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Eichler C, Himmelstoß M, Plangger R, Weber LI, Hartl M, Kreutz C, Micura R. Advances in RNA Labeling with Trifluoromethyl Groups. Chemistry 2023; 29:e202302220. [PMID: 37534701 PMCID: PMC10947337 DOI: 10.1002/chem.202302220] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2023] [Revised: 07/31/2023] [Accepted: 08/03/2023] [Indexed: 08/04/2023]
Abstract
Fluorine labeling of ribonucleic acids (RNA) in conjunction with 19 F NMR spectroscopy has emerged as a powerful strategy for spectroscopic analysis of RNA structure and dynamics, and RNA-ligand interactions. This study presents the first syntheses of 2'-OCF3 guanosine and uridine phosphoramidites, their incorporation into oligoribonucleotides by solid-phase synthesis and a comprehensive study of their properties. NMR spectroscopic analysis showed that the 2'-OCF3 modification is associated with preferential C2'-endo conformation of the U and G ribose in single-stranded RNA. When paired to the complementary strand, slight destabilization of the duplex caused by the modification was revealed by UV melting curve analysis. Moreover, the power of the 2'-OCF3 label for NMR spectroscopy is demonstrated by dissecting RNA pseudoknot folding and its binding to a small molecule. Furthermore, the 2'-OCF3 modification has potential for applications in therapeutic oligonucleotides. To this end, three 2'-OCF3 modified siRNAs were tested in silencing of the BASP1 gene which indicated enhanced performance for one of them. Importantly, together with earlier work, the present study completes the set of 2'-OCF3 nucleoside phosphoramidites to all four standard nucleobases (A, U, C, G) and hence enables applications that utilize the favorable properties of the 2'-OCF3 group without any restrictions in placing the modification into the RNA target sequence.
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Affiliation(s)
- Clemens Eichler
- Institute of Organic ChemistryCenter for Molecular Biosciences Innsbruck (CMBI)University of InnsbruckInnrain 80–826020InnsbruckAustria
| | - Maximilian Himmelstoß
- Institute of Organic ChemistryCenter for Molecular Biosciences Innsbruck (CMBI)University of InnsbruckInnrain 80–826020InnsbruckAustria
| | - Raphael Plangger
- Institute of Organic ChemistryCenter for Molecular Biosciences Innsbruck (CMBI)University of InnsbruckInnrain 80–826020InnsbruckAustria
| | - Leonie I. Weber
- Institute of BiochemistryCenter for Molecular Biosciences Innsbruck (CMBI)University of InnsbruckInnrain 80–826020InnsbruckAustria
| | - Markus Hartl
- Institute of BiochemistryCenter for Molecular Biosciences Innsbruck (CMBI)University of InnsbruckInnrain 80–826020InnsbruckAustria
| | - Christoph Kreutz
- Institute of Organic ChemistryCenter for Molecular Biosciences Innsbruck (CMBI)University of InnsbruckInnrain 80–826020InnsbruckAustria
| | - Ronald Micura
- Institute of Organic ChemistryCenter for Molecular Biosciences Innsbruck (CMBI)University of InnsbruckInnrain 80–826020InnsbruckAustria
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2
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Residues within the Foot-and-Mouth Disease Virus 3D pol Nuclear Localization Signal Affect Polymerase Fidelity. J Virol 2020; 94:JVI.00833-20. [PMID: 32581111 DOI: 10.1128/jvi.00833-20] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2020] [Accepted: 06/11/2020] [Indexed: 11/20/2022] Open
Abstract
Many RNA viruses encode a proof-reading deficient, low-fidelity RNA-dependent polymerase (RdRp), which generates genetically diverse populations that can adapt to changing environments and thwart antiviral therapies. 3Dpol, the RdRp of the foot-and-mouth disease virus (FMDV), is responsible for replication of viral genomes. The 3Dpol N terminus encodes a nuclear localization signal (NLS) sequence,MRKTKLAPT, important for import of the protein to host nucleus. Previous studies showed that substitutions at residues 18 and 20 of the NLS are defective in proper incorporation of nucleotides and RNA binding. Here, we use a systematic alanine scanning mutagenesis approach to understand the role of individual residues of the NLS in nuclear localization and nucleotide incorporation activities of 3Dpol We identify two residues of 3Dpol NLS, T19 and L21, that are important for the maintenance of enzyme fidelity. The 3Dpol NLS alanine substitutions of T19 and L21 results in aberrant incorporation of nucleoside analogs, conferring a low