1
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Dörnbrack K, Beck J, Nassal M. Structural Analysis of the Hepatitis B Virus RNA Encapsidation Signal ε by Selective 2'-Hydroxyl Acylation Analyzed by Primer Extension (SHAPE). Methods Mol Biol 2024; 2837:67-87. [PMID: 39044076 DOI: 10.1007/978-1-0716-4027-2_7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/25/2024]
Abstract
RNA structure is crucial for RNA function, including in viral cis-elements such as the hepatitis B virus (HBV) RNA encapsidation signal ε. Interacting with the viral polymerase ε mediates packaging of the pregenomic (pg) RNA into capsids, initiation of reverse transcription, and it affects the mRNA functions of pgRNA. As free RNA, the 61-nucleotide (nt) ε sequence adopts a bipartite stem-loop structure with a central bulge and an apical loop. Due to stable Watson-Crick base pairing, this was already predicted by early RNA folding programs and confirmed by classical enzymatic and chemical structure probing. A newer, high-resolution probing technique exploits the selective acylation of solvent-accessible 2'-hydroxyls in the RNA backbone by electrophilic compounds such as 2-methylnicotinic acid imidazolide (NAI), followed by mapping of the modified sites by primer extension. This SHAPE principle has meanwhile been extended to numerous applications. Here we provide a basic protocol for NAI-based SHAPE of isolated HBV ε RNA which already provided insights into the impact of mutations, and preliminarily, of polymerase binding on the RNA structural dynamics. While the focus is on NAI modification, we also briefly cover target RNA preparation by in vitro transcription, primer extension using a radiolabeled primer, and analysis of the resulting cDNAs by denaturing polyacrylamide gelelectrophoresis (PAGE). Given the high tolerance of SHAPE chemistry to different conditions, including applicability in live cells, we expect this technique to greatly facilitate deciphering the conformational dynamics underlying the various functions of the ε element, especially in concert with the recently solved three-dimensional structure of the free RNA.
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Affiliation(s)
- Katharina Dörnbrack
- Clinical Trials Unit of the Medical Center, University of Freiburg, Freiburg, Germany
| | - Jürgen Beck
- Internal Medicine II/Molecular Biology, University Hospital Freiburg, Freiburg, Germany
| | - Michael Nassal
- Internal Medicine II/Molecular Biology, University Hospital Freiburg, Freiburg, Germany.
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2
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Schneider B, Sweeney BA, Bateman A, Cerny J, Zok T, Szachniuk M. When will RNA get its AlphaFold moment? Nucleic Acids Res 2023; 51:9522-9532. [PMID: 37702120 PMCID: PMC10570031 DOI: 10.1093/nar/gkad726] [Citation(s) in RCA: 21] [Impact Index Per Article: 21.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2023] [Revised: 08/13/2023] [Accepted: 08/22/2023] [Indexed: 09/14/2023] Open
Abstract
The protein structure prediction problem has been solved for many types of proteins by AlphaFold. Recently, there has been considerable excitement to build off the success of AlphaFold and predict the 3D structures of RNAs. RNA prediction methods use a variety of techniques, from physics-based to machine learning approaches. We believe that there are challenges preventing the successful development of deep learning-based methods like AlphaFold for RNA in the short term. Broadly speaking, the challenges are the limited number of structures and alignments making data-hungry deep learning methods unlikely to succeed. Additionally, there are several issues with the existing structure and sequence data, as they are often of insufficient quality, highly biased and missing key information. Here, we discuss these challenges in detail and suggest some steps to remedy the situation. We believe that it is possible to create an accurate RNA structure prediction method, but it will require solving several data quality and volume issues, usage of data beyond simple sequence alignments, or the development of new less data-hungry machine learning methods.
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Affiliation(s)
- Bohdan Schneider
- Institute of Biotechnology of the Czech Academy of Sciences, Prumyslova 595, CZ-252 50 Vestec, Czech Republic
| | - Blake Alexander Sweeney
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, CB10 1SD, UK
| | - Alex Bateman
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, CB10 1SD, UK
| | - Jiri Cerny
- Institute of Biotechnology of the Czech Academy of Sciences, Prumyslova 595, CZ-252 50 Vestec, Czech Republic
| | - Tomasz Zok
- Institute of Computing Science and European Centre for Bioinformatics and Genomics, Poznan University of Technology, Piotrowo 2, 60-965 Poznan, Poland
| | - Marta Szachniuk
- Institute of Computing Science and European Centre for Bioinformatics and Genomics, Poznan University of Technology, Piotrowo 2, 60-965 Poznan, Poland
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12/14, 61-704 Poznan, Poland
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3
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Mao G, Srivastava AS, Wu S, Kosek D, Kirsebom LA. Importance of residue 248 in Escherichia coli RNase P RNA mediated cleavage. Sci Rep 2023; 13:14140. [PMID: 37644068 PMCID: PMC10465520 DOI: 10.1038/s41598-023-41203-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2023] [Accepted: 08/23/2023] [Indexed: 08/31/2023] Open
Abstract
tRNA genes are transcribed as precursors and RNase P generates the matured 5' end of tRNAs. It has been suggested that residue - 1 (the residue immediately 5' of the scissile bond) in the pre-tRNA interacts with the well-conserved bacterial RNase P RNA (RPR) residue A248 (Escherichia coli numbering). The way A248 interacts with residue - 1 is not clear. To gain insight into the role of A248, we analyzed cleavage as a function of A248 substitutions and N-1 nucleobase identity by using pre-tRNA and three model substrates. Our findings are consistent with a model where the structural topology of the active site varies and depends on the identity of the nucleobases at, and in proximity to, the cleavage site and their potential to interact. This leads to positioning of Mg2+ that activates the water that acts as the nucleophile resulting in efficient and correct cleavage. We propose that in addition to be involved in anchoring the substrate the role of A248 is to exclude bulk water from access to the amino acid acceptor stem, thereby preventing non-specific hydrolysis of the pre-tRNA. Finally, base stacking is discussed as a way to protect functionally important base-pairing interactions from non-specific hydrolysis, thereby ensuring high fidelity during RNA processing and the decoding of mRNA.
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Affiliation(s)
- Guanzhong Mao
- Department of Cell and Molecular Biology, Biomedical Centre, Box 596, 751 24, Uppsala, Sweden
| | - Abhishek S Srivastava
- Department of Cell and Molecular Biology, Biomedical Centre, Box 596, 751 24, Uppsala, Sweden
| | - Shiying Wu
- Department of Cell and Molecular Biology, Biomedical Centre, Box 596, 751 24, Uppsala, Sweden
| | - David Kosek
- Department of Cell and Molecular Biology, Biomedical Centre, Box 596, 751 24, Uppsala, Sweden
| | - Leif A Kirsebom
- Department of Cell and Molecular Biology, Biomedical Centre, Box 596, 751 24, Uppsala, Sweden.
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4
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Combination of DNA walker and Pb2+-specific DNAzyme-based signal amplification with a signal-off electrochemical DNA sensor for Staphylococcus aureus detection. Anal Chim Acta 2022; 1222:340179. [DOI: 10.1016/j.aca.2022.340179] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2022] [Revised: 07/09/2022] [Accepted: 07/15/2022] [Indexed: 12/18/2022]
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5
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Rapid and selective electrochemical detection of pb2+ ions using aptamer-conjugated alloy nanoparticles. SN APPLIED SCIENCES 2020. [DOI: 10.1007/s42452-020-03840-6] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
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6
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Patra D, Banerjee S, Sova Mandi C, Haseena KS, Basu G, Dutta S. A Pyrimido-Quinoxaline Fused Heterocycle Lights Up Transfer RNA upon Binding at the Mg 2+ Binding Site. Chembiochem 2020; 22:359-363. [PMID: 32869357 DOI: 10.1002/cbic.202000584] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2020] [Indexed: 11/07/2022]
Abstract
Transfer RNAs (tRNAs) are fundamental molecules in cellular translation. In this study we have highlighted a fluorescence-based perceptive approach for tRNAs by using a quinoxaline small molecule. We have synthesised a water-soluble fluorescent pyrimido-quinoxaline-fused heterocycle containing a mandatory piperazine tail (DS1) with a large Stokes shift (∼160 nm). The interaction between DS1 and tRNA results in significant fluorescence enhancement of the molecule with Kd ∼5 μM and multiple binding sites. Our work reveals that the DS1 binding site overlaps with the specific Mg2+ ion binding site in the D loop of tRNA. As a proof-of-concept, the molecule inhibited Pb2+ -induced cleavage of yeast tRNAPhe in the D loop. In competitive binding assays, the fluorescence of DS1-tRNA complex is quenched by a known tRNA-binder, tobramycin. This indicates the displacement of DS1 and, indeed, a substantiation of specific binding at the site of tertiary interaction in the central region of tRNA. The ability of compound DS1 to bind tRNA with a higher affinity compared to DNA and single-stranded RNA offers a promising approach to developing tRNA-based biomarker diagnostics in the future.
