Optimization and performance evaluation of double-stranded probe in real-time PCR.
Anal Biochem 2022;
650:114711. [PMID:
35561816 DOI:
10.1016/j.ab.2022.114711]
[Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2022] [Revised: 04/18/2022] [Accepted: 05/01/2022] [Indexed: 11/22/2022]
Abstract
BACKGROUND
TaqMan probe-based real-time PCR (qPCR/RT-qPCR) has been widely used in various fields because of its high sensitivity and specificity. However, TaqMan probes are associated with a relatively higher background signal, and hence negatively affect the detection results.
METHODS
Double-stranded probes (DSPs) were designed for the high sensitive detection of hepatitis B virus (HBV) DNA and severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) RNA using qPCR/RT-qPCR. DSPs consist of different lengths of positive and negative strands with complementary oligonucleotides. We systematically optimized DSP length, the free energy of hybridization (ΔG) between complementary oligonucleotides, and the length of sticky ends, and DSP performance was evaluated in comparison with other types of probes.
RESULTS
By using similar length positive and negative strands, controlling ΔG between complementary oligonucleotides to approximately -30 kcal/mol, and maintaining the sticky end length at 4-6 nt, the analytical performance of DSP was significantly improved. Compared with other types of probes, DSP is advantageous in fluorescence signal intensity and sensitivity.
CONCLUSION
DSPs can further improve the detection sensitivity and the detection rate of low-concentration samples in molecular diagnosis.
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