1
|
Advanced approaches for elucidating structures of large RNAs using NMR spectroscopy and complementary methods. Methods 2020; 183:93-107. [DOI: 10.1016/j.ymeth.2020.01.009] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2019] [Revised: 11/11/2019] [Accepted: 01/16/2020] [Indexed: 11/23/2022] Open
|
2
|
Campbell ID, Dobson CM. The application of high resolution nuclear magnetic resonance to biological systems. METHODS OF BIOCHEMICAL ANALYSIS 2006; 25:1-133. [PMID: 34772 DOI: 10.1002/9780470110454.ch1] [Citation(s) in RCA: 65] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
|
3
|
Abstract
NMR spectroscopy is a powerful tool for studying proteins and nucleic acids in solution. This is illustrated by the fact that nearly half of all current RNA structures were determined by using NMR techniques. Information about the structure, dynamics, and interactions with other RNA molecules, proteins, ions, and small ligands can be obtained for RNA molecules up to 100 nucleotides. This review provides insight into the resonance assignment methods that are the first and crucial step of all NMR studies, into the determination of base-pair geometry, into the examination of local and global RNA conformation, and into the detection of interaction sites of RNA. Examples of NMR investigations of RNA are given by using several different RNA molecules to illustrate the information content obtainable by NMR spectroscopy and the applicability of NMR techniques to a wide range of biologically interesting RNA molecules.
Collapse
Affiliation(s)
- Boris Fürtig
- Institute for Organic Chemistry and Chemical Biology, Center for Biomolecular Magnetic Resonance, Johann Wolfgang Goethe University, Marie-Curie-Strasse 11, 60439 Frankfurt am Main, Germany
| | | | | | | |
Collapse
|
4
|
Choi BS, Redfield AG. NMR study of nitrogen-15-labeled Escherichia coli valine transfer RNA. Biochemistry 1992; 31:12799-802. [PMID: 1463750 DOI: 10.1021/bi00166a013] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
1,3-15N-Labeled uracil was synthesized chemically and used to prepare labeled Escherichia coli tRNA(Val) biosynthetically. 500-MHz measurements of 15N and proton chemical shift were obtained, for all uridine and uridine-related bases, by heteronuclear multiple-quantum coherence spectroscopy. All the uracil NH group resonances were assigned and were in agreement with previous proton-only assignments. The temperature dependence of intensities of resonances was used to infer the relative stability of parts of the molecule. The acceptor stem was the least thermally stable structural feature, while the anticodon and T loop were relatively more stable.
Collapse
Affiliation(s)
- B S Choi
- Graduate Department of Biochemistry, Brandeis University, Waltham, Massachusetts 02254
| | | |
Collapse
|
5
|
Pease AC, Wemmer DE. Characterization of the secondary structure and melting of a self-cleaved RNA hammerhead domain by 1H NMR spectroscopy. Biochemistry 1990; 29:9039-46. [PMID: 1702996 DOI: 10.1021/bi00490a022] [Citation(s) in RCA: 36] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
We have completely assigned the extreme low-field ring-NH nuclear magnetic resonance spectrum of a self-cleaving RNA in the absence of magnesium ions by experiments involving sequential Overhauser enhancements between adjacent base pairs. These assignments substantiate the hammerhead secondary folding model proposed by Symons and co-workers for this class of self-cleaving RNA [Hutchins, C. J., Rathjen, P. D., Forster, A. C., & Symons, R. H. (1986) Nucleic Acids Res. 14, 3627-3640; Forster, A. C. & Symons, R. H. (1987) Cell 49, 211-220; Kneese, P., & Symons, R. H. (1987) in Viroids and Viroid-like Pathogens (Semancick, J. S., Ed.) pp 1-47, CRC Press, Boca Raton, FL]. No resonances due to tertiary base pairs could be identified in the low-field spectrum, and addition of MgCl2 to the sample did not produce additional resonances in this region of the spectrum.
