High Resolution NMR Studies of the Structure and Dynamics of tRNA in Solution

Abstract

Ribonucleic acids are composed of a sugar-phosphate backbone with bases attached at position l' of the sugar ring (Fig. 1). The backbone consists of six rotatable bonds defined by the angles 0/, cp', 1/1', 1/1, cp, and w, while the base and sugar rings are joined by the rotatable glycosidic bond, x. The four major bases are the purines guanine· (G) and adenine (A), and the pyrimidines cytosine (C) and uracil (U). Polynucleotide strands can interact with each other to form duplex structures by formation of complementary Watson-Crick adenine-uracil and guanine· cytosine base pairs. tRNA is composed of a single ribonucleic acid chain that ranges between 73 and 93 nucleotides in length with a terminal phosphate at its 5' end (residue 1). The nucleotide sequence of known tRNAs (2, 3) suggests that the polynucleotide chain can fold back on itself to generate double-stranded helical regions, as well as single­ stranded loop regions of the hairpin (chain reversal) and bulge types (Fig. 2)_ There are three hairpin loops defined as the D loop (contains the dihydrouracil base), the anticodon loop (contains the trinucleotide sequence complementary to the trinucleotide codon on messenger RNA), and the TljlC loop (contains the common sequence ribothymine-pseudouridine-cytosine). Each of these three loops is asso­ ciated with its corresponding double helical region called the stem. There is in addition a variable loop whose length depends on individual tRNAs and the acceptor stem whose 3' terminus is the site of aminoacylation. A survey of the known tRNA sequences demonstrates the presence of invariant and semi-invariant bases and they are defined in Figure 2 with purines and pyrimidines designated by Y and R, respectively (4, 5).