Studies of oligonucleotide interactions by hybridisation to arrays: the influence of dangling ends on duplex yield

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Abstract
Effects of dangling ends on duplex yield have been assessed by hybridisation of oligonucleotldes to an array of oligonucleotldes syntheslsed on the surface of a solid support. The array consists of deca-nucleotldes and shorter sequences. One of the deca-nucleotides in the array was fully complementary to the decanucleotide used as solution target. Others were complementary over seven to nine bases, with overhangs of one to three bases. Duplexes involving different decanucleotldes had different overhangs at the 3′ and 5′ ends. Some duplexes involving shorter oligonucleotldes had the same regions of complementarity as these decanucleotldes, but with fewer overhanging bases. This analysis allows simultaneous assessment of the effects of differing bases at both 5′ and 3′ ends of the oligonucleotide in duplexes formed under identical reaction conditions. The results indicate that a 5′ overhang is more stabilising than a 3′ overhang, which is consistent with previous results obtained with DNA overhangs. However, it is not clear whether this is due to the orientation of the overhang or to the effect of specific bases.