structure that inhibits the initiation of elongation by telomerase, the analysis of telomerase-elongation steps revealed that only a few molecules interfered with the processivity of telomerase (i.e., inhibit elongation once one or more repeats have been incorporated). The demonstration that these molecules are actually more effective inhibitors of telomeric DNA amplification than extension by telomerase contributes to the already growing suspicion that quadruplex ligands are not simple telomerase inhibitors but, rather, constitute a different class of biologically active molecules. We also demonstrate that the popular telomeric repeat amplification protocol is completely inappropriate for the determination of telomerase inhibition by quadruplex ligands, even when PCR controls are included. As a consequence, the inhibitory effect of many quadruplex ligands has been overestimated.
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Affiliation(s)
- Anne De Cian
- *Institut National de la Santé et de la Recherche Médicale, U565, F-75231 Paris Cedex 05, France
- Centre National de la Recherche Scientifique, Unité Mixte de Recherche 5153, F-75231 Paris Cedex 05, France
- Régulation et Dynamique des Génomes, Muséum National d'Histoire Naturelle, USM 503, 43 Rue Cuvier, CP26, F-75231 Paris Cedex 05, France
| | - Gael Cristofari
- Swiss Institute for Experimental Cancer Research (ISREC) and National Center of Competence in Research “Frontiers in Genetics,” Ecole Polytechnique Federale de Lausanne (EPFL), Chemin des Boveresses 155, CH-1066 Epalinges s/Lausanne Switzerland
| | - Patrick Reichenbach
- Swiss Institute for Experimental Cancer Research (ISREC) and National Center of Competence in Research “Frontiers in Genetics,” Ecole Polytechnique Federale de Lausanne (EPFL), Chemin des Boveresses 155, CH-1066 Epalinges s/Lausanne Switzerland
| | - Elsa De Lemos
- Institut Curie, Section Recherche, Centre National de la Recherche Scientifique Unité Mixte de Recherche 176, Centre Universitaire Paris XI, Bât. 110, 91405 Orsay, France; and
| | - David Monchaud
- Institut Curie, Section Recherche, Centre National de la Recherche Scientifique Unité Mixte de Recherche 176, Centre Universitaire Paris XI, Bât. 110, 91405 Orsay, France; and
| | - Marie-Paule Teulade-Fichou
- Institut Curie, Section Recherche, Centre National de la Recherche Scientifique Unité Mixte de Recherche 176, Centre Universitaire Paris XI, Bât. 110, 91405 Orsay, France; and
| | - Kazuo Shin-ya
- **Chemical Biology Team, Biological Information Research Center (BIRC), National Institute of Advanced Industrial Science and Technology (AIST), Tokyo Waterfront Bio-IT Research Building 2-42 Aomi, Koto-ku, Tokyo 135-0064, Japan
| | - Laurent Lacroix
- *Institut National de la Santé et de la Recherche Médicale, U565, F-75231 Paris Cedex 05, France
- Centre National de la Recherche Scientifique, Unité Mixte de Recherche 5153, F-75231 Paris Cedex 05, France
- Régulation et Dynamique des Génomes, Muséum National d'Histoire Naturelle, USM 503, 43 Rue Cuvier, CP26, F-75231 Paris Cedex 05, France
| | - Joachim Lingner
- Swiss Institute for Experimental Cancer Research (ISREC) and National Center of Competence in Research “Frontiers in Genetics,” Ecole Polytechnique Federale de Lausanne (EPFL), Chemin des Boveresses 155, CH-1066 Epalinges s/Lausanne Switzerland
| | - Jean-Louis Mergny
- *Institut National de la Santé et de la Recherche Médicale, U565, F-75231 Paris Cedex 05, France
- Centre National de la Recherche Scientifique, Unité Mixte de Recherche 5153, F-75231 Paris Cedex 05, France
- Régulation et Dynamique des Génomes, Muséum National d'Histoire Naturelle, USM 503, 43 Rue Cuvier, CP26, F-75231 Paris Cedex 05, France