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Affiliation(s)
- Dipendu Patra
- Department of Organic and Medicinal Chemistry, CSIR - Indian Institute of Chemical Biology, 4 Raja S. C. Mullick Road, Kolkata, 700032, WB, India.,Academy of Scientific and Innovative Research (AcSIR) CSIR - Human Resource Development Centre, (CSIR-HRDC) Campus, Postal Staff College Area, Sector 19, Kamla Nehru Nagar, Ghaziabad, Uttar Pradesh, 201002, India
| | - Sayanika Banerjee
- Department of Organic and Medicinal Chemistry, CSIR - Indian Institute of Chemical Biology, 4 Raja S. C. Mullick Road, Kolkata, 700032, WB, India
| | - Chandra Sova Mandi
- Department of Organic and Medicinal Chemistry, CSIR - Indian Institute of Chemical Biology, 4 Raja S. C. Mullick Road, Kolkata, 700032, WB, India
| | - K S Haseena
- Department of Organic and Medicinal Chemistry, CSIR - Indian Institute of Chemical Biology, 4 Raja S. C. Mullick Road, Kolkata, 700032, WB, India
| | - Gautam Basu
- Department of Biophysics, Bose Institute, P-1/12 CIT Scheme VIIM, Kolkata, 700054, India
| | - Sanjay Dutta
- Department of Organic and Medicinal Chemistry, CSIR - Indian Institute of Chemical Biology, 4 Raja S. C. Mullick Road, Kolkata, 700032, WB, India.,Academy of Scientific and Innovative Research (AcSIR) CSIR - Human Resource Development Centre, (CSIR-HRDC) Campus, Postal Staff College Area, Sector 19, Kamla Nehru Nagar, Ghaziabad, Uttar Pradesh, 201002, India
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7
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Twittenhoff C, Brandenburg VB, Righetti F, Nuss AM, Mosig A, Dersch P, Narberhaus F. Lead-seq: transcriptome-wide structure probing in vivo using lead(II) ions. Nucleic Acids Res 2020; 48:e71. [PMID: 32463449 PMCID: PMC7337928 DOI: 10.1093/nar/gkaa404] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2019] [Revised: 04/08/2020] [Accepted: 05/06/2020] [Indexed: 12/24/2022] Open
Abstract
The dynamic conformation of RNA molecules within living cells is key to their function. Recent advances in probing the RNA structurome in vivo, including the use of SHAPE (Selective 2'-Hydroxyl Acylation analyzed by Primer Extension) or kethoxal reagents or DMS (dimethyl sulfate), provided unprecedented insights into the architecture of RNA molecules in the living cell. Here, we report the establishment of lead probing in a global RNA structuromics approach. In order to elucidate the transcriptome-wide RNA landscape in the enteric pathogen Yersinia pseudotuberculosis, we combined lead(II) acetate-mediated cleavage of single-stranded RNA regions with high-throughput sequencing. This new approach, termed 'Lead-seq', provides structural information independent of base identity. We show that the method recapitulates secondary structures of tRNAs, RNase P RNA, tmRNA, 16S rRNA and the rpsT 5'-untranslated region, and that it reveals global structural features of mRNAs. The application of Lead-seq to Y. pseudotuberculosis cells grown at two different temperatures unveiled the first temperature-responsive in vivo RNA structurome of a bacterial pathogen. The translation of candidate genes derived from this approach was confirmed to be temperature regulated. Overall, this study establishes Lead-seq as complementary approach to interrogate intracellular RNA structures on a global scale.
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Affiliation(s)
| | | | | | - Aaron M Nuss
- Department of Molecular Infection Biology, Helmholtz Centre for Infection Research, 381214 Braunschweig, Germany
| | - Axel Mosig
- Department of Biophysics, Ruhr University Bochum, 44780 Bochum, Germany
| | - Petra Dersch
- Department of Molecular Infection Biology, Helmholtz Centre for Infection Research, 381214 Braunschweig, Germany
- Institute of Infectiology, Center for Molecular Biology of Inflammation, University of Münster, 48149 Münster, Germany
| | - Franz Narberhaus
- Microbial Biology, Ruhr University Bochum, 44780 Bochum, Germany
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8
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Li J, Mohammed-Elsabagh M, Paczkowski F, Li Y. Circular Nucleic Acids: Discovery, Functions and Applications. Chembiochem 2020; 21:1547-1566. [PMID: 32176816 DOI: 10.1002/cbic.202000003] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2020] [Revised: 02/13/2020] [Indexed: 12/14/2022]
Abstract
Circular nucleic acids (CNAs) are nucleic acid molecules with a closed-loop structure. This feature comes with a number of advantages including complete resistance to exonuclease degradation, much better thermodynamic stability, and the capability of being replicated by a DNA polymerase in a rolling circle manner. Circular functional nucleic acids, CNAs containing at least a ribozyme/DNAzyme or a DNA/RNA aptamer, not only inherit the advantages of CNAs but also offer some unique application opportunities, such as the design of topology-controlled or enabled molecular devices. This article will begin by summarizing the discovery, biogenesis, and applications of naturally occurring CNAs, followed by discussing the methods for constructing artificial CNAs. The exploitation of circular functional nucleic acids for applications in nanodevice engineering, biosensing, and drug delivery will be reviewed next. Finally, the efforts to couple functional nucleic acids with rolling circle amplification for ultra-sensitive biosensing and for synthesizing multivalent molecular scaffolds for unique applications in biosensing and drug delivery will be recapitulated.
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Affiliation(s)
- Jiuxing Li
- M.G. DeGroote Institute for Infectious Disease Research Department of Biochemistry and Biomedical Sciences, McMaster University, 1280 Main Street West, Hamilton, L8S 4K1, Canada
| | - Mostafa Mohammed-Elsabagh
- M.G. DeGroote Institute for Infectious Disease Research Department of Biochemistry and Biomedical Sciences, McMaster University, 1280 Main Street West, Hamilton, L8S 4K1, Canada
| | - Freeman Paczkowski
- M.G. DeGroote Institute for Infectious Disease Research Department of Biochemistry and Biomedical Sciences, McMaster University, 1280 Main Street West, Hamilton, L8S 4K1, Canada
| | - Yingfu Li
- M.G. DeGroote Institute for Infectious Disease Research Department of Biochemistry and Biomedical Sciences, McMaster University, 1280 Main Street West, Hamilton, L8S 4K1, Canada
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9
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Singh G, Sharma G, Sanchita, Kalra P, Satija P, Pawan, Singh B, Aulakh D, Wreidt M. Click‐Derived Uracil‐Appended Organosilatranyl Scaffolds: Synthesis, Antibacterial Characteristics, Pb2+ Binding and Fabrication of Hybrid Silica Nanoparticles. ChemistrySelect 2020. [DOI: 10.1002/slct.201903464] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Affiliation(s)
| | - Geetika Sharma
- Department of ChemistryPanjab University Chandigarh 160014 India
| | - Sanchita
- Department of ChemistryPanjab University Chandigarh 160014 India
| | - Pooja Kalra
- Department of Chemistry and BiochemistrySharda University 201306 Sharda Greater Noida
| | - Pinky Satija
- Department of ChemistryPanjab University Chandigarh 160014 India
| | - Pawan
- Department of ChemistryPanjab University Chandigarh 160014 India
| | - Baljinder Singh
- Department of BiotechnologyPanjab University Chandigarh 160014 India
| | - Darpandeep Aulakh
- Functional Materials Design & X-ray Diffraction Lab, Department of Chemistry & Bimolecular ScienceClarkson University, Box 5810 Potsdam, NY 13699 USA
| | - Mario Wreidt
- Functional Materials Design & X-ray Diffraction Lab, Department of Chemistry & Bimolecular ScienceClarkson University, Box 5810 Potsdam, NY 13699 USA
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10
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Dwyer BG, Johnson E, Cazares E, McFarlane Holman KL, Kirk SR. Ruthenium anticancer agent KP1019 binds more tightly than NAMI-A to tRNA Phe. J Inorg Biochem 2018; 182:177-183. [PMID: 29501978 DOI: 10.1016/j.jinorgbio.2018.02.019] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2018] [Revised: 02/22/2018] [Accepted: 02/23/2018] [Indexed: 12/29/2022]
Abstract
The ruthenium-based anticancer agent NAMI-A (ImH[trans-RuCl4(dmso)(Im)], where Im = imidazole) has been shown to interact with RNA in vivo and in vitro. We hypothesized that the similarly structured drug KP1019 (IndH[trans-RuCl4(Ind)2], where Ind = indazole) binds to RNA as well. Fluorescence spectroscopy was employed to assay the interactions between either NAMI-A or KP1019 and tRNAPhe through an intrinsic fluorophore wybutosine (Y) base and by extrinsic displacement of the intercalating agent ethidium bromide. In both the intrinsic Y-base and extrinsic ethidium bromide studies, KP1019 exhibited tighter binding to phenylalanine-specific tRNA (tRNAPhe) than NAMI-A. In the ethidium bromide study, reducing both drugs from RuIII to RuII resulted in a significant decrease in binding. Our findings suggest that the relatively large heteroaromatic indazole ligands of KP1019 intercalate in the π-stacks of tRNAPhe within structurally complex binding pockets. In addition, NAMI-A appears to be sensitive to destabilizing electrostatic interactions with the negative phosphate backbone of tRNAPhe. Interactions with additional tRNA molecules and other types of RNA require further evaluation to determine the role of RNA in the mechanisms of action for KP1019 and to better understand how Ru drugs fundamentally interact with biomolecules that are more structurally sophisticated than short DNA oligonucleotides. To the best of our knowledge, this is the first study to report KP1019 binding interactions with RNA.
