1
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Kotkowiak W, Roxo C, Pasternak A. Physicochemical and antiproliferative characteristics of RNA and DNA sequence-related G-quadruplexes. ACS Med Chem Lett 2023; 14:35-40. [PMID: 36655120 PMCID: PMC9841586 DOI: 10.1021/acsmedchemlett.2c00361] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2022] [Accepted: 10/03/2022] [Indexed: 01/21/2023] Open
Abstract
In this article the physicochemical and biological properties of sequence-related G-quadruplex forming oligonucleotides in RNA and DNA series are analyzed and compared. The intermolecular G-quadruplexes vary in loop length, number of G-tetrads and homogeneity of the core. Our studies show that even slight variations in sequence initiate certain changes of G-quadruplex properties. DNA G-quadruplexes are less thermally stable than their RNA counterparts, more topologically diversified and are better candidates as inhibitors of cancer cells proliferation. The most efficient antiproliferative activity within the studied group of molecules was observed for two DNA G-quadruplexes with unperturbed core and lower content of thymidine residues within the loops leading to reduction of cells viability up to 65% and 33% for HeLa and MCF-7 cell lines, respectively.
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Affiliation(s)
- Weronika Kotkowiak
- Department of Nucleic Acids
Bioengineering, Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12/14, 61-704 Poznan, Poland
| | - Carolina Roxo
- Department of Nucleic Acids
Bioengineering, Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12/14, 61-704 Poznan, Poland
| | - Anna Pasternak
- Department of Nucleic Acids
Bioengineering, Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12/14, 61-704 Poznan, Poland
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2
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Reversal of G-Quadruplexes’ Role in Translation Control When Present in the Context of an IRES. Biomolecules 2022; 12:biom12020314. [PMID: 35204814 PMCID: PMC8869680 DOI: 10.3390/biom12020314] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2021] [Revised: 02/08/2022] [Accepted: 02/14/2022] [Indexed: 02/01/2023] Open
Abstract
G-quadruplexes (GQs) are secondary nucleic acid structures that play regulatory roles in various cellular processes. G-quadruplex-forming sequences present within the 5′ UTR of mRNAs can function not only as repressors of translation but also as elements required for optimum function. Based upon previous reports, the majority of the 5′ UTR GQ structures inhibit translation, presumably by blocking the ribosome scanning process that is essential for detection of the initiation codon. However, there are certain mRNAs containing GQs that have been identified as positive regulators of translation, as they are needed for translation initiation. While most cellular mRNAs utilize the 5′ cap structure to undergo cap-dependent translation initiation, many rely on cap-independent translation under certain conditions in which the cap-dependent initiation mechanism is not viable or slowed down, for example, during development, under stress and in many diseases. Cap-independent translation mainly occurs via Internal Ribosomal Entry Sites (IRESs) that are located in the 5′ UTR of mRNAs and are equipped with structural features that can recruit the ribosome or other factors to initiate translation without the need for a 5′ cap. In this review, we will focus only on the role of RNA GQs present in the 5′ UTR of mRNAs, where they play a critical role in translation initiation, and discuss the potential mechanism of this phenomenon, which is yet to be fully delineated.
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3
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Banco MT, Ferré-D'Amaré AR. The emerging structural complexity of G-quadruplex RNAs. RNA (NEW YORK, N.Y.) 2021; 27:390-402. [PMID: 33483368 PMCID: PMC7962482 DOI: 10.1261/rna.078238.120] [Citation(s) in RCA: 50] [Impact Index Per Article: 16.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/12/2023]
Abstract
G-quadruplexes (G4s) are four-stranded nucleic acid structures that arise from the stacking of G-quartets, cyclic arrangements of four guanines engaged in Hoogsteen base-pairing. Until recently, most RNA G4 structures were thought to conform to a sequence pattern in which guanines stacking within the G4 would also be contiguous in sequence (e.g., four successive guanine trinucleotide tracts separated by loop nucleotides). Such a sequence restriction, and the stereochemical constraints inherent to RNA (arising, in particular, from the presence of the 2'-OH), dictate relatively simple RNA G4 structures. Recent crystallographic and solution NMR structure determinations of a number of in vitro selected RNA aptamers have revealed RNA G4 structures of unprecedented complexity. Structures of the Sc1 aptamer that binds an RGG peptide from the Fragile-X mental retardation protein, various fluorescence turn-on aptamers (Corn, Mango, and Spinach), and the spiegelmer that binds the complement protein C5a, in particular, reveal complexity hitherto unsuspected in RNA G4s, including nucleotides in syn conformation, locally inverted strand polarity, and nucleotide quartets that are not all-G. Common to these new structures, the sequences folding into G4s do not conform to the requirement that guanine stacks arise from consecutive (contiguous in sequence) nucleotides. This review highlights how emancipation from this constraint drastically expands the structural possibilities of RNA G-quadruplexes.
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Affiliation(s)
- Michael T Banco
- Biochemistry and Biophysics Center, National Heart, Lung, and Blood Institute, Bethesda, Maryland 20892-8012, USA
| | - Adrian R Ferré-D'Amaré
- Biochemistry and Biophysics Center, National Heart, Lung, and Blood Institute, Bethesda, Maryland 20892-8012, USA
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4
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RNA and DNA G-quadruplexes bind to human dicer and inhibit its activity. Cell Mol Life Sci 2021; 78:3709-3724. [PMID: 33733306 PMCID: PMC8038994 DOI: 10.1007/s00018-021-03795-w] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2020] [Revised: 01/27/2021] [Accepted: 02/19/2021] [Indexed: 01/17/2023]
Abstract
Guanine (G)-rich single-stranded nucleic acids can adopt G-quadruplex structures. Accumulating evidence indicates that G-quadruplexes serve important regulatory roles in fundamental biological processes such as DNA replication, transcription, and translation, while aberrant G-quadruplex formation is linked to genome instability and cancer. Understanding the biological functions played by G-quadruplexes requires detailed knowledge of their protein interactome. Here, we report that both RNA and DNA G-quadruplexes are bound by human Dicer in vitro. Using in vitro binding assays, mutation studies, and computational modeling we demonstrate that G-quadruplexes can interact with the Platform-PAZ-Connector helix cassette of Dicer, the region responsible for anchoring microRNA precursors (pre-miRNAs). Consequently, we show that G-quadruplexes efficiently and stably inhibit the cleavage of pre-miRNA by Dicer. Our data highlight the potential of human Dicer for binding of G-quadruplexes and allow us to propose a G-quadruplex-driven sequestration mechanism of Dicer regulation.
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5
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Amato J, Mashima T, Kamatari YO, Kuwata K, Novellino E, Randazzo A, Giancola C, Katahira M, Pagano B. Improved Anti-Prion Nucleic Acid Aptamers by Incorporation of Chemical Modifications. Nucleic Acid Ther 2020; 30:414-421. [PMID: 32991255 DOI: 10.1089/nat.2020.0899] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
Abstract
Nucleic acid aptamers are innovative and promising candidates to block the hallmark event in the prion diseases, that is the conversion of prion protein (PrP) into an abnormal form; however, they need chemical modifications for effective therapeutic activity. This communication reports on the development and biophysical characterization of a small library of chemically modified G-quadruplex-forming aptamers targeting the cellular PrP and the evaluation of their anti-prion activity. The results show the possibility of enhancing anti-prion aptamer properties through straightforward modifications.
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Affiliation(s)
- Jussara Amato
- Department of Pharmacy, University of Naples Federico II, Naples, Italy
| | - Tsukasa Mashima
- Institute of Advanced Energy, Kyoto University, Uji, Japan.,Graduate School of Energy Science, Kyoto University, Uji, Japan
| | | | - Kazuo Kuwata
- United Graduate School of Drug Discovery and Medical Information Sciences, Gifu University, Gifu, Japan
| | - Ettore Novellino
- Department of Pharmacy, University of Naples Federico II, Naples, Italy
| | - Antonio Randazzo
- Department of Pharmacy, University of Naples Federico II, Naples, Italy
| | - Concetta Giancola
- Department of Pharmacy, University of Naples Federico II, Naples, Italy
| | - Masato Katahira
- Institute of Advanced Energy, Kyoto University, Uji, Japan.,Graduate School of Energy Science, Kyoto University, Uji, Japan
| | - Bruno Pagano
- Department of Pharmacy, University of Naples Federico II, Naples, Italy
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6
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Zok T, Popenda M, Szachniuk M. ElTetrado: a tool for identification and classification of tetrads and quadruplexes. BMC Bioinformatics 2020; 21:40. [PMID: 32005130 PMCID: PMC6995151 DOI: 10.1186/s12859-020-3385-1] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2019] [Accepted: 01/24/2020] [Indexed: 12/13/2022] Open
Abstract
Background Quadruplexes are specific structure motifs occurring, e.g., in telomeres and transcriptional regulatory regions. Recent discoveries confirmed their importance in biomedicine and led to an intensified examination of their properties. So far, the study of these motifs has focused mainly on the sequence and the tertiary structure, and concerned canonical structures only. Whereas, more and more non-canonical quadruplex motifs are being discovered. Results Here, we present ElTetrado, a software that identifies quadruplexes (composed of guanine- and other nucleobase-containing tetrads) in nucleic acid structures and classifies them according to the recently introduced ONZ taxonomy. The categorization is based on the secondary structure topology of quadruplexes and their component tetrads. It supports the analysis of canonical and non-canonical motifs. Besides the class recognition, ElTetrado prepares a dot-bracket and graphical representations of the secondary structure, which reflect the specificity of the quadruplex’s structure topology. It is implemented as a freely available, standalone application, available at https://github.com/tzok/eltetrado. Conclusions The proposed software tool allows to identify and classify tetrads and quadruplexes based on the topology of their secondary structures. It complements existing approaches focusing on the sequence and 3D structure.