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86
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Pedroso IM, Duarte LF, Yanez G, Burkewitz K, Fletcher TM. Sequence specificity of inter- and intramolecular G-quadruplex formation by human telomeric DNA. Biopolymers 2007; 87:74-84. [PMID: 17549693 DOI: 10.1002/bip.20790] [Citation(s) in RCA: 47] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Human telomeric DNA consists of tandem repeats of the sequence 5'-d(TTAGGG)-3'. Guanine-rich DNA, such as that seen at telomeres, forms G-quadruplex secondary structures. Alternative forms of G-quadruplex structures can have differential effects on activities involved in telomere maintenance. With this in mind, we analyzed the effect of sequence and length of human telomeric DNA on G-quadruplex structures by native polyacrylamide gel electrophoresis and circular dichroism. Telomeric oligonucleotides shorter than four, 5'-d(TTAGGG)-3' repeats formed intermolecular G-quadruplexes. However, longer telomeric repeats formed intramolecular structures. Altering the 5'-d(TTAGGG)-3' to 5'-d(TTAGAG)-3' in any one of the repeats of 5'-d(TTAGGG)(4)-3' converted an intramolecular structure to intermolecular G-quadruplexes with varying degrees of parallel or anti-parallel-stranded character, depending on the length of incubation time and DNA sequence. These structures were most abundant in K(+)-containing buffers. Higher-order structures that exhibited ladders on polyacrylamide gels were observed only for oligonucleotides with the first telomeric repeat altered. Altering the sequence of 5'-d(TTAGGG)(8)-3' did not result in the substantial formation of intermolecular structures even when the oligonucleotide lacked four consecutive telomeric repeats. However, many of these intramolecular structures shared common features with intermolecular structures formed by the shorter oligonucleotides. The wide variability in structure formed by human telomeric sequence suggests that telomeric DNA structure can be easily modulated by proteins, oxidative damage, or point mutations resulting in conversion from one form of G-quadruplex to another.
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Affiliation(s)
- Ilene M Pedroso
- Department of Biochemistry and Molecular Biology, University of Miami School of Medicine, Miami, FL 33101-6129, USA
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87
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Phan AT, Kuryavyi V, Luu KN, Patel DJ. Structure of two intramolecular G-quadruplexes formed by natural human telomere sequences in K+ solution. Nucleic Acids Res 2007; 35:6517-25. [PMID: 17895279 PMCID: PMC2095816 DOI: 10.1093/nar/gkm706] [Citation(s) in RCA: 422] [Impact Index Per Article: 23.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Intramolecular G-quadruplexes formed by human telomere sequences are attractive anticancer targets. Recently, four-repeat human telomere sequences have been shown to form two different intramolecular (3 + 1) G-quadruplexes in K(+) solution (Form 1 and Form 2). Here we report on the solution structures of both Form 1 and Form 2 adopted by natural human telomere sequences. Both structures contain the (3 + 1) G-tetrad core with one double-chain-reversal and two edgewise loops, but differ in the successive order of loop arrangements within the G-quadruplex scaffold. Our results provide the structural details at the two ends of the G-tetrad core in the context of natural sequences and information on different loop conformations. This structural information might be important for our understanding of telomere G-quadruplex structures and for anticancer drug design targeted to such scaffolds.
