An NMR study of the exchange rates for protons involved in the secondary and tertiary structure of yeast tRNA<sup>phe</sup>

Johnston, Paul D.; Redfield, Alfred G.

doi:10.1093/nar/4.10.3599

Cited by 91 publications

(57 citation statements)

References 27 publications

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“…U wobble base pair in the molecule and thus the only base pair containing two hydrogen-bonded imino protons rather than one. These two imino protons are much closer to each other than those in neighbouring base pairs and therefore give much larger mutual NOEs [32]. As shown at the bottom of Fig.2, peaks R' and P give large mutual NOEs and are therefore assigned to the imino protons of G49 .…”

Section: The Ribosylthymine Stemmentioning

confidence: 90%

“…This is a Watson-Crick base pair far in space from other hydrogen-bonded imino protons and so may not give NOEs. This tertiary base pair has been assigned at 12.9 ppm in yeast tRNA"' [32]. The low-field proton NMR spectrum of E. coli tRNAYlY has thus been assigned with only a few ambiguities.…”

Section: Remaining Assignmentsmentioning

confidence: 97%

“…As the temperature increases the imino protons exchange with water via helix opening and their resonances decrease in intensity (spectroscopic melting) [32]. The temperature at which most of the imino peaks disappear increases with magnesium concentration; however the same order of melting is observed at all magnesium concentrations.…”

Section: Temperature Efffctsmentioning

confidence: 99%

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Imino proton NMR assignments and ion‐binding studies on Escherichia coli tRNA₃^Gly

Hyde¹

1986

European Journal of Biochemistry

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The imino region of the proton NMR spectrum of Escherichia coli tRNAQIY has been assigned mainly by sequential nuclear Overhauser effects between neighbouring base pairs and by comparison of assignments of other tRNAs. The effects of magnesium, spermine and temperature on the 'H and 31P NMR spectra of this tRNA were studied. Both ions affect resonances close to the G 15 . C48 tertiary base pair and in the ribosylthymine loop. The magnesium studies indicate the presence of an altered tRNA conformer at low magnesium concentrations in equilibrium with the high magnesium form. The temperature studies show that the A7 . U66 imino proton (from a secondary base pair) melts before some of the tertiary hydrogen bonds and that the anticodon stem does not melt sequentially from the ends. Correlation of the ion effects in the 'H and 31P NMR spectra has led to the tentative assignment of two 31P resonances not assigned in the comparable 31P NMR spectrum of yeast tRNAPhe. 31P NMR spectra of E. coli tRNAF'y lack resolved peaks corresponding to peaks C and F in the spectra of E. coli tRNAPhe and yeast tRNAPhe. In the latter tRNAs these peaks have been assigned to phosphate groups in the anticodon loop. Ion binding to E. coli tRNA?lY and E. coli tRNAPhe has different effects on their 'H NMR spectra which may reflect further differences in their charge distribution and conformation.The conformation of transfer ribonucleic acids in solution is of interest because of their role in protein synthesis. All tRNAs within a cell interact with the same initiation and elongation factors and ribosomes and hence must have elements of similar structure. Indeed most tRNAs can form cloverleaf secondary structures and have invariant or semiinvariant bases at tertiary folding sites. However, each group of isoaccepting tRNAs is charged with the appropriate aminoacid by a specific aminoacyl-tRNA synthetase. This specificity could derive either from direct interaction of the synthetase with base sequences unique to the isoaccepting tRNAs or from differences in the solution conformation of tRNAs. Differences in the conformation of tRNAs would result in differences in their charge distribution and hence in the binding of ions. I have therefore studied the binding of ions to tRNAs in solution in order to probe their conformational differences or similarities.The method of choice for such a study is nuclear magnetic resonance spectroscopy as NMR spectra are very sensitive to the chemical environment around each observed nucleus. In this study both low-field 'H NMR spectra and 31P NMR spectra have been used. The low-field 'H NMR spectra contain resonances from the hydrogen-bonded imino protons of the secondary and tertiary base pairs. In general, each base pair gives rise to a separate signal which can be monitored (reviewed in [I]). 31P NMR spectra give information complementary to the low-field 'H NMR spectra. Although phosphates in the helical stems and stacked regions of the tRNA resonate at similar frequencies and are not resolved,Correspondence to ...

