Many of the applications of oligonucleotide arrays, especially the complex and quantitative applications such as Sequence By Hybridization (SBH) are hampered by errors resulting from the variable hybridization properties of the small probes and the stability of their hybrids. Non-specific hybridization also cause a low signal to noise ratio. We propose a method that is aimed at addressing these drawbacks by use of 'snap-back' oligonucleotide probes and novel detection methods. Hairpin oligonucleotide probes that are composed of mixed backbone of ribose, and deoxyribose or modified or non-natural phosphodiester linkages such as methyl phosphonates will be used to setup pseudo-competitive hybridization reactions to increase specificity. Such oligonudeotide probes will be designed in a way that would render a region of the probe susceptible to RNase H digestion when hybridized to the target DNA sequence. The 'snap-back' hairpin oligonucleotide probe containing methyl phosphonate residues in one strand and RNA in the opposite strand of the stem will not be digestible by RNase-H. After hybridization of the RNA strand to the target DNA stand, the RNA strand can be digested with RNase-H. The hairpins with single stranded region that are left attached to the substrate will be detected using one of the novel detection methods such as fluorescent-labeled oligonucleotide mixture. The intact and un-hybridized probe would snap back rendering themselves un-reactive in the detection stage, resulting in a low background. We propose to validate this approach and compare it with the current SBH methods by sequencing short segments of DNA. Subsequently, these studies will be extended to typing of rifampicin resistant Mycobacterium tuberculosis. Our long-term goal for Phase II of the project will be to use the snap-back probes in genotyping mutations such as those in the presenilin I gene that are related to Alzheimer. Ultimately, we would extend its application in genotyping mutations for other genetic diseases in clinical settings and physicians' offices.
