Thermal cyclers and qPCR machines both perform DNA amplification—but they aren’t interchangeable. One is a foundational tool in nearly every molecular biology lab; the other adds real-time detection and quantification, unlocking deeper insights for diagnostics, gene expression, and beyond.
If you're setting up a new lab, scaling your PCR workflows, or evaluating equipment options for specific assays, it’s critical to know the difference. Choosing the wrong platform can bottleneck your research—or saddle you with features (and costs) you don’t actually need.
In this post, we’ll break down the key differences between thermal cyclers and qPCR machines, explain when you need one vs. the other, and show how leasing can help you access the right system without blowing your budget. Whether you're running endpoint PCR, quantitative assays, or both, understanding your amplification needs is the first step toward building an efficient, scalable workflow.
What Is a Thermal Cycler?
A thermal cycler—also called a PCR machine or thermocycler—is the backbone of standard PCR (polymerase chain reaction). It’s designed to precisely heat and cool samples through a series of temperature cycles that enable DNA amplification.
Here’s how it works:
The basics: controlled temperature cycling
The thermal cycler moves samples through repeated cycles of:
- Denaturation: Heating to ~94–98°C to separate double-stranded DNA
- Annealing: Cooling to ~50–65°C so primers can bind to the target DNA
- Extension: Heating to ~72°C so DNA polymerase can synthesize new strands
This thermal cycling repeats 25–40 times, exponentially amplifying the target DNA sequence.
What it does—and doesn’t do
Thermal cyclers execute the PCR process with precision, but they don’t measure anything. After amplification, you typically run your samples on an agarose gel using electrophoresis to visualize results. This makes thermal cyclers ideal for workflows like:
- Cloning and plasmid prep
- Genotyping
- Detecting presence/absence of target DNA
- Endpoint PCR validation
Key features to consider
Modern PCR thermal cyclers often include:
- Gradient capabilities: Allow optimization of annealing temperatures across a plate
- Heated lids: Prevent sample evaporation
- Fast ramp rates: Speed up cycling for high-throughput labs
- Flexible block formats: Accommodate different tube or plate sizes
Standard thermal cyclers are reliable, cost-effective, and widely used across life science research. But if your application requires quantification or real-time data, you’ll need more than just temperature control.
What Is a qPCR Machine—and How Is It Different?
A qPCR machine (short for quantitative PCR, also known as real-time PCR) builds on standard thermal cycler functionality—but adds real-time fluorescence detection that allows you to monitor DNA amplification as it happens. This real-time signal makes qPCR essential for applications where you need both detection and quantification of nucleic acids.
Real-time detection using fluorescence
qPCR machines use fluorescent dyes or probes that bind to DNA. As amplification progresses, the fluorescence signal increases. The system captures this signal during each cycle—providing a quantitative readout of how much target DNA or RNA is present in the sample.
This allows labs to:
- Measure gene expression levels
- Quantify pathogens or viral load in diagnostics
- Detect rare mutations or single-nucleotide polymorphisms (SNPs)
- Validate results with more precision than endpoint PCR alone
Core differences from standard thermal cyclers
- Built-in optics and sensors: qPCR instruments have an integrated fluorescence detection system with excitation/emission filters, cameras, and software
- Quantitative output: Rather than just amplifying DNA, qPCR instruments generate Ct (cycle threshold) values that reflect the starting quantity of target nucleic acid
- Software-driven workflows: Most real-time PCR machines come with robust analysis platforms for plotting amplification curves, generating standard curves, and analyzing results
When you need a qPCR system
You’ll likely need a real-time PCR system if you’re doing:
- Gene expression profiling
- Pathogen detection and quantification
- High-throughput diagnostics
- Molecular diagnostics in clinical or public health labs
These systems are more complex—and more expensive—than standard thermal cyclers, but they offer critical advantages for quantitative assays.
Thermal Cycler or qPCR? How to Choose Based on Your Workflow
Choosing the right PCR platform isn’t about which system is “better”—it’s about which one matches your goals, throughput needs, and budget. Here’s how to think through the decision.
