ArticleNucleic acids research2007
Base-specific spin-labeling of RNA for structure determination.
Article in Nucleic acids research, 2007. The graph could read no effect estimate from its abstract, so it casts no vote on the map. An erratum has been issued. Cited by 37 papers.
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Who cites it
37 citing papers in PubMed, 141 citations in OpenAlex.
- Spin-Labeled Riboswitch Synthesized from a Protected TPA Phosphoramidite Building Block.Chemistry (Weinheim an der Bergstrasse, Germany) · 2022Article
- Paramagnetic Chemical Probes for Studying Biological Macromolecules.Chemical reviews · 2022Review
- Spin Labeling of Long RNAs Via Click Reaction and Enzymatic Ligation.Methods in molecular biology (Clifton, N.J.) · 2022Article
- Preparation of Site-Specifically Spin-Labeled RNA by in Vitro Transcription Using an Expanded Genetic Alphabet.Methods in molecular biology (Clifton, N.J.) · 2022Article
- Covalent labeling of nucleic acids.Chemical Society reviews · 2020Review
- Lanthanide Tagging of Oligonucleotides to Nucleobase for Paramagnetic NMR.Chembiochem : a European journal of chemical biology · 2020Article
- Synthesis of Nucleobase-Modified RNA Oligonucleotides by Post-Synthetic Approach.Molecules (Basel, Switzerland) · 2020Review
- EPR Distance Measurements on Long Non-coding RNAs Empowered by Genetic Alphabet Expansion Transcription.Angewandte Chemie (International ed. in English) · 2020Article
- 2'-Alkynyl spin-labelling is a minimally perturbing tool for DNA structural analysis.Nucleic acids research · 2020Article
- "End-to-end" stacking of small dsRNA.RNA (New York, N.Y.) · 2019Article
- Influence of MgRNA (New York, N.Y.) · 2019Article
- Post-transcriptional labeling by using Suzuki-Miyaura cross-coupling generates functional RNA probes.Nucleic acids research · 2018Article
- Structural rearrangements in mRNA upon its binding to human 80S ribosomes revealed by EPR spectroscopy.Nucleic acids research · 2018Article
- Impact of spin label rigidity on extent and accuracy of distance information from PRE data.Journal of biomolecular NMR · 2017Article
- Complementary-addressed site-directed spin labeling of long natural RNAs.Nucleic acids research · 2016Article
- High-resolution measurement of long-range distances in RNA: pulse EPR spectroscopy with TEMPO-labeled nucleotides.Chemical science · 2016Article
- New developments in spin labels for pulsed dipolar EPR.Molecules (Basel, Switzerland) · 2014Review
- A novel paramagnetic relaxation enhancement tag for nucleic acids: a tool to study structure and dynamics of RNA.ACS chemical biology · 2013Article
- Pulsed electron double resonance in structural studies of spin-labeled nucleic acids.Acta naturae · 2013Article
- Design, synthesis, and spectroscopic properties of extended and fused pyrrolo-dC and pyrrolo-C analogs.Organic letters · 2012Article
Corrections and comments
- Erratum issued
Authors and funding
6 authors at 1 institution in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
To facilitate the measurement of intramolecular distances in solvated RNA systems, a combination of spin-labeling, electron paramagnetic resonance (EPR), and molecular dynamics (MD) simulation is presented. The fairly rigid spin label 2,2,5,5-tetramethyl-pyrrolin-1-yloxyl-3-acetylene (TPA) was base and site specifically introduced into RNA through a Sonogashira palladium catalyzed cross-coupling on column. For this purpose 5-iodo-uridine, 5-iodo-cytidine and 2-iodo-adenosine phosphoramidites were synthesized and incorporated into RNA-sequences. Application of the recently developed ACE chemistry presented the main advantage to limit the reduction of the nitroxide to an amine during the oligonucleotide automated synthesis and thus to increase substantially the reliability of the synthesis and the yield of labeled oligonucleotides. 4-Pulse Electron Double Resonance (PELDOR) was then successfully used to measure the intramolecular spin-spin distances in six doubly labeled RNA-duplexes. Comparison of these results with our previous work on DNA showed that A- and B-Form can be differentiated. Using an all-atom force field with explicit solvent, MD simulations gave results in good agreement with the measured distances and indicated that the RNA A-Form was conserved despite a local destabilization effect of the nitroxide label. The applicability of the method to more complex biological systems is discussed.
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