共查询到20条相似文献,搜索用时 31 毫秒
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Hagan NA Smith CA Antoine MD Lin JS Feldman AB Demirev PA 《Journal of the American Society for Mass Spectrometry》2012,23(4):773-777
The capability to rapidly and confidently determine or confirm the sequences of short oligonucleotides, including native and
chemically-modified DNA and RNA, is important for a number of fields. While matrix-assisted laser desorption/ionization (MALDI)
time-of-flight (TOF) mass spectrometry (MS) has been used previously to sequence short oligonucleotides, the typically low
fragmentation efficiency of in-source or post-source decay processes necessitates the accumulation of a large number of spectra,
thus limiting the throughput of these methods. Here we introduce a novel matrix, 1,5-diaminonapthalene (DAN), for facile in-source
decay (ISD) of DNA and RNA molecular anions, which allows for rapid sequence confirmation. d-, w-, and y-series ions are prominent in the spectra, complementary to the (a-B)- and w- ions that are typically produced by MALDI post-source decay (PSD). Results are shown for several model DNA and RNA oligonucleotides,
including combinations of DAN-induced fragmentation with true tandem TOF MS (MS/MS) for pseudo-MS3 and “activated-ion PSD.” 相似文献
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Mohammad Ghaem Maghami Surjendu Dey Ann‐Kathrin Lenz Claudia Hbartner 《Angewandte Chemie (International ed. in English)》2020,59(24):9335-9339
In vitro selected ribozymes are promising tools for site‐specific labeling of RNA. Previously known nucleic acid catalysts attached fluorescently labeled adenosine or guanosine derivatives through 2′,5′‐branched phosphodiester bonds to the RNA of interest. Herein, we report new ribozymes that use orthogonal substrates, derived from the antiviral drug tenofovir, and attach bioorthogonal functional groups, as well as affinity handles and fluorescent reporter units through a hydrolytically more stable phosphonate ester linkage. The tenofovir transferase ribozymes were identified by in vitro selection and are orthogonal to nucleotide transferase ribozymes. As genetically encodable functional RNAs, these ribozymes may be developed for potential cellular applications. The orthogonal ribozymes addressed desired target sites in large RNAs in vitro, as shown by fluorescent labeling of E. coli 16S and 23S rRNAs in total cellular RNA. 相似文献
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Mohammad Ghaem Maghami Dr. Surjendu Dey Ann-Kathrin Lenz Prof. Dr. Claudia Höbartner 《Angewandte Chemie (Weinheim an der Bergstrasse, Germany)》2020,132(24):9421-9425
In vitro selected ribozymes are promising tools for site-specific labeling of RNA. Previously known nucleic acid catalysts attached fluorescently labeled adenosine or guanosine derivatives through 2′,5′-branched phosphodiester bonds to the RNA of interest. Herein, we report new ribozymes that use orthogonal substrates, derived from the antiviral drug tenofovir, and attach bioorthogonal functional groups, as well as affinity handles and fluorescent reporter units through a hydrolytically more stable phosphonate ester linkage. The tenofovir transferase ribozymes were identified by in vitro selection and are orthogonal to nucleotide transferase ribozymes. As genetically encodable functional RNAs, these ribozymes may be developed for potential cellular applications. The orthogonal ribozymes addressed desired target sites in large RNAs in vitro, as shown by fluorescent labeling of E. coli 16S and 23S rRNAs in total cellular RNA. 相似文献
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A Vastly Increased Chemical Variety of RNA Modifications Containing a Thioacetal Structure
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Christina Dal Magro Patrick Keller Dr. Annika Kotter Stephan Werner Dr. Victor Duarte Dr. Virginie Marchand Dr. Michael Ignarski Anja Freiwald Dr. Roman‐Ulrich Müller Prof. Dr. Christoph Dieterich Prof. Dr. Yuri Motorin Dr. Falk Butter Dr. Mohamed Atta Prof. Dr. Mark Helm 《Angewandte Chemie (International ed. in English)》2018,57(26):7893-7897
Recently discovered new chemical entities in RNA modifications have involved surprising functional groups that enlarge the chemical space of RNA. Using LC‐MS, we found over 100 signals of RNA constituents that contained a ribose moiety in tRNAs from E. coli. Feeding experiments with variegated stable isotope labeled compounds identified 37 compounds that are new structures of RNA modifications. One structure was elucidated by deuterium exchange and high‐resolution mass spectrometry. The structure of msms2i6A (2‐methylthiomethylenethio‐N6‐isopentenyl‐adenosine) was confirmed by methione‐D3 feeding experiments and by synthesis of the nucleobase. The msms2i6A contains a thioacetal, shown in vitro to be biosynthetically derived from ms2i6A by the radical‐SAM enzyme MiaB. This enzyme performs thiomethylation, forming ms2i6A from i6A in a first turnover. The new thioacetal is formed by a second turnover. Along with the pool of 36 new modifications, this work describes a new layer of RNA modification chemistry. 相似文献
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Site‐Specific Isotope‐Labeling of Inosine Phosphoramidites and NMR Analysis of an Inosine‐Containing RNA Duplex
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Dr. Andre Dallmann Dr. Alexander V. Beribisky Dr. Felix Gnerlich Martin Rübbelke Dr. Stefan Schiesser Prof. Dr. Thomas Carell Prof. Dr. Michael Sattler 《Chemistry (Weinheim an der Bergstrasse, Germany)》2016,22(43):15350-15359
