Secondary structure in single-stranded ONA and RNA is a significant barrier to the efficient hybridization of short oligonucleotide probes. While some probes to a given target hybridize efficiently, other probes to the same target may not hybridize at all. Use of longer probes, on the order of 60 nucleotides in length, is one way to overcome this problem. Unfortunately, such probes cannot be used to directly detect single nucieotide polymorphisms or point mutations. Use of pseudo-complementary (pc) DNA or RNA targets that lack secondary structure should facilitate the use of short probes and enable the development of generic oligonucleotide microarrays wherein every permutation of a short probe (e.g., an 8-mer) is represented on the array. Such arrays are ideally suited to the resequencing of DNA for SNP identification and to the acquisition of genetic profiles for identification purposes. We have shown that nucleoside triphosphates (NTPs) of 2-aminoadenine (nATP) and 2-thiothymine/2-thiouracii (sTTP/sUTP) can be enzymatically incorporated into DNA or RNA. These bases are pseudo-complementary since they don't interact with each other but can individually pair to the regular base complement. In this Phase I proposal we will evaluate whether dNTP analogues of dGTP and dCTP can be used together with dnATP and dsTTP in a primer extension assay to generate structure-free single-stranded DNA that can hybridize to short DNA or RNA probes with high efficiency and specificity. Existing data from ourselves and others indicate that this goal should be readily attainable and would form the basis for evaluating pseudo-complementary DNA and RNA targets for use in conjunction with short probes in a microarray format.
| Lahoud, Georges; Arar, Khalil; Hou, Ya-Ming et al. (2008) RecA-mediated strand invasion of DNA by oligonucleotides substituted with 2-aminoadenine and 2-thiothymine. Nucleic Acids Res 36:6806-15 |
| Lahoud, Georges; Timoshchuk, Victor; Lebedev, Alexandre et al. (2008) Properties of pseudo-complementary DNA substituted with weakly pairing analogs of guanine or cytosine. Nucleic Acids Res 36:6999-7008 |
| Lahoud, Georges; Timoshchuk, Victor; Lebedev, Alexandre et al. (2008) Enzymatic synthesis of structure-free DNA with pseudo-complementary properties. Nucleic Acids Res 36:3409-19 |