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Affiliation(s)
- Tomasz Zok
- Institute of Computing Science and European Centre for Bioinformatics and Genomics, Poznan University of Technology, Piotrowo 2, Poznan, 60-965, Poland.,Poznan Supercomputing and Networking Center, Jana Pawla II 10, Poznan, 61-139, Poland
| | - Mariusz Popenda
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12/14, Poznan, 61-704, Poland
| | - Marta Szachniuk
- Institute of Computing Science and European Centre for Bioinformatics and Genomics, Poznan University of Technology, Piotrowo 2, Poznan, 60-965, Poland. .,Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12/14, Poznan, 61-704, Poland.
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7
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Lightfoot HL, Hagen T, Tatum NJ, Hall J. The diverse structural landscape of quadruplexes. FEBS Lett 2019; 593:2083-2102. [PMID: 31325371 DOI: 10.1002/1873-3468.13547] [Citation(s) in RCA: 86] [Impact Index Per Article: 17.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2019] [Revised: 07/09/2019] [Accepted: 07/15/2019] [Indexed: 12/15/2022]
Abstract
G-quadruplexes are secondary structures formed in G-rich sequences in DNA and RNA. Considerable research over the past three decades has led to in-depth insight into these unusual structures in DNA. Since the more recent exploration into RNA G-quadruplexes, such structures have demonstrated their in cellulo existence, function and roles in pathology. In comparison to Watson-Crick-based secondary structures, most G-quadruplexes display highly redundant structural characteristics. However, numerous reports of G-quadruplex motifs/structures with unique features (e.g. bulges, long loops, vacancy) have recently surfaced, expanding the repertoire of G-quadruplex scaffolds. This review addresses G-quadruplex formation and structure, including recent reports of non-canonical G-quadruplex structures. Improved methods of detection will likely further expand this collection of novel structures and ultimately change the face of quadruplex-RNA targeting as a therapeutic strategy.
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Affiliation(s)
- Helen L Lightfoot
- Department of Chemistry and Applied Biosciences, Institute of Pharmaceutical Sciences, ETH Zurich, Switzerland
| | - Timo Hagen
- Department of Chemistry and Applied Biosciences, Institute of Pharmaceutical Sciences, ETH Zurich, Switzerland
| | - Natalie J Tatum
- Newcastle Cancer Centre, Northern Institute for Cancer Research, Medical School, Newcastle University, Newcastle upon Tyne, UK
| | - Jonathan Hall
- Department of Chemistry and Applied Biosciences, Institute of Pharmaceutical Sciences, ETH Zurich, Switzerland
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8
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Jodoin R, Perreault JP. G-quadruplexes formation in the 5'UTRs of mRNAs associated with colorectal cancer pathways. PLoS One 2018; 13:e0208363. [PMID: 30507959 PMCID: PMC6277105 DOI: 10.1371/journal.pone.0208363] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2018] [Accepted: 11/15/2018] [Indexed: 11/24/2022] Open
Abstract
RNA G-quadruplexes (rG4) are stable non-canonical secondary structures composed of G-rich sequences. Many rG4 structures located in the 5'UTRs of mRNAs act as translation repressors due to their high stability which is thought to impede ribosomal scanning. That said, it is not known if these are mRNA-specific examples, or if they are indicative of a global expression regulation mechanism of the mRNAs involved in a common pathway based on structure folding recognition. Gene-ontology analysis of mRNAs bearing a predicted rG4 motif in their 5'UTRs revealed an enrichment for mRNAs associated with the colorectal cancer pathway. Bioinformatic tools for rG4 prediction, and experimental in vitro validations were used to confirm and compare the folding of the predicted rG4s of the mRNAs associated with dysregulated pathways in colorectal cancer. The rG4 folding was confirmed for the first time for 9 mRNAs. A repressive effect of 3 rG4 candidates on the expression of a reporter gene was also measured in colorectal cancer cell lines. This work highlights the fact that rG4 prediction is not yet accurate, and that experimental characterization is still essential in order to identify the precise rG4 folding sequences and the possible common features shared between the rG4 overrepresented in important biological pathways.
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Affiliation(s)
- Rachel Jodoin
- Département de Biochimie, Faculté de médecine et des sciences de la santé, Université de Sherbrooke, Sherbrooke, Québec, Canada
| | - Jean-Pierre Perreault
- Département de Biochimie, Faculté de médecine et des sciences de la santé, Université de Sherbrooke, Sherbrooke, Québec, Canada
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9
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Antiparallel RNA G-quadruplex Formed by Human Telomere RNA Containing 8-Bromoguanosine. Sci Rep 2017; 7:6695. [PMID: 28751647 PMCID: PMC5532209 DOI: 10.1038/s41598-017-07050-w] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2017] [Accepted: 06/21/2017] [Indexed: 11/09/2022] Open
Abstract
In this study, by combining nuclear magnetic resonance (NMR), circular dichroism (CD), liquid chromatography-electrospray ionization-mass spectrometry (LC-ESI-MS), and gel electrophoresis, we report an unusual topological structure of the RNA G-quadruplex motif formed by human telomere RNA r(UAGGGU) containing 8-bromoguanosine. Results showed that the RNA sequence formed an antiparallel tetramolecular G-quadruplex, in which each pair of diagonal strands run in opposite directions. Furthermore, guanosines were observed both in syn- and anti-conformations. In addition, two of these G-quadruplex subunits were found to be stacking on top of each other, forming a dimeric RNA G-quadruplex. Our findings provide a new insight into the behavior of RNA G-quadruplex structures.
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10
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Dickerhoff J, Appel B, Müller S, Weisz K. Zuckerseitige Wechselwirkungen in einem DNA-RNA-G-Quadruplex: Hinweise auf sequentielle C−H⋅⋅⋅O-Wasserstoffbrücken als Beitrag zur RNA-Quadruplex-Faltung. Angew Chem Int Ed Engl 2016. [DOI: 10.1002/ange.201608275] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
- Jonathan Dickerhoff
- Institut für Biochemie; Ernst-Moritz-Arndt-Universität Greifswald; Felix-Hausdorff-Str. 4 17487 Greifswald Deutschland
| | - Bettina Appel
- Institut für Biochemie; Ernst-Moritz-Arndt-Universität Greifswald; Felix-Hausdorff-Str. 4 17487 Greifswald Deutschland
| | - Sabine Müller
- Institut für Biochemie; Ernst-Moritz-Arndt-Universität Greifswald; Felix-Hausdorff-Str. 4 17487 Greifswald Deutschland
| | - Klaus Weisz
- Institut für Biochemie; Ernst-Moritz-Arndt-Universität Greifswald; Felix-Hausdorff-Str. 4 17487 Greifswald Deutschland
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11
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Dickerhoff J, Appel B, Müller S, Weisz K. Sugar-Edge Interactions in a DNA-RNA G-Quadruplex: Evidence of Sequential C-H⋅⋅⋅O Hydrogen Bonds Contributing to RNA Quadruplex Folding. Angew Chem Int Ed Engl 2016; 55:15162-15165. [PMID: 27860177 DOI: 10.1002/anie.201608275] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2016] [Revised: 09/29/2016] [Indexed: 11/11/2022]
Abstract
DNA G-quadruplexes were systematically modified by single riboguanosine (rG) substitutions at anti-dG positions. Circular dichroism and NMR experiments confirmed the conservation of the native quadruplex topology for most of the DNA-RNA hybrid structures. Changes in the C8 NMR chemical shift of guanosines following rG substitution at their 3'-side within the quadruplex core strongly suggest the presence of C8-H⋅⋅⋅O hydrogen-bonding interactions with the O2' position of the C2'-endo ribonucleotide. A geometric analysis of reported high-resolution structures indicates that such interactions are a more general feature in RNA quadruplexes and may contribute to the observed preference for parallel topologies.
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Affiliation(s)
- Jonathan Dickerhoff
- Institut für Biochemie, Ernst-Moritz-Arndt-Universität Greifswald, Felix-Hausdorff-Strasse 4, 17487, Greifswald, Germany
| | - Bettina Appel
- Institut für Biochemie, Ernst-Moritz-Arndt-Universität Greifswald, Felix-Hausdorff-Strasse 4, 17487, Greifswald, Germany
| | - Sabine Müller
- Institut für Biochemie, Ernst-Moritz-Arndt-Universität Greifswald, Felix-Hausdorff-Strasse 4, 17487, Greifswald, Germany
| | - Klaus Weisz
- Institut für Biochemie, Ernst-Moritz-Arndt-Universität Greifswald, Felix-Hausdorff-Strasse 4, 17487, Greifswald, Germany
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12
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Kumar J, Pratibha, Verma S. Crystallographic signatures of silver-purine frameworks with an azide functionality. Inorganica Chim Acta 2016. [DOI: 10.1016/j.ica.2016.03.016] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
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13
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Bhattacharyya D, Mirihana Arachchilage G, Basu S. Metal Cations in G-Quadruplex Folding and Stability. Front Chem 2016; 4:38. [PMID: 27668212 PMCID: PMC5016522 DOI: 10.3389/fchem.2016.00038] [Citation(s) in RCA: 364] [Impact Index Per Article: 45.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2016] [Accepted: 08/25/2016] [Indexed: 12/23/2022] Open
Abstract
This review is focused on the structural and physicochemical aspects of metal cation coordination to G-Quadruplexes (GQ) and their effects on GQ stability and conformation. G-quadruplex structures are non-canonical secondary structures formed by both DNA and RNA. G-quadruplexes regulate a wide range of important biochemical processes. Besides the sequence requirements, the coordination of monovalent cations in the GQ is essential for its formation and determines the stability and polymorphism of GQ structures. The nature, location, and dynamics of the cation coordination and their impact on the overall GQ stability are dependent on several factors such as the ionic radii, hydration energy, and the bonding strength to the O6 of guanines. The intracellular monovalent cation concentration and the localized ion concentrations determine the formation of GQs and can potentially dictate their regulatory roles. A wide range of biochemical and biophysical studies on an array of GQ enabling sequences have generated at a minimum the knowledge base that allows us to often predict the stability of GQs in the presence of the physiologically relevant metal ions, however, prediction of conformation of such GQs is still out of the realm.
