title: Quenching of Unincorporated Amplification Signal Reporters in Reverse-Transcription Loop-Mediated Isothermal Amplification Enabling Bright, Single-Step, Closed-Tube, and Multiplexed Detection of RNA Viruses.
abstract: Reverse-transcription-loop-mediated isothermal amplification (RT-LAMP) has frequently been proposed as an enabling technology for simplified diagnostic tests for RNA viruses. However, common detection techniques used for LAMP and RT-LAMP have drawbacks, including poor discrimination capability, inability to multiplex targets, high rates of false positives, and (in some cases) the requirement of opening reaction tubes postamplification. Here, we present a simple technique that allows closed-tube, target-specific detection, based on inclusion of a dye-labeled primer that is incorporated into a target-specific amplicon if the target is present. A short, complementary quencher hybridizes to unincorporated primer upon cooling down at the end of the reaction, thereby quenching fluorescence of any unincorporated primer. Our technique, which we term QUASR (for quenching of unincorporated amplification signal reporters, read "quasar"), does not significantly reduce the amplification efficiency or sensitivity of RT-LAMP. Equipped with a simple LED excitation source and a colored plastic gel filter, the naked eye or a camera can easily discriminate between positive and negative QUASR reactions, which produce a difference in signal of approximately 10:1 without background subtraction. We demonstrate that QUASR detection is compatible with complex sample matrices such as human blood, using a novel LAMP primer set for bacteriophage MS2 (a model RNA virus particle). Furthermore, we demonstrate single-tube duplex detection of West Nile virus (WNV) and chikungunya virus (CHIKV) RNA.
authors.affiliation: Sandia National Laboratories , P.O. Box 969, MS 9291, Livermore, California 94551, United States.
authors.forename: Cameron S
authors.initials: CS
authors.lastname: Ball
authors.affiliation: Sandia National Laboratories , P.O. Box 969, MS 9291, Livermore, California 94551, United States.
authors.forename: Yooli K
authors.initials: YK
authors.lastname: Light
authors.affiliation: Sandia National Laboratories , P.O. Box 969, MS 9291, Livermore, California 94551, United States.
authors.forename: Chung-Yan
authors.initials: CY
authors.lastname: Koh
authors.affiliation: University of California Davis , School of Veterinary Medicine, Department of Pathology, Microbiology and Immunology, One Shield Avenue, Davis, California 95616, United States.
authors.forename: Sarah S
authors.initials: SS
authors.lastname: Wheeler
authors.affiliation: University of California Davis , School of Veterinary Medicine, Department of Pathology, Microbiology and Immunology, One Shield Avenue, Davis, California 95616, United States.
authors.forename: Lark L
authors.initials: LL
authors.lastname: Coffey
authors.affiliation: Sandia National Laboratories , P.O. Box 969, MS 9291, Livermore, California 94551, United States.
authors.forename: Robert J
authors.initials: RJ
authors.lastname: Meagher
mesh_terms: D021141:Nucleic Acid Amplification Techniques; D012328:RNA Viruses / Q000235:genetics / Q000302:isolation & purification*; D013696:Temperature