2-AMINOPURINE LABELED RNA BULGE LOOPS - SYNTHESIS AND THERMODYNAMICS

The chemical introduction of the blue-fluorescent 2-aminopurine ribosi de into oligoribonucleotides synthesized using the 2'-O-t-butyl-dimeth ylsilyl protection is reported. The proposed purification procedure le d to the synthetic RNAs of high purity required for spectrofluorimetry studies. Thermodynamic parameters for the RNA bulge loops of type (A) , labelled with the 2-aminopurine (2AP) have been determined by optica l melting. Results indicate that a bulge (B) in the RNA duplexes GUCG( B)GCUG + CAGCCGAC destabilize a regular helix structure and the destab ilization increases monotonically as bulge length increases in the fol lowing order of (B)=A-2AP-A > 2AP-A; A-2AP > 2AP. The analysis of the free energy increments for bulged loops, Delta G(37)(o)(bulge), allows to conclude that the structural properties of 2-aminopurine in RNA bu lge loops are very similar to those of isomeric adenine. The fluoresce nt 2-aminopurine could therefore be used as non-invasive conformationa l probe.