Nuclear magnetic resonance and nuclear Overhauser effect study of yeast phenylalanine transfer ribonucleic acid imino protons

Johnston, Paul D.; Redfield, Alfred G.

doi:10.1021/bi00508a016

Cited by 86 publications

(91 citation statements)

References 38 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…However, even if uti had an error as high as 25%, our estimate of ru would have an uncertainty of less than 5%. The present estimate is similar to the value of 0.288 nm estimated by Johnston & Redfield (1981) for the imino-imino distance of the GU-4 base pair in yeast tRNAPhe. Since the latter workers did not have an independent measure of rR but had to guess a value, the present estimate of ru = 0.272 nm may be considered the more reliable value.…”

Section: R O T a T I O N A L D Y N A M I C S O F T R Nsupporting

confidence: 90%

Rotational dynamics of transfer ribonucleic acid: effect of ionic strength and concentration

Jc¹,

Schurr²,

Dr³

1984

Biochemistry

View full text Add to dashboard Cite

We have investigated the influence of ionic strength and nucleic acid concentration on the rotational Brownian motion of Escherichia coli tRNA1Val by studying the decay of the fluorescence polarization anisotropy (FPA) of intercalated ethidium on a nanosecond time scale. The rotational relaxation time tau R remains essentially constant as the ionic strength is varied from 2 to 100 mM at a tRNA concentration of 54 mg/mL. tau R also remains practically unchanged as the tRNA concentration is varied from 0.3 to 54 mg/mL at an ionic strength of 130 mM. Present hydrodynamic theories generally predict a more pronounced concentration dependence for rotational diffusion than we observe. This disagreement may result from a nonrandom distribution of the tRNA molecules in solution due to electrostatic interactions. By combining independent data from time-resolved nuclear Overhauser effect (NOE) cross-relaxation experiments and FPA experiments on the same tRNA, we are able to estimate the interproton spacing for the guanine N1-H and the uracil N3-H of the GU-50 base pair in E. coli tRNA1Val. This distance is 0.272 nm.

show abstract

Section: R O T a T I O N A L D Y N A M I C S O F T R Nsupporting

confidence: 90%

Rotational dynamics of transfer ribonucleic acid: effect of ionic strength and concentration

Jc¹,

Schurr²,

Dr³

1984

Biochemistry

View full text Add to dashboard Cite

show abstract

“…In the parameter set of Gralla and Crothers it is assumed that the thermodyanmic properties of G:U pairs are identical to those of A:U pairs. This assumption is also used in this work: it is supported by experimental results from oligonucleotide binding to tRNA (20,21,22), NMR-studies on G:U containing RNA-double helices (23,24,25,26), and calculations on the stability of G:U containing tRNAs.…”

Section: ) Helix Growthmentioning

confidence: 82%

Conformational Transitions in Viroids and Virusoids: Comparison of Results from Energy Minimization Algorithm and from Experimental Data

Steger

Hofmann

Förtsch

et al. 1984

Journal of Biomolecular Structure and Dynamics

126

View full text Add to dashboard Cite

Viroids are single-stranded circular RNA molecules of 240 to 400 nucleotides which are pathogens of certain higher plants and replicate autonomously in the host cell. Virusoids are similar to viroids in respect to size and circularity but replicate only as genomic part of a plant virus. Their structure and structural transitions have been investigated by thermo-dynamic, kinetic and hydrodynamic methods. The special features of the sequences of these RNAs, which are the basis for their secondary structures and structural flexibility, are investigated with theoretical methods. A set of thermodynamic parameters for helix growth and loop formation is selected from the literature to calculate secondary structures and structural transitions of single-stranded RNAs. Appropriate modifications of the chosen parameter set are discussed. For calculations we used either Tinoco-plots and the model of "cooperative helices" or the Zuker-program based on the exact algorithm of Nussinov et al, or both. Calculations were done for viroids and virusoids. As both are single-stranded, circular RNAs we had to modify the Zuker-program as described in the appendix. Calculations are done for different viroids, i.e. potato spindle tuber, citrus exocortis, chrysanthemum stunt, coconut cadang-cadang, and avocado sunblotch, and for two virusoids, i.e. the circular RNAs of Solanum nodiflorum mottle virus, and velvet tobacco mottle virus. For viroids the calculations confirm our earlier theoretical and experimental results about the extended native structure and the highly cooperative transition into a branched structure. Virusoids show less base pairing, branching in the native secondary structure, and only low cooperativity during denaturation. They resemble more closely the properties of random sequences with length, G:C content, and circularity as in viroids but statistical sequences. The comparison of viroids, virusoids, and circular RNA or random sequences confirms the uniqueness of viroid structure.

show abstract

“…The sample was later lyophilized and redissolved in 99.8% 2H20 for the deuterium exchange experiment. Both Redfield 2-1-4 soft-pulse (8) and single ('90°) strong-pulse experiments were performed on a Bruker WM-500 NMR spectrometer located at the Chemical Instrumentation Center, Department of Chemistry, Yale University. Proton NMR spectra were obtained in 'H20 and 2H20.…”

Section: Methodsmentioning

confidence: 99%

Detection of a guanine X adenine base pair in a decadeoxyribonucleotide by proton magnetic resonance spectroscopy.

Kan

Chandrasegaran

Pulford

et al. 1983

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

134

View full text Add to dashboard Cite

A decadeoxyribonucleotide, d(C-C-A-A-G-A-T-T-G-G) (I), forms a duplex in solution. The base pairing pattern in this duplex was studied by proton nuclear magnetic resonance spectroscopy. Five NH...N hydrogen-bonded proton resonances were observed, and they were assigned by nuclear Overhauser enhancement experiments as well as by comparison to five previously assigned NH...N hydrogen-bonded proton resonances in a self-complementary duplex of similar sequence, d(C-C-A-A-G-C-T-T-G-G) (II). The results suggest that the central -G-A- residues of I form G X A base pairs in the helical state. The fact that the H2 proton of A at the sixth position from the 5' end of I showed nuclear Overhauser enhancement when the NH...N hydrogen-bonded proton resonance of G X A was irradiated suggests that the bases of the G X A base pair are oriented in an anti-anti conformation. Comparison of the linewidths at the half height of the NH...N hydrogen-bonded proton resonances of I at 1 degree C suggest that the G X A base pairs are less stable than adjacent A X T base pairs.

show abstract

Nuclear magnetic resonance and nuclear Overhauser effect study of yeast phenylalanine transfer ribonucleic acid imino protons

Cited by 86 publications

References 38 publications

Rotational dynamics of transfer ribonucleic acid: effect of ionic strength and concentration

Rotational dynamics of transfer ribonucleic acid: effect of ionic strength and concentration

Conformational Transitions in Viroids and Virusoids: Comparison of Results from Energy Minimization Algorithm and from Experimental Data

Detection of a guanine X adenine base pair in a decadeoxyribonucleotide by proton magnetic resonance spectroscopy.

Contact Info

Product

Resources

About