Go with a thermal cycler if you need:
- Standard DNA amplification without real-time quantification
- A cost-effective tool for cloning, genotyping, or basic detection
- Flexibility to run a range of assays with manual downstream analysis
- A reliable system for teaching labs, R&D, or non-diagnostic workflows
- The ability to optimize PCR conditions using gradient blocks
Thermal cyclers are ideal when you're running endpoint PCR and plan to analyze results via gel electrophoresis or another post-PCR method. They’re also simpler to operate, require fewer reagents, and have lower ongoing costs.
Choose a qPCR machine if your application demands:
- Quantification of nucleic acids, such as measuring gene expression
- Real-time tracking of amplification curves for high-sensitivity detection
- Running clinical diagnostics, such as pathogen testing or viral load assays
- Multiplexing capabilities to detect multiple targets in a single reaction
- Automation and integration into a high-throughput molecular workflow
qPCR systems are more advanced and enable fluorescence-based detection without additional post-PCR steps. They reduce sample handling, improve sensitivity, and offer robust data analysis tools—but come with higher equipment and reagent costs.
Consider both for a hybrid workflow
Some labs benefit from having both: a standard thermal cycler for routine amplification and a qPCR system for quantitative work. If budget or bench space is a concern, think about your assay mix—what percentage of your PCR work actually needs real-time quantification?
Understanding your current and future needs helps you avoid over- or under-investing—and ensures your PCR setup supports your research, diagnostics, or assay development goals.
How Leasing Can Help You Access the Right System
Thermal cyclers and qPCR machines vary widely in cost—and not every lab has the capital to buy the system it actually needs. Whether you're outfitting a new space, upgrading outdated equipment, or expanding your PCR capacity, leasing can be a smart way to stay flexible and cost-effective.
Reduce upfront costs
qPCR machines—especially high-throughput or multiplex-capable models—can cost tens of thousands of dollars. Leasing allows you to spread those costs over time and preserve your cash for other essentials, like hiring, reagents, or scaling up your workflow.
Access better technology now
Instead of settling for a lower-spec thermal cycler because it’s all your budget allows, leasing gives you access to more advanced systems—whether that’s a gradient-capable thermocycler or a real-time PCR instrument with built-in optimization software. This can accelerate research progress and improve data quality.
Match equipment to your use case
Leasing gives you the flexibility to choose the right PCR system based on actual assay needs, not just your capital availability. Need a standard thermocycler now, but expect to shift into diagnostics later? Leasing terms can often accommodate upgrades, swaps, or expansions.
Minimize downtime and maintenance headaches
Many leasing agreements include service and support—meaning you can focus on running assays instead of troubleshooting breakdowns or worrying about long-term repairs. That’s especially important in diagnostics labs or any setting where instrument uptime is critical.
Scale as your PCR workload grows
As your lab’s PCR needs evolve—whether you're adding new assays, increasing sample volume, or moving into real-time qPCR—you can scale up your equipment accordingly. Leasing supports that growth without locking you into a static system or forcing a large one-time purchase.
Final Thoughts: Start with the Workflow, Then Scale
Whether you're running standard endpoint PCR or diving into quantitative gene expression, choosing the right amplification system comes down to understanding your workflow, not just your wishlist. Thermal cyclers are reliable, versatile, and cost-effective for many research labs. qPCR machines offer real-time insight, quantification, and streamlined analysis—but at a higher price point.
If you're building a new lab, expanding your assay capabilities, or entering the diagnostics space, the decision between these platforms can shape your workflow for years to come. That’s why access matters.
Excedr helps life science labs lease the right PCR equipment—whether it's a thermal cycler, a real-time qPCR system, or both—without large capital expenditures. With flexible lease terms, equipment bundles, and service included, you can get the performance you need today and the scalability to support what’s next.
Need help choosing the right PCR setup for your lab? Talk to our team.