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Affiliation(s)
| | | | - Soumitra Basu
- Department of Chemistry and Biochemistry, Kent State UniversityKent, OH, USA
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14
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Mittelberger F, Meyer C, Waetzig GH, Zacharias M, Valentini E, Svergun DI, Berg K, Lorenzen I, Grötzinger J, Rose-John S, Hahn U. RAID3--An interleukin-6 receptor-binding aptamer with post-selective modification-resistant affinity. RNA Biol 2016; 12:1043-53. [PMID: 26383776 DOI: 10.1080/15476286.2015.1079681] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022] Open
Abstract
Aptamers are an emerging class of highly specific targeting ligands. They can be selected in vitro for a large variety of targets, ranging from small molecules to whole cells. Most aptamers selected are nucleic acid-based, allowing chemical synthesis and easy modification. Although their properties make them interesting drug candidates for a broad spectrum of applications and an interesting alternative to antibodies or fusion proteins, they are not yet broadly used. One major drawback of aptamers is their susceptibility to abundant serum nucleases, resulting in their fast degradation in biological fluids. Using modified nucleic acids has become a common strategy to overcome these disadvantages, greatly increasing their half-life under cell culture conditions or even in vivo. Whereas pre-selective modifications of the initial library for aptamer selection are relatively easy to obtain, post-selective modifications of already selected aptamers are still generally very labor-intensive and often compromise the aptamers ability to bind its target molecule. Here we report the selection, characterization and post-selective modification of a 34 nucleotide (nt) RNA aptamer for a non-dominant, novel target site (domain 3) of the interleukin-6 receptor (IL-6R). We performed structural analyses and investigated the affinity of the aptamer to the membrane-bound and soluble forms (sIL-6R) of the IL-6R. Further, we performed structural analyses of the aptamer in solution using small-angle X-ray scattering and determined its overall shape and oligomeric state. Post-selective exchange of all pyrimidines against their 2'-fluoro analogs increased the aptamers stability significantly without compromising its affinity for the target protein. The resulting modified aptamer could be shortened to its minimal binding motif without loss of affinity.
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Affiliation(s)
- Florian Mittelberger
- a Institute for Biochemistry and Molecular Biology ; Department of Chemistry ; University of Hamburg ; Hamburg , Germany
| | - Cindy Meyer
- b Howard Hughes Medical Institute; Laboratory of RNA Molecular Biology; Rockefeller University ; New York , NY USA
| | | | - Martin Zacharias
- d Physics Department ; Technical University Munich ; Garching , Germany
| | - Erica Valentini
- a Institute for Biochemistry and Molecular Biology ; Department of Chemistry ; University of Hamburg ; Hamburg , Germany.,e European Molecular Biology Laboratory; Hamburg Unit ; Hamburg , Germany
| | - Dmitri I Svergun
- e European Molecular Biology Laboratory; Hamburg Unit ; Hamburg , Germany
| | - Katharina Berg
- a Institute for Biochemistry and Molecular Biology ; Department of Chemistry ; University of Hamburg ; Hamburg , Germany
| | - Inken Lorenzen
- f Institute of Biochemistry; University of Kiel ; Kiel , Germany
| | | | - Stefan Rose-John
- f Institute of Biochemistry; University of Kiel ; Kiel , Germany
| | - Ulrich Hahn
- a Institute for Biochemistry and Molecular Biology ; Department of Chemistry ; University of Hamburg ; Hamburg , Germany
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15
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Tan W, Zhou J, Gu J, Xu M, Xu X, Yuan G. Probing the G‑quadruplex from hsa-miR-3620-5p and inhibition of its interaction with the target sequence. Talanta 2016; 154:560-6. [PMID: 27154715 DOI: 10.1016/j.talanta.2016.02.037] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2015] [Revised: 02/12/2016] [Accepted: 02/17/2016] [Indexed: 12/21/2022]
Abstract
G-quadruplexes have been reported to exist both in human genome and transcriptome and are of great interests due to their important biological functions. Up to now, the formation and property of G-quadruplex in human mature microRNAs has not been explored yet. In this study, we discovered that hsa-miR-3620-5p, a guanine rich human mature microRNA, could fold into a stable parallel G-quadruplex in near physiological condition for the first time. We explored the formation, folding pattern and binding affinity of the miR-3620-5p G-quadruplex by ESI-MS, CD, NMR and SPR. The results indicated that its high-order structure was comprised of three G-quartets with two bases in each parallel loop stretching outward and two bases flanking at each end. In addition, sanguinarine, a natural alkaloid screened from traditional Chinese medicine was characterized to have high binding affinity and thermodynamic stabilization effects through π-π stacking interaction with the external G-quartets. Furthermore, the potent interaction of sanguinarine with miR-3620-5p G-quadruplex could block the base pairing between miR-3620-5p and its target sequence. Therefore, our study revealed the possibility of regulating microRNA functions using potent G-quadruplex binders, and could provide a new approach to affect the microRNA:mRNA interactions.
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Affiliation(s)
- Wei Tan
- Beijing National Laboratory for Molecular Sciences, Key Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education, Department of Chemical Biology, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China
| | - Jiang Zhou
- Beijing National Laboratory for Molecular Sciences, Key Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education, Department of Chemical Biology, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China.
| | - Jiangyong Gu
- Beijing National Laboratory for Molecular Sciences, Key Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education, Department of Chemical Biology, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China
| | - Ming Xu
- Department of Cardiology, Institute of Vascular Medicine, Peking University Third Hospital, Beijing 100191, China
| | - Xiaojie Xu
- Beijing National Laboratory for Molecular Sciences, Key Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education, Department of Chemical Biology, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China
| | - Gu Yuan
- Beijing National Laboratory for Molecular Sciences, Key Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education, Department of Chemical Biology, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China.
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16
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Modelska A, Turro E, Russell R, Beaton J, Sbarrato T, Spriggs K, Miller J, Gräf S, Provenzano E, Blows F, Pharoah P, Caldas C, Le Quesne J. The malignant phenotype in breast cancer is driven by eIF4A1-mediated changes in the translational landscape. Cell Death Dis 2015; 6:e1603. [PMID: 25611378 PMCID: PMC4669741 DOI: 10.1038/cddis.2014.542] [Citation(s) in RCA: 113] [Impact Index Per Article: 12.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2014] [Revised: 10/29/2014] [Accepted: 11/03/2014] [Indexed: 01/09/2023]
Abstract
Human mRNA DeXD/H-box helicases are ubiquitous molecular motors that are required for the majority of cellular processes that involve RNA metabolism. One of the most abundant is eIF4A, which is required during the initiation phase of protein synthesis to unwind regions of highly structured mRNA that would otherwise impede the scanning ribosome. Dysregulation of protein synthesis is associated with tumorigenesis, but little is known about the detailed relationships between RNA helicase function and the malignant phenotype in solid malignancies. Therefore, immunohistochemical analysis was performed on over 3000 breast tumors to investigate the relationship among expression of eIF4A1, the helicase-modulating proteins eIF4B, eIF4E and PDCD4, and clinical outcome. We found eIF4A1, eIF4B and eIF4E to be independent predictors of poor outcome in ER-negative disease, while in contrast, the eIF4A1 inhibitor PDCD4 was related to improved outcome in ER-positive breast cancer. Consistent with these data, modulation of eIF4A1, eIF4B and PCDC4 expression in cultured MCF7 cells all restricted breast cancer cell growth and cycling. The eIF4A1-dependent translatome of MCF7 cells was defined by polysome profiling, and was shown to be highly enriched for several classes of oncogenic genes, including G-protein constituents, cyclins and protein kinases, and for mRNAs with G/C-rich 5'UTRs with potential to form G-quadruplexes and with 3'UTRs containing microRNA target sites. Overall, our data show that dysregulation of mRNA unwinding contributes to the malignant phenotype in breast cancer via preferential translation of a class of genes involved in pro-oncogenic signaling at numerous levels. Furthermore, immunohistochemical tests are promising biomarkers for tumors sensitive to anti-helicase therapies.
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Affiliation(s)
- A Modelska
- Department of Oncology and Cancer Research UK Cambridge Institute, University of Cambridge, Li Ka Shing Centre, Robinson Way, Cambridge CB2 0RE, UK
| | - E Turro
- Department of Oncology and Cancer Research UK Cambridge Institute, University of Cambridge, Li Ka Shing Centre, Robinson Way, Cambridge CB2 0RE, UK
- Department of Haematology, University of Cambridge, NHS Blood and Transplant, Long Road, Cambridge CB2 0PT, UK
| | - R Russell
- Department of Oncology and Cancer Research UK Cambridge Institute, University of Cambridge, Li Ka Shing Centre, Robinson Way, Cambridge CB2 0RE, UK
| | - J Beaton
- Department of Oncology and Cancer Research UK Cambridge Institute, University of Cambridge, Li Ka Shing Centre, Robinson Way, Cambridge CB2 0RE, UK
| | - T Sbarrato
- Medical Research Council Toxicology Unit, Lancaster Road, Leicester LE1 9HN, UK
| | - K Spriggs
- School of Pharmacy, University of Nottingham, Nottingham NG7 2RD, UK
| | - J Miller
- Department of Oncology and Cancer Research UK Cambridge Institute, University of Cambridge, Li Ka Shing Centre, Robinson Way, Cambridge CB2 0RE, UK
| | - S Gräf
- Department of Oncology and Cancer Research UK Cambridge Institute, University of Cambridge, Li Ka Shing Centre, Robinson Way, Cambridge CB2 0RE, UK
- Department of Haematology, University of Cambridge, NHS Blood and Transplant, Long Road, Cambridge CB2 0PT, UK
- Department of Medicine, University of Cambridge, Addenbrooke's Hospital, Hills Road, Cambridge CB2 0QQ, UK
| | - E Provenzano
- Cambridge Experimental Cancer Medicine Centre (ECMR) and NIHR Cambridge Biomedical Research Centre, Cambridge University Hospitals NHS Foundation Trust, Cambridge CB2 0QQ, UK
- Cambridge Breast Unit and Cambridge University Hospitals NHS Foundation Trust, Hills Road, Cambridge CB2 0QQ, UK
| | - F Blows
- Strangeways Research Institute, 2 Worts' Causeway, Cambridge CB1 8RN, UK
| | - P Pharoah
- Cambridge Experimental Cancer Medicine Centre (ECMR) and NIHR Cambridge Biomedical Research Centre, Cambridge University Hospitals NHS Foundation Trust, Cambridge CB2 0QQ, UK
- Strangeways Research Institute, 2 Worts' Causeway, Cambridge CB1 8RN, UK
| | - C Caldas
- Department of Oncology and Cancer Research UK Cambridge Institute, University of Cambridge, Li Ka Shing Centre, Robinson Way, Cambridge CB2 0RE, UK
- Cambridge Experimental Cancer Medicine Centre (ECMR) and NIHR Cambridge Biomedical Research Centre, Cambridge University Hospitals NHS Foundation Trust, Cambridge CB2 0QQ, UK
| | - J Le Quesne
- Department of Oncology and Cancer Research UK Cambridge Institute, University of Cambridge, Li Ka Shing Centre, Robinson Way, Cambridge CB2 0RE, UK
- Medical Research Council Toxicology Unit, Lancaster Road, Leicester LE1 9HN, UK
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A targeted oligonucleotide enhancer of SMN2 exon 7 splicing forms competing quadruplex and protein complexes in functional conditions. Cell Rep 2014; 9:193-205. [PMID: 25263560 PMCID: PMC4536295 DOI: 10.1016/j.celrep.2014.08.051] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2013] [Revised: 07/17/2014] [Accepted: 08/21/2014] [Indexed: 01/20/2023] Open
Abstract
The use of oligonucleotides to activate the splicing of selected exons is limited by a poor understanding of the mechanisms affected. A targeted bifunctional oligonucleotide enhancer of splicing (TOES) anneals to SMN2 exon 7 and carries an exonic splicing enhancer (ESE) sequence. We show that it stimulates splicing specifically of intron 6 in the presence of repressing sequences in intron 7. Complementarity to the 5' end of exon 7 increases U2AF65 binding, but the ESE sequence is required for efficient recruitment of U2 snRNP. The ESE forms at least three coexisting discrete states: a quadruplex, a complex containing only hnRNP F/H, and a complex enriched in the activator SRSF1. Neither hnRNP H nor quadruplex formation contributes to ESE activity. The results suggest that splicing limited by weak signals can be rescued by rapid exchange of TOES oligonucleotides in various complexes and raise the possibility that SR proteins associate transiently with ESEs.