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Affiliation(s)
- Brendan G Dwyer
- Department of Chemistry, Willamette University, 900 State Street, Salem, Oregon 97301, United States
| | - Emily Johnson
- Department of Chemistry, Willamette University, 900 State Street, Salem, Oregon 97301, United States
| | - Efren Cazares
- Department of Chemistry, Willamette University, 900 State Street, Salem, Oregon 97301, United States
| | - Karen L McFarlane Holman
- Department of Chemistry, Willamette University, 900 State Street, Salem, Oregon 97301, United States
| | - Sarah R Kirk
- Department of Chemistry, Willamette University, 900 State Street, Salem, Oregon 97301, United States.
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11
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Vakiloroayaei A, Shah NS, Oeffinger M, Bayfield MA. The RNA chaperone La promotes pre-tRNA maturation via indiscriminate binding of both native and misfolded targets. Nucleic Acids Res 2017; 45:11341-11355. [PMID: 28977649 PMCID: PMC5737608 DOI: 10.1093/nar/gkx764] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2017] [Accepted: 08/17/2017] [Indexed: 12/14/2022] Open
Abstract
Non-coding RNAs have critical roles in biological processes, and RNA chaperones can promote their folding into the native shape required for their function. La proteins are a class of highly abundant RNA chaperones that contact pre-tRNAs and other RNA polymerase III transcripts via their common UUU-3′OH ends, as well as through less specific contacts associated with RNA chaperone activity. However, whether La proteins preferentially bind misfolded pre-tRNAs or instead engage all pre-tRNA substrates irrespective of their folding status is not known. La deletion in yeast is synthetically lethal when combined with the loss of tRNA modifications predicted to contribute to the native pre-tRNA fold, such as the N2, N2-dimethylation of G26 by the methyltransferase Trm1p. In this work, we identify G26 containing pre-tRNAs that misfold in the absence of Trm1p and/or La (Sla1p) in Schizosaccharomyces pombe cells, then test whether La preferentially associates with such tRNAs in vitro and in vivo. Our data suggest that La does not discriminate a native from misfolded RNA target, and highlights the potential challenges faced by RNA chaperones in preferentially binding defective substrates.
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Affiliation(s)
- Ana Vakiloroayaei
- Department of Biology, York University, Toronto, Ontario M3J 1P3, Canada
| | - Neha S Shah
- Department of Biology, York University, Toronto, Ontario M3J 1P3, Canada
| | - Marlene Oeffinger
- Institut de Recherches Cliniques de Montréal (IRCM), 110 Avenue des Pins Ouest, Montréal, Québec H2W 1R7, Canada.,Faculty of Medicine, Division of Experimental Medicine, McGill University, Montréal, Québec H3A 1A3, Canada.,Département de Biochimie, Faculté de Médecine, Université de Montréal, Montréal, Québec H3T 1J4, Canada
| | - Mark A Bayfield
- Department of Biology, York University, Toronto, Ontario M3J 1P3, Canada
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12
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Affiliation(s)
- Wenhu Zhou
- Xiangya
School of Pharmaceutical Sciences, Central South University, Changsha, Hunan 410013, China
- Department
of Chemistry, Water Institute, and Waterloo Institute for Nanotechnology, University of Waterloo, Waterloo, Ontario N2L 3G1, Canada
| | - Runjhun Saran
- Department
of Chemistry, Water Institute, and Waterloo Institute for Nanotechnology, University of Waterloo, Waterloo, Ontario N2L 3G1, Canada
| | - Juewen Liu
- Department
of Chemistry, Water Institute, and Waterloo Institute for Nanotechnology, University of Waterloo, Waterloo, Ontario N2L 3G1, Canada
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13
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Andersen KL, Beckert B, Masquida B, Johansen SD, Nielsen H. Accumulation of Stable Full-Length Circular Group I Intron RNAs during Heat-Shock. Molecules 2016; 21:molecules21111451. [PMID: 27809244 PMCID: PMC6274462 DOI: 10.3390/molecules21111451] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2016] [Revised: 10/25/2016] [Accepted: 10/27/2016] [Indexed: 02/07/2023] Open
Abstract
Group I introns in nuclear ribosomal RNA of eukaryotic microorganisms are processed by splicing or circularization. The latter results in formation of full-length circular introns without ligation of the exons and has been proposed to be active in intron mobility. We applied qRT-PCR to estimate the copy number of circular intron RNA from the myxomycete Didymium iridis. In exponentially growing amoebae, the circular introns are nuclear and found in 70 copies per cell. During heat-shock, the circular form is up-regulated to more than 500 copies per cell. The intron harbours two ribozymes that have the potential to linearize the circle. To understand the structural features that maintain circle integrity, we performed chemical and enzymatic probing of the splicing ribozyme combined with molecular modeling to arrive at models of the inactive circular form and its active linear counterpart. We show that the two forms have the same overall structure but differ in key parts, including the catalytic core element P7 and the junctions at which reactions take place. These differences explain the relative stability of the circular species, demonstrate how it is prone to react with a target molecule for circle integration and thus supports the notion that the circular form is a biologically significant molecule possibly with a role in intron mobility.
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Affiliation(s)
- Kasper L Andersen
- Department of Cellular and Molecular Medicine, The Panum Institute, University of Copenhagen, DK-2200 Copenhagen N, Denmark.
| | - Bertrand Beckert
- Department of Cellular and Molecular Medicine, The Panum Institute, University of Copenhagen, DK-2200 Copenhagen N, Denmark.
- Molecular Genetics Genomics Microbiology, Université de Strasbourg, CNRS, UMR 7156, Strasbourg 67081, France.
| | - Benoit Masquida
- Molecular Genetics Genomics Microbiology, Université de Strasbourg, CNRS, UMR 7156, Strasbourg 67081, France.
| | - Steinar D Johansen
- Department of Medical Biology, UiT, The Arctic University of Norway, Tromsø N-9037, Norway.
| | - Henrik Nielsen
- Department of Cellular and Molecular Medicine, The Panum Institute, University of Copenhagen, DK-2200 Copenhagen N, Denmark.
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14
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Kabir A, Dutta D, Mandal C, Suresh Kumar G. Molecular Recognition of tRNA with 1-Naphthyl Acetyl Spermine, Spermine, and Spermidine: A Thermodynamic, Biophysical, and Molecular Docking Investigative Approach. J Phys Chem B 2016; 120:10871-10884. [PMID: 27690446 DOI: 10.1021/acs.jpcb.6b05391] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The role of tRNA in protein translational machinery and the influence of polyamines on the interaction of acylated and deacylated tRNA with ribosomes make polyamine-tRNA interaction conspicuous. We studied the interaction of two biogenic polyamines, spermine (SPM) and spermidine (SPD), with tRNAPhe and compared the results to those of the analogue 1-naphthyl acetyl spermine (NASPM). The binding affinity of SPM was comparable to that of NASPM; both were higher than that of SPD. The interactions led to significant thermal stabilization of tRNAPhe and an increase in the enthalpy of transition. All the interactions were exothermic in nature and displayed prominent enthalpy-entropy compensation behavior. The entropy-driven nature of the interaction, the structural perturbations observed, and docking results proved that the polyamines were bound in the groove of the anticodon arm of tRNAPhe. The amine groups of polyamines were involved in extensive electrostatic, H-bonding, and van der Waals interactions with tRNAPhe. The naphthyl group of NASPM showed an additional stacking interaction with G24 and G26 of tRNAPhe, which was absent in others. The results demonstrate that 1-naphthyl acetyl spermine can target the same binding sites as the biogenic polyamines without substituting for the functions played by them, which may lead to exhibition of selective anticancer cytotoxicity.
