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Biomedical subjects

R Griffey

Publications and source records attributed to R Griffey.

4 recordsLinked to original sources

Computational methods for RNA structure determination.

During the past year, major improvements have been made in methods used to solve RNA structures from crystals, find RNA patterns in sequence data and determine RNA secondary structure. Computational methods for assisting an interactive computer graphics human modeler, searching the conformational space of RNA tertiary structure, studying the dynamics of complexes involving RNA and simulating RNA catalytic activities have also been advanced.

Base Sequence↗

Kinetic characteristics of Escherichia coli RNase H1: cleavage of various antisense oligonucleotide-RNA duplexes.

1. The effects of variations in substrates on the kinetic properties of Escherichia coli RNase H were studied using antisense oligonucleotides of various types hybridized to complementary oligoribonucleotides. The enzyme displayed minimal sequence preference, initiated cleavage through an endonucleolytic mechanism near the 3' terminus of the RNA in a DNA-RNA chimera and then was processively exonucleolytic. Phosphorothioate oligodeoxynucleotides hybridized to RNA supported cleavage more effectively than phosphodiester oligodeoxynucleotides. Oligonucleotides comprised of 2'-methoxy-, 2'-fluoro- or 2'-propoxy-nucleosides did not support RNase H1 activity. 2. The Km and Vmax. of cleavage of RNA duplexes with full phosphorothioate oligodeoxynucleotides were compared with methoxy-deoxy 'gapmers', i.e.; oligonucleotides with 2'-methoxy wings surrounding a deoxynucleotide centre. Such structural modifications resulted in substantial increases in affinity, but significant reductions in cleavage efficiency. The initial rates of cleavage increased as the deoxynucleotide gap size was increased. Multiple deoxynucleotide gaps increased the Vmax. but had little effect on Km. 3. The effects of several base modifications on the site of initial cleavage, processivity and initial rate of cleavage were also studied.

Base Sequence↗

Dissociation of decreases in renal cellular energetics and recovery of renal microsomal translation during chronic cyclosporine A administration.

Male Sprague-Dawley rats were given oral cyclosporine A or control vehicle, and renal protein synthesis and renal ATP levels were examined. Acute oral cyclosporine A at 5, 10, 25 and 50 mg/kg/day for 6 days reduced [3H]L-leucine incorporation by isolated renal microsomes to 76.2, 56.8, 44.3 and 29.5% of control incorporations, respectively. No significant changes in renal ATP levels were detected by NMR spectroscopy after acute oral cyclosporine A administration at the doses indicated. However, during chronic exposure to cyclosporine A at doses of 5 and 25 mg/kg/day for 30, 60 and 90 days, there was a recovery of renal microsomal protein synthesis by day 30 at 5 mg/kg/day, and by day 45 at 25 mg/kg/day. NMR spectroscopy of the kidneys of these rats demonstrated decreases in renal ATP level by day 60 in animals given cyclosporine A at 25 mg/kg/day. Cyclosporine A administration produced a renal acidosis and up to a 40% decrease in renal ATP level by day 90 in rats fed cyclosporine A at 25 mg/kg. No apparent histologic abnormalities were observed in the ATP-deficient renal tissue by NMR imaging. Reductions in renal ATP level suggest that the recovery of renal microsomal protein synthesis is aberrant in the continued presence of cyclosporine A, or that mitochondria are direct sites of cyclosporine A toxicity.

Adenosine Diphosphate↗

Effect of the sampling rate on magnetic resonance imaging.

Effects of the sampling rate on spatial resolution and the signal-to-noise ratio in spin-echo MR imaging were calculated. The theoretical results suggest that as T2* decreases, due to either static magnetic field inhomogeneities or shortened T2 relaxation times, the calculated optimum sampling rate increases accordingly. Since biological tissues exhibit wide variations in their magnetic susceptibilities and T2 relaxation times for various isotopes but modern magnets are characterized by good magnetic field homogeneity, the optimum sampling rate should exhibit an observable dependence on the tissue type. Proton and sodium imaging experiments confirm this conclusion.

Animals↗