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18
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Malgowska M, Gudanis D, Kierzek R, Wyszko E, Gabelica V, Gdaniec Z. Distinctive structural motifs of RNA G-quadruplexes composed of AGG, CGG and UGG trinucleotide repeats. Nucleic Acids Res 2014; 42:10196-207. [PMID: 25081212 PMCID: PMC4150804 DOI: 10.1093/nar/gku710] [Citation(s) in RCA: 50] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Trinucleotide repeats are microsatellite sequences that are polymorphic in length. Their expansion in specific genes underlies a number of neurodegenerative disorders. Using ultraviolet-visible, circular dichroism, nuclear magnetic resonance (NMR) spectroscopies and electrospray ionization mass spectrometry, the structural preferences of RNA molecules composed of two and four repeats of AGG, CGG and UGG in the presence of K+, Na+ and NH4+ were analysed. (AGG)2A, (AGG)4A, p(UGG)2U and p(UGG)4U strongly prefer folding into G-quadruplexes, whereas CGG-containing sequences can adopt different types of structure depending on the cation and on the number of repeats. In particular, the two-repeat CGG sequence folds into a G-quadruplex in potassium buffer. We also found that each G-quadruplex fold is different: A:(G:G:G:G)A hexads were found for (AGG)2A, whereas mixed G:C:G:C tetrads and U-tetrads were observed in the NMR spectra of G(CGG)2C and p(UGG)2U, respectively. Finally, our NMR study highlights the influence of the strand sequence on the structure formed, and the influence of the intracellular environment on the folding. Importantly, we highlight that although potassium ions are prevalent in cells, the structures observed in the HeLa cell extract are not always the same as those prevailing in biophysical studies in the presence of K+ ions.
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Affiliation(s)
- Magdalena Malgowska
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, 61-704 Poznan, Noskowskiego 12/14, Poland
| | - Dorota Gudanis
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, 61-704 Poznan, Noskowskiego 12/14, Poland
| | - Ryszard Kierzek
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, 61-704 Poznan, Noskowskiego 12/14, Poland
| | - Eliza Wyszko
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, 61-704 Poznan, Noskowskiego 12/14, Poland
| | - Valérie Gabelica
- Laboratoire de Spectrométrie de Masse, Institut de Chimie, Bat. B6c, Université de Liège, B-4000 Liège, Belgium Inserm, U869 ARNA Laboratory, F-33000 Bordeaux, France University of Bordeaux, IECB, ARNA Laboratory, F-33600 Pessac, France
| | - Zofia Gdaniec
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, 61-704 Poznan, Noskowskiego 12/14, Poland
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19
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Zhou J, Sayre DA, Zheng Y, Szmacinski H, Sintim HO. Unexpected complex formation between coralyne and cyclic diadenosine monophosphate providing a simple fluorescent turn-on assay to detect this bacterial second messenger. Anal Chem 2014; 86:2412-20. [PMID: 24494631 PMCID: PMC3983017 DOI: 10.1021/ac403203x] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
![]()
Cyclic
diadenosine monophosphate (c-di-AMP) has emerged as an important
dinucleotide that is involved in several processes in bacteria, including
cell wall remodeling (and therefore resistance to antibiotics that
target bacterial cell wall). Small molecules that target c-di-AMP
metabolism enzymes have the potential to be used as antibiotics. Coralyne
is known to form strong complexes with polyadenine containing eight
or more adenine stretches but not with short polyadenine oligonucleotides.
Using a panel of techniques (UV, both steady state fluorescence and
fluorescence lifetime measurements, circular dichroism (CD), NMR,
and Job plots), we demonstrate that c-di-AMP, which contains only
two adenine bases is an exception to this rule and that it can form
complexes with coralyne, even at low micromolar concentrations. Interestingly,
pApA (the linear analog of c-di-AMP that also contains two adenines)
or cyclic diguanylate (c-di-GMP, another nucleotide second messenger
in bacteria) did not form any complex with coralyne. Unlike polyadenine,
which forms a 2:1 complex with coralyne, c-di-AMP forms a higher order
complex with coralyne (≥6:1). Additionally, whereas polyadenine
reduces the fluorescence of coralyne when bound, c-di-AMP enhances
the fluorescence of coralyne. We use the quenching property of halides
to selectively quench the fluorescence of unbound coralyne but not
that of coralyne bound to c-di-AMP. Using this simple selective quenching
strategy, the assay could be used to monitor the synthesis of c-di-AMP
by DisA or the degradation of c-di-AMP by YybT. Apart from the practical
utility of this assay for c-di-AMP research, this work also demonstrates
that, when administered to cells, intercalators might not only associate
with polynucleotides, such as DNA or RNA, but also could associate
with cyclic dinucleotides to disrupt or modulate signal transduction
processes mediated by these nucleotides.
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Affiliation(s)
- Jie Zhou
- Department of Chemistry and Biochemistry, University of Maryland , College Park, Maryland 20742, United States
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20
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Blice-Baum AC, Mihailescu MR. Biophysical characterization of G-quadruplex forming FMR1 mRNA and of its interactions with different fragile X mental retardation protein isoforms. RNA (NEW YORK, N.Y.) 2014; 20:103-114. [PMID: 24249225 PMCID: PMC3866639 DOI: 10.1261/rna.041442.113] [Citation(s) in RCA: 43] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/18/2013] [Accepted: 10/14/2013] [Indexed: 06/02/2023]
Abstract
Fragile X syndrome, the most common form of inherited mental impairment in humans, is caused by the absence of the fragile X mental retardation protein (FMRP) due to a CGG trinucleotide repeat expansion in the 5'-untranslated region (UTR) and subsequent translational silencing of the fragile x mental retardation-1 (FMR1) gene. FMRP, which is proposed to be involved in the translational regulation of specific neuronal messenger RNA (mRNA) targets, contains an arginine-glycine-glycine (RGG) box RNA binding domain that has been shown to bind with high affinity to G-quadruplex forming mRNA structures. FMRP undergoes alternative splicing, and the binding of FMRP to a proposed G-quadruplex structure in the coding region of its mRNA (named FBS) has been proposed to affect the mRNA splicing events at exon 15. In this study, we used biophysical methods to directly demonstrate the folding of FMR1 FBS into a secondary structure that contains two specific G-quadruplexes and analyze its interactions with several FMRP isoforms. Our results show that minor splice isoforms, ISO2 and ISO3, created by the usage of the second and third acceptor sites at exon 15, bind with higher affinity to FBS than FMRP ISO1, which is created by the usage of the first acceptor site. FMRP ISO2 and ISO3 cannot undergo phosphorylation, an FMRP post-translational modification shown to modulate the protein translation regulation. Thus, their expression has to be tightly regulated, and this might be accomplished by a feedback mechanism involving the FMRP interactions with the G-quadruplex structures formed within FMR1 mRNA.
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21
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Martadinata H, Phan AT. Structure of human telomeric RNA (TERRA): stacking of two G-quadruplex blocks in K(+) solution. Biochemistry 2013; 52:2176-83. [PMID: 23445442 DOI: 10.1021/bi301606u] [Citation(s) in RCA: 71] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Abstract
Telomeric repeat-containing RNAs (TERRA) are transcription products of the telomeres. Human TERRA sequences containing UUAGGG repeats can form parallel-stranded G-quadruplexes. The stacking interaction of such structures was shown to be important for ligand targeting and higher-order arrangement of G-quadruplexes in long TERRA sequences. Here we report on the first high-resolution structure of a stacked G-quadruplex formed by the 10-nucleotide human TERRA sequence r(GGGUUAGGGU) in potassium solution. This structure comprises two dimeric three-layer parallel-stranded G-quadruplex blocks, which stack on each other at their 5'-ends. The adenine in each UUA loop is nearly coplanar with the 5'-end G-tetrad forming an A·(G·G·G·G)·A hexad, thereby increasing the stacking contacts between the two blocks. Interestingly, this stacking and loop conformation is different from all structures previously reported for the free human TERRA but resembles the structure previously determined for a complex between a human TERRA sequence and an acridine ligand. This stacking conformation is a potential target for drugs that recognize or induce the stacking interface.