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Affiliation(s)
- Anh Tuân Phan
- Structural Biology Program, Memorial Sloan-Kettering Cancer Center, New York, NY 10021, USA and Division of Physics and Applied Physics, School of Physical and Mathematical Sciences, Nanyang Technological University, Singapore 637551, Singapore
- *To whom correspondence should be addressed. +65 6514 1915+65 6794 1325 Correspondence may also be addressed to Dinshaw J. Patel. Tel:+ 1 212 639 7207+ 1 212 717 3066
| | - Vitaly Kuryavyi
- Structural Biology Program, Memorial Sloan-Kettering Cancer Center, New York, NY 10021, USA and Division of Physics and Applied Physics, School of Physical and Mathematical Sciences, Nanyang Technological University, Singapore 637551, Singapore
| | - Kim Ngoc Luu
- Structural Biology Program, Memorial Sloan-Kettering Cancer Center, New York, NY 10021, USA and Division of Physics and Applied Physics, School of Physical and Mathematical Sciences, Nanyang Technological University, Singapore 637551, Singapore
| | - Dinshaw J. Patel
- Structural Biology Program, Memorial Sloan-Kettering Cancer Center, New York, NY 10021, USA and Division of Physics and Applied Physics, School of Physical and Mathematical Sciences, Nanyang Technological University, Singapore 637551, Singapore
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88
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Luu KN, Phan AT, Kuryavyi V, Lacroix L, Patel DJ. Structure of the human telomere in K+ solution: an intramolecular (3 + 1) G-quadruplex scaffold. J Am Chem Soc 2007; 128:9963-70. [PMID: 16866556 PMCID: PMC4692383 DOI: 10.1021/ja062791w] [Citation(s) in RCA: 681] [Impact Index Per Article: 37.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
We present the intramolecular G-quadruplex structure of human telomeric DNA in physiologically relevant K(+) solution. This G-quadruplex, whose (3 + 1) topology differs from folds reported previously in Na(+) solution and in a K(+)-containing crystal, involves the following: one anti.syn.syn.syn and two syn.anti.anti.anti G-tetrads; one double-chain reversal and two edgewise loops; three G-tracts oriented in one direction and the fourth in the opposite direction. The topological characteristics of this (3 + 1) G-quadruplex scaffold should provide a unique platform for structure-based anticancer drug design targeted to human telomeric DNA.
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Affiliation(s)
- Kim Ngoc Luu
- Structural Biology Program, Memorial Sloan-Kettering Cancer Center, New York, New York 10021
| | - Anh Tuân Phan
- Structural Biology Program, Memorial Sloan-Kettering Cancer Center, New York, New York 10021
| | - Vitaly Kuryavyi
- Structural Biology Program, Memorial Sloan-Kettering Cancer Center, New York, New York 10021
| | - Laurent Lacroix
- Laboratoire de Biophysique, Muséum National d’Histoire Naturelle, INSERM UR565, CNRS UMR5153, 75231 Paris Cedex 05, France
| | - Dinshaw J. Patel
- Structural Biology Program, Memorial Sloan-Kettering Cancer Center, New York, New York 10021
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89
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Oganesian L, Graham ME, Robinson PJ, Bryan TM. Telomerase Recognizes G-Quadruplex and Linear DNA as Distinct Substrates. Biochemistry 2007; 46:11279-90. [PMID: 17877374 DOI: 10.1021/bi700993q] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Telomeric DNA can assemble into a nonlinear, higher-order conformation known as a G-quadruplex. Here, we demonstrate by electrospray ionization mass spectrometry that the two repeat telomeric sequence d(TGGGGTTGGGGT) from Tetrahymena thermophila gives rise to a novel parallel four-stranded G-quadruplex in the presence of sodium. The G-quadruplex directly interacts with the catalytic subunit of Tetrahymena telomerase (TERT) with micromolar affinity, and the presence of telomerase RNA is not obligatory for this interaction. Both N- and C-terminal halves of TERT bind the G-quadruplex independently. This G-quadruplex is a robust substrate for both recombinant and cell extract-derived telomerase in vitro. Furthermore, the G-quadruplex weakens the affinity of wild-type telomerase for the incoming nucleotide (dTTP) and likely perturbs the nucleotide binding pocket of the enzyme. In agreement with this, a lysine to alanine substitution at amino acid 538 (K538A) within motif 1 of TERT dramatically reduces the ability of telomerase to extend G-quadruplex but not linear DNA. The K538A mutant retains binding affinity for the quadruplex. This suggests that telomerase undergoes changes in conformation in its active site to specifically accommodate binding and subsequent extension of G-quadruplex DNA. We propose that telomerase recognizes G-quadruplex DNA as a substrate that is distinct from linear DNA.