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Affiliation(s)
| | | | - Chhabinath Mandal
- National Institute of Pharmaceutical and Educational Research , Kolkata 700032, India
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15
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Ageely EA, Kartje ZJ, Rohilla KJ, Barkau CL, Gagnon KT. Quadruplex-Flanking Stem Structures Modulate the Stability and Metal Ion Preferences of RNA Mimics of GFP. ACS Chem Biol 2016; 11:2398-406. [PMID: 27467146 DOI: 10.1021/acschembio.6b00047] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
The spinach family of RNA aptamers are RNA mimics of green fluorescent protein (GFP) that have previously been designed to address the challenges of imaging RNA inside living cells. However, relatively low levels of free intracellular magnesium limited the practical use of these aptamers. Recent cell-based selections identified the broccoli RNA aptamer, which requires less magnesium for fluorescence, but the basis for magnesium preference remained unclear. Here, we find that the broccoli RNA structure is very similar to that of baby spinach, a truncated version of the spinach aptamer. Differences in stability and metal ion preferences between these two aptamers, and among broccoli mutants, are primarily associated with the sequence and structure of predicted quadruplex-flanking stem structures. Mutation of purine-purine pairs in broccoli at the terminal stem-quadruplex transition caused reversion of broccoli to a higher magnesium dependence. Unique duplex-to-quadruplex transitions in GFP-mimic RNAs likely explain their sensitivity to magnesium for stability and fluorescence. Thus, optimizations designed to improve aptamers should take into consideration the role of metal ions in stabilizing the transitions and interactions between independently folding RNA structural motifs.
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Affiliation(s)
- Eman A. Ageely
- Department
of Chemistry and Biochemistry, Southern Illinois University, Carbondale, Illinois 62901, United States
| | - Zachary J. Kartje
- Department
of Chemistry and Biochemistry, Southern Illinois University, Carbondale, Illinois 62901, United States
| | - Kushal J. Rohilla
- Department
of Biochemistry and Molecular Biology, Southern Illinois University, School of Medicine, Carbondale, Illinois 62901, United States
| | - Christopher L. Barkau
- Department
of Biochemistry and Molecular Biology, Southern Illinois University, School of Medicine, Carbondale, Illinois 62901, United States
| | - Keith T. Gagnon
- Department
of Chemistry and Biochemistry, Southern Illinois University, Carbondale, Illinois 62901, United States
- Department
of Biochemistry and Molecular Biology, Southern Illinois University, School of Medicine, Carbondale, Illinois 62901, United States
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16
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Wu S, Mao G, Kirsebom LA. Inhibition of Bacterial RNase P RNA by Phenothiazine Derivatives. Biomolecules 2016; 6:biom6030038. [PMID: 27618117 PMCID: PMC5039424 DOI: 10.3390/biom6030038] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2016] [Revised: 08/24/2016] [Accepted: 08/26/2016] [Indexed: 12/19/2022] Open
Abstract
There is a need to identify novel scaffolds and targets to develop new antibiotics. Methylene blue is a phenothiazine derivative, and it has been shown to possess anti-malarial and anti-trypanosomal activities. Here, we show that different phenothiazine derivatives and pyronine G inhibited the activities of three structurally different bacterial RNase P RNAs (RPRs), including that from Mycobacterium tuberculosis, with Ki values in the lower μM range. Interestingly, three antipsychotic phenothiazines (chlorpromazine, thioridazine, and trifluoperazine), which are known to have antibacterial activities, also inhibited the activity of bacterial RPRs, albeit with higher Ki values than methylene blue. Phenothiazines also affected lead(II)-induced cleavage of bacterial RPR and inhibited yeast tRNA(Phe), indicating binding of these drugs to functionally important regions. Collectively, our findings provide the first experimental data showing that long, noncoding RNAs could be targeted by different phenothiazine derivatives.
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Affiliation(s)
- Shiying Wu
- Department of Cell and Molecular Biology, Box 596, Biomedical Centre, Uppsala SE-751 24, Sweden.
| | - Guanzhong Mao
- Department of Cell and Molecular Biology, Box 596, Biomedical Centre, Uppsala SE-751 24, Sweden.
| | - Leif A Kirsebom
- Department of Cell and Molecular Biology, Box 596, Biomedical Centre, Uppsala SE-751 24, Sweden.
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17
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Hwang K, Hosseinzadeh P, Lu Y. Biochemical and Biophysical Understanding of Metal Ion Selectivity of DNAzymes. Inorganica Chim Acta 2016; 452:12-24. [PMID: 27695134 DOI: 10.1016/j.ica.2016.04.017] [Citation(s) in RCA: 71] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
This review summarizes research into the metal-binding properties of catalytic DNAzymes, towards the goal of understanding the structural properties leading to metal ion specificity. Progress made and insight gained from a range of biochemical and biophysical techniques are covered, and promising directions for future investigations are discussed.
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Affiliation(s)
- Kevin Hwang
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, IL 61801
| | - Parisa Hosseinzadeh
- Department of Biochemistry, University of Illinois at Urbana-Champaign, Urbana, IL 61801
| | - Yi Lu
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, IL 61801; Department of Biochemistry, University of Illinois at Urbana-Champaign, Urbana, IL 61801
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18
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Saran R, Chen Q, Liu J. Searching for a DNAzyme Version of the Leadzyme. J Mol Evol 2015; 81:235-44. [PMID: 26458991 DOI: 10.1007/s00239-015-9702-z] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2015] [Accepted: 10/02/2015] [Indexed: 11/25/2022]
Abstract
The leadzyme refers to a small ribozyme that cleaves a RNA substrate in the presence of Pb(2+). In an optimized form, the enzyme strand contains only two unpaired nucleotides. Most RNA-cleaving DNAzymes are much longer. Two classical Pb(2+)-dependent DNAzymes, 8-17 and GR5, both contain around 15 nucleotides in the enzyme loop. This is also the size of most RNA-cleaving DNAzymes that use other metal ions for their activity. Such large enzyme loops make spectroscopic characterization difficult and so far no high-resolution structural information is available for active DNAzymes. The goal of this work is to search for DNAzymes with smaller enzyme loops. A simple replacement of the ribonucleotides in the leadzyme by deoxyribonucleotides failed to produce an active enzyme. A Pb(2+)-dependent in vitro selection combined with deep sequencing was then performed. After sequence alignment and DNA folding, a new DNAzyme named PbE22 was identified, which contains only 5 nucleotides in the enzyme catalytic loop. The biochemical characteristics of PbE22 were compared with those of the leadzyme and the two classical Pb(2+)-dependent DNAzymes. The rate of PbE22 rises with increase in Pb(2+) concentration, being 1.7 h(-1) in the presence of 100 μM Pb(2+) and reaching 3.5 h(-1) at 500 µM Pb(2+). The log of PbE22 rate rises linearly in a pH-dependent fashion (20 µM Pb(2+)) with a slope of 0.74. In addition, many other abundant sequences in the final library were studied. These sequences are quite varied in length and nucleotide composition, but some contain a few conserved nucleotides consistent with the GR5 structure. Interestingly, some sequences are active with Pb(2+) but none of them were active with even 50 mM Mg(2+), which is reminiscent of the difference between the GR5 and 8-17 DNAzymes.
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Affiliation(s)
- Runjhun Saran
- Department of Chemistry, Waterloo Institute for Nanotechnology, University of Waterloo, Waterloo, ON, N2L 3G1, Canada
| | - Qingyun Chen
- Department of Chemistry, Waterloo Institute for Nanotechnology, University of Waterloo, Waterloo, ON, N2L 3G1, Canada
| | - Juewen Liu
- Department of Chemistry, Waterloo Institute for Nanotechnology, University of Waterloo, Waterloo, ON, N2L 3G1, Canada.
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19
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Qi X, Xia T. Structure, dynamics, and mechanism of the lead-dependent ribozyme. Biomol Concepts 2015; 2:305-14. [PMID: 25962038 DOI: 10.1515/bmc.2011.029] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2011] [Accepted: 06/06/2011] [Indexed: 12/24/2022] Open
Abstract
Leadzyme is a small catalytic RNA that was identified by in vitro selection for Pb2+-dependent cleavage from a tRNA library. Leadzyme employs a unique two-step Pb2+-specific mechanism to cleave within its active site. NMR and crystal structures of the active site revealed different folding patterns, but neither features the in-line alignment for attack by the 2'-OH nucleophilic group. These experimentally determined structures most likely represent ground states and are catalytically inactive. There are significant dynamics of the active site and the motif samples multiple conformations at the ground states. Various metal ion binding sites have been identified, including one that may be occupied by a catalytic Pb2+. Based on functional group analysis, a computational model of the transition state has been proposed. This model features a unique base triple that is consistent with sequence and functional group requirements for catalysis. This structure is likely only populated transiently, but imposing appropriate conformational constraints may significantly stabilize this state thereby promoting catalysis. Other ions may inhibit the cleavage by competing for the Pb2+ binding site, or by stabilizing the ground state thereby suppressing its transition to the catalytically active conformation. Some rare earth ions can enhance the reaction via an unknown mechanism. Because of its unique chemistry and dynamic behavior, leadzyme can continue to serve as an excellent model system for teaching us RNA biology and chemistry.
