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Kurkowiak M, Arcimowicz Ł, Chruściel E, Urban-Wójciuk Z, Papak I, Keegan L, O'Connell M, Kowalski J, Hupp T, Marek-Trzonkowska N. The effects of RNA editing in cancer tissue at different stages in carcinogenesis. RNA Biol 2021; 18:1524-1539. [PMID: 33593231 PMCID: PMC8582992 DOI: 10.1080/15476286.2021.1877024] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
RNA editing is one of the most prevalent and abundant forms of post-transcriptional RNA modification observed in normal physiological processes and often aberrant in diseases including cancer. RNA editing changes the sequences of mRNAs, making them different from the source DNA sequence. Edited mRNAs can produce editing-recoded protein isoforms that are functionally different from the corresponding genome-encoded protein isoforms. The major type of RNA editing in mammals occurs by enzymatic deamination of adenosine to inosine (A-to-I) within double-stranded RNAs (dsRNAs) or hairpins in pre-mRNA transcripts. Enzymes that catalyse these processes belong to the adenosine deaminase acting on RNA (ADAR) family. The vast majority of knowledge on the RNA editing landscape relevant to human disease has been acquired using in vitro cancer cell culture models. The limitation of such in vitro models, however, is that the physiological or disease relevance of results obtained is not necessarily obvious. In this review we focus on discussing in vivo occurring RNA editing events that have been identified in human cancer tissue using samples surgically resected or clinically retrieved from patients. We discuss how RNA editing events occurring in tumours in vivo can identify pathological signalling mechanisms relevant to human cancer physiology which is linked to the different stages of cancer progression including initiation, promotion, survival, proliferation, immune escape and metastasis.
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Affiliation(s)
- Małgorzata Kurkowiak
- International Centre for Cancer Vaccine Science (ICCVS), University of Gdańsk, Gdańsk, Poland
| | - Łukasz Arcimowicz
- International Centre for Cancer Vaccine Science (ICCVS), University of Gdańsk, Gdańsk, Poland
| | - Elżbieta Chruściel
- International Centre for Cancer Vaccine Science (ICCVS), University of Gdańsk, Gdańsk, Poland
| | - Zuzanna Urban-Wójciuk
- International Centre for Cancer Vaccine Science (ICCVS), University of Gdańsk, Gdańsk, Poland
| | - Ines Papak
- International Centre for Cancer Vaccine Science (ICCVS), University of Gdańsk, Gdańsk, Poland
| | - Liam Keegan
- CEITEC Masaryk University, Brno, CZ, Czech Republic
| | | | - Jacek Kowalski
- International Centre for Cancer Vaccine Science (ICCVS), University of Gdańsk, Gdańsk, Poland.,Department of Pathomorphology, Medical University of Gdańsk, Gdańsk, Poland
| | - Ted Hupp
- International Centre for Cancer Vaccine Science (ICCVS), University of Gdańsk, Gdańsk, Poland.,University of Edinburgh, Edinburgh Cancer Research Centre, Edinburgh, Scotland, UK
| | - Natalia Marek-Trzonkowska
- International Centre for Cancer Vaccine Science (ICCVS), University of Gdańsk, Gdańsk, Poland.,Laboratory of Immunoregulation and Cellular Therapies, Department of Family Medicine, Medical University of Gdańsk, Gdańsk, Poland
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Špačková N, Réblová K. Role of Inosine⁻Uracil Base Pairs in the Canonical RNA Duplexes. Genes (Basel) 2018; 9:genes9070324. [PMID: 29958383 PMCID: PMC6070904 DOI: 10.3390/genes9070324] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2018] [Revised: 06/13/2018] [Accepted: 06/26/2018] [Indexed: 01/09/2023] Open
Abstract
Adenosine to inosine (A–I) editing is the most common modification of double-stranded RNA (dsRNA). This change is mediated by adenosine deaminases acting on RNA (ADARs) enzymes with a preference of U>A>C>G for 5′ neighbor and G>C=A>U or G>C>U=A for 3′ neighbor. A–I editing occurs most frequently in the non-coding regions containing repetitive elements such as ALUs. It leads to disruption of RNA duplex structure, which prevents induction of innate immune response. We employed standard and biased molecular dynamics (MD) simulations to analyze the behavior of RNA duplexes with single and tandem inosine–uracil (I–U) base pairs in different sequence context. Our analysis showed that the I–U pairs induce changes in base pair and base pair step parameters and have different dynamics when compared with standard canonical base pairs. In particular, the first I–U pair from tandem I–U/I–U systems exhibited increased dynamics depending on its neighboring 5′ base. We discovered that UII sequence, which is frequently edited, has lower flexibility compared with other sequences (AII, GII, CII), hence it only modestly disrupts dsRNA. This might indicate that the UAA motifs in ALUs do not have to be sufficiently effective in preventing immune signaling.
