STUDIES OF OLIGONUCLEOTIDE INTERACTIONS BY HYBRIDIZATION TO ARRAYS - THE INFLUENCE OF DANGLING ENDS ON DUPLEX YIELD

Effects of dangling ends on duplex yield have been assessed by hybridi sation of oligonucleotides to an array of oligonucleotides synthesised on the surface of a solid support. The array consists of decanucleoti des and shorter sequences. One of the decanucleotides in the array was fully complementary to the decanucleotide used as solution target. Ot hers were complementary over seven to nine bases, with overhangs of on e to three bases. Duplexes involving different decanucleotides had dif ferent overhangs at the 3' and 5' ends. Some duplexes involving shorte r oligonucleotides had the same regions of complementarity as these de canucleotides, but with fewer overhanging bases. This analysis allows simultaneous assessment of the effects of differing bases at both 5' a nd 3' ends of the oligonucleotide in duplexes formed under identical r eaction conditions. The results indicate that a 5' overhang is more st abilising than a 3' overhang, which is consistent with previous result s obtained with DNA overhangs. However, it is not clear whether this i s due to the orientation of the overhang or to the effect of specific bases.