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Affiliation(s)
- Herry Martadinata
- School of Physical and Mathematical Sciences, Nanyang Technological University, Singapore
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22
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Abstract
G-quadruplexes constitute a class of nucleic acid structures defined by stacked guanine tetrads (or G-tetrads) with guanine bases from neighboring tetrads stacking with one another within the G-tetrad core. Individual G-quadruplexes can also stack with one another at their G-tetrad interface leading to higher-order structures as observed in telomeric repeat-containing DNA and RNA. In this study, we investigate how guanine base stacking influences the stability of G-quadruplexes and their stacked higher-order structures. A structural survey of the Protein Data Bank is conducted to characterize experimentally observed guanine base stacking geometries within the core of G-quadruplexes and at the interface between stacked G-quadruplex structures. We couple this survey with a systematic computational examination of stacked G-tetrad energy landscapes using quantum mechanical computations. Energy calculations of stacked G-tetrads reveal large energy differences of up to 12 kcal/mol between experimentally observed geometries at the interface of stacked G-quadruplexes. Energy landscapes are also computed using an AMBER molecular mechanics description of stacking energy and are shown to agree quite well with quantum mechanical calculated landscapes. Molecular dynamics simulations provide a structural explanation for the experimentally observed preference of parallel G-quadruplexes to stack in a 5′–5′ manner based on different accessible tetrad stacking modes at the stacking interfaces of 5′–5′ and 3′–3′ stacked G-quadruplexes.
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Affiliation(s)
- Christopher Jacques Lech
- Division of Physics and Applied Physics, School of Physical and Mathematical Sciences, Nanyang Technological University, Singapore 637371, Singapore
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23
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Abstract
Carbon-oxygen (CH···O) hydrogen bonding represents an unusual category of molecular interactions first documented in biological structures over 4 decades ago. Although CH···O hydrogen bonding has remained generally underappreciated in the biochemical literature, studies over the last 15 years have begun to yield direct evidence of these interactions in biological systems. In this minireview, we provide a historical context of biological CH···O hydrogen bonding and summarize some major advancements from experimental studies over the past several years that have elucidated the importance, prevalence, and functions of these interactions. In particular, we examine the impact of CH···O bonds on protein and nucleic acid structure, molecular recognition, and enzyme catalysis and conclude by exploring overarching themes and unresolved questions regarding unconventional interactions in biomolecular structure.
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24
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Nagata T, Sakurai Y, Hara Y, Mashima T, Kodaki T, Katahira M. ‘Intelligent’ ribozyme whose activity is altered in response to K+ as a result of quadruplex formation. FEBS J 2012; 279:1456-63. [DOI: 10.1111/j.1742-4658.2012.08538.x] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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25
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26
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Bruelle C, Bédard M, Blier S, Gauthier M, Traish AM, Vincent M. The mitotic phosphorylation of p54nrb modulates its RNA binding activity. Biochem Cell Biol 2011; 89:423-33. [DOI: 10.1139/o11-030] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
The RNA-binding protein p54nrb is involved in many nuclear processes including transcription, RNA processing, and retention of hyperedited RNAs. In interphase cells, p54nrb localizes to the nucleoplasm and concentrates with protein partners in the paraspeckles via an interaction with the non-coding RNA Neat1. During mitosis, p54nrb becomes multiphosphorylated and the effects of this modification are not known. In the present study, we show that p54nrb phosphorylation does not affect the interactions with its protein partners but rather diminishes its general RNA-binding ability. Biochemical assays indicate that in vitro phosphorylation of a GST-p54nrb construct by CDK1 abolishes the interaction with 5′ splice site RNA sequence. Site-directed mutagenesis shows that the threonine 15 residue, located N-terminal to the RRM tandem domains of p54nrb, is involved in this inhibition. In vivo analysis reveals that Neat1 ncRNA co-immunoprecipitates with p54nrb in either interphase or mitotic cells, suggesting that p54nrb–Neat1 interaction is not modulated by phosphorylation. Accordingly, in vitro phosphorylated GST-p54nrb still interacts with PIR-1 RNA, a G-rich Neat1 sequence known to interact with p54nrb. In vitro RNA binding assays show that CDK1-phosphorylation of a GST-p54nrb construct abolishes its interaction with homoribopolymers poly(A), poly(C), and poly(U) but not with poly(G). These data suggest that p54nrb interaction with RNA could be selectively modulated by phosphorylation during mitosis.
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Affiliation(s)
- Céline Bruelle
- PROTEO Research Center and Département de biologie moléculaire, biochimie médicale et pathologie, Université Laval, Québec, QC G1V 0A6, Canada
| | - Mikaël Bédard
- PROTEO Research Center and Département de biologie moléculaire, biochimie médicale et pathologie, Université Laval, Québec, QC G1V 0A6, Canada
| | - Stéphanie Blier
- PROTEO Research Center and Département de biologie moléculaire, biochimie médicale et pathologie, Université Laval, Québec, QC G1V 0A6, Canada
| | - Martin Gauthier
- PROTEO Research Center and Département de biologie moléculaire, biochimie médicale et pathologie, Université Laval, Québec, QC G1V 0A6, Canada
| | - Abdulmaged M. Traish
- Department of Biochemistry, Boston University School of Medicine, Center for Advanced Biomedical Research, 700 Albany Street, W607, Boston, MA 02118, USA
| | - Michel Vincent
- PROTEO Research Center and Département de biologie moléculaire, biochimie médicale et pathologie, Université Laval, Québec, QC G1V 0A6, Canada
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27
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Halder K, Largy E, Benzler M, Teulade-Fichou MP, Hartig JS. Efficient Suppression of Gene Expression by Targeting 5′-UTR-Based RNA Quadruplexes with Bisquinolinium Compounds. Chembiochem 2011; 12:1663-8. [DOI: 10.1002/cbic.201100228] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2011] [Indexed: 12/30/2022]
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28
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Horowitz S, Yesselman JD, Al-Hashimi HM, Trievel RC. Direct evidence for methyl group coordination by carbon-oxygen hydrogen bonds in the lysine methyltransferase SET7/9. J Biol Chem 2011; 286:18658-63. [PMID: 21454678 PMCID: PMC3099682 DOI: 10.1074/jbc.m111.232876] [Citation(s) in RCA: 49] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2011] [Revised: 03/17/2011] [Indexed: 12/27/2022] Open
Abstract
SET domain lysine methyltransferases (KMTs) are S-adenosylmethionine (AdoMet)-dependent enzymes that catalyze the site-specific methylation of lysyl residues in histone and non-histone proteins. Based on crystallographic and cofactor binding studies, carbon-oxygen (CH · · · O) hydrogen bonds have been proposed to coordinate the methyl groups of AdoMet and methyllysine within the SET domain active site. However, the presence of these hydrogen bonds has only been inferred due to the uncertainty of hydrogen atom positions in x-ray crystal structures. To experimentally resolve the positions of the methyl hydrogen atoms, we used NMR (1)H chemical shift coupled with quantum mechanics calculations to examine the interactions of the AdoMet methyl group in the active site of the human KMT SET7/9. Our results indicated that at least two of the three hydrogens in the AdoMet methyl group engage in CH · · · O hydrogen bonding. These findings represent direct, quantitative evidence of CH · · · O hydrogen bond formation in the SET domain active site and suggest a role for these interactions in catalysis. Furthermore, thermodynamic analysis of AdoMet binding indicated that these interactions are important for cofactor binding across SET domain enzymes.
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Affiliation(s)
- Scott Horowitz
- Chemistry, and Biophysics, University of Michigan, Ann Arbor, Michigan 48109
| | - Joseph D. Yesselman
- Chemistry, and Biophysics, University of Michigan, Ann Arbor, Michigan 48109
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Abstract
Opposed to DNA quadruplex sequences, RNA quadruplexes are still less well characterized. On the other hand, RNA quadruplexes are found to be at least as stable as their DNA counterparts. They show the same dependence on metal ions but seem to be much more restricted with respect to the adopted conformations. Other than DNA, which is mostly found to be double-stranded inside cells, RNAs are produced during transcription without its complementary sequence. The absence of a second strand that is able to hybridize and form a duplex makes the folding of RNA quadruplexes a likely event of intramolecular structure formation. Consequently, the formation of RNA quadruplexes in cellular RNAs has recently been suggested and the study of their influence and potential roles in cellular processes has just started. Here we give an overview of the RNA quadruplex field, summarizing issues such as structures, stabilities, and anticipated roles of these interesting four-stranded, guanosine-rich sequences.
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Affiliation(s)
- Kangkan Halder
- Department of Chemistry, University of Konstanz, Universitätsstrasse 10, D-78457 Konstanz, Germany
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30
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Joachimi A, Benz A, Hartig JS. A comparison of DNA and RNA quadruplex structures and stabilities. Bioorg Med Chem 2009; 17:6811-5. [PMID: 19736017 DOI: 10.1016/j.bmc.2009.08.043] [Citation(s) in RCA: 168] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2009] [Revised: 08/18/2009] [Accepted: 08/19/2009] [Indexed: 11/30/2022]
Abstract
Guanosine-rich sequences are prone to fold into four-stranded nucleic acid structures. Such quadruplex sequences have long been suspected to play important roles in regulatory processes within cells. Although DNA quadruplexes have been studied in great detail, four-stranded structures made up from RNA have received only minor attention, although it is known that RNA is able to form stable quadruplexes as well. Here, we compare quadruplex structures and stabilities of a variety of DNA and RNA sequences. We focus on well established DNA sequences and determine the topologies and stabilities of the corresponding RNA sequences by CD spectroscopy and CD thermal melting experiments. We find that the RNA sequences exclusively fold into the all-parallel conformation in contrast to the diverse topologies adopted by DNA quadruplexes. The thermal stabilities of the RNA structures rival those of the corresponding DNA sequences, often displaying enhanced stabilities compared to their DNA counterparts. Especially thermodynamically less stable sequences show a strong preference for potassium, with the RNA quadruplexes exhibiting much higher stabilities than the corresponding DNAs. The latter finding suggests that quadruplexes formed at critical positions in mRNAs might perturb gene expression to a larger extend than previously anticipated.