fidelity phenotype of the enzyme. A molecular dynamics simulation of RNA- and mutagen (RTP)-bound 3Dpol revealed that the T19 residue participates in a hydrogen bond network, including D165 in motif F and R416 at the C terminus of the FMDV 3Dpol and RNA template-primer. Based on these findings and previous studies, we conclude that at least the first six residues of theMRKTKLAPT sequence motif play a vital role in the maintenance of faithful RNA synthesis activity (fidelity) of FMDV 3Dpol, suggesting that the role of the NLS motif in similar viral polymerases needs to be revisited.IMPORTANCE In this study, we employed genetic and molecular dynamics approaches to analyze the role of individual amino acids of the FMDV 3Dpol nuclear localization signal (NLS). The NLS residues were mutated to alanine using a type A full-genome cDNA clone, and the virus progeny was analyzed for defects in growth and in competition with the parental virus. We identified two mutants in 3Dpol, T19A and L21A, that exhibited high rate of mutation, were sensitive to nucleotide analogs, and displayed reduced replicative fitness compared to the parental virus. Using molecular dynamics simulation, we demonstrated that residues T19 and L21 played a role in the structural configuration of the interaction network at the 3Dpol palm subdomain. Cumulatively, our data suggest that the T19 and L21 3Dpol amino acids are important for maintaining the fidelity of the FMDV polymerase and ensuring faithful replication of the FMDV genome.
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3
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Alswaidan IA, Sooknah K, Rhyman L, Parlak C, Ndinteh DT, Elzagheid MI, Ramasami P. 2,4-Ditellurouracil and its 5-fluoro derivative: Theoretical investigations of structural, energetics and ADME parameters. Comput Biol Chem 2017; 68:56-63. [PMID: 28236747 DOI: 10.1016/j.compbiolchem.2017.02.002] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2016] [Revised: 12/17/2016] [Accepted: 02/02/2017] [Indexed: 11/29/2022]
Abstract
2,4-Ditellurouracil exhibits keto-enol tautomerism via different pathways resulting in seven tautomers. These pathways were studied in the gas phase using density functional theory method. The functionals used were BLYP, B3LYP and BHLYP and the basis sets were 6-311++G(d,p) for all atoms except that LanL2DZ ECP was used for tellurium atom only. The results indicate that the diketo form is more stable as observed for uracil and its sulfur and selenium analogues. The effect of introducing fluorine at position 5 was also investigated and the energy difference between the diketo and dienol forms is reduced. 2,4-Ditellurouracil and its 5-fluoro analogue are expected to exist exclusively as the diketo form due to the high interconversion energy barrier. We extended the investigation to predict ADME parameters of the most stable diketo and dienol tautomers in view of understanding their biological properties. This research enlightens keto-enol tautomerism of 2,4-ditellurouracil and its 5-fluoro derivative with additional insights to biological functions.
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Affiliation(s)
- Ibrahim A Alswaidan
- Department of Pharmaceutical Chemistry, College of Pharmacy, King Saud University, Riyadh 11451, Saudi Arabia
| | - Kritish Sooknah
- Computational Chemistry Group, Department of Chemistry, Faculty of Science, University of Mauritius, Réduit 80837, Mauritius
| | - Lydia Rhyman
- Department of Applied Chemistry, University of Johannesburg, Doornfontein Campus, Johannesburg 2028, South Africa; Department of Chemistry, University of Johannesburg, PO Box 524, Auckland Park, Johannesburg, 2006, South Africa
| | - Cemal Parlak
- Department of Physics, Science Faculty, Ege University, Bornova, Izmir, 35100, Turkey
| | - Derek T Ndinteh
- Department of Applied Chemistry, University of Johannesburg, Doornfontein Campus, Johannesburg 2028, South Africa
| | - Mohamed I Elzagheid
- Department of Chemical and Process Engineering, Jubail Industrial College, Jubail Industrial City 31961, Saudi Arabia
| | - Ponnadurai Ramasami
- Computational Chemistry Group, Department of Chemistry, Faculty of Science, University of Mauritius, Réduit 80837, Mauritius; Department of Applied Chemistry, University of Johannesburg, Doornfontein Campus, Johannesburg 2028, South Africa; Department of Chemistry, University of Johannesburg, PO Box 524, Auckland Park, Johannesburg, 2006, South Africa.
