Martina Gaňová‡
a,
Xinlu Wang‡b,
Zhiqiang Yanc,
Haoqing Zhangb,
Tomáš Lednickýa,
Marie Korabečnád and
Pavel Neužil*b
aCentral European Institute of Technology, Brno University of Technology, Purkyňova 123, 612 00 Brno, Czech Republic
bNorthwestern Polytechnical University, School of Mechanical Engineering, Department of Microsystem Engineering, 127 West Youyi Road, Xi'an, Shaanxi 710072, PR China. E-mail: pavel.neuzil@gmail.com
cNorthwestern Polytechnical University, School of Marine Science and Technology, 127 West Youyi Road, Xi'an, Shaanxi 710072, PR China
dInstitute of Biology and Medical Genetics, First Faculty of Medicine, Charles University and General University Hospital in Prague, Albertov 4, 128 00 Prague, Czech Republic
First published on 17th January 2022
A microfluidic-based digital polymerase chain reaction (dPCR) chip requires precise temperature control as well as uniform temperature distribution to ensure PCR efficiency. However, measuring local temperature and its distribution over thousands of μL/nL-volume samples with minimum disturbance is challenging. Here, we present a method of non-contact localized temperature measurement for determination of the non-uniformity of temperature distribution over a dPCR chip. We filled the dPCR chip with a PCR solution containing amplified DNA fragments with a known melting temperature (TM). We then captured fluorescent images of the chip when it was heated from 70 to 99 °C, plotted the fluorescence intensity of each partition as a function of temperature, and calculated measured TM values from each partition. Finally, we created a 3-D map of the dPCR chip with the measured TM as the parameter. Even when the actual TM of the PCR solution was constant, the measured TM value varied between locations due to temperature non-uniformity in the dPCR chip. The method described here thereby characterized the distribution of temperature non-uniformity using a PCR solution with known TM as a temperature sensor. Among the non-contact temperature measurement methods, the proposed TM-based method can determine the temperature distribution within the chip, instead of only at the chip surface. The method also does not suffer from the undesirable photobleaching effect of fluorescein-based temperature measurement method. Temperature determination over the dPCR chip based on TM allowed us to calibrate the temperature sensor and improve the dPCR configuration and precision. This method is also suitable for determining the temperature uniformity of other microarray systems where there is no physical access to the system and thus direct temperature measurement is not possible.
Temperature uniformity between partitions is critical as the temperature during thermal cycling affects PCR efficiency.7 The thermal uniformity of the dPCR device depends on its heating/cooling elements and the thermal conductance between the elements.8 The most commonly used heating/cooling techniques are based on thermoelectric coolers (TEC).9 Other techniques, based on different principles, can also be used such as photonic heating with airflow cooling.10 Additional problems arise from non-uniform temperature distribution11 due to insufficient heat transfer or non-uniform cooling in open systems such as those using air convection.12 This is a significant problem as the relative PCR efficiency between partitions is strongly affected by poor temperature uniformity during thermal cycling.13
Therefore, each dPCR assay must be optimized carefully and reasons causing false positive signals are more easily detectable than the causes of false negative partitions. Attempts to prevent false negative dropouts mainly focus on optimizing the surface to volume ratio of partitions, which potentially inhibit PCR process, or on pre-analytical steps associated with the preparation of the DNA template.14 When optimizing dPCR on a chip, thermal non-uniformity is usually not considered as measurement of sample temperature (TS) inside partitions with a sample volume of pico-/nano-liters is a challenging job.15,16 An accurate system to calibrate a temperature sensor with respect to the fluid inside the partitions, and enable determination of the temperature distribution over the dPCR chip, or even between the partitions, would benefit the optimization of temperature uniformity,17 thus improving PCR efficiency.
TS can be measured by contact or non-contact methods. Contact methods primarily use temperature sensors10,18,19 such as resistive temperature detectors (RTD),20 thermistors19 or thermocouples21 for point measurement. However, it is impossible to determine TS within a single micro/nano partition using those sensors due to the size limitations.22,23 The most popular non-contact temperature measurement method is based on an emitted infrared (IR) power determination.10,19 This only determines the power of the IR radiation emitted from the surface, which for these chips is typically that of a glass covering the partitions inside the chip, meant to prevent water evaporation from the PCR master mix.24 Unfortunately the glass is not transparent at IR wavelengths, making it impossible to determine the temperature (T) of the master mix, which is the most critical information for optimal PCR operation. The measurement precision can also be affected by surface contamination.
