title: Effects of mismatches and insertions on discrimination accuracy of nucleic acid probes.
abstract: 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 approximately G:G > G:A > A:A approximately T:T > A:C approximately 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.
authors.affiliation: Department of Biochemistry and Molecular Biology, China Medical University Shenyang, China.
authors.forename: Xianyu
authors.initials: X
authors.lastname: Piao
authors.forename: Liancheng
authors.initials: L
authors.lastname: Sun
authors.forename: Tianbiao
authors.initials: T
authors.lastname: Zhang
authors.forename: Youlin
authors.initials: Y
authors.lastname: Gan
authors.forename: Yifu
authors.initials: Y
authors.lastname: Guan
mesh_terms: D020137:Base Pair Mismatch; D001483:Base Sequence; D009693:Nucleic Acid Hybridization; D015341:Nucleic Acid Probes; D016133:Polymerase Chain Reaction
chemical_list: D015341:Nucleic Acid Probes