2-Aminopurine labelled RNA bulge loops. Synthesis and thermodynamics

The chemical introduction of the blue-fluorescent 2-aminopurine riboside into oligoribonucleotides synthesized using the 2'-O-t-butyl-dimethylsilyl protection is reported. The proposed purification procedure led to the synthetic RNAs of high purity required for spectrofluorimetry studies. Thermodynamic parameters for the RNA bulge loops of type (A)n labelled with the 2-aminopurine (2AP) have been determined by optical melting. Results indicate that a bulge (B) in the RNA duplexes GUCG(B)GCUG + CAGCCGAC destabilize a regular helix structure and the destabilization increases monotonically as bulge length increases in the following order of (B) = A-2AP-A > 2AP-A; A-2AP > 2AP. The analysis of the free energy increments for bulged loops, delta G(o)37(bulge), allows to conclude that the structural properties of 2-aminopurine in RNA bulge loops are very similar to those of isomeric adenine. The fluorescent 2-aminopurine could therefore be used as non-invasive conformational probe.