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4
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Palafox MA, Rastogi V. 6-Aminouracil: Geometries and spectra in the isolated state and in the solid state simulation. A comparison with 5-aminouracil. J Mol Struct 2016. [DOI: 10.1016/j.molstruc.2015.12.004] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
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5
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A DFT analysis of the molecular structure, vibrational spectra and other molecular properties of 5-nitrouracil and comparison with uracil. J Mol Struct 2016. [DOI: 10.1016/j.molstruc.2015.10.096] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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6
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Zhao C, Bachu R, Popović M, Devany M, Brenowitz M, Schlatterer JC, Greenbaum NL. Conformational heterogeneity of the protein-free human spliceosomal U2-U6 snRNA complex. RNA (NEW YORK, N.Y.) 2013; 19:561-73. [PMID: 23426875 PMCID: PMC3677266 DOI: 10.1261/rna.038265.113] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/11/2013] [Accepted: 01/16/2013] [Indexed: 05/24/2023]
Abstract
The complex formed between the U2 and U6 small nuclear (sn)RNA molecules of the eukaryotic spliceosome plays a critical role in the catalysis of precursor mRNA splicing. Here, we have used enzymatic structure probing, (19)F NMR, and analytical ultracentrifugation techniques to characterize the fold of a protein-free biophysically tractable paired construct representing the human U2-U6 snRNA complex. Results from enzymatic probing and (19)F NMR for the complex in the absence of Mg(2+) are consistent with formation of a four-helix junction structure as a predominant conformation. However, (19)F NMR data also identify a lesser fraction (up to 14% at 25°C) of a three-helix conformation. Based upon this distribution, the calculated ΔG for inter-conversion to the four-helix structure from the three-helix structure is approximately -4.6 kJ/mol. In the presence of 5 mM Mg(2+), the fraction of the three-helix conformation increased to ∼17% and the Stokes radius, measured by analytical ultracentrifugation, decreased by 2%, suggesting a slight shift to an alternative conformation. NMR measurements demonstrated that addition of an intron fragment to the U2-U6 snRNA complex results in displacement of U6 snRNA from the region of Helix III immediately 5' of the ACAGAGA sequence of U6 snRNA, which may facilitate binding of the segment of the intron adjacent to the 5' splice site to the ACAGAGA sequence. Taken together, these observations indicate conformational heterogeneity in the protein-free human U2-U6 snRNA complex consistent with a model in which the RNA has sufficient conformational flexibility to facilitate inter-conversion between steps of splicing in situ.
