Magnetic Stir Plate Speeds DNA Measurements

Scientists have demonstrated that they can measure the amount of DNA in a sample within minutes using only magnetic beads, a laboratory stir plate, and a digital camera (J. Am. Chem. Soc., DOI: 10.1021/ja300839n). This simple, rapid method could find use detecting and quantifying DNA in the field, such as spotting bacterial DNA sequences at slaughterhouses, the researchers say.

The most common methods to quantify DNA are fluorescence-based techniques and quantitative polymerase chain reaction. Both require expensive equipment.

James Landers of the University of Virginia and his colleagues stumbled across a cheap and fast method based on the aggregation of magnetic microparticles. Similar methods have recently been developed to quantify biomolecules, including one in which proteins glom onto magnetic beads, causing the beads to aggregate into chains (Nano Lett., DOI: 10.1021/nl9030488). In that method, the researchers use a spectrophotometer to measure how much light passes through the sample, and thereby determine the length of the chains and the amount of protein present.

The new DNA quantification method simplifies the detection step by producing large, visible clusters of beads and DNA. Instead of relying on an expensive spectrophotometer, Landers’ team can use a digital camera to determine the DNA concentration.

To form the DNA-particle clusters, the researchers suspend silica-coated magnetic microparticles about 8 µm in diameter in a solution of guanidine hydrochloride and then add the DNA sample. Guanidine separates the DNA double strand into single strands that then wrap themselves around several silica beads, Landers says. Placing the solution over a rotating magnetic field, like one generated by certain types of laboratory stir plates, causes the nanoparticles to gather into clusters that look like spinning pinwheels. Landers says these clusters form within five minutes.

The researchers then snap a digital photograph of the suspension and use a computer program to determine the amount of aggregation. Without DNA, the magnetic beads disperse through the solution and the percentage of dark pixels in the picture is large. The number of dark pixels drops as larger clumps form with increasing amounts of DNA. The program converts the percentage of dark pixels into a DNA concentration. With this method, the scientists could detect DNA concentrations as low as 3 pg/μL, comparable to the sensitivity of fluorescence-based techniques.

The team also could detect specific DNA sequences with their method. To do so, they combined two sets of beads, each decorated with short strands of a DNA sequence that complemented each end of a single 26-base strand target. The beads only clustered into pinwheels when the target strand was present.

Landers hopes to build a handheld device that generates a rotating magnetic field to use in the field, as in remote areas or in a meat packing plant.

Jérôme Bibette, a chemist and physicist at the City of Paris Industrial Physics and Chemistry Higher Educational Institution, says the method’s key advance is the rotating magnetic field. Other researchers have used static fields to aggregate DNA on magnetic beads, but the rotating magnetic field leads to better contrast for optical detection.

But for the method to be practical, says chemist Itamar Willner, of the Hebrew University of Jerusalem, the researchers need to increase its sensitivity by 1,000-fold and make it selective enough to detect mismatches of single DNA base pairs.

Landers says his colleagues are working on improvements to sensitivity.

CORRECTION: This story was updated on April 10, 2012, to correct several errors. The original version inaccurately stated that both common methods to quantify DNA take hours of work; it incorrectly said that the new technique built on other researchers’ recent work; and it also said, inappropriately, that Landers agreed with Itamar Willner’s statement about sensitivity and selectivity. A clarification was added that the technique works only with certain types of laboratory stir plates. The video was originally credited to the journal instead of to James Landers.