Probing the anticodon loop structure in yeast tRNA(Phe-Y) with single strand-specific nuclease S1

Yeast tRNA(Phe) and tRNA(Phe-Y) are cleaved by single strand-specific endonuclease S1 at the same positions within the anticodon loop (phosphates 34, 36 and 37) and at the 3'-terminus (phosphates 75 and 76). The efficiency of the anticodon loop hydrolysis is much higher in tRNA(Phe-Y) while the cutting at the 3'-terminus is not influenced considerably by the Y-base1 removal from yeast tRNA(Phe). The effect of the Y-base excision on the structure of the anticodon loop is discussed on the basis of the S1 digestion studies as well as other relevant results.