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Affiliation(s)
- Caijie Zhao
- Department of Chemistry and Biochemistry, Hunter College of the City University of New York, New York, New York 10065, USA
- The Graduate Center, City University of New York, New York, New York 10016, USA
| | - Ravichandra Bachu
- Department of Chemistry and Biochemistry, Hunter College of the City University of New York, New York, New York 10065, USA
- The Graduate Center, City University of New York, New York, New York 10016, USA
| | - Milena Popović
- Department of Chemistry and Biochemistry, Hunter College of the City University of New York, New York, New York 10065, USA
- Department of Chemistry and Biochemistry, Florida State University, Tallahassee, Florida 32306, USA
| | - Matthew Devany
- Department of Chemistry and Biochemistry, Hunter College of the City University of New York, New York, New York 10065, USA
| | - Michael Brenowitz
- Department of Biochemistry, Albert Einstein College of Medicine, Bronx, New York 10461, USA
| | - Jörg C. Schlatterer
- Department of Biochemistry, Albert Einstein College of Medicine, Bronx, New York 10461, USA
| | - Nancy L. Greenbaum
- Department of Chemistry and Biochemistry, Hunter College of the City University of New York, New York, New York 10065, USA
- The Graduate Center, City University of New York, New York, New York 10016, USA
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7
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Nucleic Acid Based Fluorinated Derivatives: New Tools for Biomedical Applications. APPLIED SCIENCES-BASEL 2012. [DOI: 10.3390/app2020245] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
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8
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Rastogi V, Alcolea Palafox M, Guerrero-Martínez A, Tardajos G, Vats J, Kostova I, Schlucker S, Kiefer W. FT-IR and FT-Raman spectra, ab initio and density functional computations of the vibrational spectra, molecular geometry, atomic charges and some molecular properties of the biomolecule 5-iodouracil. ACTA ACUST UNITED AC 2010. [DOI: 10.1016/j.theochem.2009.10.003] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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9
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Reif B, Wittmann V, Schwalbe H, Griesinger C, Wörner K, Jahn-Hofmann K, Engels JW, Bermel W. Structural Comparison of Oligoribonucleotides and Their 2′-Deoxy-2′-fluoro Analogs by heteronuclear NMR spectroscopy. Helv Chim Acta 2004. [DOI: 10.1002/hlca.19970800614] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
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10
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Pariente N, Airaksinen A, Domingo E. Mutagenesis versus inhibition in the efficiency of extinction of foot-and-mouth disease virus. J Virol 2003; 77:7131-8. [PMID: 12768034 PMCID: PMC156209 DOI: 10.1128/jvi.77.12.7131-7138.2003] [Citation(s) in RCA: 88] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
RNA viruses replicate near the error threshold for maintenance of genetic information, and an increase in mutation frequency during replication may drive RNA viruses to extinction in a process termed lethal mutagenesis. This report addresses the efficiency of extinction (versus escape from extinction) of foot-and-mouth disease virus (FMDV) by combinations of the mutagenic base analog 5-fluorouracil (FU) and the antiviral inhibitors guanidine hydrochloride (G) and heparin (H). Selection of G- or H-resistant, extinction-escape mutants occurred with low-fitness virus only in the absence of FU and with high-fitness virus with some mutagen-inhibitor combinations tested. The combination of FU, G, and H prevented selection of extinction-escape mutants in all cases examined, and extinction of high-fitness FMDV could not be achieved by equivalent inhibitory activity exerted by the nonmutagenic agents. The G-resistant phenotype was mapped in nonstructural protein 2C by introducing the relevant mutations in infectious cDNA clones. Decreases in FMDV infectivity were accompanied by modest decreases in the intracellular and extracellular levels of FMDV RNA, maximal intracellular concentrations of FU triphosphate, and a decrease in the intracellular concentrations of UTP. In addition to indicating a key participation of mutagenesis in virus extinction, the results suggest that picornaviruses provide versatile experimental systems to approach the problem of extinction failure associated with inhibitor-escape mutants during treatments based on enhanced mutagenesis.
