Silver Nanoparticles Make DNA Assembly Up to Five Times More Efficient, Japanese Study Finds

Researchers in Japan have developed a technique that uses silver nanoparticles to cut and reconnect DNA at chosen sites, achieving assembly efficiencies two to five times higher than conventional methods, according to a study published in Nucleic Acids Research. The team, led by Professor Hiroshi Abe and Assistant Professor Masahito Inagaki at Nagoya University with Professor Natsuhisa Oka at Gifu University, was seeking an alternative to standard restriction enzymes, which can only cut certain DNA sequences and tend to produce short overhanging sections called sticky ends that limit how efficiently fragments join together.

The researchers revisited a chemical reaction first reported between 1990 and 1992, in which silver ions cut specially modified DNA at specific sites, but the reaction originally recovered only about 14% of the DNA because silver ions attached nonspecifically and caused precipitation. Replacing silver ions with silver nanoparticles, separable from the mixture by centrifugation, solved the recovery problem, and coating them with polyethylene glycol (PEG) raised DNA cleavage efficiency from 36% to 92% at body temperature, with unwanted fragments sticking to the nanoparticle surfaces and raising overall DNA recovery to 98%.

The technique also produced sticky ends up to 18 bases long, far longer than those from conventional restriction enzymes. Using an 18-base overhang, the researchers achieved a DNA-joining efficiency of 44%, compared with just 8% for a conventional 4-base overhang, a fivefold improvement. To test the method biologically, the team assembled a DNA fragment encoding green fluorescent protein (GFP) and introduced it into human HeLa cells, which successfully produced the glowing protein, confirming accurate assembly.

"We believe this technology will be useful for synthesizing genomic DNA, with many possible applications in areas such as mRNA library establishment for cancer vaccines and gene therapy, as well as the development of artificial protein drugs and genome crops," Inagaki said. The researchers next want to determine whether multiple DNA fragments can be joined at the same time, a step they say is needed for building genome-scale DNA.