Improving Yield and Quality in Nucleic Acid Extraction

High-quality nucleic acid extraction is an essential first step in most molecular biology workflows. Whether studying genomes, transcripts, epigenetic markers, or combinations of these, the quality of the nucleic acids influences the success of downstream analyses. In recent years, advances in extraction have produced faster, higher-yield, and more consistent results across a range of sample types. This article explores new approaches in nucleic acid extraction and how they are helping meet the growing demands of genomics, diagnostics, and personalized medicine.

Developments in extraction methods

Since Friedrich Miescher first succeeded in isolating DNA, methods for nucleic acid extraction have undergone major improvements.¹ Some of the earliest routine methods relied on density gradient centrifugation and solubility differences in alkaline buffer. With continued innovation and commercialization, techniques expanded to include organic solvent and detergent-based separations. More recently, solid-phase methods employing silica, glass, diatomaceous earth, magnetic beads, or anion exchangers have enabled faster and cleaner purification.

“The most exciting advance I'm seeing right now is the development of automated high molecular weight (HMW) DNA extraction solutions enabling the full potential of long-read sequencing,” stated Catherine Goh, Product Manager of chemagen Nucleic Acid Purification and Molecular Cytogenetics at Revvity. While long-read platforms can produce reads over 10 kb, their progress has been limited by the difficulty of extracting high-quality, intact DNA. Goh explained that traditional HMW methods are difficult because they require careful manual handling to avoid shearing fragments over 50 kb. Automated chemagic™ magnetic bead-based systems use gentler handling and optimized protocols that recover DNA over 100 kb quickly, while reducing labor and expanding access to long-read sequencing and clinical testing.

Improvements in binding chemistry have also had a major impact. “The big leap has been in binding formats,” stated Kevin Mayer, Sr Research Scientist at Promega. “The move from rigid silica membranes to semi-solid magnetic phases has allowed for far more flexibility in workflow design, throughput capabilities, and automation.” While silica membranes once defined the standard, magnetic phases are now enabling gentler handling, reduced shearing, and compatibility with high-throughput automation.

Goh highlighted similar advantages to this shift toward magnetic separation and its automation potential. She added that these integrated workflows reduce manual steps and cut hands-on time from hours to minutes while improving consistency.

At the same time, extractions are becoming increasingly specialized and multifunctional. Mayer described recent advances that produce ultra-pure nucleic acids for biologics such as mRNA vaccines, as well as selective recovery from sources like extracellular vesicles or specific cell types. He also emphasized new multi-analyte workflows that can capture DNA, RNA, and even proteins from the same sample to maximize data from limited material.

Working with difficult samples

Alongside these innovations, researchers continue to face the challenge of working with degraded or scarce samples. Nucleic acids extracted from archival biopsies, forensic traces, environmental material, ancient DNA, and formalin-fixed paraffin-embedded (FFPE) tissues are often fragmented, chemically modified, or present in trace amounts. “These samples are often the most valuable yet most difficult to work with,” noted Mayer.

The formalin fixation and embedding process, while essential for tissue preservation, introduces crosslinking and artifacts like cytosine deamination. Mayer explained that “repair” enzymes, such as uracil-DNA glycosylase, can reduce some sequencing artifacts in FFPE DNA but also lower sequence complexity. Since high temperature decrosslinking itself promotes cytosine deamination, Mayer’s team at Promega has been working on technologies that limit deamination during the extraction process. “We have developed chemical catalysts that accelerate reversal of DNA-DNA and DNA-protein crosslinks, enabling shorter, gentler pre-processing conditions during extraction,” he said.

