Thursday, July 14, 2011

GpU dinucleotide platform, the smallest unit with key RNA structural features

Compared to DNA, RNA has three salient structural features: it contains ribose sugar, uracil, and is normally single-standed. The O2'(G)...O2P(U) H-bond stabilized GpU dinucleotide platform may turn out to be the smallest unit with all those RNA hallmarks (see Figure below).

Firstly, it must have the guanosine ribose to form the O2'(G)...O2P(U) H-bond.

Secondly, the methyl group in position 5 of thymine would cause steric clash with guanosine, thus disrupting the N2(G)...O4(U) base-base H-bond to form the GpU dinucleotide platform.

Thirdly, a dinucleotide, by definition, is single-standed. The two H-bonds, plus the covalent linkage, makes the GpU platform extremely rigid (see Figure 1 of our 2010 NAR paper).

Moreover, the GpU platform is directional: swapping the two bases while keeping the sugar-phosphate backbone fixed does not allow for a base-base H-bond, thus no UpG dinucleotide platform.