Biomedical subjects

D R Kearns

Publications and source records attributed to D R Kearns.

125 records · Page 7Linked to original sources

PubMed1973

Effect of the removal of the Y base on the conformation of yeast tRNA.

The effect of removing the Y base from the anticodon loop of yeast tRNA(Phe) has been examined by high-resolution proton nuclear magnetic resonance spectroscopy and optical melting. Analysis of the changes in the nuclear magnetic resonance spectra indicate that the removal of the Y base produces a small conformational change in the anticodon stem in which all the interbase separations are increased by approximately 0.2 A. The temperature dependence of the nuclear magnetic resonance spectra and the optical melting measurements indicate that the high temperature stability of tRNA(Phe) is decreased by removal of the Y base. With the exception of the anticodon stem, the secondary structure of the other helical stems of the molecule appear to be unaltered when the Y base is excised.

Hydrochloric Acid↗

PubMed1973

Determination of secondary and tertiary structural features of transfer RNA molecules in solution by nuclear magnetic resonance.

High-resolution 300-MHz proton nuclear magnetic resonance spectra of the hydrogen-bounded protons in three different purified tRNA molecules are presented. The resonances in the region between -11 and -15 ppm from 2,2-dimethyl-2-silapentane-5-sulfonate (DSS) are assigned to the ring NH protons of specific base pairs by two approaches. First, intrinsic positions of -14.8 ppm and -13.7 ppm are taken for the AU and GC ring NH protons, respectively, and the spectra are calculated by including ring current shifts from the nearest neighbors. The spectra calculated in this way on the basis of the cloverleaf are in good agreement with the observed. Second, fragments of yeast tRNA(Phe) were obtained, which helped in assignments of the spectrum of intact molecules. The close agreement strongly supports the cloverleaf model. Tertiary structural features were determined in a few cases where the ring currents at the terminal base pairs of helical regions depended upon stacking of the helices. In this way, we were able to show that in Escherichia coli tRNA(Glu) the CCA stem forms a continuous helix with the TPsiC stem, which is in accord with the preliminary x-ray structure of yeast tRNA(Phe), suggesting that this stacking is observed in solution and may be a general property of different tRNA molecules. Similar reasoning suggests that in E. coli tRNA(fMet) G-27 is stacked upon the dihydrouridine helix.

Base Sequence↗

PubMed1973

Conformation of charged and uncharged tRNA.

The effect of aminoacylation on the conformation of yeast tRNA(Phe) was investigated by high-resolution (300 MHz) proton nuclear magnetic resonance (NMR) spectroscopy. Resonances in the low-field (-11 to -15 ppm) region of the spectra are due to ring NH protons of Watson-Crick base pairs, and to a very high degree of approximation (within 0.05 ppm) the low-field spectra of tRNA(Phe) and phenylalanyl-tRNA(Phe) are identical. From this observation and analysis of the low-field NMR spectra we conclude that the secondary structures of the two tRNAs are identical with respect to base-pairing schemes and interbase distances in the helical region (0.1-0.2 A). Several tertiary structural features, including conformation of the dihydro-U loop, conformation of the minor loop, relative orientations of the acceptor and the TPsiC stems, dihydro-U and anticodon stems, and probably conformation of the anticodon loop are shown to be the same in tRNA(Phe) and phenylalanyl-tRNA(Phe). Our results leave little remaining opportunity for changes in tertiary structure that would not have been observed by the NMR method.

Base Sequence↗

PubMed1973