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Aleksandr Osipenko Alexandra Plotnikova Milda Nainytė Dr. Viktoras Masevičius Prof. Saulius Klimašauskas Dr. Giedrius Vilkaitis 《Angewandte Chemie (Weinheim an der Bergstrasse, Germany)》2017,129(23):6607-6610
The HEN1 RNA 2′-O-methyltransferase plays important roles in the biogenesis of small non-coding RNAs in plants and proved a valuable tool for selective transfer of functional groups from cofactor analogues onto miRNA and siRNA duplexes in vitro. Herein, we demonstrate the versatile HEN1-mediated methylation and alkylation of small RNA strands in heteroduplexes with a range of complementary synthetic DNA oligonucleotides carrying user-defined moieties such as internal or 3′-terminal extensions or chemical reporter groups. The observed DNA-guided covalent functionalization of RNA broadens our understanding of the substrate specificity of HEN1 and paves the way for the development of novel chemo-enzymatic tools with potential applications in miRNomics, synthetic biology, and nanomedicine. 相似文献
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Fabrice Freville Tristan Richard Katell Bathany Serge Moreau 《Helvetica chimica acta》2006,89(12):2958-2974
A new strategy to cyclize short synthetic oligonucleotides on DNA or RNA target strands is described. The approach is based on metal‐templated cyclization of short synthetic oligonucleotides conjugated with two chelating 2,2′ : 6′,2′′‐terpyridine (Tpy) moieties at their 3′‐ and 5′‐ends. Cyclization after metal addition (Zn2+, Fe2+) was demonstrated by means of thermal‐denaturation experiments, MALDI‐Q‐TOF‐MS, and gel electrophoresis (PAGE). 1D‐ and 2D‐NMR Experiments were performed to analyze the association of complementary strands after metal‐mediated cyclization. Our protocol allows the efficient circularization of synthetic oligonucleotides. Thereby, the hybridization on a complementary strand was more efficient with an RNA target strand and a 2′‐O‐methylated circularized oligomer. 相似文献
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《Magnetic resonance in chemistry : MRC》2002,40(5):377-379
The temperature dependence of internucleotide nitrogen–nitrogen scalar couplings 2hJ(N,N) across hydrogen bonds in adenine–uracil (A–U) and guanine–cytosine (G–C) base pairs of the 22 nucleotide RNA oligomer GGCGAAGUCGAAAGAUGGCGCC was studied between 280 and 310 K. The value of 2hJ(N,N) was observed to decrease monotonically for all four base pairs with increasing temperature. The temperature dependence of 2hJ(N,N) was found to be more pronounced for the A–U base pair than for G–C base pairs. An earlier study of cross‐correlation effects at 296 K appeared to indicate a reduced mobility of the A–U base pair, as evidenced by small contributions of chemical shift modulation to relaxation rates. Copyright © 2002 John Wiley & Sons, Ltd. 相似文献
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A Non‐Invasive NMR Method Based on Histidine Imidazoles to Analyze the pH‐Modulation of Protein–Nucleic Acid Interfaces
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Dr. Isabel Cruz‐Gallardo Dr. Rebecca Del Conte Dr. Adrián Velázquez‐Campoy Dr. Sofía M. García‐Mauriño Dr. Irene Díaz‐Moreno 《Chemistry (Weinheim an der Bergstrasse, Germany)》2015,21(20):7588-7595
A useful 2J(N?H) coupling‐based NMR spectroscopic approach is proposed to unveil, at the molecular level, the contribution of the imidazole groups of histidines from RNA/DNA‐binding proteins on the modulation of binding to nucleic acids by pH. Such protonation/deprotonation events have been monitored on the single His96 located at the second RNA/DNA recognition motif (RRM2) of T‐cell intracellular antigen‐1 (TIA‐1) protein. The pKa values of the His96 ionizable groups were substantially higher in the complexes with short U‐rich RNA and T‐rich DNA oligonucleotides than those of the isolated TIA‐1 RRM2. Herein, the methodology applied to determine changes in pKa of histidine side chains upon DNA/RNA binding, gives valuable information to understand the pH effect on multidomain DNA/RNA‐binding proteins that shuttle among different cellular compartments. 相似文献
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Dipl.‐Chem. Christoph Kröner Dr. Martin Thunemann Dipl.‐Chem. Sven Vollmer Manuela Kinzer Prof. Robert Feil Prof. Clemens Richert 《Angewandte Chemie (International ed. in English)》2014,53(35):9198-9202
It is becoming increasingly clear that nature uses RNAs extensively for regulating vital functions of the cell, and short sequences are frequently used to suppress gene expression. However, controlling the concentration of small molecules intracellularly through designed RNA sequences that fold into ligand‐binding structures is difficult. The development of “endless”, a triplex‐based folding motif that can be expressed in mammalian cells and binds the second messenger 3′,5′‐cyclic guanosine monophosphate (cGMP), is described. In vitro, DNA or RNA versions of endless show low micromolar to nanomolar dissociation constants for cGMP. To test its functionality in vivo, four endless RNA motifs arranged in tandem were co‐expressed with a fluorescent cGMP sensor protein in murine vascular smooth muscle cells. Nitric oxide induced endogenous cGMP signals were suppressed in endless‐expressing cells compared to cells expressing a control motif, which suggests that endless can act as a genetically encoded cGMP sink to modulate signal transduction in cells. 相似文献