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Section: The Ribosylthymine Stemmentioning

confidence: 90%

Section: Remaining Assignmentsmentioning

confidence: 97%

Section: Temperature Efffctsmentioning

confidence: 99%

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Imino proton NMR assignments and ion‐binding studies on Escherichia coli tRNA₃^Gly

Hyde¹

1986

European Journal of Biochemistry

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“…Crosslinking strategies can also help identify the contacts between nucleic acids and cognate proteins [154 -157] and reveal the organization of multisubunit functional complexes [158 -160]. The possible application of hydrogen/deuterium exchange (HDX) to characterize the contact interfaces between assembled units has been hampered by the fast exchange rate exhibited in solution by the nucleic acid components [161,162]. However, this approach has been successfully employed to highlight the protein surfaces in contact with them and to study the dynamics associated with the specific interactions [163][164][165].…”

Section: Elucidating Structure-function Relationshipsmentioning

confidence: 99%

A eole for the MS analysis of nucleic acids in the post-genomics age

Fabris

2010

J. Am. Soc. Mass Spectrom.

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The advances of mass spectrometry in the analysis of nucleic acids have tracked very closely the exciting developments of instrumentation and ancillary technologies, which have taken place over the years. However, their diffusion in the broader life sciences community has been and will be linked to the ever evolving focus of biomedical research and its changing demands. Before the completion of the Human Genome Project, great emphasis was placed on sequencing technologies that could help accomplish this project of exceptional scale. After the publication of the human genome, the emphasis switched toward techniques dedicated to the exploration of sequences not coding for actual protein products, which amount to the vast majority of transcribed elements. The broad range of capabilities offered by mass spectrometry is rapidly advancing this platform to the forefront of the technologies employed for the structure-function investigation of these noncoding elements. Increasing focus on the characterization of functional assemblies and their specific interactions has prompted a re-evaluation of what has been traditionally construed as nucleic acid analysis by mass spectrometry. Inspired by the accelerating expansion of the broader field of nucleic acid research, new applications to fundamental biological studies and drug discovery will help redefine the evolving role of MS-analysis of nucleic acids in the post-genomics age. (J Am Soc Mass Spectrom 2010, 21, 1-13)

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“…This leads to the saturation of the latter imino proton resonances so that they cannot be observed anymore. 5 Several alternative experimental techniques have been proposed in the past, the current one being the application of a semiselective observation pulse. The underlying principle of this method is to excite the resonances of interest without disturbing the water peak.…”

Section: Introductionmentioning

confidence: 99%

Effective water resonance suppression in 1D‐ and 2D‐FT–¹H‐nmr spectroscopy of biopolymers in aqueous solution

Haasnoot¹,

Hilbers²

1983

Biopolymers

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An NMR study of the exchange rates for protons involved in the secondary and tertiary structure of yeast tRNA^phe

Cited by 91 publications

References 27 publications

Imino proton NMR assignments and ion‐binding studies on Escherichia coli tRNA₃^Gly

Imino proton NMR assignments and ion‐binding studies on Escherichia coli tRNA₃^Gly

A eole for the MS analysis of nucleic acids in the post-genomics age

Effective water resonance suppression in 1D‐ and 2D‐FT–¹H‐nmr spectroscopy of biopolymers in aqueous solution

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An NMR study of the exchange rates for protons involved in the secondary and tertiary structure of yeast tRNAphe

Cited by 91 publications

References 27 publications

Imino proton NMR assignments and ion‐binding studies on Escherichia coli tRNA3Gly

Imino proton NMR assignments and ion‐binding studies on Escherichia coli tRNA3Gly

A eole for the MS analysis of nucleic acids in the post-genomics age

Effective water resonance suppression in 1D‐ and 2D‐FT–1H‐nmr spectroscopy of biopolymers in aqueous solution

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An NMR study of the exchange rates for protons involved in the secondary and tertiary structure of yeast tRNA^phe

Imino proton NMR assignments and ion‐binding studies on Escherichia coli tRNA₃^Gly

Imino proton NMR assignments and ion‐binding studies on Escherichia coli tRNA₃^Gly

Effective water resonance suppression in 1D‐ and 2D‐FT–¹H‐nmr spectroscopy of biopolymers in aqueous solution