Collapse
Affiliation(s)
- A C Pease
- Department of Chemistry, Lawrence Berkeley Laboratory, University of California, Berkeley 94720
| | | |
Collapse
|
6
|
Schweizer MP, Olsen JI, Stolk JA, Lee YC, Reeves PM, Perry C, De N. Interactions of Escherichia coli SO-187 tRNA(IVal) with Bacillus stearothermophilus valine-tRNA synthetase studied by 13C-NMR. BIOCHIMICA ET BIOPHYSICA ACTA 1989; 1008:293-300. [PMID: 2667642 DOI: 10.1016/0167-4781(89)90019-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
Uracil isotopically labelled with 13C at C4 and C5 has been incorporated into nucleic acids of the Escherichia coli uracil auxotroph, SO-187. [4,5-13C]uracil-labeled tRNA(IVal) was isolated and purified. 13C longitudinal relaxation times measured at 67.8 MHz demonstrated that the C5 dipole caused a 20-50% increase in the C4 relaxation. Interactions of this tRNA with valine-tRNA synthetase (VTS) purified from Bacillus stearothermophilus were established by 13C-NMR. Specific spectral changes were seen at 4-thiouridine, ribothymidine and pseudouridine of the 'bend' in the three-dimensional structure, and particularly at the uridine-5-oxyacetic acid in the wobble position of the anticodon. Thus, the protein seems to be in contact along the entire tRNA molecule, including the anticodon loop.
Collapse
Affiliation(s)
- M P Schweizer
- Department of Medicinal Chemistry, University of Utah, Salt Lake City 84112
| | | | | | | | | | | | | |
Collapse
|
7
|
Abstract
The early NMR research on nucleic acids was of a qualitative nature and was restricted to partial characterization of short oligonucleotides in aqueous solution. Major advances in magnet design, spectrometer electronics, pulse techniques, data analysis and computational capabilities coupled with the availability of pure and abundant supply of long oligonucleotides have extended these studies towards the determination of the 3-D structure of nucleic acids in solution.
Collapse
Affiliation(s)
- D J Patel
- Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY 10032
| | | | | |
Collapse
|
8
|
Griffey RH, Davis DR, Yamaizumi Z, Nishimura S, Hawkins BL, Poulter CD. 15N-labeled tRNA. Identification of 4-thiouridine in Escherichia coli tRNASer1 and tRNATyr2 by 1H-15N two-dimensional NMR spectroscopy. J Biol Chem 1986. [DOI: 10.1016/s0021-9258(18)67204-7] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022] Open
|
9
|
Carter CW, Green DC, Toomim CS, Betts L. Two-step purification of tryptophan-accepting tRNA from Bacillus stearothermophilus. Anal Biochem 1985; 151:515-9. [PMID: 3854274 DOI: 10.1016/0003-2697(85)90213-1] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
Tryptophan-accepting tRNA has been purified essentially to homogeneity from Bacillus stearothermophilus. Crude tRNA was chromatographed first on benzoylated DEAE-cellulose and then on Sepharose 4B with reverse salt gradient elution. The product has tryptophan acceptor activity in excess of 2 nmol [14C]tryptophan per A260 unit. This procedure avoids costly aminoacylation, a step characteristic of other one- and two-step procedures. In two separate purifications 7 and 11 mg of tRNAtrp were prepared from 750 and 1000 g of frozen cells, respectively. This yield compares favorably with that from other procedures. The pure tRNAtrp has been crystallized under several different conditions.