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Affiliation(s)
- Nonia Pariente
- Centro de Biología Molecular Severo Ochoa, Universidad Autónoma de Madrid, Cantoblanco, 28049 Madrid, Spain
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11
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Fukai S, Nureki O, Sekine SI, Shimada A, Vassylyev DG, Yokoyama S. Mechanism of molecular interactions for tRNA(Val) recognition by valyl-tRNA synthetase. RNA (NEW YORK, N.Y.) 2003; 9:100-111. [PMID: 12554880 PMCID: PMC1370374 DOI: 10.1261/rna.2760703] [Citation(s) in RCA: 51] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/04/2002] [Accepted: 09/23/2002] [Indexed: 05/24/2023]
Abstract
The molecular interactions between valyl-tRNA synthetase (ValRS) and tRNA(Val), with the C34-A35-C36 anticodon, from Thermus thermophilus were studied by crystallographic analysis and structure-based mutagenesis. In the ValRS-bound structure of tRNA(Val), the successive A35-C36 residues (the major identity elements) of tRNA(Val) are base-stacked upon each other, and fit into a pocket on the alpha-helix bundle domain of ValRS. Hydrogen bonds are formed between ValRS and A35-C36 of tRNA(Val) in a base-specific manner. The C-terminal coiled-coil domain of ValRS interacts electrostatically with A20 and hydrophobically with the G19*C56 tertiary base pair. The loss of these interactions by the deletion of the coiled-coil domain of ValRS increased the K(M) value for tRNA(Val) 28-fold and decreased the k(cat) value 19-fold in the aminoacylation. The tRNA(Val) K(M) and k(cat) values were increased 21-fold and decreased 32-fold, respectively, by the disruption of the G18*U55 and G19*C56 tertiary base pairs, which associate the D- and T-loops for the formation of the L-shaped tRNA structure. Therefore, the coiled-coil domain of ValRS is likely to stabilize the L-shaped tRNA structure during the aminoacylation reaction.
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Affiliation(s)
- Shuya Fukai
- Department of Biophysics and Biochemistry, Graduate School of Science, The University of Tokyo, Bunkyo-ku, Japan
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12
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Hammann C, Norman DG, Lilley DM. Dissection of the ion-induced folding of the hammerhead ribozyme using 19F NMR. Proc Natl Acad Sci U S A 2001; 98:5503-8. [PMID: 11331743 PMCID: PMC33242 DOI: 10.1073/pnas.091097498] [Citation(s) in RCA: 67] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
We have used (19)F NMR to analyze the metal ion-induced folding of the hammerhead ribozyme by selective incorporation of 5fluorouridine. We have studied the chemical shift and linewidths of (19)F resonances of 5-fluorouridine at the 4 and 7 positions in the ribozyme core as a function of added Mg(2+). The data fit well to a simple two-state model whereby the formation of domain 1 is induced by the noncooperative binding of Mg(2+) with an association constant in the range of 100 to 500 M(-1), depending on the concentration of monovalent ions present. The results are in excellent agreement with data reporting on changes in the global shape of the ribozyme. However, the NMR experiments exploit reporters located in the center of the RNA sections undergoing the folding transitions, thereby allowing the assignment of specific nucleotides to the separate stages. The results define the folding pathway at high resolution and provide a time scale for the first transition in the millisecond range.
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Affiliation(s)
- C Hammann
- Cancer Research Campaign Nucleic Acid Structure Research Group, Department of Biochemistry, University of Dundee, Dundee DD1 4HN, United Kingdom
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14
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Naumov P, Anastasova F. Experimental and theoretical vibrational study of isatin, its 5-(NO2, F, Cl, Br, I, CH3) analogues and the isatinato anion. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2001; 57:469-481. [PMID: 11300558 DOI: 10.1016/s1386-1425(00)00393-0] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/23/2023]
Abstract
Effects of 5-R substitution (R = NO2, F, Cl, Br, I, CH3) and N-deprotonation on the 4000-400 cm(-1) region of the low temperature FT IR spectrum and the molecular structure of solid isatin are investigated. Harmonic IR spectra and molecular geometries of the 5-R isatins (except for Br and I analogues) are calculated at the HF/6-31G(d, p) level and compared with the experimental solid-state data. In general, substitution has small effect on the molecular structure and the IR spectrum of isatin. The v(CO) triplet in the IR spectra of isatin and its 5-substituted analogues is resulted by vibrational splitting of the out-of-phase CO stretching, v(op)[(CO)2]. While the frequency of the v(op)[(CO)2] mode is relatively less affected by 5-substitution and mainly depends on the substituent mass, the frequency of the in-phase stretching, v(ip)[(CO)2], is strongly sensitive to both mass and electronic properties of the substituent. Substitution at C5 has relatively greater influence on the electron density and the force constant of the amide than on the ketone carbonyl group. Strong electron-donors shorten and stabilize the unusually long alpha-dicarbonyl CC bond, while electron-accepting groups tend to stretch this bond further. N-Deprotonation brings to elongation of the five membered-ring along the N-C(CO(ketone)) vector and expansion of the bonds within the alpha-dicarbonyl part. Theoretical v(CO) frequency of isatin is lowered for about 180 cm(-1) upon conversion into isatinato ion. Harmonic vibrational analysis reveals that only the highest-frequency v(CO) mode of the isolated isatinato anion can be considered good group vibration for empirical assignments in spectra of solid isatinates. Owing to the solid-state influences on the v[(CO)2] modes, no reliable spectra structure correlations could be established from the present experimental spectroscopic data.
