Proofreading and Error-Correction

Graphic: A piece of DNA

Despite much progress made in the self-assembly of nanomaterials, defects that occur during the assembly process still present major obstacles. "Instead of trying to avoid defects or work around them, it makes more sense to correct them during and after the assembly process," said Yi Lu, a chemistry professor at Illinois.

Lu and graduate students Juewen Liu and Daryl Wernette utilized catalytic DNA to locate and remove errors in a DNA-templated gold nanoparticle assembly process. Catalytic DNA contains a substrate strand and an enzyme strand. In the presence of certain ions, the substrate is cleaved by the enzyme into two pieces of unequal length. The cleaved fragment with the shorter binding arm can be easily released. This catalytic DNA serves as a template for assembly of nanoparticles.

There are three kinds of nanoparticles encoded by different DNA in the system: two are defined as "correct" particles and one is defined as a "wrong" particle. Besides the difference in coding DNA, the nanoparticles can also be different in other aspects, such as size.

"To allow the catalytic DNA substrate to be a template for nanoparticle assembly, the substrate strand must be complementary to the DNA attached to the nanoparticles," Lu said. "A defect can occur in a DNA-templated gold nanoparticle assembly when the wrong particle is incorporated into the structure."

When a particle of the correct size is encountered, binding of the longer arm of the enzyme to the DNA template is permitted, while binding of the shorter arm to the DNA template is inhibited. "The active structure of the catalytic DNA cannot form," Lu said. "As a result, the template is not cleaved and the particle is incorporated into the assembly."

When a particle of the wrong size is mistakenly incorporated into the assembly, the enzyme can bind both its arms to the substrate template and form an active structure to cleave the substrate and remove the particle.

The researchers demonstrated that proofreading and error-correction can take place during and after the assembly of nanoparticles.; Source: University of Illinois at Urbana-Champaign