Identification of tertiary base pair resonances in the nuclear magnetic resonance spectra of transfer ribonucleic acid

Br, Reid; McCollum, Lillian; Ns, Ribeiro; Abbate, Joseph; Hurd, Re

doi:10.1021/bi00585a024

Cited by 33 publications

(22 citation statements)

References 39 publications

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“… 66 Chemical shifts for UH3 in AU pairs resonated between 13 and 15 ppm and GH1 in GC pairs resonated from 12 to 13.5 ppm, as expected. 67 , 68 The absence of an imino peak for a terminal base pair in r(CU G GC U AG) 2 indicates exchange with water. The G3-H1 and U7–H3 resonances of r(CUG G AU U CAG) 2 appear to overlap, as evident by the presence of a single large peak.…”

Section: Resultsmentioning

confidence: 99%

Testing the Nearest Neighbor Model for Canonical RNA Base Pairs: Revision of GU Parameters

et al. 2012

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Thermodynamic parameters for GU pairs are important for predicting the secondary structures of RNA and for finding genomic sequences that code for structured RNA. Optical melting curves were measured for 29 RNA duplexes with GU pairs to improve nearest neighbor parameters for predicting stabilities of helixes. The updated model eliminates a prior penalty assumed for terminal GU pairs. Six additional duplexes with the 5′GG/3′UU motif were added to the single representation in the previous database. This revises the ΔG°37 for the 5′GG/3′UU motif from an unfavorable 0.5 kcal/mol to a favorable −0.2 kcal/mol. Similarly, the ΔG°37 for the 5′UG/3′GU motif changes from 0.3 to −0.6 kcal/mol. The correlation coefficients between predicted and experimental ΔG°37, ΔH°, and ΔS° for the expanded database are 0.95, 0.89, and 0.87, respectively. The results should improve predictions of RNA secondary structure.

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Section: Resultsmentioning

confidence: 99%

Testing the Nearest Neighbor Model for Canonical RNA Base Pairs: Revision of GU Parameters

et al. 2012

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“…In the case of E. coli tRNAyal, Reid and co-workers (4,6,12) have shown that the low field imino proton spectrum can be interpreted in terms of a folded structure with X 7 tertiary hydrogen bond interactions and X 20 secondary base-pairs, two of the latter shown by Johnston and Redfield (13) to be due to the G50-U64 wobble base pair (Fig. 1).…”

Section: Nucleic Acids Researchmentioning

confidence: 96%

Carbon-13 NMR relaxation studies of pre-melt structural dynamics in [4-¹³C-uracil] labeledE. colitransfer RNA₁^Val*

Oslen

Schweizer

et al. 1982

Nucl Acids Res

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We report 67.8 MHz carbon-13 spin-lattice relaxation studies on [4-13C-uracil] labeled tRNAIVal purified from E. coli SO-187. Following 13C-enriched C4 carbonyl resonances from modified and unsubstituted uridines scattered throughout the polymer backbone enables us to determine dynamical features in both loop and helical stem regions. The experimental results have been analyzed in terms of a model of isotropic overall molecular reorientation. "Anomalous" residues for which the experimental data cannot be accounted for in terms of the model provide an assessment of local and regional properties. Thus, "native" tRNAIVal under physiological conditions of magnesium (10 mM) and temperature (20 degrees - 40 degrees C), exhibits the following characteristics: 1) uridines held rigidly in helical stems and tertiary interactions display correlation times for rotational reorientation of 15-20 nsecs, typical for overall tRNA motion; 2) uridines in loops such as the wobble residue uridine-5-oxyacetic acid (V34) are quite accessible to solvent; moreover V34 and another loop residue, D17, exhibit local mobility; 3) the tertiary interactions involving 4-thio uridine (s4U8) and A14 and ribothymidine (rT54) and A58 are weakened as temperature increases.

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“…The presence of these stabilizing ions would be consistent with the proposal that the slowly exchanging protons that we observe arise from the D stem of the molecule and are dependent on the tertiary structure. In the absence of such ions, tertiary structural interactions are not completely lost because the seven or so low-field imino proton nuclear magnetic resonances associated with tertiary interactions are still present, meaning that the exchange time for these protons is still longer than about 5 msec (24). However, saturation recovery experiments indicate that the exchange with water for these resonances in the absence of magnesium is much faster than that of secondary structural resonances, which is consistent with their being no longer observable in tritium-exchange experiments (25).…”

Section: Discussionmentioning

confidence: 99%

“…3). These two molecules are identical, except that the suppressor has an A in place of the G in position 24 of the-D stem; thus a G.U pair is replaced by an A-U pair in this stem (27). This change widens the translational specificity of the molecule (27,28).…”

Section: Discussionmentioning

confidence: 99%

Tritium exchange on transfer RNA: slowly exchanging protons sensitive to a change in the dihydrouridine stem.