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Affiliation(s)
- Astrid Joachimi
- Department of Chemistry and Konstanz Research School Chemical Biology, University of Konstanz, Universitätsstr. 10, 78457 Konstanz, Germany
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31
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Mashima T, Matsugami A, Nishikawa F, Nishikawa S, Katahira M. Unique quadruplex structure and interaction of an RNA aptamer against bovine prion protein. Nucleic Acids Res 2009; 37:6249-58. [PMID: 19666719 PMCID: PMC2764455 DOI: 10.1093/nar/gkp647] [Citation(s) in RCA: 70] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Abstract
RNA aptamers against bovine prion protein (bPrP) were obtained, most of the obtained aptamers being found to contain the r(GGAGGAGGAGGA) (R12) sequence. Then, it was revealed that R12 binds to both bPrP and its β-isoform with high affinity. Here, we present the structure of R12. This is the first report on the structure of an RNA aptamer against prion protein. R12 forms an intramolecular parallel quadruplex. The quadruplex contains G:G:G:G tetrad and G(:A):G:G(:A):G hexad planes. Two quadruplexes form a dimer through intermolecular hexad–hexad stacking. Two lysine clusters of bPrP have been identified as binding sites for R12. The electrostatic interaction between the uniquely arranged phosphate groups of R12 and the lysine clusters is suggested to be responsible for the affinity of R12 to bPrP. The stacking interaction between the G:G:G:G tetrad planes and tryptophan residues may also contribute to the affinity. One R12 dimer molecule is supposed to simultaneously bind the two lysine clusters of one bPrP molecule, resulting in even higher affinity. The atomic coordinates of R12 would be useful for the development of R12 as a therapeutic agent against prion diseases and Alzheimer's disease.
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Affiliation(s)
- Tsukasa Mashima
- Department of Supramolecular Biology, Graduate School of Nanobioscience, Yokohama City University, 1-7-29 Suehiro-cho, Tsurumi-ku, Yokohama 230-0045, Japan
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32
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Nishikawa F, Murakami K, Matsugami A, Katahira M, Nishikawa S. Structural studies of an RNA aptamer containing GGA repeats under ionic conditions using microchip electrophoresis, circular dichroism, and 1D-NMR. Oligonucleotides 2009; 19:179-90. [PMID: 19355811 DOI: 10.1089/oli.2008.0167] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
Nuclear magnetic resonance (NMR) studies have shown that RNA/DNA oligomers with GGA repeat sequences contain unique G-quadruplex structures in the presence of K(+) or Na(+) ions. In this study, we used microchip electrophoresis to study the structure of an RNA aptamer against bovine prion protein that possessed four GGA-triplet repeats (wt2). We analyzed the structural changes and characterized dimer formation of the aptamer. Mutational, circular dichroism, and one-dimensional NMR studies of wt2 revealed that K(+) ions induce wt2 to assume a thermostable dimer in an intramolecular G-quadruplex with parallel orientation.
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Affiliation(s)
- Fumiko Nishikawa
- Age Dimension Research Center, National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba, Ibaraki, Japan
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Morris MJ, Basu S. An unusually stable G-quadruplex within the 5'-UTR of the MT3 matrix metalloproteinase mRNA represses translation in eukaryotic cells. Biochemistry 2009; 48:5313-9. [PMID: 19397366 DOI: 10.1021/bi900498z] [Citation(s) in RCA: 120] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
MT3-MMP is a matrix metalloproteinase involved in the regulation of cancer cell invasion and metastasis. The MT3-MMP mRNA contains a 20-nucleotide G-rich region (M3Q) upstream of the initiation codon. Herein, we report that the M3Q purine-only sequence forms an extremely stable intramolecular G-quadruplex structure and has an inhibitory role on translation of a reporter gene in eukaryotic cells. The formation of the G-quadruplex structure was indicated by circular dichroism (CD) spectroscopy and enzymatic footprinting with RNase T1. The unusual stability of the G-quadruplex was evidenced when addition of only 1 mM KCl resulted in about a 30 degrees C increase in the melting temperature (T(m)), as compared to that obtained in the absence of added salt. The T(m) was independent of the RNA concentration, suggesting an intramolecular G-quadruplex structure. Additionally, in a dual luciferase reporter assay performed in eukaryotic cells, the M3Q motif present in the context of the entire 5'-UTR of MT3-MMP repressed activity of its downstream gene by more than half. To the best of our knowledge, the naturally occurring M3Q sequence forms one of the most stable, intramolecular RNA G-quadruplexes reported. This report is the first to establish a functional role of a G-quadruplex forming sequence within the MT3-MMP 5'-UTR in the regulation of translation in eukaryotic cells.
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Affiliation(s)
- Mark J Morris
- Department of Chemistry, Kent State University, Kent, Ohio 44242, USA
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Affiliation(s)
- Jitendra Kumar
- Department of Chemistry, Indian Institute of Technology Kanpur, Kanpur 208016 (UP), India
| | - Sandeep Verma
- Department of Chemistry, Indian Institute of Technology Kanpur, Kanpur 208016 (UP), India
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35
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Martadinata H, Phan AT. Structure of propeller-type parallel-stranded RNA G-quadruplexes, formed by human telomeric RNA sequences in K+ solution. J Am Chem Soc 2009; 131:2570-8. [PMID: 19183046 DOI: 10.1021/ja806592z] [Citation(s) in RCA: 180] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Very recent studies showed that mammalian telomeres were transcribed into telomeric-repeat-containing RNAs and suggested that these RNA molecules were biologically important. Here we report on a structural study of RNA G-quadruplexes formed by human telomeric RNA sequences in K(+) solution. Our data indicated that these sequences formed propeller-type parallel-stranded RNA G-quadruplexes. We have determined the NMR-based solution structure of a dimeric propeller-type RNA G-quadruplex formed by the 12-nt human telomeric RNA sequence r(UAGGGUUAGGGU). We also observed the stacking of two such propeller-type G-quadruplex blocks for the 10-nt human telomeric RNA sequence r(GGGUUAGGGU) and a higher-order G-quadruplex structure for the 9-nt human telomeric RNA sequence r(GGGUUAGGG). Based on these findings we proposed how higher-order structures might be formed by long telomeric RNA.
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Affiliation(s)
- Herry Martadinata
- Division of Physics and Applied Physics, School of Physical and Mathematical Sciences, Nanyang Technological University, Singapore 637371
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36
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Morgado CA, Jurečka P, Svozil D, Hobza P, Šponer J. Balance of Attraction and Repulsion in Nucleic-Acid Base Stacking: CCSD(T)/Complete-Basis-Set-Limit Calculations on Uracil Dimer and a Comparison with the Force-Field Description. J Chem Theory Comput 2009; 5:1524-44. [DOI: 10.1021/ct9000125] [Citation(s) in RCA: 45] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Affiliation(s)
- Claudio A. Morgado
- Institute of Biophysics, Academy of Sciences of the Czech Republic, Královopolská 135, 612 65 Brno, Czech Republic, Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, Flemingovo náměstí 2, 166 10 Prague 6, Czech Republic, and Department of Physical Chemistry, Palacky University, tr. Svobody 26, 771 46, Olomouc, Czech Republic
| | - Petr Jurečka
- Institute of Biophysics, Academy of Sciences of the Czech Republic, Královopolská 135, 612 65 Brno, Czech Republic, Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, Flemingovo náměstí 2, 166 10 Prague 6, Czech Republic, and Department of Physical Chemistry, Palacky University, tr. Svobody 26, 771 46, Olomouc, Czech Republic
| | - Daniel Svozil
- Institute of Biophysics, Academy of Sciences of the Czech Republic, Královopolská 135, 612 65 Brno, Czech Republic, Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, Flemingovo náměstí 2, 166 10 Prague 6, Czech Republic, and Department of Physical Chemistry, Palacky University, tr. Svobody 26, 771 46, Olomouc, Czech Republic
| | - Pavel Hobza
- Institute of Biophysics, Academy of Sciences of the Czech Republic, Královopolská 135, 612 65 Brno, Czech Republic, Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, Flemingovo náměstí 2, 166 10 Prague 6, Czech Republic, and Department of Physical Chemistry, Palacky University, tr. Svobody 26, 771 46, Olomouc, Czech Republic
| | - Jiří Šponer
- Institute of Biophysics, Academy of Sciences of the Czech Republic, Královopolská 135, 612 65 Brno, Czech Republic, Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, Flemingovo náměstí 2, 166 10 Prague 6, Czech Republic, and Department of Physical Chemistry, Palacky University, tr. Svobody 26, 771 46, Olomouc, Czech Republic
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Lipay JM, Mihailescu MR. NMR spectroscopy and kinetic studies of the quadruplex forming RNA r(UGGAGGU). MOLECULAR BIOSYSTEMS 2009; 5:1347-55. [DOI: 10.1039/b911555b] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
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Huppert JL, Bugaut A, Kumari S, Balasubramanian S. G-quadruplexes: the beginning and end of UTRs. Nucleic Acids Res 2008; 36:6260-8. [PMID: 18832370 PMCID: PMC2577360 DOI: 10.1093/nar/gkn511] [Citation(s) in RCA: 318] [Impact Index Per Article: 19.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2008] [Revised: 07/20/2008] [Accepted: 07/25/2008] [Indexed: 01/17/2023] Open
Abstract
Molecular mechanisms that regulate gene expression can occur either before or after transcription. The information for post-transcriptional regulation can lie within the sequence or structure of the RNA transcript and it has been proposed that G-quadruplex nucleic acid sequence motifs may regulate translation as well as transcription. Here, we have explored the incidence of G-quadruplex motifs in and around the untranslated regions (UTRs) of mRNA. We observed a significant strand asymmetry, consistent with a general depletion of G-quadruplex-forming RNA. We also observed a positional bias in two distinct regions, each suggestive of a specific function. We observed an excess of G-quadruplex motifs towards the 5'-ends of 5'-UTRs, supportive of a hypothesis linking 5'-UTR RNA G-quadruplexes to translational control. We then analysed the vicinity of 3'-UTRs and observed an over-representation of G-quadruplex motifs immediately after the 3'-end of genes, especially in those cases where another gene is in close proximity, suggesting that G-quadruplexes may be involved in the termination of gene transcription.
