Tail variation of the folding primer affects the SmartAmp2 process differently.
Folding primer (FP), together with turn-back primer (TP) and boost primer (BP), is one of the major components of SmartAmp2, a rapid amplification-based method for SNP detection. FP has a unique design where the annealing region is combined with a tail that can fold back. FP tails can be classified as either "strong" or "weak", depending on the melting temperature and free energy of the hairpin structure. We report that FP tails affect the amplification process differently; by changing the FP concentration, we can increase the amplification reaction speed with "strong tails". Unlike "strong tails", concentration change of FP with "weak tails" did not show significant impact on the amplification speed. The comparative analyses using gel electrophoresis demonstrate that the FP type and FP ratio in the reaction change the amplification pattern. The above observations can be used to optimize the reaction and manipulate the reaction speed of SmartAmp2.
Kimura
Yasumasa
Y
Technology Development Unit, Omics Science Center (OSC), RIKEN Yokohama Institute, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan.
Oguchi-Katayama
Atsuko
A
Kawai
Yuki
Y
Naito
Kana
K
Mitani
Yasumasa
Y
Morlighem
Jean-Etienne
JE
Hayashizaki
Yoshihide
Y
Lezhava
Alexander
A
D004247:DNA / Q000032:analysis; D017931:DNA Primers / Q000737:chemistry* / Q000235:genetics; D004591:Electrophoresis, Polyacrylamide Gel; D009690:Nucleic Acid Conformation; D016133:Polymerase Chain Reaction / Q000379:methods*; D020641:Polymorphism, Single Nucleotide; D012680:Sensitivity and Specificity; D044366:Transition Temperature
D017931:DNA Primers; D004247:DNA