1
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Ahmed MA, Ahmed MA, Mohamed AA. Facile adsorptive removal of dyes and heavy metals from wastewaters using magnetic nanocomposite of zinc ferrite@reduced graphene oxide. INORG CHEM COMMUN 2022. [DOI: 10.1016/j.inoche.2022.109912] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
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2
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Gende M, Schmeling M. Development of an analytical method for determination of lead and cadmium in biological materials by GFAAS using Escherichia coli as model substance. PLoS One 2022; 17:e0267775. [PMID: 35503792 PMCID: PMC9064108 DOI: 10.1371/journal.pone.0267775] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2022] [Accepted: 04/14/2022] [Indexed: 11/18/2022] Open
Abstract
In this work, an analytical method was developed for the determination of lead and cadmium in biological samples using graphite furnace atomic absorption spectrometry. Escherichia coli (E. coli) was chosen as model substance for this purpose as it is readily available in most laboratories and can be quickly and easily prepared with a high turnaround rate. Four different sample preparation methods were initially evaluated with respect to percent recovery, limit of detection, and limit of quantification, and the most promising one was developed further. The final process involving microwave assisted digestion of the sample with nitric acid and hydrogen peroxide showed high recovery, repeatability, and specificity. The process was first applied to lead and then extended for the determination of cadmium in the same E. coli substrates. Finally, to validate the process, a certified references material was analyzed, and the results obtained were evaluated with respect to accuracy by comparing them to the reported ones.
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Affiliation(s)
- Michelle Gende
- Department of Chemistry and Biochemistry, Loyola University Chicago, Chicago, IL, United States of America
| | - Martina Schmeling
- Department of Chemistry and Biochemistry, Loyola University Chicago, Chicago, IL, United States of America
- * E-mail:
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3
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Streckerová T, Kurfürst J, Curtis EA. Single-round deoxyribozyme discovery. Nucleic Acids Res 2021; 49:6971-6981. [PMID: 34133739 PMCID: PMC8266665 DOI: 10.1093/nar/gkab504] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2021] [Revised: 05/14/2021] [Accepted: 05/31/2021] [Indexed: 01/23/2023] Open
Abstract
Artificial evolution experiments typically use libraries of ∼1015 sequences and require multiple rounds of selection to identify rare variants with a desired activity. Based on the simple structures of some aptamers and nucleic acid enzymes, we hypothesized that functional motifs could be isolated from significantly smaller libraries in a single round of selection followed by high-throughput sequencing. To test this idea, we investigated the catalytic potential of DNA architectures in which twelve or fifteen randomized positions were embedded in a scaffold present in all library members. After incubating in either the presence or absence of lead (which promotes the nonenzymatic cleavage of RNA), library members that cleaved themselves at an RNA linkage were purified by PAGE and characterized by high-throughput sequencing. These selections yielded deoxyribozymes with activities 8- to 30-fold lower than those previously isolated under similar conditions from libraries containing 1014 different sequences, indicating that the disadvantage of using a less diverse pool can be surprisingly small. It was also possible to elucidate the sequence requirements and secondary structures of deoxyribozymes without performing additional experiments. Due to its relative simplicity, we anticipate that this approach will accelerate the discovery of new catalytic DNA and RNA motifs.
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Affiliation(s)
- Tereza Streckerová
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Prague 160 00, Czech Republic
- Department of Biochemistry and Microbiology, University of Chemistry and Technology, Prague 160 00, Czech Republic
| | - Jaroslav Kurfürst
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Prague 160 00, Czech Republic
- Department of Informatics and Chemistry, University of Chemistry and Technology, Prague 166 28, Czech Republic
| | - Edward A Curtis
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Prague 160 00, Czech Republic
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4
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Martínez-Giménez JA, Tabares-Seisdedos R. Possible Ancestral Functions of the Genetic and RNA Operational Precodes and the Origin of the Genetic System. ORIGINS LIFE EVOL B 2021; 51:167-183. [PMID: 34097191 DOI: 10.1007/s11084-021-09610-7] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2021] [Accepted: 05/17/2021] [Indexed: 11/24/2022]
Abstract
The origin of genetic systems is the central problem in the study of the origin of life for which various explanatory hypotheses have been presented. One model suggests that both ancestral transfer ribonucleic acid (tRNA) molecules and primitive ribosomes were originally involved in RNA replication (Campbell 1991). According to this model the early tRNA molecules catalyzed their own self-loading with a trinucleotide complementary to their anticodon triplet, while the primordial ribosome (protoribosome) catalyzed the transfer of these terminal trinucleotides from one tRNA to another tRNA harboring the growing RNA polymer at the 3´-end.Here we present the notion that the anticodon-codon-like pairs presumably located in the acceptor stem of primordial tRNAs (Rodin et al. 1996) (thus being and remaining, after the code and translation origins, the major contributor to the RNA operational code (Schimmel et al. 1993)) might have originally been used for RNA replication rather than translation; these anticodon and acceptor stem triplets would have been involved in accurately loading the 3'-end of tRNAs with a trinucleotide complementary to their anticodon triplet, thus allowing the accurate repair of tRNAs for their use by the protoribosome during RNA replication.We propose that tRNAs could have catalyzed their own trinucleotide self-loading by forming catalytic tRNA dimers which would have had polymerase activity. Therefore, the loading mechanism and its evolution may have been a basic step in the emergence of new genetic mechanisms such as genetic translation. The evolutionary implications of this proposed loading mechanism are also discussed.
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Affiliation(s)
| | - Rafael Tabares-Seisdedos
- Departamento de Medicina, Facultad de Medicina de Valencia, Universidad de Valencia, Av. Blasco Ibañez 17, 46010, Valencia, Spain.
