Circular Dichroism Study of Nine Species of Transfer Ribonucleic Acid

A detailed circular dichroism (CD) study of nine species of tRNA has been done to obtain as much information about the structure of these molecules as possible. CD spectra are calculated from sums of mononucleotide, dinucleoside monophosphate, and double-strand polynucleotide spectra and compared with experimental CD spectra. Absorbance-temperature profiles show that tRNA in less than 10-5 m magnesium is single stranded at 40° while tRNA in the presence of 1 mM magnesium is native. Comparison of the CD spectrum of the single-stranded tRNA with appropriate sums of dinucleoside monophosphate spectra shows that the CD of the dinucleoside monophosphates is not a good model for the CD of single-stranded tRNA. The CD of native tRNA at 40° may be calculated using the experimental single-strand spectrum to represent the CD of the single-strand regions of the tRNA, and double-strand pairing interaction spectra to represent the double-strand regions. Any unique contribution of tertiary structure of the tRNA to the CD is thus shown to be small. For most tRNAs, two to four base pairs in addition to those due to the commonly accepted cloverleaf secondary structure improve the agreement between calculated and experimental spectra. Comparison of the difference between the CD of native and denatured tRNA3Leu (yeast) with sums of double-strand pairing interactions suggests that the native to denatured transition for tRNALeu involves the loss of 4-5 base pairs. On the other hand, the native to denatured CD difference spectrum for tRNATrp could not be fit by any combination of double-strand pairing-interaction spectra.