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Affiliation(s)
- Naďa Špačková
- Department of Condensed Matter Physics, Faculty of Science, Masaryk University, Kotlářská 2, 611 37 Brno, Czech Republic.
| | - Kamila Réblová
- CEITEC-Central European Institute of Technology, Masaryk University, Kamenice 5, 625 00 Brno, Czech Republic.
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Spasic A, Kennedy SD, Needham L, Manoharan M, Kierzek R, Turner DH, Mathews DH. Molecular dynamics correctly models the unusual major conformation of the GAGU RNA internal loop and with NMR reveals an unusual minor conformation. RNA (NEW YORK, N.Y.) 2018; 24:656-672. [PMID: 29434035 PMCID: PMC5900564 DOI: 10.1261/rna.064527.117] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/17/2017] [Accepted: 01/19/2018] [Indexed: 05/08/2023]
Abstract
The RNA "GAGU" duplex, (5'GACGAGUGUCA)2, contains the internal loop (5'-GAGU-3')2 , which has two conformations in solution as determined by NMR spectroscopy. The major conformation has a loop structure consisting of trans-Watson-Crick/Hoogsteen GG pairs, A residues stacked on each other, U residues bulged outside the helix, and all sugars with a C2'-endo conformation. This differs markedly from the internal loops, (5'-GAGC-3')2, (5'-AAGU-3')2, and (5'-UAGG-3')2, which all have cis-Watson-Crick/Watson-Crick AG "imino" pairs flanked by cis-Watson-Crick/Watson-Crick canonical pairs resulting in maximal hydrogen bonding. Here, molecular dynamics was used to test whether the Amber force field (ff99 + bsc0 + OL3) approximates molecular interactions well enough to keep stable the unexpected conformation of the GAGU major duplex structure and the NMR structures of the duplexes containing (5'-GAGC-3')2, (5'-AAGU-3')2, and (5'-UAGG-3')2 internal loops. One-microsecond simulations were repeated four times for each of the duplexes starting in their NMR conformations. With the exception of (5'-UAGG-3')2, equivalent simulations were also run starting with alternative conformations. Results indicate that the Amber force field keeps the NMR conformations of the duplexes stable for at least 1 µsec. They also demonstrate an unexpected minor conformation for the (5'-GAGU-3')2 loop that is consistent with newly measured NMR spectra of duplexes with natural and modified nucleotides. Thus, unrestrained simulations led to the determination of the previously unknown minor conformation. The stability of the native (5'-GAGU-3')2 internal loop as compared to other loops can be explained by changes in hydrogen bonding and stacking as the flanking bases are changed.
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Affiliation(s)
- Aleksandar Spasic
- Department of Biochemistry and Biophysics, University of Rochester Medical Center, Rochester, New York 14642, USA
- Center for RNA Biology, University of Rochester Medical Center, Rochester, New York 14642, USA
| | - Scott D Kennedy
- Department of Biochemistry and Biophysics, University of Rochester Medical Center, Rochester, New York 14642, USA
| | - Laura Needham
- Department of Biochemistry and Biophysics, University of Rochester Medical Center, Rochester, New York 14642, USA
- Center for RNA Biology, University of Rochester Medical Center, Rochester, New York 14642, USA
| | - Muthiah Manoharan
- Department of Discovery, Alnylam Pharmaceuticals, Cambridge, Massachusetts 02142, USA
| | - Ryszard Kierzek
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, 61-704 Poznan Noskowskiego, Poland
| | - Douglas H Turner
- Center for RNA Biology, University of Rochester Medical Center, Rochester, New York 14642, USA
- Department of Chemistry, University of Rochester, Rochester, New York 14627-0216, USA
| | - David H Mathews
- Department of Biochemistry and Biophysics, University of Rochester Medical Center, Rochester, New York 14642, USA
- Center for RNA Biology, University of Rochester Medical Center, Rochester, New York 14642, USA
- Department of Biostatistics and Computational Biology, University of Rochester Medical Center, Rochester, New York 14642, USA
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Keegan L, Khan A, Vukic D, O'Connell M. ADAR RNA editing below the backbone. RNA (NEW YORK, N.Y.) 2017; 23:1317-1328. [PMID: 28559490 PMCID: PMC5558901 DOI: 10.1261/rna.060921.117] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/22/2023]
Abstract