Other non-contact temperature measurement methods use the fluid in the partitions as a sensing element, via the inclusion of thermochromic dyes, such as organic leuco dyes, with specific temperature-dependent optical properties.25 However, these methods are restricted to temperatures up to ≈50 °C, insufficient for dPCR applications. An obvious alternative would seem to be fluorescein, as its amplitude of fluorescence (F) is a function of T,26 and fluorescence measurements are compatible with the instrumentation used for dPCR quantification. Unfortunately, this technique is susceptible to photobleaching and thus the system cannot be calibrated for precise temperature determination.
An alternative fluorescence measurement technique, based on melting curve analysis (MCA) of DNA, has been utilized.27 At the melting temperature (TM) of DNA, ≈50% of the double-stranded DNA is denatured, leading to a drop in the emitted F value.28 The TM depends only on the composition of the DNA template and the PCR master mix, making it independent of photobleaching. The F value decreases with exposure time, however the first derivation of the melting curves with respect to TS provides the constant value of TM with minimal deviation.27 This MCA-based non-contact temperature measurement technique was previously applied to determine the temperature uniformity inside of the microfluidic channel of a microcalorimeter, and the device was subsequently calibrated accordingly.22,29
Here we proposed a non-contact temperature sensing technique based on MCA to determine the temperature non-uniformity of the fluid within the micro partitions of a dPCR chip. We also used this technique to calibrate temperature sensor using two points calibration. The proposed method is non-contact thus it does not affect the temperature of the device such as contact methods do. It measures temperature of the fluid, which is the temperature of interest instead of infrared technique measuring only radiation from the surface. Finally the MCA-based technique is not suffering from undesirable photobleaching effect such as earlier used fluorescein-based temperature measurement method.
This method provided information about T inside the partitions where precision is required. We loaded the dPCR chip with the PCR master mix after amplification and then captured fluorescence images of the chip in the temperature range from 70 to 99 °C. We subsequently performed image processing to extract and plot the F values of each partition as a function of T. We then performed MCA and extracted TM values from each partition. We finally plotted the TM values as a function of partition location, determining the temperature distribution over the dPCR chip. Our method of determining temperature uniformity is particularly suitable for microfluidic systems where access for even a miniaturized temperature sensor is challenging or impossible. Once the temperature distribution of the device has been determined, should there be any undesirable variation or other non-uniformity, researchers can check the heat transfer system and improve it to ensure that the system functions properly.
The TEC was powered by electrical current pulses using an H-bridge system. The temperatures of the brass plate (Fig. 1D) and the TEC itself (Fig. 1E) were monitored with an RTD-type Pt100 temperature sensor. Temperature was controlled via PWM from a personal computer using software based on proportional integral derivative regulation. The dPCR chip, with a TEC, was placed on another brass plate equipped with a fan for cooling. The bottom part of the TEC was mounted on a Z-stage located on two sliders, allowing convenient dPCR chip filling and replacements. The dPCR chip was placed either in a brass holder on top of the TEC (configuration A) or directly on the TEC surface with silicon wafer interface (configuration B), yielding different chip temperature uniformity. We assembled two systems with different configurations just to demonstrate the different temperature distribution between two different types of system using the proposed method.
We performed the following PCR protocol using a commercial qPCR instrument: a hot start for 120 s at 95 °C, followed by 40 cycles of three-step PCR amplification consisting of denaturation for 15 s at 95 °C, annealing for 15 s at 56 °C, and extension for 30 s at 72 °C, followed by MCA from 65 to 95 °C. We then plotted F as a function of T (Fig. 2B for HBV as an example), thereby obtaining the melting temperature of HBV (TMB) equal to (87.17 ± 0.04) °C (mean ± standard deviation [σ] from 7 measurements), as shown in an inset of Fig. 2B. We also performed the same experiment for the Chr21 gene target, obtaining its melting temperature (TMC) equal to (83.69 ± 0.20) °C (mean ± σ from 16 measurements) as described in ESI Section A.†
We pipetted ≈4 μL of the amplified sample onto the edge of the dPCR chip, and the sample was then spread by the glass to fill each partition of the chip. Then ≈10 μL of mineral oil was pipetted on the edge of the cover glass, coated with parylene and polydimethylsiloxane,24 and placed on top of the dPCR chip to cover the sample in the micro partitions and prevent the sample's evaporation. The Chr21 and HBV genes were tested with dPCR configuration A and dPCR configuration B, respectively.