Collapse
|
10
|
Cenatiempo Y, Twardowski T, Redfield B, Reid BR, Dauerman H, Weissbach H, Brot N. Simplified in vitro system for study of eukaryotic mRNA translation by measuring di- and tripeptide formation. Proc Natl Acad Sci U S A 1983; 80:3223-6. [PMID: 6574481 PMCID: PMC394012 DOI: 10.1073/pnas.80.11.3223] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023] Open
Abstract
An in vitro system for measurement of rabbit globin mRNA translation has been developed based on the formation of the NH2-terminal dipeptide, fMet-Val. The basic components include a partially purified initiation factor preparation from rabbit reticulocytes supplemented with eukaryotic initiation factor 4A, purified and formylated yeast Met-tRNAi, and rabbit liver or Escherichia coli Val-tRNA1Val. Picomole quantities of fMet-Val are synthesized, dependent on mRNA, and the dipeptide is readily assayed by a simple extraction procedure. In the presence of Leu-tRNA or His-tRNA, the tripeptides fMet-Val-Leu and fMet-Val-His are synthesized, corresponding to the NH2-terminal sequence of alpha- and beta-globin, respectively. Therefore, tripeptide synthesis provides a simple means to distinguish between the expression of the alpha- and beta-globin mRNA species.
Collapse
|
11
|
Johnston PD, Redfield AG. Study of transfer ribonucleic acid unfolding by dynamic nuclear magnetic resonance. Biochemistry 1981; 20:3996-4006. [PMID: 7025889 DOI: 10.1021/bi00517a008] [Citation(s) in RCA: 45] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Abstract
Nuclear magnetic resonance (NMR) measurements of proton exchange were performed on yeast tRNAPhe, and in much less detail on Escherichia coli tRNAfMet, over a range of Mg2+ concentrations and temperatures, at neutral pH and 0.1 M NaCl. The resonances studied were those of ring nitrogen protons, resonating between 10 and 15 ppm downfield from sodium 3-(trimethylsilyl)-1-propanesulfonate, which partake in hydrogen bonding between bases of secondary and tertiary pairs. Methods include saturation--recovery, line width, and real-time observation after a change to deuterated solvent. The relevant theory is briefly reviewed. We believe that most of the higher temperature rates reflect major unfolding of the molecule. For E. coli tRNAfMet, the temperature dependence of the rate for the U8--A14 resonance maps well onto previous optical T-jump studies for a transition assigned to tertiary melting. For yeast tRNAPhe, exchange rates of several resolved protons could be studied from 30 to 45 degrees C in zero Mg2+ concentration and had activation energies on the order of 40 kcal/mol. Initially, the tertiary structure melts, followed shortly by the acceptor stem. At high Mg2+ concentration, relatively few exchange rates are measurable below the general cooperative melt at about 60 degrees C; these are attributed to tertiary changes. Real-time observations suggest a change in the exchange mechanism at room temperature with a lower activation energy. The results are compared with those obtained by other methods directed toward assaying ribonucleic acid dynamics.
Collapse
|
12
|
Rittschof D, Traugh JA. Purification of messenger ribonucleoprotein particles from rabbit reticulocytes by zonal centrifugation in metrizamide. EUROPEAN JOURNAL OF BIOCHEMISTRY 1981; 115:45-52. [PMID: 7227370 DOI: 10.1111/j.1432-1033.1981.tb06195.x] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Abstract
A large-scale purification procedure for messenger ribonucleoprotein (mRNP) particles from rabbit reticulocyte polysomes is described. The mRNP particles were dissociated from polysomes by treatment with urea and separated by differential centrifugation under conditions of high ionic strength. Zonal centrifugation in a metrizamide buoyant density gradient was the final purification step. One major class of mRNA particle was observed. The RNA was defined as mRNA by polyacrylamide gel electrophoresis and by globin production in a cell-free protein-synthesizing system. The twenty-three different proteins associated with the particle were a discrete set of proteins, which ranged in molecular weight from 175,000 to 23,500. The relative amount of each peptide in the particle was determined from a gel scan of the stained protein by computer simulation. None of the polypeptides comigrated with proteins from the 40-S and 60-S ribosomal subunits when analyzed by two-dimensional polyacrylamide gel electrophoresis.
