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D H Turner

Publications and source records attributed to D H Turner.

117 records · Page 7Linked to original sources
PubMed1976

The kinetics of binding of U-U-C-A to a dodecanucleotide anticodon fragment from yeast tRNA-Phe.

The kinetics of U-U-C-A binding to the dodecanucleotide (A-Cm-U-Gm-A-A-Y-A-psi-m5C-U-Gp) isolated from the anticodon region of yeast tRNA-Phe are similar to the kinetics of binding of U-U-C-A to intact tRNA-Phe. A large enhancement in binding constant over that predicted for U-U-C-A-U-G-A-A is observed for both the complexes of dodecanucleotide and tRNA-Phe with U-U-C-A. This strongly suggests that both the anticodon loop in tRNA-Phe and the dodecanucleotide can form four base pairs with U-U-C-A. Furthermore, the enhanced stability cannot be attributed to a special conformation of the anticodon loop, but instead the anticodon loop is probably flexible. A likely explanation for the increased binding is the effect of non-base-paired ends. This increased thermodynamic stability comes from a larger entropy gain rather than a larger enthalpy decrease.

Adenine Nucleotides↗
PubMed1975

Fluorescence detected circular dichroism study of the anticodon loop of yeast tRNAPhe.

Fluorescence detected circular dichroism (FDCD) measurements have been used to study the conformations of the anticodon loop of yeast phenylalanine tRNA. To our knowledge this is the first application of fluorescence detected circular dichroism. Much smaller amounts of tRNA are needed for the measurement of FDCD than for the conventionally measured circular dichroism. Furthermore, FDCD is specific for conformational changes near the anticodon loop. The FDCD measurements suggest a transition in the anticodon loop near 20 degrees in 0.01 M MgCl2-0.1 M NaCl (pH 7). This is followed by a broad transition from 30 to 60 degrees and finally a sharp melting at 75 degrees consistent with the absorbance detected melting of the entire tRNA. Removal of Mg2+ from the tRNA at 1 degrees causes nearly a factor of two decrease in the FDCD near 230 nm. This indicates a decrease in conformational rigidity in the anticodon loop on removal of Mg2+.

Anticodon↗
PubMedDate not supplied

The energetics of small internal loops in RNA.

The energetics of small internal loops are important for prediction of RNA secondary and tertiary structure, selection of drug target sites, and understanding RNA structure-function relationships. Hydrogen bonding, base stacking, electrostatic interactions, backbone distortion, and base-pair size compatibility all contribute to the energetics of small internal loops. Thus, the sequence dependence of these energetics are idiosyncratic. Current approximations for predicting the free energies of internal loops consider size, asymmetry, closing base pairs, and the potential to form GA, GG, or UU pairs. The database of known three-dimensional structures allows for comparison with the models used for predicting stability from sequence.

Base Pairing↗
PubMedDate not supplied

The chemical synthesis of oligoribonucleotides with selectively placed 2'-O-phosphates.

A phosphoramidite, solid support method for the chemical synthesis of oligoribonucleotides containing 2'-O-phosphate at a selected position is presented. Synthesis of these oligoribonucleotides is based on uridine- and adenosine-(2'-O-phosphate)-3'-phosphoramidites, and a new condition for removal of 2'-O-phosphate protecting groups, which does not cleave internucleotide bonds. The structure of oligoribonucleotides with 2'-O-phosphate has been proven by enzymatic digestions and dephosphorylation by yeast 2'-phosphotransferase.

Adenosine↗