Loop accessibility in transfer RNA.

Summary Endonuclease digestion of tRNA and unfractionated tRNA mixtures results in only discrete fragment sizes which are quarters or multiples thereof, thus strongly supporting the validity of the cloverleaf structure for all tRNAs. Kinetic studies with individual tRNA species and with unfractionated tRNA using pancreatic RNase as well as RNase T1 indicate that the anticodon loop is by far the most accessible region of the tRNA structure, being at least ten times more susceptible to cleavage than either side loop. RNase T1 fragmentation kinetics of species containing free guanine in one, two or all three major loops reveal that the dihydrouridine loop is the second most susceptible to attack, being several times more accessible than the ribothymidine loop. This has been confirmed with unfractionated tRNA and appears to be a general feature of tRNA structure in solution.