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5
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Zhou Y, Li X, McBride MB. Aqueous solubility of Pb at equilibrium with hydroxypyromorphite over a range of phosphate concentrations. ENVIRONMENTAL SCIENCE. PROCESSES & IMPACTS 2021; 23:170-178. [PMID: 33399599 DOI: 10.1039/d0em00430h] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
Hydroxypyromorphite (HPM) is a low-solubility Pb phosphate mineral that has the potential to limit solubility and bioavailability of Pb in soils and water. Because of reported uncertainty regarding the solubility product of this important mineral, we re-evaluated the solubility of Pb and activity of the free Pb2+ ion in aqueous suspensions of microcrystalline HPM equilibrated up to 30 days over a wide range of added soluble phosphate. A small addition of phosphate (0.1 mM) reduced Pb solubility as measured by ICP-OES, but greater phosphate additions (up to 50 mM) had no further effect in lowering HPM solubility. However, free Pb2+ ion activity measured by ion-selective electrode progressively decreased from about 10-6.5 with no added phosphate to 10-9 as soluble phosphate was increased. The effect of soluble phosphate in lowering Pb2+ activity is attributed to inhibited dissolution of HPM as well as increased Pb2+-phosphate ion pair formation in solution at higher solution concentrations of phosphate. Measurement of the ion activity products (IAP) of the solutions at equilibrium with HPM gave highly variable IAP values that were sensitive to pH and were generally not consistent with the reported solubility product of this mineral. The high variability of the IAPs for solutions with variable pH and phosphate concentrations indicates that dissolution-precipitation reactions of HPM are not described by a constant solubility product at equilibrium, possibly because of the incongruent dissolution behavior of this mineral at near-neutral pH.
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Affiliation(s)
- Yuting Zhou
- College of Environmental and Resource Science, Zhejiang University, Hangzhou, China
| | - Xinxin Li
- School of Environmental Science and Engineering, Shandong University, Qingdao, China
| | - Murray B McBride
- Section of Soil and Crop Sciences, Cornell University, Ithaca, NY 14850, USA.
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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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Yang H, Peng D, Zhou Y, Liu J. Pb 2+ as a Substrate and a Cofactor of a Porphyrin Metalation DNAzyme. Chembiochem 2020; 21:2259-2263. [PMID: 32202058 DOI: 10.1002/cbic.202000073] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2020] [Revised: 03/21/2020] [Indexed: 11/11/2022]
Abstract
We herein report a DNAzyme named T30695 (sequence: (G3 T)4 ) that can catalyze Zn2+ insertion into three different porphyrins in the presence of Pb2+ as a cofactor. Meanwhile, T30695 with Pb2+ alone was found to cause a shift in both the fluorescence and UV-vis spectra of protoporphyrin IX (PPIX), thus suggesting that metalation of Pb2+ was also achieved at room temperature. From kinetic measurements, the reaction required two Pb2+ ions; this is consistent with one being a cofactor and the other being a substrate. No previous reports inserted Pb2+ into porphyrins by using DNAzymes or protein-based enzymes. This reaction was most significantly inhibited in the presence of K+ followed by Na+ and Li+ , suggesting the importance of the Pb2+ -stabilized G-quadruplex. When Pb2+ is inserted into PPIX, its emission blue shifts from 635 to 590 nm, thus allowing simple ratiometric fluorescent sensing with a detection limit of 1.2 nM Pb2+ .
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Affiliation(s)
- Hualin Yang
- College of Life Science, Yangtze University, 266 Jingmi Road, Jingzhou, Hubei, 434025, China.,Department of Chemistry, Waterloo Institute for Nanotechnology, University of Waterloo, Waterloo, Ontario, N2 L 3G1, Canada
| | - Dong Peng
- Department of Chemistry, Waterloo Institute for Nanotechnology, University of Waterloo, Waterloo, Ontario, N2 L 3G1, Canada.,College of Chemistry20, Nanchang University, 999 Xuefu Avenue, Nanchang, 330031, Jiangxi, China
| | - Yu Zhou
- College of Life Science, Yangtze University, 266 Jingmi Road, Jingzhou, Hubei, 434025, China
| | - Juewen Liu
- Department of Chemistry, Waterloo Institute for Nanotechnology, University of Waterloo, Waterloo, Ontario, N2 L 3G1, 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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Water Soluble Schiff Base Functinalized Fe3O4 Magnetic Nano-Particles as a Novel Adsorbent for the Removal of Pb(II) and Cu(II) Metal Ions from Aqueous Solutions. J Inorg Organomet Polym Mater 2017. [DOI: 10.1007/s10904-017-0770-y] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
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11
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Li Y, Kluger R. Increased efficiency in biomimetic Lewis acid–base pair catalyzed monoacylation of diols by acyl phosphate monoesters. Facets (Ott) 2017. [DOI: 10.1139/facets-2017-0047] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
Acyl phosphate monoesters are biomimetic acylation reagents that require coordination to metal ions to react with cis-diol substrates in water. With lanthanide catalysts, outcomes are compromised by (1) the competitive lanthanide-promoted hydrolysis of the acyl phosphate reagents as well as by (2) the high affinity of lanthanum ions for the phosphate monoester by-product. Based on analysis of the mechanism of the process, optimizing reaction conditions can selectively inhibit the lanthanum-promoted hydrolysis of acyl phosphate monoesters. Furthermore, using zinc salts and lead salts in place of lanthanides enhances the reactivity of the reactants and causes less complexation of the metal ion with the by-products.
