Key Labeling Technologies to Tackle Sizeable Problems in RNA Structural Biology

The ability to adopt complex three-dimensional (3D) structures that can rapidly interconvert between multiple functional states (folding and dynamics) is vital for the proper functioning of RNAs. Consequently, RNA structure and dynamics necessarily determine their biological function. In the post-genomic era, it is clear that RNAs comprise a larger proportion (>50%) of the transcribed genome compared to proteins (≤2%). Yet the determination of the 3D structures of RNAs lags considerably behind those of proteins and to date there are even fewer investigations of dynamics in RNAs compared to proteins. Site specific incorporation of various structural and dynamic probes into nucleic acids would likely transform RNA structural biology. Therefore, various methods for introducing probes for structural, functional, and biotechnological applications are critically assessed here. These probes include stable isotopes such as 2H, 13C, 15N, and 19F. Incorporation of these probes using improved RNA ligation strategies promises to change the landscape of structural biology of supramacromolecules probed by biophysical tools such as nuclear magnetic resonance (NMR) spectroscopy, X-ray crystallography and Raman spectroscopy. Finally, some of the structural and dynamic problems that can be addressed using these technological advances are outlined.

• Publication year

  2008

• Venue

  International Journal of Molecular Sciences

• Publication date

  2008-06-01

• Fields of study

  Biology, Medicine, Materials Science, Chemistry

• Identifiers
  DOI 10.3390/ijms9071214PMID 19325801PMCID 2635727
• External record

  Open on Semantic Scholar

• Source metadata

  Semantic Scholar, PubMed

• No claims are published for this paper.

• No concepts are published for this paper.

• Metabolic labeling: Taking advantage of bacterial pathways to prepare spectroscopically useful isotope patterns in proteins and nucleic acids

  2008cited by this paper
• A structural understanding of the dynamic ribosome machine

  2008cited by this paper
• A glimpse into the active site of a group II intron and maybe the spliceosome, too.

  2008cited by this paper
• Selenium Derivatization of Nucleic Acids for Phase and Structure Determination in Nucleic Acid X-ray Crystallography

  2008cited by this paper
• Isolation of an active step I spliceosome and composition of its RNP core

  2008cited by this paper
• Crystal Structure of a Self-Spliced Group II Intron

  2008cited by this paper
• The Eukaryotic Genome as an RNA Machine

  2008cited by this paper
• Improved native affinity purification of RNA.

  2007cited by this paper
• The ribosome in focus: new structures bring new insights.

  2007cited by this paper
• Purification and characterization of transcribed RNAs using gel filtration chromatography

  2007cited by this paper
• Solution NMR studies of the maturation intermediates of a 13 MDa viral capsid.

  2007cited by this paper
• Molecular replacement.

  2007cited by this paper
• Preparation and crystallization of RNA.

  2007cited by this paper
• Riboswitches: small-molecule recognition by gene regulatory RNAs.

  2007cited by this paper
• Internal bulge and tetraloop of the catalytic domain 5 of a group II intron ribozyme are flexible: implications for catalysis.

  2007influential reference
• Recombinant RNA technology: the tRNA scaffold

  2007influential reference
• In-gel fluorescence probing of RNA-RNA interactions.

  2007cited by this paper
• Molecular replacement

  2007cited by this paper
• Synthesis of 5-fluoropyrimidine nucleotides as sensitive NMR probes of RNA structure.

  2007cited by this paper
• A general strategy to solve the phase problem in RNA crystallography.

  2007cited by this paper
• The multifunctional nucleolus

  2007cited by this paper
• The relationship between non-protein-coding DNA and eukaryotic complexity.

  2007cited by this paper
• Preparation of large RNA oligonucleotides with complementary isotope-labeled segments for NMR structural studies

  2007cited by this paper
• Substitution of the use of radioactivity by fluorescence for biochemical studies of RNA.

  2007cited by this paper
• Recent advances in DNA catalysis.

  2007cited by this paper
• A novel approach to the synthesis of DNA and RNA lariats.

  2007cited by this paper
• Structural features of metabolite-sensing riboswitches.

  2007cited by this paper
• An RNA ligase-mediated method for the efficient creation of large, synthetic RNAs.

  2006cited by this paper
• Cryo-electron microscopy of spliceosomal components.

  2006cited by this paper
• NMR techniques for very large proteins and rnas in solution.

  2006cited by this paper
• Alternate-site isotopic labeling of ribonucleotides for NMR studies of ribose conformational dynamics in RNA

  2006cited by this paper
• 17 Group II Introns: Ribozymes That Splice RNA and Invade DNA

  2006cited by this paper
• Tertiary contacts distant from the active site prime a ribozyme for catalysis.