Ramstein¹,

Buckingham²

1981

Proc. Natl. Acad. Sci. U.S.A.

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Measurements of tritium exchange on tRNA were made for periods from 0.5 min to 8 hr after separation from labeled solvent. The exchange curve was analysed in terms of three kinetic classes of exchanging protons with half-lives of 5 hr (12 protons), 0.54 hr (37 protons and about 3.5 min (58 protons) at 00C in 0.14 M K+/10 mM Mge. The behaviour under varying ionic conditions of protons in the slowest exchange class and of some protons in the intermediate class suggests that they are dependent on the tertiary structure of the molecule. Moreover, in the same range of exchange times characteristic of these latter protons, about 9 more protons were observed in the case of a mutant form of tRNATrP, the UGA-suppressor species, than in the wild-type tRNATrP. These two species differ only in base 24 in the dihydrouridine stem. This dynamic difference between the wildtype and suppressor species may be related to a functionally important difference in coupling between the conformation of the molecule and interactions at the anticodon.ture of tRNA and suggest that tertiary structure contributes an additional source of slowly exchanging hydrogens (6, 7, 12).There is little information available to account for the overall kinetic behaviour of the protons within tRNA structure that exchange slowly. We describe here protons exchanging with a half-life of the order of hours, observable in the presence of Mg2e or spermine or 1.4 M KC1 but not in 0.14 M KCI alone.This suggests that these protons owe their slow exchange to the integrity of the tRNA tertiary structure. Furthermore, the number of these protons is sensitive to a base change in the D stem in the case of tRNATrP (Escherichia coli). We have analyzed the overall behavior of the slowly exchanging protons in terms of three classes, with average half-lives of 5 hr, 0.5 hr, and 3.5 min. We describe the behavior of these three classes under different ionic conditions and discuss their origin.During the course of its biological function, a tRNA molecule interacts with many different macromolecular species (1). Many authors have emphasized the essentially dynamic molecular structure that tRNA must have to account for these diverse interactions (2-4). Indeed, the isolated molecule in solution is conformationally heterogeneous and strongly affected by ionic conditions, such as the presence of monovalent and divalent cations and polyamines (3-7). One particularly useful probe of the dynamic aspects of nucleic acid structure is the tritium-exchange technique largely developed by Englander et aL (8). It has been shown with this technique that in double helices, five protons associated with G-C base pairs (bp) and three protons in A-U bp exchange slowly enough to be labeled with tritium and measured by Sephadex-column or fast-dialysis techniques (9, 10). All except the guanine exocyclic amino protons are dependent on transitory opening of the bp for exchange.Models favored for the opening process have usually supposed that there is a cooperative opening of several bp in ord...

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Identification of tertiary base pair resonances in the nuclear magnetic resonance spectra of transfer ribonucleic acid

Cited by 33 publications

References 39 publications

Testing the Nearest Neighbor Model for Canonical RNA Base Pairs: Revision of GU Parameters

Testing the Nearest Neighbor Model for Canonical RNA Base Pairs: Revision of GU Parameters

Carbon-13 NMR relaxation studies of pre-melt structural dynamics in [4-¹³C-uracil] labeledE. colitransfer RNA₁^Val*

Tritium exchange on transfer RNA: slowly exchanging protons sensitive to a change in the dihydrouridine stem.

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Identification of tertiary base pair resonances in the nuclear magnetic resonance spectra of transfer ribonucleic acid

Cited by 33 publications

References 39 publications

Testing the Nearest Neighbor Model for Canonical RNA Base Pairs: Revision of GU Parameters

Testing the Nearest Neighbor Model for Canonical RNA Base Pairs: Revision of GU Parameters

Carbon-13 NMR relaxation studies of pre-melt structural dynamics in [4-13C-uracil] labeledE. colitransfer RNA1Val*

Tritium exchange on transfer RNA: slowly exchanging protons sensitive to a change in the dihydrouridine stem.

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Carbon-13 NMR relaxation studies of pre-melt structural dynamics in [4-¹³C-uracil] labeledE. colitransfer RNA₁^Val*