From Manual to Mastermind: Guide to PCR Automation Solutions

Quantitative polymerase chain reaction (qPCR) is a pivotal technique in molecular biology that supports the quantification of DNA within a sample (Fig. 1). By incorporating a fluorescent dye, qPCR facilitates the real-time monitoring and measurement of PCR product formation. As the DNA is amplified with each cycle, the fluorescence intensity increases proportionally, providing precise and sensitive quantification against a standard curve of known DNA concentrations¹. 

Figure 1. qPCR supports the precise quantification of the amount of DNA in a sample. 

Due to its high sensitivity, accuracy, and adaptability, qPCR has become integral to several areas of research^2–5. In fundamental research, PCR is used for analyzing gene expression, detecting genetic variations, and identifying pathogens. Moreover, on a more clinical level, qPCR aids in pinpointing biomarkers, tracking disease progression, and evaluating the effects of novel treatments on gene expression.

Notwithstanding its importance, qPCR workflows are abundant with challenges, many of which can be attributed to the multitude of liquid handling steps in a workflow⁶. Here, we explore these challenges and discuss how PCR automation solutions can help overcome obstacles and turn your workflows around⁷. 

Optimizing PCR Workflow: Mastering Liquid Handling Techniques and the Role of Automation

One of the most important aspects of setting up a PCR workflow is optimization⁶. Efficient liquid handling is essential for optimizing PCR workflows, as it directly impacts accuracy, consistency, and contamination control. Precise pipetting techniques are crucial for transferring small liquid volumes, ensuring correct reagent concentrations, and successful amplification. Moreover, regular calibration and maintenance of pipettes can minimize errors and enhance data integrity. 

However, manual liquid handling has inherent limitations that cannot be overcome even when best pipetting practices are followed. It is time-consuming and monotonous and leaves scientists prone to repetitive strain injury (RSI), especially when dealing with large sample volumes. 

PCR automation solutions such as the I.DOT Liquid Handler (Fig. 2) address these challenges by improving accuracy, reproducibility, and efficiency. They streamline workflows, reduce human error, and increase throughput, making them indispensable for high-volume PCR processing. They also mitigate the risk of RSI, creating a safer work environment and offering scalability to accommodate various sample sizes and experimental protocols. Thus, implementing PCR automation solutions is a pivotal step in enhancing PCR workflow optimization^6,7.

Figure 2. The I.DOT Non-Contact Dispenser has several features that make it a great choice for automating qPCR workflows. 

To learn more about PCR workflow optimization and how PCR automation solutions like the I.DOT Non-Contact Dispenser can support this, check out the full article. 

qPCR Troubleshooting: Ensuring Successful Experiments

qPCR assays, though widely used, present several challenges that require effective troubleshooting for optimal results, such as low yield, non-specific amplification, and Ct value variations⁶. Low yield, often due to poor RNA quality, inefficient cDNA synthesis, or suboptimal primer design, can be mitigated by optimizing RNA purification⁸, adjusting cDNA synthesis conditions, and using specialized primer design software. Non-specific amplification, frequently caused by primer dimers or mismatches, can be reduced by redesigning primers or optimizing annealing temperatures⁹. Ct value variations, typically resulting from inconsistent pipetting, can be minimized with proper pipetting techniques and reliable PCR automation solutions. 

PCR automation solutions offer significant advantages in qPCR workflows, including improved accuracy and reproducibility, reduced contamination risk, and increased throughput. The I.DOT Non-Contact Dispenser, with its compact design and closed tipless system, ensures minimal cross-contamination and precise handling of small volumes (Fig. 3), providing confidence in assay success and result validity. Effectively implementing PCR automation solutions like the I.DOT Non-Contact Dispenser can greatly simplify qPCR troubleshooting and enhance workflow efficiency¹⁰.

Figure 3. The I.DOT Non-Contact Dispenser is equipped with droplet detection sensors for integrated volume verification, enabling an unparalleled degree of accuracy in qPCR workflows. 

For more useful PCR troubleshooting tips and tricks, read our recent article. 

Investing in qPCR Automation: Saving Time and Money to Advance Research

The true cost of manual qPCR workflows extends far beyond the initial equipment purchase, encompassing significant expenses related to time, labor, and errors. Manual workflows are time-consuming and labor-intensive, with skilled scientists performing repetitive pipetting tasks representing a hugely inefficient use of resources. Additionally, human errors and cross-contamination necessitate repeat experiments, wasting reagents and delaying timelines⁷. 

PCR automation solutions such as the I.DOT Liquid Handler address these issues by enhancing throughput, reducing labor costs, and minimizing errors^7,11. Automated systems enable simultaneous processing of multiple samples, accelerating research and allowing researchers to focus on more valuable tasks (Fig. 4). Precision in automated liquid handling minimizes inaccuracies and cross-contamination, conserving reagents and ensuring reliable, reproducible results. Moreover, qPCR automation improves data quality, enhances workflow consistency, and reduces the risk of RSI.

Figure 4. PCR automation solutions free up scientists for tasks that require their knowledge, skills, and experience. 

To ensure the investment in PCR automation solutions is worthwhile and offers a good long-term return, it's essential to carefully evaluate your lab's workflow needs and budget, selecting a system that meets specific demands without overspending. Labs with limited automation experience should opt for a user-friendly system with minimal training requirements.

Additionally, it is important to choose a system that can adapt to evolving project needs, handle increased workloads, and integrate seamlessly with other equipment, providing a flexible and future-proof solution that grows with your research.

To discover more valuable information about how PCR automation solutions could help you save time and money and for tips on choosing the best solution for your lab’s needs, read more here. 

Conclusion

Transitioning from manual to automated qPCR workflows offers substantial benefits in terms of accuracy, efficiency, and cost-effectiveness. Automation not only addresses the common challenges of manual qPCR workflows, such as time constraints, labor costs, and errors, but also enhances overall workflow efficiency and data quality.

By integrating PCR automation solutions like the I.DOT Liquid Handler, labs can significantly reduce human error, prevent cross-contamination, and increase throughput. This allows researchers to focus on high-value tasks, streamline their processes, and ultimately accelerate scientific discovery.

Ready to explore how PCR automation solutions can transform your lab? Book a demo today and discover the perfect solution to unleash the full potential of your PCR research!

References

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9. Delghandi M, Delghandi MP, Goddard S. The Significance of PCR Primer Design in Genetic Diversity Studies: Exemplified by Recent Research into the Genetic Structure of Marine Species. In: Basu C, ed. PCR Primer Design. Vol 2392. Methods in Molecular Biology. Springer US; 2022:3-15. doi:10.1007/978-1-0716-1799-1_1
10. Annona G, Liberti A, Pollastro C, Spagnuolo A, Sordino P, De Luca P. Reaping the benefits of liquid handlers for high-throughput gene expression profiling in a marine model invertebrate. BMC Biotechnol. 2024;24(1):4. doi:10.1186/s12896-024-00831-y
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