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Affiliation(s)
- Yuyang Li
- Davenport Laboratories, Department of Chemistry, University of Toronto, 80 St. George Street, Toronto, ON M5S 3H6, Canada
| | - Ronald Kluger
- Davenport Laboratories, Department of Chemistry, University of Toronto, 80 St. George Street, Toronto, ON M5S 3H6, Canada
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12
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Rolfsson Ó, Middleton S, Manfield IW, White SJ, Fan B, Vaughan R, Ranson NA, Dykeman E, Twarock R, Ford J, Kao CC, Stockley PG. Direct Evidence for Packaging Signal-Mediated Assembly of Bacteriophage MS2. J Mol Biol 2016; 428:431-48. [PMID: 26608810 PMCID: PMC4751978 DOI: 10.1016/j.jmb.2015.11.014] [Citation(s) in RCA: 71] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2015] [Revised: 11/06/2015] [Accepted: 11/08/2015] [Indexed: 01/20/2023]
Abstract
Using cross-linking coupled to matrix-assisted laser desorption/ionization mass spectrometry and CLIP-Seq sequencing, we determined the peptide and oligonucleotide sequences at the interfaces between the capsid proteins and the genomic RNA of bacteriophage MS2. The results suggest that the same coat protein (CP)-RNA and maturation protein (MP)-RNA interfaces are used in every viral particle. The portions of the viral RNA in contact with CP subunits span the genome, consistent with a large number of discrete and similar contacts within each particle. Many of these sites match previous predictions of the locations of multiple, dispersed and degenerate RNA sites with cognate CP affinity termed packaging signals (PSs). Chemical RNA footprinting was used to compare the secondary structures of protein-free genomic fragments and the RNA in the virion. Some PSs are partially present in protein-free RNA but others would need to refold from their dominant solution conformations to form the contacts identified in the virion. The RNA-binding peptides within the MP map to two sections of the N-terminal half of the protein. Comparison of MP sequences from related phages suggests a similar arrangement of RNA-binding sites, although these N-terminal regions have only limited sequence conservation. In contrast, the sequences of the C-termini are highly conserved, consistent with them encompassing pilin-binding domains required for initial contact with host cells. These results provide independent and unambiguous support for the assembly of MS2 virions via a PS-mediated mechanism involving a series of induced-fit viral protein interactions with RNA.
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Affiliation(s)
- Óttar Rolfsson
- Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds LS2 9JT, United Kingdom
| | - Stefani Middleton
- Department of Molecular and Cellular Biochemistry, Indiana University, Bloomington, IN 47405, USA; The Center for Genomics and Bioinformatics, Indiana University, Bloomington, IN 47405, USA
| | - Iain W Manfield
- Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds LS2 9JT, United Kingdom
| | - Simon J White
- Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds LS2 9JT, United Kingdom
| | - Baochang Fan
- Department of Molecular and Cellular Biochemistry, Indiana University, Bloomington, IN 47405, USA
| | - Robert Vaughan
- Department of Molecular and Cellular Biochemistry, Indiana University, Bloomington, IN 47405, USA
| | - Neil A Ranson
- Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds LS2 9JT, United Kingdom
| | - Eric Dykeman
- Department of Biology and Mathematics and York Centre for Complex Systems Analysis, University of York, York YO10 5DD, United Kingdom
| | - Reidun Twarock
- Department of Biology and Mathematics and York Centre for Complex Systems Analysis, University of York, York YO10 5DD, United Kingdom
| | - James Ford
- The Center for Genomics and Bioinformatics, Indiana University, Bloomington, IN 47405, USA
| | - C Cheng Kao
- Department of Molecular and Cellular Biochemistry, Indiana University, Bloomington, IN 47405, USA
| | - Peter G Stockley
- Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds LS2 9JT, United Kingdom
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13
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PENG RP, XING LB, WANG XJ, WU CJ, CHEN B, JI HF, WU LZ, TUNG CH. Detection of Pb 2+ in Aqueous Solution by Using a DNA-modified Microcantilever. ANAL SCI 2016; 32:1065-1069. [DOI: 10.2116/analsci.32.1065] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Affiliation(s)
- Rong-Peng PENG
- Key Laboratory of Photochemical Conversion and Optoelectronic Materials, Technical Institute of Physics and Chemistry, Chinese Academy of Sciences and Graduate University of Chinese Academy of Sciences
- College of Chemistry, Nanchang University
- Department of Chemistry, Drexel University
| | - Ling-Bao XING
- Key Laboratory of Photochemical Conversion and Optoelectronic Materials, Technical Institute of Physics and Chemistry, Chinese Academy of Sciences and Graduate University of Chinese Academy of Sciences
| | - Xiao-Jun WANG
- Key Laboratory of Photochemical Conversion and Optoelectronic Materials, Technical Institute of Physics and Chemistry, Chinese Academy of Sciences and Graduate University of Chinese Academy of Sciences
| | - Cheng-juan WU
- Key Laboratory of Photochemical Conversion and Optoelectronic Materials, Technical Institute of Physics and Chemistry, Chinese Academy of Sciences and Graduate University of Chinese Academy of Sciences
| | - Bin CHEN
- Key Laboratory of Photochemical Conversion and Optoelectronic Materials, Technical Institute of Physics and Chemistry, Chinese Academy of Sciences and Graduate University of Chinese Academy of Sciences
| | | | - Li-Zhu WU
- Key Laboratory of Photochemical Conversion and Optoelectronic Materials, Technical Institute of Physics and Chemistry, Chinese Academy of Sciences and Graduate University of Chinese Academy of Sciences
| | - Chen-Ho TUNG
- Key Laboratory of Photochemical Conversion and Optoelectronic Materials, Technical Institute of Physics and Chemistry, Chinese Academy of Sciences and Graduate University of Chinese Academy of Sciences
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14
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Saran R, Liu J. A comparison of two classic Pb2+-dependent RNA-cleaving DNAzymes. Inorg Chem Front 2016. [DOI: 10.1039/c5qi00125k] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
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15
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Huang PJJ, Vazin M, Liu J. Desulfurization Activated Phosphorothioate DNAzyme for the Detection of Thallium. Anal Chem 2015; 87:10443-9. [PMID: 26393365 DOI: 10.1021/acs.analchem.5b02568] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
Thallium (Tl) is a highly toxic heavy metal situated between mercury and lead in the periodic table. While its neighbors have been thoroughly studied for DNA-based sensing, little is known about thallium detection. In this work, in vitro selection of RNA-cleaving DNAzymes is carried out using Tl(3+) as the target metal cofactor. Both normal DNA and phosphorothioate (PS)-modified DNA are tested for this purpose. While no Tl(3+)-dependent DNAzymes are obtained, a DNA oligonucleotide containing a single PS-modified RNA nucleotide is found to cleave by ∼7% by Tl(3+) at the RNA position. The remaining 93% are desulfurized. By hybridization of this PS-modified oligonucleotide with the Tm7 DNAzyme, the cleavage yield increases to ∼40% in the presence of Tl(3+) and Er(3+). Tm7 is an Er(3+)-dependent RNA-cleaving DNAzyme. It cleaves only the normal substrate but is completely inactive using the PS-modified substrate. Tl(3+) desulfurizes the PS substrate to the normal substrate to be cleaved by Tm7 and Er(3+). This system is engineered into a catalytic beacon for Tl(3+) with a detection limit of 1.5 nM, which is below its maximal contamination limit defined by the U.S. Environmental Protection Agency (10 nM).