  2006cited by this paper
• Fluorescence and solution NMR study of the active site of a 160-kDa group II intron ribozyme.

  2006influential reference
• Evidence for preorganization of the glmS ribozyme ligand binding pocket.

  2006cited by this paper
• Rapid purification of RNAs using fast performance liquid chromatography (FPLC).

  2006cited by this paper
• Efficient substrate cleavage catalyzed by hammerhead ribozymes derivatized with selenium for X-ray crystallography.

  2006cited by this paper
• New RNA labeling methods offer dramatic sensitivity enhancements in 2H NMR relaxation spectra.

  2006cited by this paper
• Resolution enhanced homonuclear carbon decoupled triple resonance experiments for unambiguous RNA structural characterization

  2005cited by this paper
• Structure of a self-splicing group II intron catalytic effector domain 5: parallels with spliceosomal U6 RNA.

  2005cited by this paper
• RNA helical packing in solution: NMR structure of a 30 kDa GAAA tetraloop-receptor complex.

  2005influential reference
• How retroviruses select their genomes

  2005cited by this paper
• General deoxyribozyme-catalyzed synthesis of native 3'-5' RNA linkages.

  2005cited by this paper
• NMR Methods for Studying the Structure and Dynamics of RNA

  2005cited by this paper
• New NMR experiments for RNA nucleobase resonance assignment and chemical shift analysis of an RNA UUCG tetraloop

  2004cited by this paper
• Large-scale preparation and purification of polyacrylamide-free RNA oligonucleotides.

  2004cited by this paper
• New applications of 2D filtered/edited NOESY for assignment and structure elucidation of RNA and RNA-protein complexes

  2004cited by this paper
• Enzymatic synthesis and 19F NMR studies of 2-fluoroadenine-substituted RNA.

  2004cited by this paper
• Control of gene expression by a natural metabolite-responsive ribozyme

  2004cited by this paper
• Structural basis for packaging the dimeric genome of Moloney murine leukaemia virus

  2004cited by this paper
• Crystallization of RNA and RNA-protein complexes.

  2004cited by this paper
• NMR structure of the 101-nucleotide core encapsidation signal of the Moloney murine leukemia virus.

  2004cited by this paper
• Superior 5' homogeneity of RNA from ATP-initiated transcription under the T7 phi 2.5 promoter.

  2004cited by this paper
• Rapid preparation of RNA samples for NMR spectroscopy and X-ray crystallography.

  2004cited by this paper
• A general method for rapid and nondenaturing purification of RNAs.

  2004cited by this paper
• RNA crystallization.

  2003cited by this paper
• RNA footprinting analysis using ion pair reverse phase liquid chromatography.

  2002influential reference
• NMR study of 100 kDa HCV IRES RNA using segmental isotope labeling.

  2002cited by this paper
• RNA analysis by ion-pair reversed-phase high performance liquid chromatography.

  2001influential reference
• Preparation and use of 2H-labeled RNA oligonucleotides in nuclear magnetic resonance studies.

  2001cited by this paper
• Resonance assignment and structure determination for RNA.

  2001cited by this paper
• Base-type-selective high-resolution 13C edited NOESY for sequential assignment of large RNAs

  2001cited by this paper
• RNA oligonucleotide synthesis via 5'-silyl-2'-orthoester chemistry.

  2001cited by this paper
• Solving large RNA structures by X-ray crystallography.

  2000cited by this paper
• Purification, crystallization, and X-ray diffraction analysis of small ribozymes.

  2000cited by this paper
• [8] Heavy atom derivatives of RNA

  2000cited by this paper
• Preparation of specifically 2H- and 13C-labeled ribonucleotides.

  2000cited by this paper
• 2.8 A crystal structure of the malachite green aptamer.

  2000cited by this paper
• Heavy atom derivatives of RNA.

  2000cited by this paper
• Joining of RNAs by splinted ligation.

  2000cited by this paper
• Crystallization and structure determination of a hepatitis delta virus ribozyme: use of the RNA-binding protein U1A as a crystallization module.

  2000cited by this paper
• High-performance liquid chromatography purification of homogenous-length RNA produced by trans cleavage with a hammerhead ribozyme.

  1999influential reference
• A simple and efficient method to reduce nontemplated nucleotide addition at the 3 terminus of RNAs transcribed by T7 RNA polymerase.

  1999cited by this paper
• More mistakes by T7 RNA polymerase at the 5' ends of in vitro-transcribed RNAs.