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Affiliation(s)
- P Naumov
- Institute of Chemistry, Faculty of Sciences, Sv. Kiril i Metodij University, Skopje, Macedonia.
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15
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Abstract
Recent advances in structural and conformational analysis of fluorinated carbohydrates by NMR spectroscopy are reviewed. Characteristic 1H, 13C, and 19F NMR chemical shifts and coupling constants for selected examples are given and the spectral data of a series of fluorinated carbohydrates were collected in continuation of the review of Csuk and Glänzer [Adv. Carbohydr. Chem. Biochem., 46 (1988) 73-177].
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Affiliation(s)
- M Michalik
- Institut für Organische Katalyseforschung an der Universität Rostock eV, Germany.
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16
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Giegé R, Sissler M, Florentz C. Universal rules and idiosyncratic features in tRNA identity. Nucleic Acids Res 1998; 26:5017-35. [PMID: 9801296 PMCID: PMC147952 DOI: 10.1093/nar/26.22.5017] [Citation(s) in RCA: 599] [Impact Index Per Article: 23.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Correct expression of the genetic code at translation is directly correlated with tRNA identity. This survey describes the molecular signals in tRNAs that trigger specific aminoacylations. For most tRNAs, determinants are located at the two distal extremities: the anticodon loop and the amino acid accepting stem. In a few tRNAs, however, major identity signals are found in the core of the molecule. Identity elements have different strengths, often depend more on k cat effects than on K m effects and exhibit additive, cooperative or anti-cooperative interplay. Most determinants are in direct contact with cognate synthetases, and chemical groups on bases or ribose moieties that make functional interactions have been identified in several systems. Major determinants are conserved in evolution; however, the mechanisms by which they are expressed are species dependent. Recent studies show that alternate identity sets can be recognized by a single synthetase, and emphasize the importance of tRNA architecture and anti-determinants preventing false recognition. Identity rules apply to tRNA-like molecules and to minimalist tRNAs. Knowledge of these rules allows the manipulation of identity elements and engineering of tRNAs with switched, altered or multiple specificities.
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MESH Headings
- Amino Acyl-tRNA Synthetases/metabolism
- Evolution, Molecular
- Genetic Code
- Humans
- Kinetics
- Models, Molecular
- Nucleic Acid Conformation
- Protein Biosynthesis
- RNA, Transfer/chemistry
- RNA, Transfer/genetics
- RNA, Transfer/metabolism
- RNA, Transfer, Amino Acyl/chemistry
- RNA, Transfer, Amino Acyl/genetics
- RNA, Transfer, Amino Acyl/metabolism
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Affiliation(s)
- R Giegé
- Unité Propre de Recherche 9002, 'Structure des Macromolécules Biologiques et Mécanismes de Reconnaissance', Scientifique, 15 rue René Descartes, F-67084, Strasbourg Cedex, France.
