title: Primers with 5' flaps improve real-time PCR.
abstract: Primers that contain portions noncomplementary to the target region are usually used to add to the PCR product a utility sequence such as a restriction site or a universal probe binding site. We have demonstrated that primers with short 5'AT-rich overhangs increase real-time PCR fluorescent signal. The improvement is particularly significant for difficult to amplify templates, such as highly variable viral sequences or bisulfite-treated DNA.
authors.affiliation: Nanogen Inc., Bothell, WA 98021, USA. iafonina@nanogen.com
authors.forename: Irina
authors.initials: I
authors.lastname: Afonina
authors.forename: Irina
authors.initials: I
authors.lastname: Ankoudinova
authors.forename: Alan
authors.initials: A
authors.lastname: Mills
authors.forename: Sergey
authors.initials: S
authors.lastname: Lokhov
authors.forename: Phan
authors.initials: P
authors.lastname: Huynh
authors.forename: Walt
authors.initials: W
authors.lastname: Mahoney
mesh_terms: D024506:5' Flanking Region / Q000235:genetics*; D017931:DNA Primers / Q000235:genetics*; D004279:DNA, Viral / Q000235:genetics; D005456:Fluorescent Dyes; D006801:Humans; D015203:Reproducibility of Results; D015183:Restriction Mapping / Q000379:methods / Q000592:standards; D020133:Reverse Transcriptase Polymerase Chain Reaction / Q000379:methods* / Q000592:standards*; D013447:Sulfites
chemical_list: D017931:DNA Primers; D004279:DNA, Viral; D005456:Fluorescent Dyes; D013447:Sulfites; C042345:hydrogen sulfite