In addition to chemistry, workflow refinements have improved extractions from degraded samples. Goh pointed to several key innovations she described as “absolute game-changers.” For instance, replacing organic solvent pretreatment with a high-heat step before extraction has improved handling while boosting PCR detection rates.^2,3 Adjustments at the sample preparation stage can also make a significant difference. Goh cited work at Memorial Sloan Kettering, where ethanol pretreatment increased cell pellet density to recover more nucleic acid from fewer block sections, and where mineral oil deparaffinization reduced losses during processing.⁴

Another priority is preserving what little intact nucleic acid remains. “To minimize nucleic acid degradation, bead-based extraction with chemagic technology is particularly effective,” Goh explained. The system uses gentle magnetic separation instead of centrifugation or vacuum methods to preserve nucleic acids in degraded samples. Its ability to handle varied input volumes and move beads instead of liquids also reduces material loss and contamination risk.

Advice for selecting a method

With so many options, choosing the right extraction method can be harder than performing it. “Start with your end goals, not the technology,” emphasized Goh. The extraction requirements follow these goals, since extraction quality impacts downstream applications. Sample diversity is another key factor. Goh explained that many labs underestimate how varied their samples will become and recommended flexible platforms that can accommodate blood, FFPE, and plant material rather than locking into a single sample type. She also advised evaluating true cost per sample, factoring in consumables, labor, and repeat extractions. “A more expensive automated system often delivers better economics when you factor in technician time and consistency,” Goh stated.

Mayer recommended labs begin their selection by focusing on the biology of the sample, ensuring it can yield the needed genetic information. Key factors such as collection method, input mass or volume, and preservation influence yield and purity, while downstream applications determine quality requirements. Throughput should also guide system choice, since the needs of small labs differ from high-volume facilities. For quality checks, he cautioned that UV absorbance can be misleading with scarce or impure samples, and recommended DNA dyes or amplification-based methods instead. “Once you know your application and throughput, the balance between yield, purity, and cost becomes clearer,” Mayer added.

The future of nucleic acid extractions

As for the future, further advances in chemistry and automation are expected to improve extraction methods. Mayer predicts that future kits will use new binding surfaces such as rationally designed polymers and natural materials, which could increase selectivity, binding strength, speed, and purity. Extractions are also likely to merge more closely with downstream analysis, with purification steps increasingly integrated into broader workflows.

While innovation continues, Mayer pointed out that extractions are still too often treated as an afterthought, even though they form the foundation for every analysis. He explained that the real goal is to make purification so reliable that users can focus entirely on biology, and that choosing the right method depends on context rather than a single “right” approach. “The mountain has many paths, and the best choice depends on the sample, the analyte, the application, and the user’s priorities, such as throughput, cost, yield, or purity,” he said.

Goh offered another perspective, emphasizing that the future of nucleic acid extraction will be driven by flexible, automated platforms designed to meet the demands of personalized medicine. As healthcare shifts toward individualized treatments that require rapid, high-quality genomic data from diverse and often challenging samples, extraction systems will need to move away from one-size-fits-all approaches. She envisions platforms that allow protocol adjustments to diverse inputs, scale efficiently, and maintain complete traceability through integrated monitoring.

“This convergence of adaptable chemistry, automated processing, and integrated monitoring will be essential for supporting population-scale genomics initiatives, clinical trials, and routine diagnostic workflows that personalized medicine demands, ultimately enabling healthcare systems to deliver truly individualized treatments at scale,” Goh concluded.

References

1. Tan SC, Yiap BC. DNA, RNA, and protein extraction: the past and the present. J Biomed Biotechnol. 2009;2009:574398. 

2. Magnusson MI, Agnarsson BA, Jonasson JG, et al. Histopathology and levels of proteins in plasma associate with survival after colorectal cancer diagnosis. Br J Cancer. 2023;129(7):1142-1151. 

3. Kofanova O, Bellora C, Garcia Frasquilho S, et al. Standardization of the preanalytical phase of DNA extraction from fixed tissue for next-generation sequencing analyses. N Biotechnol. 2020;54:52-61. 

4. Kim D, Vanderbilt CM, Yang SR, et al. Maximizing the clinical utility and performance of cytology samples for comprehensive genetic profiling. Nat Commun. 2025;16(1):116.