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17
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Dobrosz-Teperek K, Zwierzchowska Z, Lewandowski W, Bajdor K, Dobrowolski JC, Mazurek AP. Vibrational spectra of 5-halogenouracils part II—solids. J Mol Struct 1998. [DOI: 10.1016/s0022-2860(98)00395-0] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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18
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Liu M, Chu WC, Liu JC, Horowitz J. Role of acceptor stem conformation in tRNAVal recognition by its cognate synthetase. Nucleic Acids Res 1997; 25:4883-90. [PMID: 9396792 PMCID: PMC147156 DOI: 10.1093/nar/25.24.4883] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023] Open
Abstract
Although the anticodon is the primary element in Escherichia coli tRNAValfor recognition by valyl-tRNA synthetase (ValRS), nucleotides in the acceptor stem and other parts of the tRNA modulate recognition. Study of the steady state aminoacylation kinetics of acceptor stem mutants of E.coli tRNAValdemonstrates that replacing any base pair in the acceptor helix with another Watson-Crick base pair has little effect on aminoacylation efficiency. The absence of essential recognition nucleotides in the acceptor helix was confirmed by converting E.coli tRNAAlaand yeast tRNAPhe, whose acceptor stem sequences differ significantly from that of tRNAVal, to efficient valine acceptors. This transformation requires, in addition to a valine anticodon, replacement of the G:U base pair in the acceptor stem of these tRNAs. Mutational analysis of tRNAValverifies that G:U base pairs in the acceptor helix act as negative determinants of synthetase recognition. Insertion of G:U in place of the conserved U4:A69 in tRNAValreduces the efficiency of aminoacylation, due largely to an increase in K m. A smaller but significant decline in aminoacylation efficiency occurs when G:U is located at position 3:70; lesser effects are observed for G:U at other positions in the acceptor helix. The negative effects of G:U base pairs are strongly correlated with changes in helix structure in the vicinity of position 4:69 as monitored by19F NMR spectroscopy of 5-fluorouracil-substituted tRNAVal. This suggests that maintaining regular A-type RNA helix geometry in the acceptor stem is important for proper recognition of tRNAValby valyl-tRNA synthetase.19F NMR also shows that formation of the tRNAVal-valyl-tRNA synthetase complex does not disrupt the first base pair in the acceptor stem, a result different from that reported for the tRNAGln-glutaminyl-tRNA synthetase complex.
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Affiliation(s)
- M Liu
- Department of Biochemistry and Biophysics, Iowa State University, Ames, IA 50011, USA
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19
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Chu WC, Liu JC, Horowitz J. Localization of the major ethidium bromide binding site on tRNA. Nucleic Acids Res 1997; 25:3944-9. [PMID: 9380521 PMCID: PMC146966 DOI: 10.1093/nar/25.19.3944] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023] Open
Abstract
Binding of ethidium bromide to Escherichia coli tRNAVal and an RNA minihelix based on the acceptor stem and T-arm of tRNAVal was investigated by 19F and 1H NMR spectroscopy of RNAs labeled with fluorine by incorporation of 5-fluorouracil. Ethidium bromide selectively intercalates into the acceptor stem of the tRNAVal. More than one ethidium bromide binding site is found in the acceptor stem, the strongest between base pairs A6:U67 and U7:A66. 19F and 1H spectra of the 5-fluorouracil-substituted minihelix RNA indicate that the molecule exists in solution as a 12 base-paired stem and a single-stranded loop. Ethidium bromide no longer intercalates between base pairs corresponding to the tRNAVal acceptor stem in this molecule. Instead, it intercalates between base pairs at the bottom of the long stem-loop structure. These observations suggest that ethidium bromide has a preferred intercalation site close to the base of an RNA helical stem.
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Affiliation(s)
- W C Chu
- Department of Biochemistry and Biophysics, Iowa State University, Ames, Iowa 50011, USA.
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Kintanar A, Yue D, Horowitz J. Effect of nucleoside modifications on the structure and thermal stability of Escherichia coli valine tRNA. Biochimie 1994; 76:1192-204. [PMID: 7538325 DOI: 10.1016/0300-9084(94)90049-3] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
Transfer RNA transcribed in vitro lacks the base modifications found in native tRNA. To understand the effect of base modifications on the structure of tRNA, the downfield region of the 1H NMR spectrum of in vitro transcribed E coli tRNAVal in aqueous phosphate buffer in the presence of excess Mg2+ was investigated. The resonances of all imino protons involved in hydrogen bonds in the helical stem regions and in tertiary interactions were assigned using two-dimensional nuclear Overhauser enhancement spectroscopy (NOESY) and one-dimensional difference nuclear Overhauser effect (NOE) methods. In addition, some aromatic C2 and C8 proton resonances as well as one amino proton resonance were assigned. The chemical shifts of the assigned resonances of unmodified E coli tRNAVal were compared with those of the native tRNA molecule under similar solution conditions. The similarity of the NMR data for unmodified and modified tRNA indicates that the in vitro transcribed tRNA has nearly the same solution structure as the native molecule in the presence of excess Mg2+. The only significant differences were the chemical shifts of resonances corresponding to protons in (or interacting with) bases, indicating the possibility of local structural perturbations. The thermal stability of E coli modified and unmodified tRNAVal in the presence of Mg2+ was also investigated by analyzing the temperature dependence of the imino proton spectra. Several tertiary interactions involving modified nucleosides in native E coli tRNAVal are less stable in the absence of base modifications.
