Thermodynamic and kinetic properties of short RNA helices: the oligomer sequence AnGCUn

We studied the thermodynamic, kinetic and optical properties of the double helices formed by the series of self-complementary oligonucleotides, (AP)(n)GpC(pU)(n), 2 </= n </= 4, and found that the shortest helix, containing just 6 base pairs, is less stable than would be predicted from the properties of the larger molecules. It also shows a markedly smaller hyperchromism on melting than expected. These anomalous properties of a short helix indicate that one cannot always assume that base pair free energies and extinction coefficient changes are independent of helix size.