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Affiliation(s)
- Liana Oganesian
- Children's Medical Research Institute, 214 Hawkesbury Road, Westmead NSW 2145, Australia and University of Sydney, NSW 2006, Australia
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90
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Gunaratnam M, Greciano O, Martins C, Reszka AP, Schultes CM, Morjani H, Riou JF, Neidle S. Mechanism of acridine-based telomerase inhibition and telomere shortening. Biochem Pharmacol 2007; 74:679-89. [PMID: 17631279 DOI: 10.1016/j.bcp.2007.06.011] [Citation(s) in RCA: 112] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2007] [Revised: 06/02/2007] [Accepted: 06/05/2007] [Indexed: 11/28/2022]
Abstract
The trisubstituted acridine compound BRACO-19 has been developed as a ligand for stabilising G-quadruplex structures. It is shown here that BRACO-19 produces short- and long-term growth arrest in cancer cell lines, and is significantly less potent in a normal cell line. BRACO-19 reduces telomerase activity and long-term telomere length attrition is observed. It is also shown that BRACO-19 binds to telomeric single-stranded overhang DNA, consistent with quadruplex formation, and the single-stranded protein hPOT1 has been shown to be displaced from the overhang in vitro and in cellular experiments. It is concluded that the cellular activity of BRACO-19 can be ascribed both to the uncapping of 3' telomere ends and to telomere shortening that may preferentially affect cells with short telomeres.
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Affiliation(s)
- Mekala Gunaratnam
- CRUK Biomolecular Structure Group, The School of Pharmacy, University of London, 29-39 Brunswick Square, London WC1N 1AX, UK
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91
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Matsugami A, Xu Y, Noguchi Y, Sugiyama H, Katahira M. Structure of a human telomeric DNA sequence stabilized by 8-bromoguanosine substitutions, as determined by NMR in a K+
solution. FEBS J 2007; 274:3545-3556. [PMID: 17561958 DOI: 10.1111/j.1742-4658.2007.05881.x] [Citation(s) in RCA: 81] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The structure of human telomeric DNA is controversial; it depends upon the sequence contexts and the methodologies used to determine it. The solution structure in the presence of K(+) is particularly interesting, but the structure is yet to be elucidated, due to possible conformational heterogeneity. Here, a unique strategy is applied to stabilize one such structure in a K(+) solution by substituting guanosines with 8-bromoguanosines at proper positions. The resulting spectra are cleaner and led to determination of the structure at a high atomic resolution. This demonstrates that the application of 8-bromoguanosine is a powerful tool to overcome the difficulty of nucleic acid structure determination arising from conformational heterogeneity. The obtained structure is a mixed-parallel/antiparallel quadruplex. The structure of telomeric DNA was recently reported in another study, in which stabilization was brought about by mutation and resultant additional interactions [Luu KN, Phan AT, Kuryavyi V, Lacroix L & Patel DJ (2006) Structure of the human telomere in K(+) solution: an intramolecular (3+1) G-quadruplex scaffold. J Am Chem Soc 128, 9963-9970]. The structure of the guanine tracts was similar between the two. However, a difference was seen for loops connecting guanine tracts, which may play a role in the higher order arrangement of telomeres. Our structure can be utilized to design a small molecule which stabilizes the quadruplex. This type of molecule is supposed to inhibit a telomerase and thus is expected to be a candidate anticancer drug.
