title: Single-base mismatch recognition using partially double-stranded probes having various lengths.
abstract: We have focused on the nucleation-synchronized DNA strand exchange reaction (ns-SER) as a format of a single-base mismatch detection. We employed a partially double-stranded (PDS) DNA probe having a single-stranded (ss) portion. We could rapidly resolve a single-base mismatch by the ns-SER rates of the PDS probe with target DNAs. Here, we reported the influence of probe length and operating conditions, such as temperature and buffer conditions, on a single-base mismatch recognition using the PDS probes. We could reliably recognize a single-base mismatch even with a 61mer long probe. However, the ns-SER rates were decreased with increasing probe length. We considered that a rate-limiting step of the ns-SER might be sifted from nucleation to branch migration processes. By an addition of cationic comb-type copolymers (PLL-g-Dex) in the buffer, the reaction rate was considerably increased 1-2 orders without disordering the resolution power.
authors.affiliation: Institute for Materials Chemistry and Engineering, Kyushu University, 6-10-1 Hakozaki, Higashi-ku, Fukuoka 812-8581, Japan.
authors.forename: Daisuke
authors.initials: D
authors.lastname: Ishii
authors.forename: Kentaro
authors.initials: K
authors.lastname: Muraki
authors.forename: Arihiro
authors.initials: A
authors.lastname: Kano
authors.forename: Asako
authors.initials: A
authors.lastname: Yamayoshi
authors.forename: Atsushi
authors.initials: A
authors.lastname: Maruyama
mesh_terms: D020137:Base Pair Mismatch; D001483:Base Sequence; D002021:Buffers; D015342:DNA Probes / Q000737:chemistry*; D003911:Dextrans / Q000737:chemistry; D011107:Polylysine / Q000031:analogs & derivatives / Q000737:chemistry; D013696:Temperature
chemical_list: D002021:Buffers; D015342:DNA Probes; D003911:Dextrans; C113090:poly(lysine)-graft-dextran; D011107:Polylysine