Chemo-enzymatic synthesis of site-specific isotopically labeled nucleotides for use in NMR resonance assignment, dynamics and structural characterizations.
Identifieur interne : 000C86 ( PubMed/Corpus ); précédent : 000C85; suivant : 000C87Chemo-enzymatic synthesis of site-specific isotopically labeled nucleotides for use in NMR resonance assignment, dynamics and structural characterizations.
Auteurs : Andrew P. Longhini ; Regan M. Leblanc ; Owen Becette ; Carolina Salguero ; Christoph H. Wunderlich ; Bruce A. Johnson ; Victoria M. D'Souza ; Christoph Kreutz ; T Kwaku DayieSource :
- Nucleic acids research [ 1362-4962 ] ; 2016.
English descriptors
- KwdEn :
- Adenosine Triphosphate (chemical synthesis), Bacillus anthracis (chemistry), Bacillus anthracis (genetics), Carbon Isotopes, Coronavirus 229E, Human (chemistry), Coronavirus 229E, Human (genetics), Creatine Kinase (chemistry), Creatine Kinase (genetics), Guanosine Triphosphate (chemical synthesis), Isotope Labeling (methods), Magnetic Resonance Spectroscopy, Nucleotides (chemical synthesis), Pentosyltransferases (chemistry), Pentosyltransferases (genetics), Phosphotransferases (Alcohol Group Acceptor) (chemistry), Phosphotransferases (Alcohol Group Acceptor) (genetics), Recombinant Proteins (chemistry), Recombinant Proteins (genetics), Response Elements, Ribose (chemistry), Ribose-Phosphate Pyrophosphokinase (chemistry), Ribose-Phosphate Pyrophosphokinase (genetics), Riboswitch, Transcription, Genetic.
- MESH :
- chemical , chemical synthesis : Adenosine Triphosphate, Guanosine Triphosphate, Nucleotides.
- chemistry : Bacillus anthracis, Coronavirus 229E, Human, Creatine Kinase, Pentosyltransferases, Phosphotransferases (Alcohol Group Acceptor), Recombinant Proteins, Ribose, Ribose-Phosphate Pyrophosphokinase.
- genetics : Bacillus anthracis, Coronavirus 229E, Human, Creatine Kinase, Pentosyltransferases, Phosphotransferases (Alcohol Group Acceptor), Recombinant Proteins, Ribose-Phosphate Pyrophosphokinase.
- methods : Isotope Labeling.
- chemical : Carbon Isotopes, Magnetic Resonance Spectroscopy, Response Elements, Riboswitch, Transcription, Genetic.
Abstract
Stable isotope labeling is central to NMR studies of nucleic acids. Development of methods that incorporate labels at specific atomic positions within each nucleotide promises to expand the size range of RNAs that can be studied by NMR. Using recombinantly expressed enzymes and chemically synthesized ribose and nucleobase, we have developed an inexpensive, rapid chemo-enzymatic method to label ATP and GTP site specifically and in high yields of up to 90%. We incorporated these nucleotides into RNAs with sizes ranging from 27 to 59 nucleotides using in vitro transcription: A-Site (27 nt), the iron responsive elements (29 nt), a fluoride riboswitch from Bacillus anthracis(48 nt), and a frame-shifting element from a human corona virus (59 nt). Finally, we showcase the improvement in spectral quality arising from reduced crowding and narrowed linewidths, and accurate analysis of NMR relaxation dispersion (CPMG) and TROSY-based CEST experiments to measure μs-ms time scale motions, and an improved NOESY strategy for resonance assignment. Applications of this selective labeling technology promises to reduce difficulties associated with chemical shift overlap and rapid signal decay that have made it challenging to study the structure and dynamics of large RNAs beyond the 50 nt median size found in the PDB.
DOI: 10.1093/nar/gkv1333
PubMed: 26657632
Links to Exploration step
pubmed:26657632Le document en format XML
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<term>Coronavirus 229E, Human (chemistry)</term>
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<front><div type="abstract" xml:lang="en">Stable isotope labeling is central to NMR studies of nucleic acids. Development of methods that incorporate labels at specific atomic positions within each nucleotide promises to expand the size range of RNAs that can be studied by NMR. Using recombinantly expressed enzymes and chemically synthesized ribose and nucleobase, we have developed an inexpensive, rapid chemo-enzymatic method to label ATP and GTP site specifically and in high yields of up to 90%. We incorporated these nucleotides into RNAs with sizes ranging from 27 to 59 nucleotides using in vitro transcription: A-Site (27 nt), the iron responsive elements (29 nt), a fluoride riboswitch from Bacillus anthracis(48 nt), and a frame-shifting element from a human corona virus (59 nt). Finally, we showcase the improvement in spectral quality arising from reduced crowding and narrowed linewidths, and accurate analysis of NMR relaxation dispersion (CPMG) and TROSY-based CEST experiments to measure μs-ms time scale motions, and an improved NOESY strategy for resonance assignment. Applications of this selective labeling technology promises to reduce difficulties associated with chemical shift overlap and rapid signal decay that have made it challenging to study the structure and dynamics of large RNAs beyond the 50 nt median size found in the PDB.</div>
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<Abstract><AbstractText>Stable isotope labeling is central to NMR studies of nucleic acids. Development of methods that incorporate labels at specific atomic positions within each nucleotide promises to expand the size range of RNAs that can be studied by NMR. Using recombinantly expressed enzymes and chemically synthesized ribose and nucleobase, we have developed an inexpensive, rapid chemo-enzymatic method to label ATP and GTP site specifically and in high yields of up to 90%. We incorporated these nucleotides into RNAs with sizes ranging from 27 to 59 nucleotides using in vitro transcription: A-Site (27 nt), the iron responsive elements (29 nt), a fluoride riboswitch from Bacillus anthracis(48 nt), and a frame-shifting element from a human corona virus (59 nt). Finally, we showcase the improvement in spectral quality arising from reduced crowding and narrowed linewidths, and accurate analysis of NMR relaxation dispersion (CPMG) and TROSY-based CEST experiments to measure μs-ms time scale motions, and an improved NOESY strategy for resonance assignment. Applications of this selective labeling technology promises to reduce difficulties associated with chemical shift overlap and rapid signal decay that have made it challenging to study the structure and dynamics of large RNAs beyond the 50 nt median size found in the PDB.</AbstractText>
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