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Affiliation(s)
- Po-Jung Jimmy Huang
- Department of Chemistry, Waterloo Institute for Nanotechnology, University of Waterloo , Waterloo, Ontario N2L 3G1, Canada
| | - Mahsa Vazin
- Department of Chemistry, Waterloo Institute for Nanotechnology, University of Waterloo , Waterloo, Ontario N2L 3G1, Canada
| | - Juewen Liu
- Department of Chemistry, Waterloo Institute for Nanotechnology, University of Waterloo , Waterloo, Ontario N2L 3G1, Canada
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16
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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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17
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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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18
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Galaway FA, Stockley PG. MS2 Viruslike Particles: A Robust, Semisynthetic Targeted Drug Delivery Platform. Mol Pharm 2012; 10:59-68. [DOI: 10.1021/mp3003368] [Citation(s) in RCA: 95] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Affiliation(s)
- Francis A. Galaway
- Astbury Centre
for Structural Molecular Biology, University
of Leeds, Leeds, LS2 9JT, U.K
| | - Peter G. Stockley
- Astbury Centre
for Structural Molecular Biology, University
of Leeds, Leeds, LS2 9JT, U.K
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19
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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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20
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Desbouis D, Troitsky IP, Belousoff MJ, Spiccia L, Graham B. Copper(II), zinc(II) and nickel(II) complexes as nuclease mimetics. Coord Chem Rev 2012. [DOI: 10.1016/j.ccr.2011.12.005] [Citation(s) in RCA: 127] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/14/2022]
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21
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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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22
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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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23
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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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24
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Lilley DMJ, Sutherland J. The chemical origins of life and its early evolution: an introduction. Philos Trans R Soc Lond B Biol Sci 2011; 366:2853-6. [PMID: 21930575 PMCID: PMC3158915 DOI: 10.1098/rstb.2011.0133] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Can we look at contemporary biology and couple this with chemical insight to propose some plausible mechanisms for the origin of life on the planet? In what follows, we examine some promising chemical reactions by which the building blocks for nucleic acids might have been created about a billion years after the Earth formed. This could have led to self-assembling systems that were based on an all-RNA metabolism, where RNA is both catalytic and informational. We consider the breadth of RNA enzymes presently existing in biology, and to what extent these might have covered a wider range of chemistry in the RNA world. Ultimately, the RNA world would probably have given way to protein-based life quite quickly, and the origins of peptidyl transferase activity are discussed below.
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Affiliation(s)
- David M J Lilley
- Cancer Research UK Nucleic Acid Structure Research Group, MSI/WTB Complex, The University of Dundee, Dow Street, Dundee DD1 5EH, UK.
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25
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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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26
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Seshadri S, Saranya K, Kowshik M. Green synthesis of lead sulfide nanoparticles by the lead resistant marine yeast, Rhodosporidium diobovatum. Biotechnol Prog 2011; 27:1464-9. [PMID: 21710608 DOI: 10.1002/btpr.651] [Citation(s) in RCA: 123] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2011] [Revised: 04/12/2011] [Indexed: 11/07/2022]
Abstract
Biosynthesis of nanoparticles using microorganisms has attracted a lot of attention in recent years as this route has the potential to lead to synthesis of monodisperse nanoparticles. Here, we report the intracellular synthesis of stable lead sulfide nanoparticles by a marine yeast, Rhodosporidium diobovatum. The PbS nanoparticles were characterized by UV-visible absorption spectroscopy, X-ray diffraction (XRD) and energy dispersive atomic spectroscopy (EDAX). UV-visible absorption scan revealed a peak at 320 nm, a characteristic of the nanosize range. XRD confirmed the presence of PbS nanoparticles of cubic structure. Crystallite size as determined from transmission electron microscopy was found to be in the range of 2-5 nm. Elemental analysis by EDAX revealed the presence of particles composed of lead and sulfur in a 1:2 ratio indicating that PbS nanoparticles were capped by a sulfur-rich peptide. A quantitative study of lead uptake through atomic absorption spectrometry revealed that 55% of lead in the medium was accumulated in the exponential phase, whereas a further 35% was accumulated in the stationary phase; thus, the overall recovery of PbS nanoparticles was 90%. The lead-exposed yeast displayed a marked increase (280% over the control) in nonprotein thiols in the stationary phase.