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Affiliation(s)
- Akimasa Matsugami
- Supramolecular Biology, International Graduate School of Arts and Sciences, Yokohama City University, JapanGraduate School of Sciences, Kyoto University, Japan,RIKEN, Yokohama, Japan,PRESTO, Yokohama, Japan
| | - Yan Xu
- Supramolecular Biology, International Graduate School of Arts and Sciences, Yokohama City University, JapanGraduate School of Sciences, Kyoto University, Japan,RIKEN, Yokohama, Japan,PRESTO, Yokohama, Japan
| | - Yuuki Noguchi
- Supramolecular Biology, International Graduate School of Arts and Sciences, Yokohama City University, JapanGraduate School of Sciences, Kyoto University, Japan,RIKEN, Yokohama, Japan,PRESTO, Yokohama, Japan
| | - Hiroshi Sugiyama
- Supramolecular Biology, International Graduate School of Arts and Sciences, Yokohama City University, JapanGraduate School of Sciences, Kyoto University, Japan,RIKEN, Yokohama, Japan,PRESTO, Yokohama, Japan
| | - Masato Katahira
- Supramolecular Biology, International Graduate School of Arts and Sciences, Yokohama City University, JapanGraduate School of Sciences, Kyoto University, Japan,RIKEN, Yokohama, Japan,PRESTO, Yokohama, Japan
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92
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Pedroso IM, Duarte LF, Yanez G, Baker AM, Fletcher TM. Induction of parallel human telomeric G-quadruplex structures by Sr(2+). Biochem Biophys Res Commun 2007; 358:298-303. [PMID: 17485073 DOI: 10.1016/j.bbrc.2007.04.126] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2007] [Accepted: 04/18/2007] [Indexed: 11/25/2022]
Abstract
Human telomeric DNA forms G-quadruplex secondary structures, which can inhibit telomerase activity and are targets for anti-cancer drugs. Here we show that Sr(2+) can induce human telomeric DNA to form both inter- and intramolecular structures having characteristics consistent with G-quadruplexes. Unlike Na(+) or K(+), Sr(2+) facilitated intermolecular structure formation for oligonucleotides with 2 to 5 5'-d(TTAGGG)-3' repeats. Longer 5'-d(TTAGGG)-3' oligonucleotides formed exclusively intramolecular structures. Altering the 5'-d(TTAGGG)-3' to 5'-d(TTAGAG)-3' in the 1st, 3rd, or 4th repeats of 5'-d(TTAGGG)(4)-3' stabilized the formation of intermolecular structures. However, a more compact, intramolecular structure was still observed when the 2nd repeat was altered. Circular dichroism spectroscopy results suggest that the structures were parallel-stranded, distinguishing them from similar DNA sequences in Na(+) and K(+). This study shows that Sr(2+), promotes parallel-stranded, inter- and intramolecular G-quadruplexes that can serve as models to study DNA substrate recognition by telomerase.
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Affiliation(s)
- Ilene M Pedroso
- Department of Biochemistry and Molecular Biology, University of Miami, School of Medicine, P.O. Box 016129 (R629), Miami, FL 33101-6129, USA
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93
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Oganesian L, Bryan TM. Physiological relevance of telomeric G-quadruplex formation: a potential drug target. Bioessays 2007; 29:155-65. [PMID: 17226803 DOI: 10.1002/bies.20523] [Citation(s) in RCA: 251] [Impact Index Per Article: 13.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
The concept of a G-quartet, a unique structural arrangement intrinsic to guanine-rich DNA, was first introduced by Gellert and colleagues over 40 years ago. For decades, it has been uncertain whether the G-quartet and the structure that it gives rise to, the G-quadruplex, are purely in vitro phenomena. Nevertheless, the presence of signature G-rich motifs in the eukaryotic genome, and the plethora of proteins that bind to, modify or resolve this nucleic acid structure in vitro have provided circumstantial evidence for its physiological relevance. More recently, direct visualisation of G-quadruplex DNA at native telomeres was achieved, bolstering the evidence for its existence in the cell. Furthermore, G-quadruplex folded telomeric DNA has been found to perturb telomere function and to impede the action of telomerase, an enzyme overexpressed in >85% of human cancers, hence opening up a novel avenue for cancer therapy in the form of G-quadruplex stabilising agents.
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Affiliation(s)
- Liana Oganesian
- Children's Medical Research Institute, Westmead, Sydney Australia
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94
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Abstract
Recent advances have made a persuasive case for the existence of G4 DNA in living cells, but what--if any--are its functions? Experiments have established how G4 DNA may contribute to the biology of eukaryotic cells, and genomic analysis has identified new ways in which the potential to form G4 DNA may influence gene regulation and genomic stability. This Perspective highlights those advances and identifies some key open questions.
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Affiliation(s)
- Nancy Maizels
- Department of Immunology, University of Washington School of Medicine, 1959 N.E. Pacific Street, Seattle, Washington 98195-7650, USA.