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20
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Wu S, Chen Y, Mao G, Trobro S, Kwiatkowski M, Kirsebom LA. Transition-state stabilization in Escherichia coli ribonuclease P RNA-mediated cleavage of model substrates. Nucleic Acids Res 2014; 42:631-42. [PMID: 24097434 PMCID: PMC3874170 DOI: 10.1093/nar/gkt853] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2013] [Revised: 09/02/2013] [Accepted: 09/03/2013] [Indexed: 01/10/2023] Open
Abstract
We have used model substrates carrying modified nucleotides at the site immediately 5' of the canonical RNase P cleavage site, the -1 position, to study Escherichia coli RNase P RNA-mediated cleavage. We show that the nucleobase at -1 is not essential but its presence and identity contribute to efficiency, fidelity of cleavage and stabilization of the transition state. When U or C is present at -1, the carbonyl oxygen at C2 on the nucleobase contributes to transition-state stabilization, and thus acts as a positive determinant. For substrates with purines at -1, an exocyclic amine at C2 on the nucleobase promotes cleavage at an alternative site and it has a negative impact on cleavage at the canonical site. We also provide new insights into the interaction between E. coli RNase P RNA and the -1 residue in the substrate. Our findings will be discussed using a model where bacterial RNase P cleavage proceeds through a conformational-assisted mechanism that positions the metal(II)-activated H2O for an in-line attack on the phosphorous atom that leads to breakage of the phosphodiester bond.
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Affiliation(s)
- Shiying Wu
- Department of Cell and Molecular Biology, Box 596, Uppsala University, SE-751 24 Uppsala, Sweden, Department of Chemistry, University of Michigan, Ann Arbor, MI 48109, USA and Department of Molecular Biology, Swedish University of Agricultural Sciences, Box 590, SE-751 24 Uppsala, Sweden
| | - Yu Chen
- Department of Cell and Molecular Biology, Box 596, Uppsala University, SE-751 24 Uppsala, Sweden, Department of Chemistry, University of Michigan, Ann Arbor, MI 48109, USA and Department of Molecular Biology, Swedish University of Agricultural Sciences, Box 590, SE-751 24 Uppsala, Sweden
| | - Guanzhong Mao
- Department of Cell and Molecular Biology, Box 596, Uppsala University, SE-751 24 Uppsala, Sweden, Department of Chemistry, University of Michigan, Ann Arbor, MI 48109, USA and Department of Molecular Biology, Swedish University of Agricultural Sciences, Box 590, SE-751 24 Uppsala, Sweden
| | - Stefan Trobro
- Department of Cell and Molecular Biology, Box 596, Uppsala University, SE-751 24 Uppsala, Sweden, Department of Chemistry, University of Michigan, Ann Arbor, MI 48109, USA and Department of Molecular Biology, Swedish University of Agricultural Sciences, Box 590, SE-751 24 Uppsala, Sweden
| | - Marek Kwiatkowski
- Department of Cell and Molecular Biology, Box 596, Uppsala University, SE-751 24 Uppsala, Sweden, Department of Chemistry, University of Michigan, Ann Arbor, MI 48109, USA and Department of Molecular Biology, Swedish University of Agricultural Sciences, Box 590, SE-751 24 Uppsala, Sweden
| | - Leif A. Kirsebom
- Department of Cell and Molecular Biology, Box 596, Uppsala University, SE-751 24 Uppsala, Sweden, Department of Chemistry, University of Michigan, Ann Arbor, MI 48109, USA and Department of Molecular Biology, Swedish University of Agricultural Sciences, Box 590, SE-751 24 Uppsala, Sweden
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21
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Elton ES, Zhang T, Prabhakar R, Arif AM, Berreau LM. Pb(II)-Promoted Amide Cleavage: Mechanistic Comparison to a Zn(II) Analogue. Inorg Chem 2013; 52:11480-92. [DOI: 10.1021/ic401782x] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Affiliation(s)
- Eric S. Elton
- Department
of Chemistry and Biochemistry, Utah State University, 0300 Old
Main Hill, Logan, Utah 84322-0300, United States
| | - Tingting Zhang
- Department
of Chemistry, University of Miami, 1301 Memorial Drive, Coral Gables, Florida 33146-0431, United States
| | - Rajeev Prabhakar
- Department
of Chemistry, University of Miami, 1301 Memorial Drive, Coral Gables, Florida 33146-0431, United States
| | - Atta M. Arif
- Department
of Chemistry, University of Utah, 315 S. 1400 E., Salt Lake City, Utah 84112-0850, United States
| | - Lisa M. Berreau
- Department
of Chemistry and Biochemistry, Utah State University, 0300 Old
Main Hill, Logan, Utah 84322-0300, United States
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22
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Ma L, Takashima T, Koka J, Kimber HJ, Cox H, Stace AJ. Conformation-resolved UV spectra of Pb(II) complexes: A gas phase study of the sandwich structures [Pb(toluene)2]2+ and [Pb(benzene)2]2+. J Chem Phys 2013; 138:164301. [DOI: 10.1063/1.4801440] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
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23
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Giel-Pietraszuk M, Barciszewski J. Hydrostatic and osmotic pressure study of the RNA hydration. Mol Biol Rep 2012; 39:6309-18. [PMID: 22314910 PMCID: PMC3310992 DOI: 10.1007/s11033-012-1452-z] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2010] [Accepted: 01/23/2012] [Indexed: 11/17/2022]
Abstract
The tertiary structure of nucleic acids results from an equilibrium between electrostatic interactions of phosphates, stacking interactions of bases, hydrogen bonds between polar atoms and water molecules. Water interactions with ribonucleic acid play a key role in its structure formation, stabilization and dynamics. We used high hydrostatic pressure and osmotic pressure to analyze changes in RNA hydration. We analyzed the lead catalyzed hydrolysis of tRNAPhe from S. cerevisiae as well as hydrolytic activity of leadzyme. Pb(II) induced hydrolysis of the single phosphodiester bond in tRNAPhe is accompanied by release of 98 water molecules, while other molecule, leadzyme releases 86.
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Affiliation(s)
- Małgorzata Giel-Pietraszuk
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12/14, 61-704 Poznań, Poland.
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24
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Moss WN, Dela-Moss LI, Kierzek E, Kierzek R, Priore SF, Turner DH. The 3' splice site of influenza A segment 7 mRNA can exist in two conformations: a pseudoknot and a hairpin. PLoS One 2012; 7:e38323. [PMID: 22685560 PMCID: PMC3369869 DOI: 10.1371/journal.pone.0038323] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2012] [Accepted: 05/03/2012] [Indexed: 12/29/2022] Open
Abstract
The 3′ splice site of influenza A segment 7 is used to produce mRNA for the M2 ion-channel protein, which is critical to the formation of viable influenza virions. Native gel analysis, enzymatic/chemical structure probing, and oligonucleotide binding studies of a 63 nt fragment, containing the 3′ splice site, key residues of an SF2/ASF splicing factor binding site, and a polypyrimidine tract, provide evidence for an equilibrium between pseudoknot and hairpin structures. This equilibrium is sensitive to multivalent cations, and can be forced towards the pseudoknot by addition of 5 mM cobalt hexammine. In the two conformations, the splice site and other functional elements exist in very different structural environments. In particular, the splice site is sequestered in the middle of a double helix in the pseudoknot conformation, while in the hairpin it resides in a two-by-two nucleotide internal loop. The results suggest that segment 7 mRNA splicing can be controlled by a conformational switch that exposes or hides the splice site.
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Affiliation(s)
- Walter N. Moss
- Department of Chemistry, Center for RNA Biology, University of Rochester, Rochester, New York, United States of America
| | - Lumbini I. Dela-Moss
- Department of Chemistry, Center for RNA Biology, University of Rochester, Rochester, New York, United States of America
| | - Elzbieta Kierzek
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, Poznan, Noskowskiego, Poland
| | - Ryszard Kierzek
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, Poznan, Noskowskiego, Poland
| | - Salvatore F. Priore
- Department of Chemistry, Center for RNA Biology, University of Rochester, Rochester, New York, United States of America
| | - Douglas H. Turner
- Department of Chemistry, Center for RNA Biology, University of Rochester, Rochester, New York, United States of America
- * E-mail:
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25
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Aitken GDC, Cox H, Stace AJ. Moderating the Acidity of Pb(II)–Water Complexes through the Coordination of Nonaqueous Ligands: A Computational Study. J Phys Chem A 2012; 116:3035-41. [DOI: 10.1021/jp300032m] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Affiliation(s)
- Georgina D. C. Aitken
- Department of Chemistry, School of Life Sciences, University of Sussex, Falmer, Brighton BN1 9QJ, U.K
| | - Hazel Cox
- Department of Chemistry, School of Life Sciences, University of Sussex, Falmer, Brighton BN1 9QJ, U.K
| | - Anthony J. Stace
- School of Chemistry, The University of Nottingham, University Park, Nottingham NG7 2RD, U.K
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26
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Abstract
Metal ions are inextricably involved with nucleic acids due to their polyanionic nature. In order to understand the structure and function of RNAs and DNAs, one needs to have detailed pictures on the structural, thermodynamic, and kinetic properties of metal ion interactions with these biomacromolecules. In this review we first compile the physicochemical properties of metal ions found and used in combination with nucleic acids in solution. The main part then describes the various methods developed over the past decades to investigate metal ion binding by nucleic acids in solution. This includes for example hydrolytic and radical cleavage experiments, mutational approaches, as well as kinetic isotope effects. In addition, spectroscopic techniques like EPR, lanthanide(III) luminescence, IR and Raman as well as various NMR methods are summarized. Aside from gaining knowledge about the thermodynamic properties on the metal ion-nucleic acid interactions, especially NMR can be used to extract information on the kinetics of ligand exchange rates of the metal ions applied. The final section deals with the influence of anions, buffers, and the solvent permittivity on the binding equilibria between metal ions and nucleic acids. Little is known on some of these aspects, but it is clear that these three factors have a large influence on the interaction between metal ions and nucleic acids.
