Multi-Block PCR, Made for Multi-Tasking Labs
Tackle scheduling bottlenecks and streamline multi-condition workflows with 3-block flexibility of the TurboCycler 3.
Introduction
Ever feel like PCR scheduling is holding your lab back? It’s easy to hit a bottleneck when you’re trying to test multiple conditions, but can only run one protocol at a time. The TurboCycler 3 is a multi-block PCR thermal cycler with three independently controlled blocks, each with gradient temperature capability—designed specifically for labs that need a “multi-tasking” solution. In this article, we explore three common application scenarios—from genetic screening to NGS workflows to agricultural DNA analysis—showing how the TurboCycler 3 helps overcome scheduling issues and boost operational efficiency. You’ll also find a product comparison to help evaluate multi-block PCR options, making this guide especially valuable for technicians managing high-throughput workflows, diverse sample types, or limited instrument access.
Tired of PCR Scheduling Conflicts?
Many researchers in mid- to large-sized labs face the same recurring frustration: "We're not short of people—we're short of thermal cycles.”
As PCR protocols grow more diverse, those working on gene screening, NGS development, or agricultural testing, all face the same challenges:
- Shared equipment means packed schedules
- Different samples require different conditions
- Optimization demands many trial runs
- Routine calibration delays everything
Beyond manpower and workflow design, instrument flexibility has become key. That’s where multi-block thermal cyclers come in—to help labs run multiple protocols at once, cut downtime, and reduce repetitive setup.
TurboCycler 3 is built for these demands. Its independent 3-block design empowers your lab to handle multi-condition, high-throughput experiments with ease. Below, we explore three real-world use cases that show how labs can benefit from this smart flexibility.
Note: The research studies cited below used other multi-block thermal cyclers available on the market. They are included here solely to demonstrate the practical relevance and benefits of the multi-block PCR thermal cycler in real-world applications.
Scenario 1: Genetic Screening Labs—Multi-Target Demands, Solved in One Run
PCR applications are rarely one-size-fits-all. For example, in clinical genetic screening, it is common to amplify several gene targets simultaneously—each requiring different thermal conditions. Running them separately, or waiting for instrument access across multiple machines, wastes time and increases the risk of errors.
With TurboCycler 3, each block can run its own program independently, making it ideal for handling different primers, samples, or PCR protocols in parallel. When balancing condition screening and routine high-throughput PCR, this flexibility enables testing several targets in a single run—saving time and space.
In a forensic identification study, researchers working with carbonized bone samples and blood from relatives used a multi-block PCR thermal cycler to amplify STR loci under multiple conditions simultaneously—enabling sufficient DNA amplification for downstream analysis [*1].
Scenario 2: NGS Pre-PCR—When Optimization Never Ends
The PCR pre-processing phase in NGS workflows is one of the most variable and time-consuming steps. cfDNA, ctDNA, and FFPE samples all present different quality and thermal needs, from annealing temps to probe sets.
Each of the three independent modules of the TurboCycler 3 support an 8-row temperature gradient (up to 30°C). This allows three different protocols to be run in parallel—for faster, side-by-side optimization; what once took multiple runs can now be completed in one.
A study on non-invasive prenatal testing used a multi-block PCR system to amplify STR loci from trace fetal cfDNA in maternal plasma. The study showed improved success rates for low-concentration, multi-target amplifications under differentiated conditions [*2].
In another pharmacogenomic study, four genes—CYP3A5, CYP3A4, ABCB1, and POR—were simultaneously amplified, for their SNP regions, to assess drug metabolism-related variants. At this stage, the multi-block PCR thermal cycler functioned like a “photocopier,” amplifying the target segments to provide sufficient material for downstream analysis, enabling accurate interpretation of patient-specific genetic variants [*3].
Scenario 3: Agriculture and Microbiology: One Lab, Many Samples
Labs in agriculture, livestock, and aquaculture research often handle a wide range of samples—such as rice disease markers in the morning, corn genotyping by noon, and antimicrobial resistance testing for bacteria after that. Each type requires unique PCR conditions, making it nearly impossible for single-block PCR machines to keep up. The TurboCycler 3 allows each block to run a separate protocol with different temperature settings. This is especially useful for frequent task switching or handling diverse samples—reducing scheduling conflicts while maximizing throughput.
In a study targeting Xanthomonas citri, the pathogen responsible for citrus canker, researchers amplified DNA from more than 200 bacterial strains to differentiate subtypes. A multi-block PCR thermal cycler enabled them to run multiple target reactions simultaneously, maximizing sample utility and streamlining the analyses [*4].
Why Choose a Multi-Block PCR Thermal Cycler?