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95
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Sivanathan V, Allen MD, de Bekker C, Baker R, Arciszewska LK, Freund SM, Bycroft M, Löwe J, Sherratt DJ. The FtsK gamma domain directs oriented DNA translocation by interacting with KOPS. Nat Struct Mol Biol 2006; 13:965-72. [PMID: 17057717 PMCID: PMC2556771 DOI: 10.1038/nsmb1158] [Citation(s) in RCA: 87] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2006] [Accepted: 09/27/2006] [Indexed: 11/09/2022]
Abstract
The bacterial septum-located DNA translocase FtsK coordinates circular chromosome segregation with cell division. Rapid translocation of DNA by FtsK is directed by 8-base-pair DNA motifs (KOPS), so that newly replicated termini are brought together at the developing septum, thereby facilitating completion of chromosome segregation. Translocase functions reside in three domains, alpha, beta and gamma. FtsKalphabeta are necessary and sufficient for ATP hydrolysis-dependent DNA translocation, which is modulated by FtsKgamma through its interaction with KOPS. By solving the FtsKgamma structure by NMR, we show that gamma is a winged-helix domain. NMR chemical shift mapping localizes the DNA-binding site on the gamma domain. Mutated proteins with substitutions in the FtsKgamma DNA-recognition helix are impaired in DNA binding and KOPS recognition, yet remain competent in DNA translocation and XerCD-dif site-specific recombination, which facilitates the late stages of chromosome segregation.
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96
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Phan AT, Luu KN, Patel DJ. Different loop arrangements of intramolecular human telomeric (3+1) G-quadruplexes in K+ solution. Nucleic Acids Res 2006; 34:5715-9. [PMID: 17040899 PMCID: PMC1635308 DOI: 10.1093/nar/gkl726] [Citation(s) in RCA: 259] [Impact Index Per Article: 13.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022] Open
Abstract
Intramolecular G-quadruplexes formed by the human telomeric G-rich strand are promising anticancer targets. Here we show that four-repeat human telomeric DNA sequences can adopt two different intramolecular G-quadruplex folds in K+ solution. The two structures contain the (3+1) G-tetrad core, in which three G-tracts are oriented in one direction and the fourth in the opposite direction, with one double-chain-reversal and two edgewise loops, but involve different loop arrangements. This result indicates the robustness of the (3+1) core G-quadruplex topology, thereby suggesting it as an important platform for structure-based drug design. Our data also support the view that multiple human telomeric G-quadruplex conformations coexist in K+ solution. Furthermore, even small changes to flanking sequences can perturb the equilibrium between different coexisting G-quadruplex forms.
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Affiliation(s)
- Anh Tuân Phan
- Structural Biology Program, Memorial Sloan-Kettering Cancer Center, New York, NY 10021, USA.
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97
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Abstract
Chromosome stability requires a dynamic balance of DNA loss and gain in each terminal tract of telomeric repeats. Repeat addition by a specialized reverse transcriptase, telomerase, has an important role in maintaining this equilibrium. Insights that have been gained into the cellular pathways for biogenesis and regulation of telomerase ribonucleoproteins raise new questions, particularly concerning the dynamic nature of this unique polymerase.
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Affiliation(s)
- Kathleen Collins
- Department of Molecular and Cell Biology, University of California, Berkeley, California 94720-3204, USA.
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98
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Phan AT, Kuryavyi V, Patel DJ. DNA architecture: from G to Z. Curr Opin Struct Biol 2006; 16:288-98. [PMID: 16714104 PMCID: PMC4689308 DOI: 10.1016/j.sbi.2006.05.011] [Citation(s) in RCA: 215] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2006] [Revised: 04/10/2006] [Accepted: 05/10/2006] [Indexed: 12/27/2022]
Abstract
G-quadruplexes and Z-DNA are two important non-B forms of DNA architecture. Results on novel structural elements, folding and unfolding kinetics, and interactions with small molecules and proteins have been reported recently for these forms. These results will enhance our understanding of the biology of these structures and provide a platform for drug design.
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Affiliation(s)
- Anh Tuân Phan
- Structural Biology Program, Memorial Sloan-Kettering Cancer Center, New York, NY 10021, USA.
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