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Affiliation(s)
- Maria Pechlaner
- Institute of Inorganic Chemistry, University of Zürich, Zürich, Switzerland
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27
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Erat MC, Coles J, Finazzo C, Knobloch B, Sigel RK. Accurate analysis of Mg2+ binding to RNA: From classical methods to a novel iterative calculation procedure. Coord Chem Rev 2012. [DOI: 10.1016/j.ccr.2011.08.009] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/17/2022]
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28
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Salpin JY, Guillaumont S, Ortiz D, Tortajada J, Maître P. Direct evidence for tautomerization of the uracil moiety within the Pb2+/uridine-5'-monophosphate complex: a combined tandem mass spectrometry and IRMPD study. Inorg Chem 2011; 50:7769-78. [PMID: 21744847 DOI: 10.1021/ic200918q] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
The structure of the [Pb(UMP)-H](+) (UMP = uridine-5'-monophosphate) complex was studied in the gas phase by combining electrospray ionization (ESI), tandem mass spectrometry, and mid-infrared multiple photon dissociation (IRMPD) spectroscopy. The results obtained show that Pb(2+) ions interact not only with the deprotonated phosphate group but also with a carbonyl group of the nucleobase moiety by folding of the mononucleotide, resulting in macrochelates that are not likely to be present in solution. Comparison between the IRMPD and DFT-computed spectra suggests that the ESI-generated complex likely corresponds to a mixture of several structures, and establishes the enolic tautomers as the most abundant species for the [Pb(UMP)-H](+) ion, while the very weak IRMPD signal observed at ∼1763 cm(-1) points to a minor population of oxo forms. Our data also suggest that losing the nucleobase residue under CID conditions does not necessarily mean a lack of interaction between the metal and the nucleobase moiety, as commonly reported in the literature for large oligonucleotides.
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Affiliation(s)
- Jean-Yves Salpin
- Laboratoire Analyse et Modélisation pour la Biologie et l'Environnement, Université d'Evry Val d'Essonn e, Bâtiment Maupertuis, Boulevard François Mitterrand, 91025 Evry, France.
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29
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Dammertz K, Hengesbach M, Helm M, Nienhaus GU, Kobitski AY. Single-Molecule FRET Studies of Counterion Effects on the Free Energy Landscape of Human Mitochondrial Lysine tRNA. Biochemistry 2011; 50:3107-15. [DOI: 10.1021/bi101804t] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
| | - Martin Hengesbach
- Institute of Pharmacy and Molecular Biotechnology, Heidelberg University, 69120 Heidelberg, Germany
| | - Mark Helm
- Institute of Pharmacy and Molecular Biotechnology, Heidelberg University, 69120 Heidelberg, Germany
- Institute of Pharmacy and Biochemistry, University of Mainz, 55128 Mainz, Germany
| | - G. Ulrich Nienhaus
- Institute of Applied Physics and Center for Functional Nanostructures (CFN), Karlsruhe Institute of Technology (KIT), 76128 Karlsruhe, Germany
- Department of Physics, University of Illinois at Urbana−Champaign, Urbana, Illinois 61801, United States
| | - Andrei Yu. Kobitski
- Institute of Applied Physics and Center for Functional Nanostructures (CFN), Karlsruhe Institute of Technology (KIT), 76128 Karlsruhe, Germany
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30
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Joosten RP, te Beek TAH, Krieger E, Hekkelman ML, Hooft RWW, Schneider R, Sander C, Vriend G. A series of PDB related databases for everyday needs. Nucleic Acids Res 2010; 39:D411-9. [PMID: 21071423 PMCID: PMC3013697 DOI: 10.1093/nar/gkq1105] [Citation(s) in RCA: 531] [Impact Index Per Article: 37.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
Abstract
The Protein Data Bank (PDB) is the world-wide repository of macromolecular structure information. We present a series of databases that run parallel to the PDB. Each database holds one entry, if possible, for each PDB entry. DSSP holds the secondary structure of the proteins. PDBREPORT holds reports on the structure quality and lists errors. HSSP holds a multiple sequence alignment for all proteins. The PDBFINDER holds easy to parse summaries of the PDB file content, augmented with essentials from the other systems. PDB_REDO holds re-refined, and often improved, copies of all structures solved by X-ray. WHY_NOT summarizes why certain files could not be produced. All these systems are updated weekly. The data sets can be used for the analysis of properties of protein structures in areas ranging from structural genomics, to cancer biology and protein design.
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Affiliation(s)
- Robbie P Joosten
- Department of Biochemistry, Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX Amsterdam, The Netherlands
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31
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Ennifar E, Walter P, Dumas P. Cation-dependent cleavage of the duplex form of the subtype-B HIV-1 RNA dimerization initiation site. Nucleic Acids Res 2010; 38:5807-16. [PMID: 20460458 PMCID: PMC2943608 DOI: 10.1093/nar/gkq344] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023] Open
Abstract
The crystal structure of subtype-B HIV-1 genomic RNA Dimerization Initiation Site duplex revealed chain cleavage at a specific position resulting in 3'-phosphate and 5'-hydroxyl termini. A crystallographic analysis showed that Ba(2+), Mn(2+), Co(2+) and Zn(2+) bind specifically on a guanine base close to the cleaved position. The crystal structures also point to a necessary conformational change to induce an 'in-line' geometry at the cleavage site. In solution, divalent cations increased the rate of cleavage with pH/pKa compensation, indicating that a cation-bound hydroxide anion is responsible for the cleavage. We propose a 'Trojan horse' mechanism, possibly of general interest, wherein a doubly charged cation hosted near the cleavage site as a 'harmless' species is further transformed in situ into an 'aggressive' species carrying a hydroxide anion.
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Affiliation(s)
| | | | - Philippe Dumas
- *To whom correspondence should be addressed. Tel: +33 388 41 70 02; Fax: +33 388 60 22 18;
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32
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Rieder U, Lang K, Kreutz C, Polacek N, Micura R. Evidence for pseudoknot formation of class I preQ1 riboswitch aptamers. Chembiochem 2009; 10:1141-4. [PMID: 19382115 DOI: 10.1002/cbic.200900155] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
All in a knot. The smallest riboswitch forms a pseudoknot in solution. This is demonstrated for preQ(1) class I aptamers by mutational analysis in combination with (1)H NMR-based structure probing. How pseudoknot formation mediates the mRNA response through its expression platform is now open for investigation.
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Affiliation(s)
- Ulrike Rieder
- Institute of Organic Chemistry, Center for Molecular Biosciences CMBI, 6020 Innsbruck. Austria
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33
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Salpin JY, Guillaumont S, Tortajada J, Lamsabhi AM. Gas-phase interactions between lead(II) ions and thiouracil nucleobases: a combined experimental and theoretical study. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2009; 20:359-69. [PMID: 19038555 DOI: 10.1016/j.jasms.2008.10.015] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/30/2008] [Revised: 10/14/2008] [Accepted: 10/22/2008] [Indexed: 05/17/2023]
Abstract
The gas-phase interactions between lead(II) ions and 2-thiouracil, 4-thiouracil, and 2,4-dithiouracil have been investigated by combining mass spectrometry and theoretical calculations. The most abundant complexes observed, namely [Pb(thiouracil) - H](+), have been studied by MS/MS experiments. Cationization by the metal allows an unambiguous characterization of the sulfur position, several fragment ions being specific of each isomer. Moreover, compared with the uracil fragmentation, new fragmentation channels are observed: elimination of PbS or total reduction of the metal. Calculations performed on the different structures, including tautomers, show that sulfur is the preferred complexation site, suggesting the greater affinity of lead for sulfur. The most stable structures are always preferentially bidentate. Natural population analysis indicates a charge transfer from the base to the metal with a more pronounced covalent character for sulfur compared to oxygen. Energetic profiles associated with the main fragmentations have been described.
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Affiliation(s)
- Jean-Yves Salpin
- Université d'Evry Val d'Essonne, Laboratoire d'Analyse et Modélisation pour la Biologie et l'Environnement (LAMBE), Evry, France.