Some labs try to solve scheduling issues by using multiple single-block thermal cyclers. However, this consumes space, increases maintenance demands, and still cannot run different conditions simultaneously.
TurboCycler 3 integrates three 48-well blocks in a single instrument. Each can be maintained separately without interruption to the others. This not only saves lab space but also keeps operations running smoothly—even when one block is down for maintenance.
3-Block PCR Thermal Cycler Comparison: How Do You Choose?
There aren’t many 3-block PCR machines on the market, and most come from high-end international brands. We've often heard users say:
- “The specs seem similar, but the price difference is huge—what’s the actual difference?”
- “There is supposed to be ‘gradient’, but only two blocks can be adjusted. We barely use it.”
- “We have to stop the whole machine for calibration—we don’t have time for that.”
So, we have put together a comparison of three commonly used multi-block PCR thermal cyclers, looking at throughput, flexibility, and ease of daily operation.
|
Feature |
Blue-Ray Biotech TurboCycler 3 |
Thermo Fisher ProFlex |
Analytik Jena Biometra TRIO 48 |
|
Block Capacity |
3 × 48 wells (0.1/0.2 mL) |
3 × 32 wells (0.2 mL) |
3 × 48 wells (0.2 mL) |
|
Total Throughput |
144 wells |
96 wells |
144 wells |
|
Independent Block Operation |
✅ Supported |
✅ Supported |
✅ Supported |
|
Independent Block Maintenance |
✅ Yes (removable blocks) |
❌ No
|
❌ No
|
|
Temp Accuracy / Uniformity |
± 0.3 °C / ± 0.4 °C |
± 0.25 °C / < 0.5 °C |
± 0.1 °C / ± 0.2 °C |
|
Max Ramp Rate |
5.0 °C/s |
6.0 °C/s (block) / 4.4 °C/s (sample) |
5.0 °C/s |
|
Gradient Temperature |
✅ 8 zones per block |
✅ Limited (2 zones only) |
❌ No |
|
Touchscreen |
10.1” color LCD |
8.4” color LCD |
7” full-color TFT |
|
Dimensions (H×W×D) |
Compact (236×356×362 mm) |
Large (272 mm x 330 mm x 560 mm) |
Medium (250 mm x 300 mm x 410 mm) |
|
Price Tier |
Full-featured, budget-friendly |
High-priced |
High-priced |
If your lab values multitasking and flexibility, TurboCycler 3 delivers an ideal balance between high-throughput performance, ease of use, and value. Eliminate scheduling bottlenecks—run different conditions in parallel and lighten your team’s workload.
Build a Smarter PCR Workflow
At Blue-Ray Biotech, we develop a complete nucleic acid testing solution that meet lab needs—from extraction to amplification and detection. Our thermal cycler portfolio includes:
- TurboCycler 3 for flexible, high-throughput multi-condition workflows
- TurboCycler 2 for standard lab use
- TurboCycler Lite for budget-conscious labs
Our thermal cyclers are trusted for both everyday work and advanced applications and are cited in research worldwide.
We believe instruments should do more than meet technical specs—they should help your lab work be smarter every day. If your PCR scheduling is slowing you down, the TurboCycler 3 could be the solution you’ve been looking for.
Reference
*1. Dumache R, Rogobete AF, Ciocan V, Muresan CO, Enache A. DNA-Based Identification of a Carbonized Victim by Kinship Analysis. Clin Lab. 2017;63(5):1035-1040. doi:10.7754/Clin.Lab.2017.170125
*2. Dumache R, Stoicanescu D, Muresan C, Ciocan V, Enache A. Circulating Cell-Free Plasma DNA in Noninvasive Prenatal Paternity Testing with Short Tandem Repeats (STRs). Clin Lab. 2020;66(12):10.7754/Clin.Lab.2020.200337. doi:10.7754/Clin.Lab.2020.200337
*3. Abderahmene A, Khalij Y, Moussa A, et al. The pharmacogenetics of tacrolimus in renal transplant patients: association with tremors, new-onset diabetes and other clinical events. Pharmacogenomics J. 2024;24(1):3. Published 2024 Jan 22. doi:10.1038/s41397-024-00323-4
*4. Yasuhara-Bell, J., Santillana, G., Robène, I., Pruvost, O., Nakhla, M., & Mavrodieva, V. (2023). Genome-Informed Multiplex Conventional PCR for Identification and Differentiation of Xanthomonas citri pv. citri Subpathotypes, the Causal Agents of Asiatic Citrus Canker. PhytoFrontiers. https://doi.org/10.1094/PHYTOFR-04-22-0044-FI
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