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Affiliation(s)
- Sachin Seshadri
- Dept. of Biological Sciences, Birla Institute of Technology and Science, Pilani-K.K Birla Goa Campus, Zuarinagar, Goa 403726, India
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27
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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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28
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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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29
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Severcan I, Geary C, Verzemnieks E, Chworos A, Jaeger L. Square-shaped RNA particles from different RNA folds. NANO LETTERS 2009; 9:1270-7. [PMID: 19239258 PMCID: PMC2664548 DOI: 10.1021/nl900261h] [Citation(s) in RCA: 109] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/19/2023]
Abstract
The structural information encoding specific conformations of natural RNAs can be implemented within artificial RNA sequences to control both three-dimensional (3D) shape and self-assembling interfaces for nanotechnology and synthetic biology applications. We have identified three natural RNA motifs known to direct helical topology into approximately 90 degrees bends: a five-way tRNA junction, a three-way junction, and a two-helix bend. These three motifs, embedded within rationally designed RNAs (tectoRNA), were chosen for generating square-shaped tetrameric RNA nanoparticles. The ability of each motif to direct the formation of supramolecular assemblies was compared by both native gel assays and atomic force microscopy. While there are multiple structural solutions for building square-shaped RNA particles, differences in the thermodynamics and molecular dynamics of the 90 degrees motif can lead to different biophysical behaviors for the resulting supramolecular complexes. We demonstrate via structural assembly programming how the different 90 degrees motifs can preferentially direct the formation of either 2D or 3D assemblies.
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Affiliation(s)
- Isil Severcan
- Department of Chemistry and Biochemistry, University of California at Santa Barbara, Santa Barbara, CA 93106-9510
| | - Cody Geary
- Department of Chemistry and Biochemistry, University of California at Santa Barbara, Santa Barbara, CA 93106-9510
| | - Erik Verzemnieks
- Department of Chemistry and Biochemistry, University of California at Santa Barbara, Santa Barbara, CA 93106-9510
| | - Arkadiusz Chworos
- Department of Chemistry and Biochemistry, University of California at Santa Barbara, Santa Barbara, CA 93106-9510
| | - Luc Jaeger
- Department of Chemistry and Biochemistry, University of California at Santa Barbara, Santa Barbara, CA 93106-9510
- To whom correspondence should be addressed: Phone: 805-893-3628; Fax: 805-893-4120; Email;
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30
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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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31
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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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32
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Torelli AT, Krucinska J, Wedekind JE. A comparison of vanadate to a 2'-5' linkage at the active site of a small ribozyme suggests a role for water in transition-state stabilization. RNA (NEW YORK, N.Y.) 2007; 13:1052-70. [PMID: 17488874 PMCID: PMC1894929 DOI: 10.1261/rna.510807] [Citation(s) in RCA: 44] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/15/2023]
Abstract
The potential for water to participate in RNA catalyzed reactions has been the topic of several recent studies. Here, we report crystals of a minimal, hinged hairpin ribozyme in complex with the transition-state analog vanadate at 2.05 A resolution. Waters are present in the active site and are discussed in light of existing views of catalytic strategies employed by the hairpin ribozyme. A second structure harboring a 2',5'-phosphodiester linkage at the site of cleavage was also solved at 2.35 A resolution and corroborates the assignment of active site waters in the structure containing vanadate. A comparison of the two structures reveals that the 2',5' structure adopts a conformation that resembles the reaction intermediate in terms of (1) the positioning of its nonbridging oxygens and (2) the covalent attachment of the 2'-O nucleophile with the scissile G+1 phosphorus. The 2',5'-linked structure was then overlaid with scissile bonds of other small ribozymes including the glmS metabolite-sensing riboswitch and the hammerhead ribozyme, and suggests the potential of the 2',5' linkage to elicit a reaction-intermediate conformation without the need to form metalloenzyme complexes. The hairpin ribozyme structures presented here also suggest how water molecules bound at each of the nonbridging oxygens of G+1 may electrostatically stabilize the transition state in a manner that supplements nucleobase functional groups. Such coordination has not been reported for small ribozymes, but is consistent with the structures of protein enzymes. Overall, this work establishes significant parallels between the RNA and protein enzyme worlds.
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Affiliation(s)
- Andrew T Torelli
- Department of Biochemistry and Biophysics, Rochester, NY 14642, USA
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33
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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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34
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Swiatek J. REVIEW: INTERACTIONS OF METAL IONS WITH NUCLEIC ACIDS AND THEIR SUBUNITS. AN ELECTROCHEMICAL APPROACH. J COORD CHEM 2006. [DOI: 10.1080/00958979408024278] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
Affiliation(s)
- Jolanta Swiatek
- a Department of Basic Medical Sciences , Medical Academy of Wroclaw , Kochanowskiego, 14, 51-601, Wroclaw , Poland
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35
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Bichenkova EV, Sadat-Ebrahimi SE, Wilton AN, O'Toole N, Marks DS, Douglas KT. Strong, Specific, Reversible Binding Ligands for Transfer Rna: Comparison By Fluorescence and Nmr Spectroscopies with Distamycin Binding for a New Structural Class of Ligand. ACTA ACUST UNITED AC 2006. [DOI: 10.1080/07328319808004698] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
Affiliation(s)
- Elena V. Bichenkova
- a School of Pharmacy and Pharmaceutical Sciences, University of Manchester Manchester , M13 9PL , U.K
| | - Seyed E. Sadat-Ebrahimi
- a School of Pharmacy and Pharmaceutical Sciences, University of Manchester Manchester , M13 9PL , U.K
| | - Amanda N. Wilton
- a School of Pharmacy and Pharmaceutical Sciences, University of Manchester Manchester , M13 9PL , U.K
| | - Niamh O'Toole
- a School of Pharmacy and Pharmaceutical Sciences, University of Manchester Manchester , M13 9PL , U.K
| | - Debora S. Marks
- a School of Pharmacy and Pharmaceutical Sciences, University of Manchester Manchester , M13 9PL , U.K
| | - Kenneth T. Douglas
- a School of Pharmacy and Pharmaceutical Sciences, University of Manchester Manchester , M13 9PL , U.K
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36
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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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Affiliation(s)
- Roland K. O. Sigel
- Institute of Inorganic Chemistry, University of Zürich, Winterthurerstrasse 190, 8057 Zürich, Switzerland, Fax: +41‐44‐635‐6802
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Darnell JC, Fraser CE, Mostovetsky O, Stefani G, Jones TA, Eddy SR, Darnell RB. Kissing complex RNAs mediate interaction between the Fragile-X mental retardation protein KH2 domain and brain polyribosomes. Genes Dev 2005; 19:903-18. [PMID: 15805463 PMCID: PMC1080130 DOI: 10.1101/gad.1276805] [Citation(s) in RCA: 221] [Impact Index Per Article: 11.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
Fragile-X mental retardation is caused by loss of function of a single gene encoding the Fragile-X mental retardation protein, FMRP, an RNA-binding protein that harbors two KH-type and one RGG-type RNA-binding domains. Previous studies identified intramolecular G-quartet RNAs as high-affinity targets for the RGG box, but the relationship of RNA binding to FMRP function and mental retardation remains unclear. One severely affected patient harbors a missense mutation (I304N) within the second KH domain (KH2), and some evidence suggests this domain may be involved in the proposed role of FMRP in translational regulation. We now identify the RNA target for the KH2 domain as a sequence-specific element within a complex tertiary structure termed the FMRP kissing complex. We demonstrate that the association of FMRP with brain polyribosomes is abrogated by competition with the FMRP kissing complex RNA, but not by high-affinity G-quartet RNAs. We conclude that mental retardation associated with the I304N mutation, and likely the Fragile-X syndrome more generally, may relate to a crucial role for RNAs harboring the kissing complex motif as targets for FMRP translational regulation.
