Simplifying Nucleic Acid Extraction and Cutting Down Waste

A new approach to nucleic acid extraction efficiently frees RNA and DNA in just three steps, giving scientists back their precious time.

The Scientist Creative Services Team in collaboration with MilliporeSigma
Mar 29, 2021

Few things are as tedious as waiting for the alcohol to evaporate and an extracted DNA or RNA pellet to dry. DNA and RNA extractions are a huge time sink for scientists. The hallmark washing steps and column spins of nucleic acid extraction kits can tie scientists to the lab bench for hours depending on the number of samples.

Most nucleic acid extraction kits use spin-column technology, where DNA or RNA binds to a silica-based membrane in the presence of high concentrations of chaotropic salts, such as guanidine hydrochloride. The term chaotropic means chaos-forming, suggesting the entropic result of these salts disrupting the structure of macromolecules. This destabilizes proteins and frees the DNA or RNA from water to facilitate its binding to a silica-based membrane in a spin column. Residual chaotropic salts may creep into the final extracted product, reducing the accuracy of nucleic acid quantification and interfering with downstream applications, such as PCR. 

Washing reduces the amount of residual chaotropic salts in eluted DNA or RNA, but these steps are repetitive and dull to perform. Each step requires multiple centrifugation spins with error-prone tube handling steps that quickly add up with multiple samples. By the time the wash steps are complete, the wastebasket is overflowing with discarded plastic columns and the liquid waste container is filled with potentially toxic chaotropic- and alcohol-based solutions that need to be safely discarded. 

Each necessary centrifugation step also poses a risk to the integrity of the extracted product, as DNA or RNA may shear with each spin, resulting in DNA/RNA fragmentation. In the end, scientists rarely recover their entire eluted product; a portion of DNA or RNA remains bound to the column. GenElute™-E nucleic acid purification kits from MilliporeSigma eliminate problematic column technology.

Instead of binding DNA/RNA to silica-based membranes, GenElute™-E Single Spin technology separates nucleic acids based on size in a process known as negative chromatography. Researchers first lyse their samples to free the molecular contents of cells, and then transfer the contents to a resin matrix. Larger proteins move through the matrix more slowly than nucleotides. Impurities such as salts, detergents, and organic solvents get trapped in the matrix, allowing researchers to collect purified DNA/RNA with a single centrifugation spin. 

The technology simplifies the laborious and tedious process of nucleic acid extraction. Separating DNA/RNA based on size instead of silica-based membrane binding also eliminates the need for chaotropic salts and subsequent numerous washing steps to remove binding reagents. Reducing the number of centrifugation spins down to one also decreases the likelihood of nucleic acid sheering, maintaining the integrity of extracted DNA fragments from as small as 65 bp to as large as 49,000 bp. 

Most importantly, the volume of aliquoted solution is the same volume of recovered DNA/RNA with GenElute™-E kits. Nucleic acid solutions recovered with GenElute™-E kits are also more concentrated than silica-based methods because no DNA/RNA remains trapped in columns. And because no chaotropic salts are used in the extraction, there is no risk of salt interference in downstream applications. 

Cutting back the washing steps also decreases the amount of plastic waste produced by laboratories by as much as 55% compared to silica-based workflows, reducing laboratory costs and increasing savings. With mounting plastic waste produced by laboratories every day, researchers can rest assured that they are getting the best possible DNA/RNA extraction, with maximized purity and minimal environmental footprint with GenElute™-E Single Spin nucleic acid purification kits.