  1999cited by this paper
• Crystal structure of a hepatitis delta virus ribozyme

  1998cited by this paper
• The use of 2H, 13C, 15N multidimensional NMR to study the structure and dynamics of proteins.

  1998cited by this paper
• 3D C(CC)H TOCSY experiment for assigning protons and carbons in uniformly 13C- and selectively 2H-labeled RNA.

  1998cited by this paper
• T7 RNA polymerase produces 5' end heterogeneity during in vitro transcription from certain templates.

  1998cited by this paper
• THE USE OF NMR METHODS FOR CONFORMATIONAL STUDIES OF NUCLEIC ACIDS

  1998cited by this paper
• Structure of an RNA hairpin loop with a 5'-CGUUUCG-3' loop motif by heteronuclear NMR spectroscopy and distance geometry.

  1997influential reference
• Preparation of Specifically Deuterated and 13C-Labeled RNA for NMR Studies Using Enzymatic Synthesis†

  1997cited by this paper
• Assignment methodology for larger RNA oligonucleotides: Application to an ATP-binding RNA aptamer

  1997cited by this paper
• Use of chemically modified nucleotides to determine a 62-nucleotide RNA crystal structure: a survey of phosphorothioates, Br, Pt and Hg.

  1997cited by this paper
• X-ray crystallography of large RNAs: heavy-atom derivatives by RNA engineering.

  1996cited by this paper
• Use of cis- and trans-ribozymes to remove 5' and 3' heterogeneities from milligrams of in vitro transcribed RNA.

  1996cited by this paper
• HPLC purification of RNA for crystallography and NMR.

  1996influential reference
• Non-hydrogen bonding 'terminator' nucleosides increase the 3'-end homogeneity of enzymatic RNA and DNA synthesis.

  1996cited by this paper
• Improved large scale culture of Methylophilus methylotrophus for 13C/15N labeling and random fractional deuteration of ribonucleotides.

  1996cited by this paper
• Preparation of Specifically Deuterated RNA for NMR Studies Using a Combination of Chemical and Enzymatic Synthesis

  1996influential reference
• Synthesis, deprotection, analysis and purification of RNA and ribozymes.

  1995influential reference
• Preparation of carbon-13 labeled ribonucleotides using acetate as an isotope source.

  1995cited by this paper
• Multidimensional heteronuclear NMR experiments for structure determination of isotopically labeled RNA.

  1995cited by this paper
• Biochemical and NMR studies of RNA conformation with an emphasis on RNA pseudoknots.

  1995cited by this paper
• Effect of deuteration on the amide proton relaxation rates in proteins. Heteronuclear NMR experiments on villin 14T.

  1994cited by this paper
• In vitro transcription: preparative RNA yields in analytical scale reactions.

  1994cited by this paper
• Carbon-Proton Scalar Couplings in RNA: 3D Heteronuclear and 2D Isotope-Edited NMR of a 13C-Labeled Extra-stable Hairpin

  1994cited by this paper
• ENZYMATIC SYNTHESIS OF NAD+ WITH THE SPECIFIC INCORPORATION OF ATOMIC LABELS

  1994cited by this paper
• 6xHis-Ni-NTA chromatography as a superior technique in recombinant protein expression/purification.

  1994cited by this paper
• Selective isotopic enrichment of synthetic RNA: application to the HIV-1 TAR element.

  1993cited by this paper
• Molecular replacement

  1992cited by this paper

• Cobalt-catalysed alkene hydronitration enabled by anomeric nitroamide

  2025cites this paper
• Consolidated 3‑Fold Isotopic Lens for Probing RNAs

  2025cites this paper
• Endogenous Production and Vibrational Analysis of Heavy‐Isotope‐Labeled Peptides from Cyanobacteria

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• Efficient Scalable Hydrothermal Synthesis of MnO2 with Controlled Polymorphs and Morphologies for Enhanced Battery Cathodes

  2023cites this paper
• Atom-economical synthesis of 1,2-bis(phosphine oxide)ethanes from calcium carbide with straightforward access to deuterium- and 13C-labeled bidentate phosphorus ligands and metal complexes

  2023cites this paper
• Synthesis of [7-15N]-GTPs for RNA structure and dynamics by NMR spectroscopy

  2022cites this paper
• Isotope Labels Combined with Solution NMR Spectroscopy Make Visible the Invisible Conformations of Small-to-Large RNAs

  2022cites this paper
• Isotope-Labeled RNA Building Blocks for NMR Structure and Dynamics Studies

  2021cites this paper
• Chemo-enzymatic synthesis of [2-13C, 7-15 N]-ATP for facile NMR analysis of RNA

  2020cites this paper
• Solid-State NMR Spectroscopy of RNA.