ADAR RNA editing enzymes (adenosine deaminases acting on RNA) that convert adenosine bases to inosines were first identified biochemically 30 years ago. Since then, studies on ADARs in genetic model organisms, and evolutionary comparisons between them, continue to reveal a surprising range of pleiotropic biological effects of ADARs. This review focuses on Drosophila melanogaster, which has a single Adar gene encoding a homolog of vertebrate ADAR2 that site-specifically edits hundreds of transcripts to change individual codons in ion channel subunits and membrane and cytoskeletal proteins. Drosophila ADAR is involved in the control of neuronal excitability and neurodegeneration and, intriguingly, in the control of neuronal plasticity and sleep. Drosophila ADAR also interacts strongly with RNA interference, a key antiviral defense mechanism in invertebrates. Recent crystal structures of human ADAR2 deaminase domain-RNA complexes help to interpret available information on Drosophila ADAR isoforms and on the evolution of ADARs from tRNA deaminase ADAT proteins. ADAR RNA editing is a paradigm for the now rapidly expanding range of RNA modifications in mRNAs and ncRNAs. Even with recent progress, much remains to be understood about these groundbreaking ADAR RNA modification systems.
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Affiliation(s)
- Liam Keegan
- CEITEC at Masaryk University Brno, Pavilion A35, Brno CZ-62500, Czech Republic
| | - Anzer Khan
- CEITEC at Masaryk University Brno, Pavilion A35, Brno CZ-62500, Czech Republic
| | - Dragana Vukic
- CEITEC at Masaryk University Brno, Pavilion A35, Brno CZ-62500, Czech Republic
| | - Mary O'Connell
- CEITEC at Masaryk University Brno, Pavilion A35, Brno CZ-62500, Czech Republic
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Dallmann A, Beribisky AV, Gnerlich F, Rübbelke M, Schiesser S, Carell T, Sattler M. Site-Specific Isotope-Labeling of Inosine Phosphoramidites and NMR Analysis of an Inosine-Containing RNA Duplex. Chemistry 2016; 22:15350-15359. [DOI: 10.1002/chem.201602784] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2016] [Indexed: 01/09/2023]
Affiliation(s)
- Andre Dallmann
- Institute of Structural Biology; Helmholtz Zentrum München; Ingolstädter Landstraße 1 85764 Neuherberg Germany
- Center for Integrated Protein Science Munich at Chair Biomolecular NMR; Department Chemie; Technische Universität München; Lichtenbergstraße 4 85747 Garching Germany
- Department of Chemistry; Humboldt Universität zu Berlin; 12489 Berlin Germany
| | - Alexander V. Beribisky
- Institute of Structural Biology; Helmholtz Zentrum München; Ingolstädter Landstraße 1 85764 Neuherberg Germany
- Center for Integrated Protein Science Munich at Chair Biomolecular NMR; Department Chemie; Technische Universität München; Lichtenbergstraße 4 85747 Garching Germany
| | - Felix Gnerlich
- Center for Integrated Protein Science at the Department of Chemistry; Ludwig-Maximilians-Universität München; Butenandtstraße 5-13 81377 Munich Germany
| | - Martin Rübbelke
- Institute of Structural Biology; Helmholtz Zentrum München; Ingolstädter Landstraße 1 85764 Neuherberg Germany
- Center for Integrated Protein Science Munich at Chair Biomolecular NMR; Department Chemie; Technische Universität München; Lichtenbergstraße 4 85747 Garching Germany
| | - Stefan Schiesser
- Center for Integrated Protein Science at the Department of Chemistry; Ludwig-Maximilians-Universität München; Butenandtstraße 5-13 81377 Munich Germany
| | - Thomas Carell
- Center for Integrated Protein Science at the Department of Chemistry; Ludwig-Maximilians-Universität München; Butenandtstraße 5-13 81377 Munich Germany
| | - Michael Sattler
- Institute of Structural Biology; Helmholtz Zentrum München; Ingolstädter Landstraße 1 85764 Neuherberg Germany
- Center for Integrated Protein Science Munich at Chair Biomolecular NMR; Department Chemie; Technische Universität München; Lichtenbergstraße 4 85747 Garching Germany
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Conflict RNA modification, host-parasite co-evolution, and the origins of DNA and DNA-binding proteins1. Biochem Soc Trans 2015; 42:1159-67. [PMID: 25110019 DOI: 10.1042/bst20140147] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
