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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

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 modelmore » RNA virus particle). As a result, we demonstrate single-tube duplex detection of West Nile virus (WNV) and chikungunya virus (CHIKV) RNA.« less
Authors:
 [1] ;  [1] ;  [1] ;  [2] ;  [2] ;  [1]
  1. Sandia National Lab. (SNL-CA), Livermore, CA (United States)
  2. Univ. of California, Davis, CA (United States)
Publication Date:
Report Number(s):
SAND-2015-10119J
Journal ID: ISSN 0003-2700; 608294
Grant/Contract Number:
AC04-94AL85000; 173111
Type:
Published Article
Journal Name:
Analytical Chemistry
Additional Journal Information:
Journal Volume: 88; Journal Issue: 7; Journal ID: ISSN 0003-2700
Publisher:
American Chemical Society (ACS)
Research Org:
Sandia National Lab. (SNL-CA), Livermore, CA (United States)
Sponsoring Org:
USDOE National Nuclear Security Administration (NNSA)
Country of Publication:
United States
Language:
English
Subject:
59 BASIC BIOLOGICAL SCIENCES
OSTI Identifier:
1243142
Alternate Identifier(s):
OSTI ID: 1319449