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Affiliation(s)
- Julian Leon Huppert
- Cavendish Laboratory, University of Cambridge, JJ Thompson Ave, Cambridge CB3 0HE and University Chemical Laboratory, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, UK
| | - Anthony Bugaut
- Cavendish Laboratory, University of Cambridge, JJ Thompson Ave, Cambridge CB3 0HE and University Chemical Laboratory, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, UK
| | - Sunita Kumari
- Cavendish Laboratory, University of Cambridge, JJ Thompson Ave, Cambridge CB3 0HE and University Chemical Laboratory, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, UK
| | - Shankar Balasubramanian
- Cavendish Laboratory, University of Cambridge, JJ Thompson Ave, Cambridge CB3 0HE and University Chemical Laboratory, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, UK
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Vondrusková J, Kypr J, Kejnovská I, Fialová M, Vorlícková M. Guanine quadruplex formation by RNA/DNA hybrid analogs of Oxytricha telomere G(4)T(4)G(4) fragment. Biopolymers 2008; 89:797-806. [PMID: 18491413 DOI: 10.1002/bip.21015] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
Using circular dichroism spectroscopy, gel electrophoresis, and ultraviolet absorption spectroscopy, we have studied quadruplex folding of RNA/DNA analogs of the Oxytricha telomere fragment, G(4)T(4)G(4), which forms the well-known basket-type, antiparallel quadruplex. We have substituted riboguanines (g) for deoxyriboguanines (G) in the positions G1, G9, G4, and G12; these positions form the terminal tetrads of the G(4)T(4)G(4) quadruplex and adopt syn, syn, anti, and anti glycosidic geometries, respectively. We show that substitution of a single sugar was able to change the quadruplex topology. With the exception of G(4)T(4)G(3)g, which adopted an antiparallel structure, all the RNA/DNA hybrid analogs formed parallel, bimolecular quadruplexes in concentrated solution at low salt. In dilute solutions ( approximately 0.1 mM nucleoside), the RNA/DNA hybrids substituted at positions 4 or 12 adopted antiparallel quadruplexes, which were especially stable in Na(+) solutions. The hybrids substituted at positions 1 and 9 preferably formed parallel quadruplexes, which were more stable than the nonmodified G(4)T(4)G(4) quadruplex in K(+) solutions. Substitutions near the 3'end of the molecule affected folding more than substitutions near the 5'end. The ability to control quadruplex folding will allow further studies of biophysical and biological properties of the various folding topologies.
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Affiliation(s)
- Jitka Vondrusková
- Institute of Biophysics, v.v.i., Academy of Sciences of the Czech Republic, Department of CD Spectroscopy of Nucleic Acids, Královopolská 135, CZ-612 65 Brno, Czech Republic
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40
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Vondrusková J, Kypr J, Kejnovská I, Fialová M, Vorlícková M. Role of loops in the guanine quadruplex formation by DNA/RNA hybrid analogs of G4T4G4. Int J Biol Macromol 2008; 43:463-7. [PMID: 18812187 DOI: 10.1016/j.ijbiomac.2008.08.013] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2008] [Revised: 08/22/2008] [Accepted: 08/26/2008] [Indexed: 10/21/2022]
Abstract
CD spectroscopy, gel electrophoresis and absorption-based thermal stability were used to analyze quadruplex formation of RNA and RNA/DNA hybrid analogs of the deoxyoligonucleotide G4T4G4, which forms a well-characterized basket-type quadruplex. All RNA-containing dodecamers, g4u4g4, G4u4G4 and g4T4g4 (RNA lower-case, DNA capital letters), formed parallel, namely tetramolecular quadruplexes in Na+-containing solutions. The u4 loop forced DNA tetrads into the same conformation as adopted by g4u4g4. In contrast, the T4 loop destabilized the RNA tetrads. Potassium ions markedly stabilized parallel quadruplexes of RNA-containing analogs as well as their bimolecular folding. In the presence of K+, g4T4g4 formed exclusively bimolecular quadruplexes of both parallel and antiparallel types as indicated by CD. Thus, the T4 loop permits RNA strands to adopt an antiparallel arrangement. These findings may be useful for engineering particular quadruplex foldings in different quadruplex-forming sequences.
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Affiliation(s)
- Jitka Vondrusková
- Institute of Biophysics, v.v.i., Academy of Sciences of the Czech Republic, Královopolská 135, CZ-612 65 Brno, Czech Republic
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41
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Pagano B, Mattia CA, Cavallo L, Uesugi S, Giancola C, Fraternali F. Stability and Cations Coordination of DNA and RNA 14-Mer G-Quadruplexes: A Multiscale Computational Approach. J Phys Chem B 2008; 112:12115-23. [DOI: 10.1021/jp804036j] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Bruno Pagano
- Dipartimento di Scienze Farmaceutiche, Università di Salerno, via Ponte Don Melillo, Fisciano (SA), I-84084, Italy, Dipartimento di Chimica, Università di Salerno, via Ponte Don Melillo, Fisciano (SA), I-84084, Italy, Department of Environment and Natural Sciences, Yokohama National University, 79-7 Tokiwadai, Hodogaya-ku, Yokohama, 240-8501, Japan, Dipartimento di Chimica, Università di Napoli Federico II, via Cintia, Napoli, I-80126, Italy, and The Randall Division of Cell and Molecular Biophysics, New
| | - Carlo A. Mattia
- Dipartimento di Scienze Farmaceutiche, Università di Salerno, via Ponte Don Melillo, Fisciano (SA), I-84084, Italy, Dipartimento di Chimica, Università di Salerno, via Ponte Don Melillo, Fisciano (SA), I-84084, Italy, Department of Environment and Natural Sciences, Yokohama National University, 79-7 Tokiwadai, Hodogaya-ku, Yokohama, 240-8501, Japan, Dipartimento di Chimica, Università di Napoli Federico II, via Cintia, Napoli, I-80126, Italy, and The Randall Division of Cell and Molecular Biophysics, New
| | - Luigi Cavallo
- Dipartimento di Scienze Farmaceutiche, Università di Salerno, via Ponte Don Melillo, Fisciano (SA), I-84084, Italy, Dipartimento di Chimica, Università di Salerno, via Ponte Don Melillo, Fisciano (SA), I-84084, Italy, Department of Environment and Natural Sciences, Yokohama National University, 79-7 Tokiwadai, Hodogaya-ku, Yokohama, 240-8501, Japan, Dipartimento di Chimica, Università di Napoli Federico II, via Cintia, Napoli, I-80126, Italy, and The Randall Division of Cell and Molecular Biophysics, New
| | - Seiichi Uesugi
- Dipartimento di Scienze Farmaceutiche, Università di Salerno, via Ponte Don Melillo, Fisciano (SA), I-84084, Italy, Dipartimento di Chimica, Università di Salerno, via Ponte Don Melillo, Fisciano (SA), I-84084, Italy, Department of Environment and Natural Sciences, Yokohama National University, 79-7 Tokiwadai, Hodogaya-ku, Yokohama, 240-8501, Japan, Dipartimento di Chimica, Università di Napoli Federico II, via Cintia, Napoli, I-80126, Italy, and The Randall Division of Cell and Molecular Biophysics, New
| | - Concetta Giancola
- Dipartimento di Scienze Farmaceutiche, Università di Salerno, via Ponte Don Melillo, Fisciano (SA), I-84084, Italy, Dipartimento di Chimica, Università di Salerno, via Ponte Don Melillo, Fisciano (SA), I-84084, Italy, Department of Environment and Natural Sciences, Yokohama National University, 79-7 Tokiwadai, Hodogaya-ku, Yokohama, 240-8501, Japan, Dipartimento di Chimica, Università di Napoli Federico II, via Cintia, Napoli, I-80126, Italy, and The Randall Division of Cell and Molecular Biophysics, New
| | - Franca Fraternali
- Dipartimento di Scienze Farmaceutiche, Università di Salerno, via Ponte Don Melillo, Fisciano (SA), I-84084, Italy, Dipartimento di Chimica, Università di Salerno, via Ponte Don Melillo, Fisciano (SA), I-84084, Italy, Department of Environment and Natural Sciences, Yokohama National University, 79-7 Tokiwadai, Hodogaya-ku, Yokohama, 240-8501, Japan, Dipartimento di Chimica, Università di Napoli Federico II, via Cintia, Napoli, I-80126, Italy, and The Randall Division of Cell and Molecular Biophysics, New
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42
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Menon L, Mader SA, Mihailescu MR. Fragile X mental retardation protein interactions with the microtubule associated protein 1B RNA. RNA (NEW YORK, N.Y.) 2008; 14:1644-55. [PMID: 18579868 PMCID: PMC2491469 DOI: 10.1261/rna.1100708] [Citation(s) in RCA: 53] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/06/2023]
Abstract
Fragile X mental retardation syndrome, the most common form of inherited mental retardation, is caused by the absence of the fragile X mental retardation protein (FMRP). FMRP has been shown to use its arginine-glycine-glycine (RGG) box to bind to a subset of RNA targets that form a G quadruplex structure. We performed a detailed analysis of the interactions between the FMRP RGG box and the microtubule associated protein 1B (MAP1B) mRNA, a relevant in vivo FMRP target. We show that MAP1B RNA forms an intramolecular G quadruplex structure, which is bound with high affinity and specificity by the FMRP RGG box. We determined that hydrophobic interactions are important in the FMRP RGG box-MAP1B RNA association, with minor contributions from electrostatic interactions. Our findings that at low protein:RNA ratios the RNA G quadruplex structure is slightly stabilized, whereas at high ratios is unfolded, suggest a mechanism by which the FMRP concentration variation in response to a neurotransmitter stimulation event could act as a regulatory switch for the protein function, from translation repressor to translation activator.