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Affiliation(s)
- Jennifer C Darnell
- Howard Hughes Medical Institute and Laboratory of Molecular Neuro-Oncology, The Rockefeller University, New York, New York, USA.
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39
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Puskar L, Barran PE, Duncombe BJ, Chapman D, Stace AJ. Gas-Phase Study of the Chemistry and Coordination of Lead(II) in the Presence of Oxygen-, Nitrogen-, Sulfur-, and Phosphorus-Donating Ligands. J Phys Chem A 2004; 109:273-82. [PMID: 16839117 DOI: 10.1021/jp047637f] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Using a pickup technique in association with high-energy electron impact ionization, complexes have been formed in the gas phase between Pb(2+) and a wide range of ligands. The coordinating atoms are oxygen, nitrogen, sulfur, and phosphorus, together with complexes consisting of benzene and argon in association with Pb(2+). Certain ligands are unable to stabilze the metal dication, the most obvious group being water and the lower alcohols, but CS(2) is also unable to form [Pb(CS(2))(N)](2+) complexes. Unlike many other metal dication complexes, those associated with lead appear to exhibit very little chemical reactivity following collisional activation. Such reactions are normally promoted via charge transfer and are initiated using the energy difference between M(2+) + e(-) --> M(+) and L --> L(+) + e(-), which is typically approximately 5 eV. In the case of Pb(2+), this energy difference usually leads to the appearance of L(+) and the loss of a significant fraction of the remaining ligands as neutral species. In many instances, Pb(+) appears as a charge-transfer product. The only group of ligands to consistently exhibit chemical reactivity are those containing sulfur, where a typical product might be PbS(+)(L)(M) or PbSCH(3)(+)(L)(M).
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Affiliation(s)
- Ljiljana Puskar
- Department of Chemistry, University of Sussex, Falmer, Brighton BN1 9QJ, United Kingdom
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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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41
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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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Abstract
Understanding of lead toxicity has advanced substantially over the past three decades, and focus has shifted from high-dose effects in clinically symptomatic individuals to the consequences of exposure at lower doses that cause no symptoms, particularly in children and fetuses. The availability of more sensitive analytic methods has made it possible to measure lead at much lower concentrations. This advance, along with more refined epidemiological techniques and better outcome measures, has lowered the least observable effect level until it approaches zero. As a consequence, the segment of the population who are diagnosed with exposure to toxic levels has expanded. At the same time, environmental efforts, most importantly the removal of lead from gasoline, have dramatically reduced the amount of lead in the biosphere. The remaining major source of lead is older housing stock. Although the cost of lead paint abatement is measured in billions of dollars, the monetized benefits of such a Herculean task have been shown to far outweigh the costs.
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MESH Headings
- Adolescent
- Adult
- Aged
- Child
- Humans
- Infant
- Infant, Newborn
- Lead Poisoning, Nervous System, Adult/complications
- Lead Poisoning, Nervous System, Adult/diagnosis
- Lead Poisoning, Nervous System, Adult/therapy
- Lead Poisoning, Nervous System, Childhood/complications
- Lead Poisoning, Nervous System, Childhood/diagnosis
- Lead Poisoning, Nervous System, Childhood/therapy
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Affiliation(s)
- Herbert Needleman
- University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania 15213, USA.
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Ennifar E, Walter P, Dumas P. A crystallographic study of the binding of 13 metal ions to two related RNA duplexes. Nucleic Acids Res 2003; 31:2671-82. [PMID: 12736317 PMCID: PMC156032 DOI: 10.1093/nar/gkg350] [Citation(s) in RCA: 122] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023] Open
Abstract
Metal ions, and magnesium in particular, are known to be involved in RNA folding by stabilizing secondary and tertiary structures, and, as cofactors, in RNA enzymatic activity. We have conducted a systematic crystallographic analysis of cation binding to the duplex form of the HIV-1 RNA dimerization initiation site for the subtype-A and -B natural sequences. Eleven ions (K+, Pb2+, Mn2+, Ba2+, Ca2+, Cd2+, Sr2+, Zn2+, Co2+, Au3+ and Pt4+) and two hexammines [Co (NH3)6]3+ and [Ru (NH3)6]3+ were found to bind to the DIS duplex structure. Although the two sequences are very similar, strong differences were found in their cation binding properties. Divalent cations bind almost exclusively, as Mg2+, at 'Hoogsteen' sites of guanine residues, with a cation-dependent affinity for each site. Notably, a given cation can have very different affinities for a priori equivalent sites within the same molecule. Surprisingly, none of the two hexammines used were able to efficiently replace hexahydrated magnesium. Instead, [Co (NH3)4]3+ was seen bound by inner-sphere coordination to the RNA. This raises some questions about the practical use of [Co (NH3)6]3+ as a [Mg (H2O)6]2+ mimetic. Also very unexpected was the binding of the small Au3+ cation exactly between the Watson-Crick sites of a G-C base pair after an obligatory deprotonation of N1 of the guanine base. This extensive study of metal ion binding using X-ray crystallography significantly enriches our knowledge on the binding of middleweight or heavy metal ions to RNA, particularly compared with magnesium.
