Real-time (quantitative)
polymerase chain reaction (qPCR) has been
widely applied in molecular diagnostics due to its immense sensitivity
and specificity. qPCR multiplexing, based either on fluorescent probes
or intercalating dyes, greatly expanded PCR capability due to the
concurrent amplification of several deoxyribonucleic acid sequences.
However, probe-based multiplexing requires multiple fluorescent channels,
while intercalating dye-based multiplexing needs primers to be designed
for amplicons having different melting temperatures. Here, we report
a single fluorescent channel-based qPCR duplexing method on a model
containing the sequence of chromosomes 21 (Chr21) and 18 (Chr18).
We combined nonspecific intercalating dye EvaGreen with a 6-carboxyfluorescein
(FAM) probe specific to either Chr21 or Chr18. The copy number (
cn
) of the target linked to the FAM probe could be determined
in the entire tested range from the denaturation curve, while the
cn
of the other one was determined from the difference between
the denaturation and elongation curves. We recorded the amplitude
of fluorescence at the end of denaturation and elongation steps, thus
getting statistical data set to determine the limit of the proposed
method in detail in terms of detectable concentration ratios of both
targets. The proposed method eliminated the fluorescence overspilling
that happened in probe-based qPCR multiplexing and determined the
specificity of the PCR product via melting curve analysis. Additionally,
we performed and verified our method using a commercial thermal cycler
instead of a self-developed system, making it more generally applicable
for researchers. This quantitative single-channel duplexing method
is an economical substitute for a conventional rather expensive probe-based
qPCR requiring different color probes and hardware capable of processing
these fluorescent signals.