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Affiliation(s)
- Lakshmi Menon
- Department of Chemistry and Biochemistry, Duquesne University, Pittsburgh, Pennsylvania 15282, USA
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43
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Xu Y, Kaminaga K, Komiyama M. G-quadruplex formation by human telomeric repeats-containing RNA in Na+ solution. J Am Chem Soc 2008; 130:11179-84. [PMID: 18642813 DOI: 10.1021/ja8031532] [Citation(s) in RCA: 148] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
For a long time, telomeres have been considered to be transcriptionally silent. Very recently, a breaking finding from two groups demonstrated that telomere DNA is transcribed into telomeric repeat-containing RNA in mammalian cells (Azzalin, C. M.; Reichenbach, P.; Khoriauli, L.; Giulotto, E.; Lingner, J. Science 2007, 318, 798-801. Schoefter, S.; Blasco, M. A. Nat. Cell Biol. 2008, 10, 228-236). The telomeric RNA, a newly appeared player in telomere biology, may be a key component of telomere machinery. In the current study, we used a combination of NMR, circular dichroism (CD), matrix-assisted laser desorption/ionization-time-of-flight mass spectrometry (MALDI-TOFMS), and gel electrophoresis to investigate the structural features of a human telomere RNA sequence. We demonstrated that human telomere RNA can form a parallel G-quadruplex structure in the presence of Na(+). Importantly, we found for the first time that the G-quadruplex forming telomere RNA protects itself from enzymatic digestion. These results provide valuable information to allow understanding of the structure and function of human telomeric RNA.
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Affiliation(s)
- Yan Xu
- Research Center for Advanced Science and Technology, The University of Tokyo, 4-6-1 Komaba, Meguro-ku, Tokyo 153-8904, Japan.
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44
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Webba da Silva M. NMR methods for studying quadruplex nucleic acids. Methods 2008; 43:264-77. [PMID: 17967697 DOI: 10.1016/j.ymeth.2007.05.007] [Citation(s) in RCA: 100] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2007] [Accepted: 05/16/2007] [Indexed: 12/22/2022] Open
Abstract
Solution NMR spectroscopy has traditionally played a central role in examining quadruplex structure, dynamics, and interactions. Here, an overview is given of the methods currently applied to structural, dynamics, thermodynamics, and kinetics studies of nucleic acid quadruplexes and associated cations.
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Affiliation(s)
- Mateus Webba da Silva
- School of Biomedical Sciences, University of Ulster, Cromore Road, Coleraine BT52 1SA, UK.
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45
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Tang CF, Shafer RH. Engineering the quadruplex fold: nucleoside conformation determines both folding topology and molecularity in guanine quadruplexes. J Am Chem Soc 2007; 128:5966-73. [PMID: 16637665 PMCID: PMC2597528 DOI: 10.1021/ja0603958] [Citation(s) in RCA: 148] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Nucleic acid quadruplexes, based on the guanine quartet, can arise from one or several strands, depending on the sequence. Those consisting of a single strand are usually folded in one of two principal topologies: antiparallel, in which all or half of the guanine stretches are antiparallel to each other, or parallel, in which all guanine stretches are parallel to each other. In the latter, all guanine nucleosides possess the anti conformation about the glycosidic bond, while in the former, half possess the anti conformation, and half possess the syn conformation. While antiparallel is the more common fold, examples of biologically important, parallel quadruplexes are becoming increasingly common. Thus, it is of interest to understand the forces that determine the quadruplex fold. Here, we examine the influence of individual nucleoside conformation on the overall folding topology by selective substitution of rG for dG. We can reverse the antiparallel fold of the thrombin binding aptamer (TBA) by this approach. Additionally, this substitution converts a unimolecular quadruplex into a bimolecular one. Similar reverse substitutions in the all-RNA analogue of TBA result in a parallel to antiparallel change in topology and alter the strand configuration from bimolecular to unimolecular. On the basis of the specific substitutions made, we conclude that the strong preference of guanine ribonucleosides for the anti conformation is the driving force for the change in topology. These results demonstrate how conformational properties of guanine nucleosides govern not only the quadruplex folding topology but also impact quadruplex molecularity and provide a means to control these properties.
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Affiliation(s)
- Chung-Fei Tang
- Department of Pharmaceutical Chemistry, School of Pharmacy and Graduate Group in Chemistry and Chemical Biology, University of California, San Francisco, California 94143-0446, USA
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46
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Menon L, Mihailescu MR. Interactions of the G quartet forming semaphorin 3F RNA with the RGG box domain of the fragile X protein family. Nucleic Acids Res 2007; 35:5379-92. [PMID: 17693432 PMCID: PMC2018618 DOI: 10.1093/nar/gkm581] [Citation(s) in RCA: 62] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/04/2022] Open
Abstract
Fragile X syndrome, the most common cause of inherited mental retardation, is caused by the transcriptional silencing of the fmr1 gene due to an unstable expansion of a CGG trinucleotide repeat and its subsequent hypermethylation in its 5′ UTR. This gene encodes for the fragile X mental retardation protein (FMRP), an RNA-binding protein that has been shown to use its RGG box domain to bind to G quartet-forming RNA. In this study, we performed a detailed analysis of the interactions between the FMRP RGG box domain and one of its proposed RNA targets, human semaphorin 3F (S3F) RNA by using biophysical methods such as fluorescence, UV and circular dichroism spectroscopy. We show that this RNA forms a G quartet-containing structure, which is recognized with high affinity and specificity by the FMRP RGG box. In addition, we analyzed the interactions of human S3F RNA with the RGG box and RG cluster of the two FMRP autosomal paralogs, the FXR1P and FXR2P. We found that this RNA is bound with high affinity and specificity only by the FXR1P RGG box, but not by the FXR2P RG cluster. Both FMRP and FXR1P RGG box are able to unwind the G quartet structure of S3F RNA, however, the peptide concentrations required in this process are very different: a ratio of 1:6 RNA:FMRP RGG box versus 1:2 RNA:FXR1P RGG box.
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Li X, Nishizuka H, Tsutsumi K, Imai Y, Kurihara Y, Uesugi S. Structure, interactions and effects on activity of the 5'-terminal region of human telomerase RNA. J Biochem 2007; 141:755-65. [PMID: 17387120 DOI: 10.1093/jb/mvm081] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023] Open
Abstract
Telomerase is an enzyme that catalyzes addition of telomeric repeat sequences to the 3'-termini of eukaryotic chromosome DNA. The catalytic core of telomerase consists of a protein component, telomerase reverse transcriptase (TERT), for the catalysis and an RNA component, telomerase RNA (TR), containing the template for the sequence. Human telomerase RNA (hTR) consists of 451 nucleotides (nt) and contains consecutive G-stretches in the 5'-terminal region. We examined the effects of the 5'-terminal sequence (nt 1-17) in hTR, which is assumed to be a single-stranded region (region 1), on interaction and telomerase activity in vitro. Mutation and binding experiments for hTR and its variants suggest that region 1 has repressive effects on telomerase activity by interaction with the region(s) in the 3'-half part. We prepared various hTR variants with mutations in region 1 and two possible target regions (region 2: nt 229-244; region 3: nt 284-297). Studies on these variants showed that region 1 can interact with regions 2 and 3 and the interactions between regions 1 and 3 may contribute to the repressive effects of region 1. We found that a mutation in region 2 markedly enhances telomerase activity. We also found that some deletion and sequence mutations in region 1 enhance the activity.
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Affiliation(s)
- Xianglan Li
- Department of Environment and Natural Sciences, Graduate School of Environment and Information Sciences, Yokohama National University, 79-7 Tokiwadai, Hodogaya-ku, Yokohama 240-8501, Japan
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48
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Protoberberine Alkaloids: Physicochemical and Nucleic Acid Binding Properties. TOPICS IN HETEROCYCLIC CHEMISTRY 2007. [DOI: 10.1007/7081_2007_071] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
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Cornish PV, Stammler SN, Giedroc DP. The global structures of a wild-type and poorly functional plant luteoviral mRNA pseudoknot are essentially identical. RNA (NEW YORK, N.Y.) 2006; 12:1959-69. [PMID: 17000902 PMCID: PMC1624904 DOI: 10.1261/rna.199006] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/12/2023]
Abstract
The helical junction region of a -1 frameshift stimulating hairpin-type mRNA pseudoknot from sugarcane yellow leaf virus (ScYLV) is characterized by a novel C27.(G7-C14) loop 2-stem 1 minor groove base triple, which is stacked on a C8+.(G12-C28) loop 1-stem 2 major groove base triple. Substitution of C27 with adenosine reduces frameshifting efficiency to a level just twofold above the slip-site alone. Here, we show that the global structure of the C27A ScYLV RNA is nearly indistinguishable from the wild-type counterpart, despite the fact that the helical junction region is altered and incorporates the anticipated isostructural A27.(G7-C14) minor groove base triple. This interaction mediates a 2.3-A displacement of C8+ driven by an A27 N6-C8+ O2 hydrogen bond as part of an A(n-1).C+.G-Cn base quadruple. The helical junction regions of the C27A ScYLV and the beet western yellows virus (BWYV) pseudoknots are essentially superimposable, the latter of which contains an analogous A25.(G7-C14) minor groove base triple. These results reveal that the global ground-state structure is not strongly correlated with frameshift stimulation and point to a reduced thermodynamic stability and/or enhanced kinetic lability that derives from an altered helical junction architecture in the C27A ScYLV RNA as a significant determinant for setting frameshifting efficiencies in plant luteoviral mRNA pseudoknots.
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Affiliation(s)
- Peter V Cornish
- Department of Biochemistry and Biophysics, 2128 TAMU, Texas A&M University, College Station, Texas 77843-2128, USA
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Wieland M, Hartig JS. Turning inhibitors into activators: a hammerhead ribozyme controlled by a guanine quadruplex. Angew Chem Int Ed Engl 2006; 45:5875-8. [PMID: 16871639 DOI: 10.1002/anie.200600909] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Markus Wieland
- University of Konstanz, Department of Chemistry, Universitätsstrasse 10, 78457 Konstanz, Germany
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