Stability of tRNA-derived acceptor stem duplexes

1 Stability of tRNA-derived acceptor stem duplexes 

The unusual G-U pair, in contrast to classical Watson-Crick base pairs, gives rise to two well-separated imino lines since in this case two imino protons are involved in base pair hydrogen bonding. The G imino resonance is easily detectable since it is shifted strongly up-field to about 10-11 ppm. Moreover, the two G-U imino protons display an extraordinarily strong nuclear Overhauser effect (NOE) due to their close spatial proximity. 

In our studies the influence of the single-stranded terminus (ACCA) on the stability of the duplex was analyzed. The starting sequence used in these investigations was that of the acceptor stem of tRNA from E. coli (Fig. 19.1). 

A comparison of the imino region of the NMR spectra of the five different duplex variants reveals that after attachment of the first unpaired nucleotide (A73) onto the C72 of the first base pair (G1-C72) the imino resonance of G1 is substantially shifted as compared to the 14mer. This is also valid for the imino lines of base pairs 2 (G2-C71), and - though clearly less pronounced - for the G imino resonance of base pair 3 [32]. This upfield shift is increased upon attachment of further nucleotides of the single-strand terminus with even the fourth nucleotide (A76) causing a measurable upfield shift of the imino resonances of base pairs 1 and 2 (Fig. 19.2). 

The upfield shifts are reflected also in a quite similar dependence of melting temperature and Gibbs free energy AG of duplex formation (Tab. 19.1) on the number of singlestrand nucleotides. 

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