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Effects of mismatches and insertions on discrimination accuracy of nucleic acid probes

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Piao X., Sun L., Zhang T., Gan Y., Guan Y.

2008

vol. 55

issue 4

713-720

Effective discrimination of non-complementary nucleotides is an important factor to ensure the accuracy of hybridization-based nucleic acid analyses. The current study investigates the effects of the chemical nature, the positions, the numbers, and the cooperative behavior of mismatches as well as insertions on 20-mer and 30-mer duplexes. We observed the hybridization stability trend affected by mismatches: G:T ≈ G:G > G:A > A:A ≈ T:T > A:C ≈ T:C > C:C. The experimental data show that mismatches at the center of the oligonucleotide probes have a more profound destabilizing effect on the hybridization stability than those at either ends. Insertions also demonstrate a similar destabilizing effect as mismatches. These results provide useful information for designing DNA microarray nucleotide probes and for improving the discrimination accuracy of hybridization-based detections.

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1 Acta Biochimica Polonica

1 2008

1 Gan Y.

1 Guan Y.

1 Piao X.

1 Sun L.

1 Zhang T.

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Effects of mismatches and insertions on discrimination accuracy of nucleic acid probes