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Affiliation(s)
- Eric Ennifar
- Institut de Biologie Moléculaire et Cellulaire, CNRS-UPR 9002, 15 rue René Descartes, 67084 Strasbourg cedex, France
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Abstract
The historical existence of the RNA world, in which early life used RNA for both genetic information and catalytic ability, is widely accepted. However, there has been little discussion of whether protein synthesis arose before DNA or what preceded the RNA world (i.e. the pre-RNA world). We outline arguments of what route life may have taken out of the RNA world: whether DNA or protein followed. Metabolic arguments favor the possibility that RNA genomes preceded the use of DNA as the informational macromolecule. However, the opposite can also be argued based on the enhanced stability, reactivity, and solubility of 2-deoxyribose as compared to ribose. The possibility that DNA may have come before RNA is discussed, although it is a less parsimonious explanation than DNA following RNA.
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Affiliation(s)
- Jason P Dworkin
- Laboratory for Extraterrestrial Physics, Code 691, NASA Goddard Space Flight Center, Greenbelt, MD 20771, USA.
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45
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Knobloch B, Da Costa CP, Linert W, Sigel H. Stability constants of metal ion complexes formed with N3-deprotonated uridine in aqueous solution. INORG CHEM COMMUN 2003. [DOI: 10.1016/s1387-7003(02)00686-x] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
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46
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Abstract
The hepatitis delta virus (HDV) ribozymes are self-cleaving RNA sequences critical to the replication of a small RNA genome. A recently determined crystal structure together with biochemical and biophysical studies provides new insight into the possible catalytic mechanism of these ribozymes. The HDV ribozymes are examples of naturally occurring small ribozymes that catalyze cleavage of the RNA backbone with a rate enhancement of 10(6)- to 10(7)-fold over the uncatalyzed rate. To achieve this level of rate enhancement, the HDV ribozymes have been proposed to employ several catalytic strategies that include the use of metal ions, intrinsic binding energy, and a novel example of general acid-base catalysis with a cytosine side chain acting as a proton donor or acceptor.
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Affiliation(s)
- I-hung Shih
- Department of Biochemistry, Duke University Medical Center, Durham, North Carolina 27710, USA.
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Mielcarek M, Barciszewska MZ, Sałanski P, Stobiecki M, Jurczak J, Barciszewski J. Native transfer RNA catalyzes Diels-Alder reaction. Biochem Biophys Res Commun 2002; 294:145-8. [PMID: 12054754 DOI: 10.1016/s0006-291x(02)00452-7] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Abstract
In this paper we show that transfer ribonucleic acids (tRNAs) catalyze the Diels-Alder cycloaddition reaction. A new DNA oxidative damage product, 6-furfuryladenine (kinetin) or its riboside (diene), was transformed with dimethyl acetylenedicarboxylate or maleic anhydride (dienophile). The reaction proceeds in the presence of tRNA at high pressure but not at ambient condition. If so tRNA in prebiotic conditions (RNA world) had at least two functions: catalytic and a carrier of genetic information. It means that tRNA at high pressure shows catalytic properties and is a true Diels-Alderase.
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Affiliation(s)
- Michal Mielcarek
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12, 61704 Poznan, Poland
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48
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Acharya P, Chattopadhyaya J. The hydrogen bonding and hydration of 2'-OH in adenosine and adenosine 3'-ethyl phosphate. J Org Chem 2002; 67:1852-65. [PMID: 11895403 DOI: 10.1021/jo010960j] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The 2'-OH group has major structural implications in the recognition, processing, and catalytic properties of RNA. We report here intra- and intermolecular H-bonding of 2'-OH in adenosine 3'-ethyl phosphate (1), 3'-deoxyadenosine (2), and adenosine (3) by both temperature- and concentration-dependent NMR studies, as well as by detailed endo ((3)J(H,H)) and exocyclic ((3)J(H,OH)) coupling constant analyses. We have also examined the nature of hydration and exchange processes of 2'-OH with water by a combination of NOESY and ROESY experiments in DMSO-d(6) containing 2 mol % HOD. The NMR-constrained molecular modeling (by molecular mechanics as well as by ab initio methods both in the gas and solution phase) has been used to characterize the energy minima among the four alternative dihedrals possible from the solution of the Karplus equation for (3)J(H2',OH) and (3)J(H3',OH) to delineate the preferred orientation of 2'-O-H proton in 1 and 2 as well as for 2'/3'-O-H protons in 3. The NMR line shape analysis of 2'-OH gave the DeltaG(H-bond)(298K) of 7.5 kJ mol(-1) for 1 and 8.4 kJ mol(-1) for 3; similar analyses of the methylene protons of 3'-ethyl phosphate moiety in 1 also gave comparable DeltaG(H-bond)(298K) of 7.3 kJ mol(-1). The donor nature of the 2'-OH in the intramolecular H-bonding in 3 is evident from its relatively reduced flexibility [-TDeltaS++](2'-OH) = -17.9(+/-0.5) kJ mol(-1)] because of the loss of conformational freedom owing to the intramolecular 2'O-H...O3' H-bonding, compared to the acceptor 3'-OH in 3 [-TDeltaS++](3'-OH) = -19.8 (+/- 0.6) kJ mol(-1)] at 298 K. The presence of intramolecular 2'-OH...O3' H-bonding in 3 is also corroborated by the existence of weak long-range (4)J(H2',OH3') in 3 (i.e., W conformation of H2'-C2'-C3'-O3'-H) as well as by (3)J(H,OH) dependent orientation of the 2'- and 3'-OH groups. The ROESY spectra for 1 and 3 at 308 K, in DMSO-d(6), show a clear positive ROE contact of both 2'- and 3'-OH with water. The presence of a