Nearly 150 different enzymatically modified forms of the four canonical residues in RNA have been identified. For instance, enzymes of the ADAR (adenosine deaminase acting on RNA) family convert adenosine residues into inosine in cellular dsRNAs. Recent findings show that DNA endonuclease V enzymes have undergone an evolutionary transition from cleaving 3' to deoxyinosine in DNA and ssDNA to cleaving 3' to inosine in dsRNA and ssRNA in humans. Recent work on dsRNA-binding domains of ADARs and other proteins also shows that a degree of sequence specificity is achieved by direct readout in the minor groove. However, the level of sequence specificity observed is much less than that of DNA major groove-binding helix-turn-helix proteins. We suggest that the evolution of DNA-binding proteins following the RNA to DNA genome transition represents the major advantage that DNA genomes have over RNA genomes. We propose that a hypothetical RNA modification, a RRAR (ribose reductase acting on genomic dsRNA) produced the first stretches of DNA in RNA genomes. We discuss why this is the most satisfactory explanation for the origin of DNA. The evolution of this RNA modification and later steps to DNA genomes are likely to have been driven by cellular genome co-evolution with viruses and intragenomic parasites. RNA modifications continue to be involved in host-virus conflicts; in vertebrates, edited cellular dsRNAs with inosine-uracil base pairs appear to be recognized as self RNA and to suppress activation of innate immune sensors that detect viral dsRNA.
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Das G, Lyngdoh RHD. Role of wobble base pair geometry for codon degeneracy: purine-type bases at the anticodon wobble position. J Mol Model 2012; 18:3805-20. [PMID: 22399149 DOI: 10.1007/s00894-012-1385-4] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2011] [Accepted: 02/15/2012] [Indexed: 02/07/2023]
Abstract
Codon degeneracy is a key feature of the genetic code, explained by Crick (J Mol Biol 19:548-555, 1966) in terms of imprecision of base pairing at the codon third position (the wobble position) of the codon-anticodon duplex. The Crick wobble rules define, but do not explain, which base pairs are allowed/disallowed at the wobble position of this duplex. This work examines whether the H-bonded configurations of solitary RNA base pairs can in themselves help decide which base pairs are allowed at the wobble position during codon-anticodon pairing. Taking the purine-type bases guanine, hypoxanthine, queuine and adenine as anticodon wobble bases, H-bonded pairing energies and optimized configurations of numerous RNA base pairs are calculated in gas and modeled aqueous phase at the B3LYP/6-31 G(d,p) level. Calculated descriptors of alignment of these solitary base pairs are able to screen between allowed and disallowed base pairs for all cases studied here, except two cases which invoke base-sugar interactions in the codon wobble nucleoside. The exclusion of adenine from the anticodon wobble position cannot be explained on the basis of pairing facility or base pair geometry. These DFT results thus account for the specificity and degeneracy of the genetic code for all cases involving guanine, hypoxanthine and queuine as anticodon wobble bases.
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Affiliation(s)
- Gunajyoti Das
- Department of Chemistry, North-Eastern Hill University, Shillong, 793022, India
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Janke EMB, Riechert-Krause F, Weisz K. Low-temperature NMR studies on inosine wobble base pairs. J Phys Chem B 2011; 115:8569-74. [PMID: 21644523 DOI: 10.1021/jp200840j] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Base pairs formed by the inosine nucleoside (I) play an important role in many physiological processes as well as in various DNA technologies. Relative stabilities and favored base pair geometries of free inosine wobble base pairs in aprotic solvents have been determined through (1)H NMR measurements at room temperature and at very low temperatures in a freonic solvent. As indicated by its significantly deshielded imino proton, the Watson-Crick-type I·C base pair forms a remarkably strong NHN hydrogen bond. For the thermodynamically less stable I·A wobble base pair, two configurations of similar population coexist at 133 K in the slow hydrogen bond exchange regime, namely a Watson-Crick(I)-Watson-Crick(A) geometry and a Watson-Crick(I)-Hoogsteen(A) geometry. I·U base pairs are stabilized by two rather weak hydrogen bonds and are significantly disfavored over inosine self-associates in a low-temperature Freon solution.