  2019cites this paper
• Solid-Phase Chemical Synthesis of Stable Isotope-Labeled RNA to Aid Structure and Dynamics Studies by NMR Spectroscopy

  2019cites this paper
• RNA Characterization by Solid-State NMR Spectroscopy.

  2018cites this paper
• A guide to large-scale RNA sample preparation

  2018cites this paper
• Isotope labeling for studying RNA by solid-state NMR spectroscopy

  2018cites this paper
• RNA Structural Differentiation: Opportunities with Pattern Recognition.

  2018cites this paper
• Combining asymmetric 13C-labeling and isotopic filter/edit NOESY: a novel strategy for rapid and logical RNA resonance assignment

  2017cites this paper
• Specific labeling: An effective tool to explore the RNA world

  2016cites this paper
• STRUCTURAL ANALYSIS OF RIBOSOME BINDING ELEMENTS OF THE 3´ UTR IN TWO POSITIVE-STRAND PLANT RNA VIRUSES

  2016influential citation
• Stable isotope-labeled RNA phosphoramidites to facilitate dynamics by NMR.

  2015cites this paper
• Magic angle spinning NMR of viruses.

  2015cites this paper
• In vivo, large-scale preparation of uniformly (15)N- and site-specifically (13)C-labeled homogeneous, recombinant RNA for NMR studies.

  2015cites this paper
• Chemo-enzymatic synthesis of site-specific isotopically labeled nucleotides for use in NMR resonance assignment, dynamics and structural characterizations

  2015cites this paper
• RNA Structural Analysis Based on Thermal Denaturation

  2014cites this paper
• Regio‐Selective Chemical‐Enzymatic Synthesis of Pyrimidine Nucleotides Facilitates RNA Structure and Dynamics Studies

  2014cites this paper
• Chemo-enzymatic synthesis of selectively ¹³C/¹⁵N-labeled RNA for NMR structural and dynamics studies.

  2014cites this paper
• Probing the Structural Basis of Retroviral RNA Functions via NMR Spectroscopy

  2014cites this paper
• Biosynthetic preparation of 13C/15N-labeled rNTPs for high-resolution NMR studies of RNAs.

  2012cites this paper
• Isotope labeling and segmental labeling of larger RNAs for NMR structural studies.

  2012cites this paper
• Books and Reviews

  2012cites this paper
• NMR studies of the structure, kinetics and interactions of the conserved RNA motifs in the FMDV IRES.

  2012cites this paper
• RNAs synthesized using photocleavable biotinylated nucleotides have dramatically improved catalytic efficiency

  2011cites this paper
• Asymmetry of 13C labeled 3-pyruvate affords improved site specific labeling of RNA for NMR spectroscopy

  2011cites this paper
• Expression, purification and analysis of the activity of enzymes from the pentose phosphate pathway.

  2011cites this paper
• RNA SECONDARY STRUCTURE PREDICTION USING A COMBINED METHOD OF THERMODYNAMICS AND KINETICS

  2011cites this paper
• Biomass production of site selective 13C/15N nucleotides using wild type and a transketolase E. coli mutant for labeling RNA for high resolution NMR

  2011cites this paper
• Multiple conformations of SAM-II riboswitch detected with SAXS and NMR spectroscopy

  2011cites this paper
• Asymmetry of 13C labeled 3-pyruvate affords improved site specific labeling of RNA for NMR spectroscopy

  2011cites this paper
• Nucleic Acids: Dynamics Studies by Solution NMR

  2011cites this paper
• Structure determination and dynamics of protein-RNA complexes by NMR spectroscopy.

  2011cites this paper
• Growth of wildtype and mutant E. coli strains in minimal media for optimal production of nucleic acids for preparing labeled nucleotides

  2010cites this paper
• A fast, efficient and sequence-independent method for flexible multiple segmental isotope labeling of RNA using ribozyme and RNase H cleavage

  2010cites this paper
• Site-specific labeling of nucleotides for making RNA for high resolution NMR studies using an E. coli strain disabled in the oxidative pentose phosphate pathway

  2010influential citation
• Selective 13C labeling of nucleotides for large RNA NMR spectroscopy using an E. coli strain disabled in the TCA cycle

  2010cites this paper
• Chemical RNA Modifications for Studies of RNA Structure and Dynamics

  2010cites this paper
• Preparation of selective and segmentally labeled single-stranded DNA for NMR by self-primed PCR and asymmetrical endonuclease double digestion

  2009cites this paper
• Isotope labeling strategies for NMR studies of RNA

  2009cites this paper
• Biomolecular Structures by Solution Nuclear Magnetic Resonance

  2009cites this paper