hydrophilic 3'-phosphate group in 1 causes a much higher water activity in the vicinity of its 2'-OH, which in turn causes the 2'-OH to exchange faster, culminating in a shorter exchange lifetime (tau) for 2'-OH proton with HOD in 1 (tau2'-OH: 489 ms) compared to that in 3 (tau2'-OH: 6897 ms). The activation energy (E(a)) of the exchange with the bound-water for 2'- and 3'-OH in 3 (48.3 and 45.0 kJ mol(-1), respectively) is higher compared to that of 2'-OH in 1 (31.9 kJ mol(-1)), thereby showing that the kinetic availability of hydrated 2'-OH in 1 for any inter- and intramolecular interactions, in general, is owing to the vicinal 3'-phosphate residue. It also suggests that 2'-OH in native RNA can mediate other inter- or intramolecular interactions only in competition with the bound-water, depending upon the specific chemical nature and spatial orientation of other functions with potential for hydrogen bonding in the neighborhood. This availability of the bound water around 2'-OH in RNA would, however, be dictated by whether the vicinal phosphate is exposed to the bulk water or not. This implies that relatively poor hydration around a specific 2'-OH across a polyribonucleotide chain, owing to some hydrophobic microenvironmental pocket around that hydroxyl, may make it more accessible to interact with other donor or acceptor functions for H-bonding interactions, which might then cause the RNA to fold in a specific manner generating a new motif leading to specific recognition and function. Alternatively, a differential hydration of a specific 2'-OH may modulate its nucleophilicity to undergo stereospecific transesterification reaction as encountered in ubiquitous splicing of pre-mRNA to processed RNA or RNA catalysis, in general.
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Affiliation(s)
- Parag Acharya
- Department of Bioorganic Chemistry, Box 581, Biomedical Centre, University of Uppsala, S-751 23 Uppsala, Sweden
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49
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Wrzesinski J, Legiewicz M, Smólska B, Ciesiolka J. Catalytic cleavage of cis- and trans-acting antigenomic delta ribozymes in the presence of various divalent metal ions. Nucleic Acids Res 2001; 29:4482-92. [PMID: 11691936 PMCID: PMC60188 DOI: 10.1093/nar/29.21.4482] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Catalytic activity of four structural variants of the antigenomic delta ribozyme, two cis- and two trans-acting, has been compared in the presence of selected divalent metal ions that effectively support catalysis. The ribozymes differ in regions that are not directly involved in formation of the ribozyme active site: the region immediately preceding the catalytic cleavage site, the P4 stem and a stretch of the viral RNA sequence extending the minimal ribozyme sequence at its 3'-terminus. The variants show high cleavage activity in the presence of Mg(2+), Ca(2+) and Mn(2+), lower with Co(2+) and Sr(2+) and some variants are also active with Cd(2+) and Zn(2+) ions. In the presence of a particular metal ion the ribozymes cleave, however with different initial rates, according to pseudo-first or higher order kinetics and to different final cleavage extents. On the other hand, relatively small differences are observed in the reactions induced by various metal ions. The cleavage of trans-acting ribozymes induced by Mg(2+) is partially inhibited in the presence of Na(+), spermidine and some other divalent metal ions. The inert Co(NH(3))(6)(3+) complex is unable to support catalysis, as reported earlier for the genomic ribozyme. The results are discussed in terms of the influence of structural elements peripheral to the ribozyme active site on its cleavage rate and efficiency as well as the role of metal ions in the cleavage mechanism. Some implications concerning further studies and possible applications of delta ribozymes are also considered.
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Affiliation(s)
- J Wrzesinski
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12/14, 61-704 Poznan, Poland
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50
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Bouton CM, Hossain MA, Frelin LP, Laterra J, Pevsner J. Microarray analysis of differential gene expression in lead-exposed astrocytes. Toxicol Appl Pharmacol 2001; 176:34-53. [PMID: 11578147 DOI: 10.1006/taap.2001.9274] [Citation(s) in RCA: 41] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
The toxic metal lead is a widespread environmental health hazard that can adversely affect human health. In an effort to better understand the cellular and molecular consequences of lead exposure, we have employed cDNA microarrays to analyze the effects of acute lead exposure on large-scale gene expression patterns in immortalized rat astrocytes. Our studies identified many genes previously reported to be differentially regulated by lead exposure. Additionally, we have identified novel putative targets of lead-mediated toxicity, including members of the family of calcium/phospholipid binding annexins, the angiogenesis-inducing thrombospondins, collagens, and tRNA synthetases. We demonstrate the ability to distinguish lead-exposed samples from control or sodium samples solely on the basis of large-scale gene expression patterns using two complementary clustering methods. We have confirmed the altered expression of candidate genes and their encoded proteins by RT-PCR and Western blotting, respectively. Finally, we show that the calcium-dependent phospholipid binding protein annexin A5, initially identified as a differentially regulated gene by our microarray analysis, is directly bound and activated by nanomolar concentrations of lead. We conclude that microarray technology is an effective tool for the identification of lead-induced patterns of gene expression and molecular targets of lead.
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Affiliation(s)
- C M Bouton
- Department of Neuroscience, Johns Hopkins University, Baltimore, Maryland 21205, USA
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