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34
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Takemoto C, Spremulli LL, Benkowski LA, Ueda T, Yokogawa T, Watanabe K. Unconventional decoding of the AUA codon as methionine by mitochondrial tRNAMet with the anticodon f5CAU as revealed with a mitochondrial in vitro translation system. Nucleic Acids Res 2009; 37:1616-27. [PMID: 19151083 PMCID: PMC2655697 DOI: 10.1093/nar/gkp001] [Citation(s) in RCA: 82] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Abstract
Mitochondrial (mt) tRNAMet has the unusual modified nucleotide 5-formylcytidine (f5C) in the first position of the anticodon. This tRNA must translate both AUG and AUA as methionine. By constructing an in vitro translation system from bovine liver mitochondria, we examined the decoding properties of the native mt tRNAMet carrying f5C in the anticodon compared to a transcript that lacks the modification. The native mt Met-tRNA could recognize both AUA and AUG codons as Met, but the corresponding synthetic tRNAMet lacking f5C (anticodon CAU), recognized only the AUG codon in both the codon-dependent ribosomal binding and in vitro translation assays. Furthermore, the Escherichia coli elongator tRNAMetm with the anticodon ac4CAU (ac4C = 4-acetylcytidine) and the bovine cytoplasmic initiator tRNAMet (anticodon CAU) translated only the AUG codon for Met on mt ribosome. The codon recognition patterns of these tRNAs were the same on E. coli ribosomes. These results demonstrate that the f5C modification in mt tRNAMet plays a crucial role in decoding the nonuniversal AUA codon as Met, and that the genetic code variation is compensated by a change in the tRNA anticodon, not by a change in the ribosome. Base pairing models of f5C-G and f5C-A based on the chemical properties of f5C are presented.
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Affiliation(s)
- Chie Takemoto
- Department of Chemistry and Biotechnology, Graduate School of Engineering, University of Tokyo, Bunkyo-ku, Tokyo 113-8656, Japan.
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Lippert B. Coordinative Bond Formation Between Metal Ions and Nucleic Acid Bases. NUCLEIC ACID–METAL ION INTERACTIONS 2008. [DOI: 10.1039/9781847558763-00039] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Affiliation(s)
- Bernhard Lippert
- Fakultät für Chemie, Technische Universität Dortmund Otto-Hahn-Strasse 6 D-44227 Dortmund Germany
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37
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Lippert B. Ligand-pKaShifts through Metals: Potential Relevance to Ribozyme Chemistry. Chem Biodivers 2008; 5:1455-1474. [DOI: 10.1002/cbdv.200890135] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
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Abstract
Lead cleavage causes a transesterification reaction that breaks the 5',3'-phosphodiester backbone of RNA, leaving a 2',3'-cyclic phosphate and a 5'-hydroxyl. Since the efficiency of the reaction at the 2'-hydroxyl is related to steric and chemical constraints on particular 2'-hydroxyls embedded in the RNA, this reaction can be used to examine the structure of individual nucleotides within an RNA molecule. It is a sensitive probe of tertiary RNA structure, provided that Pb(2+)-binding sites are created in the tertiary structure.
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Affiliation(s)
- T Pan
- University of Chicago, Chicago, Illinois, USA
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Papsai P, Snygg ÅS, Aldag J, Elmroth SKC. Platination of full length tRNAAla and truncated versions of the acceptor stem and anticodon loop. Dalton Trans 2008:5225-34. [DOI: 10.1039/b719542g] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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40
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Altman S. Ribonuclease P: an enzyme with a catalytic RNA subunit. ADVANCES IN ENZYMOLOGY AND RELATED AREAS OF MOLECULAR BIOLOGY 2006; 62:1-36. [PMID: 2471397 DOI: 10.1002/9780470123089.ch1] [Citation(s) in RCA: 47] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Affiliation(s)
- S Altman
- Department of Biology, Yale University, New Haven, Connecticut 06520
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Knobloch B, Suliga D, Okruszek A, Sigel RKO. Acid-base and metal-ion binding properties of the RNA dinucleotide uridylyl-(5'-->3')-[5']uridylate (pUpU3-). Chemistry 2006; 11:4163-70. [PMID: 15861476 DOI: 10.1002/chem.200500013] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Abstract
It is well known that Mg2+ and other divalent metal ions bind to the phosphate groups of nucleic acids. Subtle differences in the coordination properties of these metal ions to RNA, especially to ribozymes, determine whether they either promote or inhibit catalytic activity. The ability of metal ions to coordinate simultaneously with two neighboring phosphate groups is important for ribozyme structure and activity. However, such an interaction has not yet been quantified. Here, we have performed potentiometric pH titrations to determine the acidity constants of the protonated dinucleotide H2(pUpU)-, as well as the binding properties of pUpU3- towards Mg2+, Mn2+, Cd2+, Zn2+, and Pb2+. Whereas Mg2+, Mn2+, and Cd2+ only bind to the more basic 5'-terminal phosphate group, Pb2+, and to a certain extent also Zn2+, show a remarkably enhanced stability of the [M(pUpU)]- complex. This can be attributed to the formation of a macrochelate by bridging the two phosphate groups within this dinucleotide by these metal ions. Such a macrochelate is also possible in an oligonucleotide, because the basic structural units are the same, despite the difference in charge. The formation degrees of the macrochelated species of [Zn(pUpU)]- and [Pb(pUpU)]- amount to around 25 and 90 %, respectively. These findings are important in the context of ribozyme and DNAzyme catalysis, and explain, for example, why the leadzyme could be selected in the first place, and why this artificial ribozyme is inhibited by other divalent metal ions, such as Mg2+.
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Affiliation(s)
- Bernd Knobloch
- Institute of Inorganic Chemistry, University of Zürich, Switzerland
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Abstract
One of the major challenges in medicine today is the development of new antibiotics as well as effective antiviral agents. The well-known aminoglycosides interact and interfere with the function of several noncoding RNAs, among which ribosomal RNAs (rRNAs) are the best studied. Aminoglycosides are also known to interact with proteins such as ribonucleases. Here we review our current understanding of the interaction between aminoglycosides and RNA. Moreover, we discuss briefly mechanisms behind the inactivation of aminoglycosides, a major concern due to the increasing appearance of multiresistant bacterial strains. Taken together, the general knowledge about aminoglycoside and RNA interaction is of utmost importance in the process of identifying/developing the next generation or new classes of antibiotics. In this perspective, previously unrecognized as well as known noncoding RNAs, apart from rRNA, are promising targets to explore.
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Affiliation(s)
- Volker Erdmann
- Institute of Chemistry/Biochemistry, Free University Berlin, Thielallee 63, 14195 Berlin, Germany
| | - Jan Barciszewski
- Institute of Bioorganic Chemistry, Polish Academy of Scienes, Noskowskiego 12/14, 61-704 Poznan, Poland
| | - Jürgen Brosius
- Institute of Experimental Pathology, Molecular Neurobiology (ZMBE), University of Münster, Von-Esmarch-Str. 56, 48149 Münster, Germany
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Schultes EA, Spasic A, Mohanty U, Bartel DP. Compact and ordered collapse of randomly generated RNA sequences. Nat Struct Mol Biol 2005; 12:1130-6. [PMID: 16273104 DOI: 10.1038/nsmb1014] [Citation(s) in RCA: 51] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2005] [Accepted: 09/21/2005] [Indexed: 11/08/2022]
Abstract
As the raw material for evolution, arbitrary RNA sequences represent the baseline for RNA structure formation and a standard to which evolved structures can be compared. Here, we set out to probe, using physical and chemical methods, the structural properties of RNAs having randomly generated oligonucleotide sequences that were of sufficient length and information content to encode complex, functional folds, yet were unbiased by either genealogical or functional constraints. Typically, these unevolved, nonfunctional RNAs had sequence-specific secondary structure configurations and compact magnesium-dependent conformational states comparable to those of evolved RNA isolates. But unlike evolved sequences, arbitrary sequences were prone to having multiple competing conformations. Thus, for RNAs the size of small ribozymes, natural selection seems necessary to achieve uniquely folding sequences, but not to account for the well-ordered secondary structures and overall compactness observed in nature.
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Affiliation(s)
- Erik A Schultes
- Whitehead Institute for Biomedical Research, 9 Cambridge Center, Cambridge, Massachusetts 02142, USA
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Knobloch B, Linert W, Sigel H. Metal ion-binding properties of (N3)-deprotonated uridine, thymidine, and related pyrimidine nucleosides in aqueous solution. Proc Natl Acad Sci U S A 2005; 102:7459-64. [PMID: 15897459 PMCID: PMC1140430 DOI: 10.1073/pnas.0501446102] [Citation(s) in RCA: 57] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2005] [Indexed: 11/18/2022] Open
Abstract
The acidity constants for (N3)H of the uridine-type ligands (U) 5-fluorouridine, 5-chloro-2'-deoxyuridine, uridine, and thymidine (2'-deoxy-5-methyluridine) and the stability constants of the M(U-H)(+) complexes for M(2+) = Mg(2+), Ca(2+), Sr(2+), Ba(2+), Mn(2+), Co(2+), Ni(2+), Cu(2+), Zn(2+), Cd(2+), and Pb(2+) were measured (potentiometric pH titrations; aqueous solution; 25 degrees C; I = 0.1 M, NaNO(3)). Plots of logK(M(U-H))(M) vs. pK(U)(H) result in straight lines that are compared with previous plots for simple pyridine-type and o-amino(methyl)pyridine-type ligands as well as with the stabilities of the corresponding M(cytidine)(2+) complexes. The results indicate monodentate coordination to (N3)(-) in M(U-H)(+) for Co(2+) and Ni(2+). For the M(U-H)(+) species of Cd(2+), Zn(2+), or Cu(2+), increased stabilities imply that semichelates form, i.e., M(2+) is (N3)(-)-bound and coordinated water molecules form hydrogen bonds to (C2)O and (C4)O; these "double" semichelates are in equilibrium with "single" semichelates involving either (C2)O or (C4)O and possibly also with four-membered chelates for which M(2+) is innersphere-coordinated to (N3)(-) and a carbonyl oxygen. For the alkaline earth ions, semichelates dominate with the M(2+) outersphere bound to (N3)(-) and innersphere to one of the carbonyl oxygens. Mn(U-H)(+) is with its properties between those of Cd(2+) (which probably also hold for Pb(2+)) and the alkaline earth ions. In nucleic acids, M(2+)-C(O) interactions are expected, if support is provided by other primary binding sites. (N3)H may possibly be acidified via carbonyl-coordinated M(2+) to become a proton donor in the physiological pH range, at which direct (N3)(-) binding of M(2+) also seems possible.