Collapse
|
13
|
Schweizer MP, Hamill WD, Walkiw IJ, Horton WJ, Grant DM. Carbon-13 NMR studies on [4-13C] uracil labelled E. coli transfer RNA1(Val1). Nucleic Acids Res 1980; 8:2075-83. [PMID: 7001371 PMCID: PMC324059 DOI: 10.1093/nar/8.9.2075] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023] Open
Abstract
In this paper we describe carbon-13 nuclear magnetic resonance results on 13C-enriched purified transfer RNAI(VAL) from from E. coli SO-187, a uracil requiring auxotroph. The organism was grown on uracil 90% 13C-enriched at the carbonyl C4 position. Transfer RNAI(Val) was purified from bulk tRNA by sequential chromatography on columns of BD cellulose, DEAE-Sephadex A-50 and reverse gradient sepharose 4B. Dihydrouridine, 4-thiouridine, and uridine 5-oxyacetic acid located at discrete positions in the polymer backbone were tentatively assigned in the highly resolved 25 MHz 13C-spectra. Chemical shift versus temperature plots reveal differential thermal perturbation of the ordered solution structure, evident in the large dispersion (ca 3-4 ppm) of the uridine C4 resonances. Over the range 26-68 degrees C, V in the anticodon displays the largest downfield shift. Whereas several uridine residues rapidly shift downfield between 50-68 degrees, one moves upfield beginning at 37 degrees. The results are qualitatively compared with proton NMR analysis of the three dimensional structure.
Collapse
|
14
|
Abstract
The addition of Ser AGC AGU tRNA to an E. coli cell-free protein synthesizing system which contains the endogenous tRNA levels results in up to 100% of the ribosomes translating the MS2 coat gene shifting into the -1 reading frame. An analogous phenomenon is seen at a much lower level without the tRNA addition, where a shift into the +1 frame can also be detected. Thus translation with the endogenous tRNA levels yields proteins which have the amino terminus of the coat protein but which are substantially larger than the coat protein and comprise about 5% of the coat translation. Since the lysis gene overlaps the 3' end of the coat gene in the +1 frame, we conclude that the reading frame shift into the +1 frame yields a hybrid protein. Also, we present evidence that ribosomes translating the synthetase gene shift into the -1 frame near the distal end of the gene. This frameshifting is promoted by thrACU ACC tRNA. Specific competitor tRNAs for both Thr and Ser tRNA-promoted frameshifting have been characterized. The generality of this new mechanism for producing additional proteins is unclear, but it investigation should increase understanding of the coding mechanism and its origin.
Collapse
|
15
|
Reid BR. The use of nuclear magnetic resonance in the study of transfer RNA structure of solution. Methods Enzymol 1979; 59:21-57. [PMID: 374939 DOI: 10.1016/0076-6879(79)59071-5] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
|
16
|
Abstract
The 5. 8S ribosomal RNA of bakers yeast contains one particularly stable hairpin helix which is isolated by partial T1 ribonuclease digestion. Thermal hyperchromism analysis of the hairpin fragment showed that it dissociates cooperatively with 18% hyperchromism, with a Tm of 83 degree C at 2.7 mM sodium ion concentration, and with a hyperchromic difference spectrum indicative of over 90% G + C content. The probable secondary structure for the fragment was used to predict a helix free energy, delta G = -16.2 kcal/mole, which was the same as that determined from the melting equilibrium. The predicted enthalpy however, was 77% of the value, delta H = -114 kcal/mole, determined from the van't Hoff relationship. The effect on these data of a G.U base pair within the 9 base pair helix is discussed.
Collapse
|
17
|
Geerdes HA, van Boom JH, Hilbers CW. Codon--anticodon interaction in yeast tRNAPhe: an 1H NMR study. FEBS Lett 1978; 88:27-32. [PMID: 346374 DOI: 10.1016/0014-5793(78)80599-7] [Citation(s) in RCA: 21] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
|
18
|
|
19
|
|
20
|
|