Fig. 3 Block diagram showing the data processing MATLAB script used to obtain the distribution of The script evaluated simultaneous MCA at each partition over the whole dPCR chip. |
We assumed that the values deviated from the mean value of TM in surrounding partitions by more than 1 °C were due to defects such as empty partitions, flaws in the cover glass or chip damage. These out-of-range values were not considered in calculations. Damaged chip or glass could also be replaced to remove the out-of-range values. A few melting curves from partitions for both targets (HBV, Chr21) were shown in the ESI Section D.†
Subsequently, we built a discrete 3D distribution map as a function of partition positions, followed by a median filtering algorithm to smooth the map (Fig. 4A and C) for both targets. Then we performed 3D parabolic function fitting on the 3D map and constructed the fitted 3D distribution map (Fig. 4B and D) of the dPCR chip. The fitted 3D map with continuity here showed a trend in dPCR chip temperature distribution more clearly than the original data, which is particularly clear in Fig. 4B with a distinguishable temperature gradient across the dPCR chip.
The mean value and deviation were estimated from the values (Fig. 4A and C) through fitting to a Gauss distribution function. The of Chr21 ( was ≈ 3.28 °C. Configuration B yielded equal to (86.49 ± 0.08) °C and the difference between TMB and was only ≈0.68 °C. This shows a better temperature homogeneity across the dPCR chip from configuration B (Fig. 4C and D) extending over the whole configuration, including the RTD sensor. Configuration A exhibits a temperature difference of ≈9 °C between the coldest and the warmest parts of the chip. Such a large temperature variance is clearly unsuitable for feasible dPCR.
The major difference between configurations was the size of TEC elements, (12 × 12) mm2 (A) vs. (30 × 30) mm2 (B), in respect to the (9 × 9) mm2 dPCR chip and the chip substrate. Configuration A used a brass block while configuration B utilized a piece of Si wafer as interface between the TEC and the dPCR chip. The contributing effects to the large dPCR chip temperature nonuniformity were presumably insufficient heat transfer, non-uniform thermal conductance, the heat capacity of the substrate, and the cooling of chip and substrate edges by the surrounding air.
We created an equivalent 3D temperature map of the chip (Fig. 4C and D) from configuration B. This configuration, with a (30 × 30) mm2 TEC and a piece of Si wafer as an interface between the TEC and the dPCR chip, has a superior performance compared to configuration A. Its σ value of fitting error was only 0.08 °C and the temperature difference between the cold and hot parts of the dPCR chip was only ≈0.22 °C. It demonstrated that the temperature fluctuation across the chip was either ≈0.22 °C or smaller. These data demonstrated that the heat transfer between the TEC and the dPCR chip was significantly better with the Si interface compared to the brass interface. All temperature data are summarized in Table 2.
The difference in and TM values between these configurations shows the importance of sensor calibration. This was also demonstrated earlier, when the readout of the RTD sensor calibrated traditionally differed from the actual fluid T by almost 10 °C.22 We used relative to TM as the first calibration point (Fig. 5A). The second calibration point was obtained by comparison of the integrated RTD sensor value with an external thermometer with, the configuration being measured having the power for the TEC off, thus assuring the temperature of the dPCR chip had equalized with the ambient environment (Fig. 5B).
The prevention of temperature non-uniformity on a dPCR chip is extremely important during assay optimization. It can contribute to the elimination of false negative partitions and to the removal of the so-called rain caused by inaccurate annealing temperature in the rain-forming partitions. The presence of this artifact makes it very difficult to interpret the results as it complicates the correct setting of the fluorescence threshold between positive and negative partitions.31 Our proposed MCA-based non-contact temperature measurement method provided an option to determine the temperature non-uniformity on a dPCR chip and it helped for the subsequent temperature non-uniformity optimization.
In principle we might measure both systems using both, HBV as well as Chr21, but the temperature distribution of the chip only depends on the system configurations and not the target thus single target measurement is sufficient.
Footnotes |
† Electronic supplementary information (ESI) available. See DOI: 10.1039/d1ra08138a |
‡ M. G. and X. W. contributed equally as they are both considered first authors. |
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