Discrimination of Single Nucleotide Mutation by Using a New Class of Immobilized Shared-Stem Double-Stranded DNA Probes

An improved technique for single nucleotide mismatch discrimination using immobilized double-stranded DNA probes with a shared-stem hairpin (SH) structure is developed. A hairpin-like double-stranded DNA probe without any chromophore was immobilized on an agarose film-coated slide. The base number of the stem area was increased to 9 similar to 19 nt and the entire shared-stem area was included in the hybridization area, in which a mutated nucleotide was introduced in the middle. For the perfect match SH probe, we introduced an inner mismatch in the middle positon of the complementary chain. After the introduction of the inner mismatch, the hybridization ability of the SHP probe with a long stem was enhanced significantly. On the other hand, the mismatch probe was not able to hybridize to the perfect matched target. The annealing properties, specificity and hybridization dynamics of this kind of double-stranded DNA probes immobilized on an agarose film are greatly improved in comparison with those for the linear ones and traditional hairpin-like ones. Collectively we demonstrated that this type of immobilized double-stranded DNA probes had an excellent discrimination ratio for single nucleotide mismatches.