title: The kinetics of binding of U-U-C-A to a dodecanucleotide anticodon fragment from yeast tRNA-Phe.
abstract: 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.
mesh_terms: D000227:Adenine Nucleotides; D000926:Anticodon; D001483:Base Sequence; D001665:Binding Sites; D003597:Cytosine Nucleotides; D007700:Kinetics; D009841:Oligonucleotides / Q000378:metabolism*; D009843:Oligoribonucleotides / Q000378:metabolism*; D010649:Phenylalanine; D012343:RNA, Transfer / Q000378:metabolism*; D012441:Saccharomyces cerevisiae; D013696:Temperature; D013816:Thermodynamics; D014500:Uracil Nucleotides
chemical_list: D000227:Adenine Nucleotides; D000926:Anticodon; D003597:Cytosine Nucleotides; D009841:Oligonucleotides; D009843:Oligoribonucleotides; D014500:Uracil Nucleotides; D010649:Phenylalanine; D012343:RNA, Transfer