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Affiliation(s)
- A Kintanar
- Department of Biochemistry and Biophysics, Iowa State University, Ames 50011, USA
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Sun WY, Ueyama N, Nakamura A. Spin–lattice relaxation time and temperature dependence of fluorine-19 nuclear magnetic resonance spectra of cysteine-containing peptide iron(II) complexes. ACTA ACUST UNITED AC 1993. [DOI: 10.1039/dt9930001871] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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Chu WC, Kintanar A, Horowitz J. Correlations between fluorine-19 nuclear magnetic resonance chemical shift and the secondary and tertiary structure of 5-fluorouracil-substituted tRNA. J Mol Biol 1992; 227:1173-81. [PMID: 1279181 DOI: 10.1016/0022-2836(92)90529-s] [Citation(s) in RCA: 20] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
To complete assignment of the 19F nuclear magnetic resonance (NMR) spectrum of 5-fluorouracil-substituted Escherichia coli tRNA(Val), resonances from 5-fluorouracil residues involved in tertiary interactions have been identified. Because these assignments could not be made directly by the base-replacement method used to assign 5-fluorouracil residues in loop and stem regions of the tRNA, alternative assignment strategies were employed. FU54 and FU55 were identified by 19F homonuclear Overhauser experiments and were then assigned by comparison of their 19F NMR spectra with those of 5-fluorouracil-labeled yeast tRNA(Phe) mutants having FU54 replaced by adenine and FU55 replaced by cytosine. FU8 and FU12, were assigned from the 19F NMR spectrum of the tRNA(Val) mutant in which the base triple G9-C23-G12 substituted for the wild-type A9-A23-FU12. Although replacement of the conserved U8 (FU8) with A or C disrupts the tertiary structure of tRNA(Val), it has only a small effect on the catalytic turnover number of valyl-tRNA synthetase, while reducing the affinity of the tRNA for enzyme. Analysis of the 19F chemical shift assignments of all 14 resonances in the spectrum of 5-fluorouracil-substituted tRNAVal indicated a strong correlation to tRNA secondary and tertiary structure. 5-Fluorouracil residues in loop regions gave rise to peaks in the central region of the spectrum, 4.4 to 4.9 parts per million (p.p.m.) downfield from free 5-fluorouracil. However, the signal from FU59, in the T-loop of tRNA(Val), was shifted more than 1 p.p.m. downfield, to 5.9 p.p.m., presumably because of the involvement of this fluorouracil in the tertiary interactions between the T and D-loops. The 19F chemical shift moved upfield, to the 2.0 to 2.8 p.p.m. range, when fluorouracil was base-paired with adenine in helical stems. This upfield shift was less pronounced for the fluorine of the FU7.A66 base-pair, located at the base of the acceptor stem, an indication that FU7 is only partially stacked on the adjacent G49 in the continuous acceptor stem/T-stem helix. An unanticipated finding was that the 19F resonances of 5-fluorouracil residues wobble base-paired with guanine were shifted 4 to 5 p.p.m. downfield of those from fluorouracil residues paired with A. In the 19F NMR spectra of all fluorinated tRNAs studied, the farthest downfield peak corresponded to FU55, which replaced the conserved pseudouridine normally found at this position.
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Affiliation(s)
- W C Chu
- Department of Biochemistry and Biophysics, Iowa State University, Ames 50011
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