title: Comparison of TaqMan and Epoch Dark Quenchers during real-time reverse transcription PCR.
abstract: Several biotechnology companies have recently introduced novel quencher fluors for use with dual-labeled fluorogenic hydrolysis probes. The Epoch Dark Quencher trade mark fluorochrome consists of a non-fluorescent moiety capable of absorption at higher wavelengths (400-650 nm). The aim of this study was to: (1) evaluate the feasibility of using Epoch Dark Quencher fluorochromes in real-time PCR pathogen detection assays that were previously optimized with TaqMan (TAMRA) quenching fluors, and (2) compare the sensitivity based on cycle threshold (CT) between probes containing either TaqMan or Epoch Dark Quencher fluors. Our data indicate Epoch Dark Quencher probes can be used in place of TaqMan probes and their performance was not better than traditional TaqMan (TAMRA) quenchers. Marginal differences observed between quenching fluorochromes may arise from concentration differences during probe synthesis.
authors.affiliation: Brooks City-Base San Antonio, TX, USA. luke.daum@brooks.af.mil
authors.forename: Luke T
authors.initials: LT
authors.lastname: Daum
authors.forename: Keying
authors.initials: K
authors.lastname: Ye
authors.forename: James P
authors.initials: JP
authors.lastname: Chambers
authors.forename: Jose
authors.initials: J
authors.lastname: Santiago
authors.forename: John R
authors.initials: JR
authors.lastname: Hickman
authors.forename: William J
authors.initials: WJ
authors.lastname: Barnes
authors.forename: Russell P
authors.initials: RP
authors.lastname: Kruzelock
authors.forename: Daniel H
authors.initials: DH
authors.lastname: Atchley
mesh_terms: D005456:Fluorescent Dyes / Q000378:metabolism; D009980:Influenza A virus / Q000235:genetics; D012367:RNA, Viral / Q000235:genetics; D020133:Reverse Transcriptase Polymerase Chain Reaction / Q000295:instrumentation / Q000379:methods*; D012680:Sensitivity and Specificity; D019914:Taq Polymerase / Q000378:metabolism*
chemical_list: D005456:Fluorescent Dyes; D012367:RNA, Viral; D019914:Taq Polymerase