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Affiliation(s)
- Bernd Knobloch
- Department of Chemistry, Inorganic Chemistry, University of Basel, Spitalstrasse 51, CH-4056 Basel, Switzerland
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Keiper S, Bebenroth D, Seelig B, Westhof E, Jäschke A. Architecture of a Diels-Alderase ribozyme with a preformed catalytic pocket. ACTA ACUST UNITED AC 2005; 11:1217-27. [PMID: 15380182 DOI: 10.1016/j.chembiol.2004.06.011] [Citation(s) in RCA: 33] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2004] [Revised: 06/06/2004] [Accepted: 06/15/2004] [Indexed: 10/26/2022]
Abstract
Artificial ribozymes catalyze a variety of chemical reactions. Their structures and reaction mechanisms are largely unknown. We have analyzed a ribozyme catalyzing Diels-Alder cycloaddition reactions by comprehensive mutation analysis and a variety of probing techniques. New tertiary interactions involving base pairs between nucleotides of the 5' terminus and a large internal loop forming a pseudoknot fold were identified. The probing data indicate a preformed tertiary structure that shows no major changes on substrate or product binding. Based on these observations, a molecular architecture featuring a Y-shaped arrangement is proposed. The tertiary structure is formed in a rather unusual way; that is, the opposite sides of the asymmetric internal loop are clamped by the four 5'-terminal nucleotides, forming two adjacent two base-pair helices. It is proposed that the catalytic pocket is formed by a wedge within one of these helices.
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Affiliation(s)
- Sonja Keiper
- Universität Heidelberg, Institut für Pharmazie und Molekulare Biotechnologie, D-69120 Heidelberg, Germany
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Krol J, Sobczak K, Wilczynska U, Drath M, Jasinska A, Kaczynska D, Krzyzosiak WJ. Structural Features of MicroRNA (miRNA) Precursors and Their Relevance to miRNA Biogenesis and Small Interfering RNA/Short Hairpin RNA Design. J Biol Chem 2004; 279:42230-9. [PMID: 15292246 DOI: 10.1074/jbc.m404931200] [Citation(s) in RCA: 131] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
We have established the structures of 10 human microRNA (miRNA) precursors using biochemical methods. Eight of these structures turned out to be different from those that were computer-predicted. The differences localized in the terminal loop region and at the opposite side of the precursor hairpin stem. We have analyzed the features of these structures from the perspectives of miRNA biogenesis and active strand selection. We demonstrated the different thermodynamic stability profiles for pre-miRNA hairpins harboring miRNAs at their 5'- and 3'-sides and discussed their functional implications. Our results showed that miRNA prediction based on predicted precursor structures may give ambiguous results, and the success rate is significantly higher for the experimentally determined structures. On the other hand, the differences between the predicted and experimentally determined structures did not affect the stability of termini produced through "conceptual dicing." This result confirms the value of thermodynamic analysis based on mfold as a predictor of strand section by RNAi-induced silencing complex (RISC).
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Affiliation(s)
- Jacek Krol
- Laboratory of Cancer Genetics, Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12/14, 61-704, Poznan, Poland
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Knobloch B, Sigel H. A quantitative appraisal of the ambivalent metal ion binding properties of cytidine in aqueous solution and an estimation of the anti–syn energy barrier of cytidine derivatives. J Biol Inorg Chem 2004; 9:365-73. [PMID: 15034770 DOI: 10.1007/s00775-004-0533-4] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2003] [Accepted: 02/19/2004] [Indexed: 10/26/2022]
Abstract
The recently defined log K (M)(M)(L) versus pK(H)(H)(L) straight-line plots for L = pyridine-type (PyN) and ortho-aminopyridine-type (oPyN) ligands now allow the evaluation in a quantitative manner of the stability of the 1:1 complexes formed between cytidine (Cyd) and Ca(2+), Mg(2+), Mn(2+), Co(2+), Ni(2+), Cu(2+), Zn(2+) or Cd(2+) (M(2+)); the corresponding stability constants, K(M)(M)(Cyd) including the acidity constant, K(H)(H)(Cyd) for the deprotonation of the (N3)H(+) site had been determined previously under exactly the same conditions as the mentioned plots. Since the stabilities of the M(PyN)(2+) and M(oPyN)(2+) complexes of Ca(2+) and Mg(2+) are practically identical, it is concluded that complex formation occurs in an outer-sphere manner, and this is in accord with the fact that in the p K(a) range 3-7 metal ion binding is independent of K(H)(H)(Pyn) or K(H)(H)(oPyN). Ca(Cyd)(2+) and Mg(Cyd)(2+) are more stable than the corresponding (outer-sphere) M(PyN)(2+) complexes and this means that the C2 carbonyl group of Cyd must participate, next to N3 which is most likely outer-sphere, in metal ion binding, leading thus to chelates; these have formation degrees of about 50% and 35%, respectively. Co(Cyd)(2+) and Ni(Cyd)(2+) show no increased stability based on the log K(M)(M)(oPyN) versus pK(H)(H)(oPyN) hence, the (C2)O group does not participate in metal ion binding, but the inner-sphere coordination to N3 is strongly inhibited by the (C4)NH(2) group. In the M(Cyd)(2+) complexes of Mn(2+), Cu(2+), Zn(2+) and Cd(2+), this inhibiting effect on M(2+) binding at N3 is partially compensated by participation of the (C2)O group in complex formation and the corresponding chelates have formation degrees between about 30% (Zn(2+)) and 83% (Cu(2+)). The different structures of the mentioned chelates are discussed in relation to available crystal structure analyses. (1). There is evidence (crystal structure studies: Cu(2+), Zn(2+), Cd(2+)) that four-membered rings form, i.e. there is a strong M(2+) bond to N3 and a weak one to (C2)O. (2). By hydrogen bond formation to (C2)O of a metal ion-bound water molecule, six-membered rings, so-called semichelates, may form. (3). For Ca(2+) and Mg(2+), and possibly Mn(2+), and their Cyd complexes, six-membered chelates are also likely with (C2)O being inner-sphere (crystal structure) and N3 outer-sphere. (4). Finally, for these metal ions also complexes with a sole outer-sphere interaction may occur. All these types of chelates are expected to be in equilibrium with each other in solution, but, depending on the metal ion, either the one or the other form will dominate. Clearly, the cytidine residue is an ambivalent binding site which adjusts well to the requirements of the metal ion to be bound and this observation is of relevance for single-stranded nucleic acids and their interactions with metal ions. In addition, the anti- syn energy barrier has been estimated as being in the order of 6-7.5 kJ/mol for cytidine derivatives in aqueous solution at 25 degrees C.
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Affiliation(s)
- Bernd Knobloch
- Department of Chemistry, Inorganic Chemistry, University of Basel, Spitalstrasse 51, CH-4056, Basel, Switzerland
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Sun M, Shangguan D, Ma H, Nie L, Li X, Xiong S, Liu G, Thiemann W. Simple PbII fluorescent probe based on PbII-catalyzed hydrolysis of phosphodiester. Biopolymers 2003; 72:413-20. [PMID: 14587063 DOI: 10.1002/bip.10484] [Citation(s) in RCA: 40] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
A new fluorescent probe for PbII, p-nitrophenyl 3H-phenoxazin-3-one-7-yl phosphoric acid (NPPA), was designed and synthesized by linking resorufin (serving as a fluorophore and electron acceptor) to p-nitrophenol (serving as a fluorescence quencher and electron donor) through phosphodiester bonds. When NPPA was irradiated with light, intramolecular fluorescence self-quenching took place because of the photoinduced electron transfer from the donor to the acceptor. However, upon the addition of PbII, the phosphate ester bonds in the probe were cleaved and the fluorophore was released, accompanying the retrievement of fluorescence.
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Affiliation(s)
- Ming Sun
- Laboratory of Chemical Biology, Institute of Chemistry, Chinese Academy of Sciences, Beijing 100080, China
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