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Nucleic Acids Symposium Series 2005 49(1):223-224; doi:10.1093/nass/49.1.223
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© 2005 Oxford University Press

Discrimination of single nucleotide polymorphisms by strand exchange assay using partially double-stranded probes

Kazuya Hirata1, Daisuke Ishii2, Arihiro Kano3, Asako Yamayoshi3, Toshihiro Akaike1 and Atsushi Maruyama3,4

1 Department of Biomolecular Engineering, Tokyo Institute of Technology, 4259 Nagatsuta-cho, Midori-ku, Yokohama 226-8501, Japan, 2 Department of Engineering, Kyushu University, 6-10-1, Hakozaki, Higashi-ku, Fukuoka 812-8581, Japan, 3 Institute for Materials Chemistry and Engineering, Kyushu University, 6-10-1 Hakozaki, Higashi-ku, Fukuoka, 812-8581, Japan, 4 Japan Science and Technology Agency, Kawaguchi Center Building, 4-1-8, Honcho, Kawaguchi-shi, Saitama 332-0012, Japan

Previously we designed the partially double-stranded (PDS) probes that have protruding single-stranded portion for a single-base mismatch analysis. The single-stranded portion is engineered to sense existences of mismatches in the counterparts and to transduce it in strand exchange rates. Here we report the influence of probe length and operating conditions, such as temperature and buffer conditions, on the mismatch resolution using the PDS probes. Reliable detection of single-base mismatches was achieved even with a 45mer-long probe. By lowering operating temperature, the higher and faster discrimination of the mismatches was demonstrated. Addition of cationic comb-type copolymers (CCCs) in the buffer increased the reaction rate 3-4 orders without disordering the resolving power.


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