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Ji X, Sun H, Zhou H, Xiang J, Tang Y, Zhao C. Research Progress of RNA Quadruplex. Nucleic Acid Ther 2011; 21:185-200. [DOI: 10.1089/nat.2010.0272] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Affiliation(s)
- Xiaohui Ji
- Key Laboratory for Cell Proliferation and Regulation Biology of Ministry of Education, Beijing Key Laboratory of Gene Engineering Drugs and Biological Technology, College of Life Sciences, Beijing Normal University, Beijing, China
| | - Hongxia Sun
- Beijing National Laboratory for Molecular Sciences, State Key Laboratory for Structural Chemistry of Unstable and Stable Species, Institute of Chemistry, Chinese Academy of Sciences, Beijing, China
| | - Huaxi Zhou
- Department of Systems Science, School of Management, Beijing Normal University, Beijing, China
| | - Junfeng Xiang
- Beijing National Laboratory for Molecular Sciences, State Key Laboratory for Structural Chemistry of Unstable and Stable Species, Institute of Chemistry, Chinese Academy of Sciences, Beijing, China
| | - Yalin Tang
- Beijing National Laboratory for Molecular Sciences, State Key Laboratory for Structural Chemistry of Unstable and Stable Species, Institute of Chemistry, Chinese Academy of Sciences, Beijing, China
| | - Changqi Zhao
- Key Laboratory for Cell Proliferation and Regulation Biology of Ministry of Education, Beijing Key Laboratory of Gene Engineering Drugs and Biological Technology, College of Life Sciences, Beijing Normal University, Beijing, China
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Ji X, Sun H, Zhou H, Xiang J, Tang Y, Zhao C. Research Progress of RNA Quadruplex. Oligonucleotides 2011:121102072334007. [PMID: 21574857 DOI: 10.1089/oli.2010.0272] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
RNA/DNA sequences rich in guanine (G) can form a 4-strand structure, G-quadruplex, which has been extensively researched and observed in mammalian, fungi, and plants, with in vivo existence in eukaryotic cells. Compared with DNA quadruplex, the potential existence of RNA quadruplex appears to be generally rare; however, it is believed by some researchers to be more inevitable in vivo and speculated to play an important role where it exists. Recently, researches concerning the function of G-quadruplexes in RNAs commence, making much progress. However, there is no available review particularly focusing on RNA quadruplex till now as we know. Therefore, we decide to give a review to comprehensively summarize research progress on it. This review highlights the diverse topologies for RNA quadruplex structure and its effect factors; outlines the current knowledge of RNA quadruplex's physiological functions in biological systems, especially in gene expression; and presents the prospects of RNA quadruplex.
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Affiliation(s)
- Xiaohui Ji
- 1 Key Laboratory for Cell Proliferation and Regulation Biology of Ministry of Education, Beijing Key Laboratory of Gene Engineering Drugs and Biological Technology, College of Life Sciences, Beijing Normal University , Beijing, China
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Pan B, Shi K, Sundaralingam M. Crystal structure of an RNA quadruplex containing inosine tetrad: implications for the roles of NH2 group in purine tetrads. J Mol Biol 2006; 363:451-9. [PMID: 16978642 DOI: 10.1016/j.jmb.2006.08.022] [Citation(s) in RCA: 34] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2006] [Revised: 07/07/2006] [Accepted: 08/10/2006] [Indexed: 11/22/2022]
Abstract
Polyinosinic acid has been known to adopt the four-stranded helical structure but its basic unit, inosine tetrad (I tetrad), has not been determined at the atomic level. Here we report the crystal structure of an RNA quadruplex containing an I tetrad at 1.4 A resolution. The I tetrad has one cyclic hydrogen bond N1...O6 with the bond length of 2.7 A. A water bridge is observed in the minor groove side of the base tetrad. Even though it is sandwiched by guanine tetrads (G tetrads), the I tetrad is buckled towards the 3' side of the tetrad plane, which results from the different interaction strength with K ions on two sides of the tetrad plane. Comparison with both G tetrad and adenine tetrad indicates that lack of NH2 in the C2 position makes the I tetrad prone to buckle for interactions with ligands. Two U*(G-G-G-G) base pentads are observed at the junction of the 5' termini of two quadruplexes. The uridine residue in the base pentad is engaged in two hydrogen bonding interactions (N2(G)-H...O2(U) and O2'(G)-H...O4(U)) and a water-mediated interaction (N3(G) and N3(U)) with the G tetrad. We also discuss the roles of amino group in purine tetrads and the inter-quadruplex interactions in RNA molecules. These quadruplexes may interact with each other by stacking, groove binding and intercalation.
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Affiliation(s)
- Baocheng Pan
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06520, USA.
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