Oligodeoxynucleotides containing conformationally constrained abasic sites: a UV and fluorescence spectroscopic investigation on duplex stability andstructure

The synthesis and incorporation into oligodeoxynucleotides of two novel, co nformationally restricted abasic (AB) site analogs are described. The stabi lity of oligonucleotide 18mer duplexes containing one such AB site opposite any of the four natural DNA bases was investigated by UV melting curve ana lysis and compared to that of duplexes containing a conformationally flexib le propanediol unit 1 or a tetrahydrofuran unit 2 as an AB site analog. No major differences in the melting temperatures (Delta T-m 0-3 degrees C) bet ween the different abasic duplexes were observed, All AB duplexes were foun d to have T(m)s that were lower by 9-15 degrees C relative to a fully match ed 18mer control duplex, and by 4-10 degrees C relative to the correspondin g 19mer duplexes in which the AB site is replaced by a mismatched nucleobas e, Thus we conclude that the loss of stability of a duplex that is encounte red by removal of a nucleobase from the stack cannot be compensated with co nformational restriction of the AB site. From the van't Hoff transition ent halpies obtained from the melting curves, it appears that melting cooperati vity is higher for the duplexes containing the conformationally rigid AB si tes. Fluorescence quenching experiments with duplexes containing the fluore scent base 2-amino-purine (2AP) opposite the AB sites showed a weak tendenc y towards more efficient stacking of this base in duplexes containing the c onformationally constrained AB sites. Thus, such AB sites may structurally stabilize the cavity formed by the removal of a base, Potential application s emerging from the properties of such conformationally constrained AB site s in DNA diagnostics are discussed.