Proton magnetic resonance studies on the conformation of the hexanucleotide, GmpApApYpApsiP, and Related fragments from the anticodong loop of baker's yeast phenylalanine transfer ribonucleic acid.

A hexanucleotide, GmpApApYpAppsiP, and 11 related compounds from the anticodon loop of Baker's yeast tRNA-Phe were studied by proton magnetic resonance from 100 to 250 MHz. Totally 19 resonance lines from all the base protons (H8, H6, and H2), H1', and methyl proton resonances of the hexamer have been assigned by a systematic "incremental procedure" in comparing all the related shorter fragments. Emphasis is given to the Y base and its stacking conformation with respect to its nearest neighboring bases. The results reveal a strong tendency of the purine bases to have a maximal extent of base-base overlap with their neighbors in the sequence. This tendency is manifested in a zigzag (or balcony-like) mode of base-stacking pattern of the -ApYpA-sequence in the hexamer in which the -pA-residue tends to stack toward the adduct ring (C10, C11, and N12) of Y. This tendency is also shown in the formation of a stack of GmAAA closing the gap left behind by the excision of Y in the hexamer GmpApAp--pApp. The implication of these findings to the structure and function of tRNA is discussed.