Catenanes are mechanically interlocked rings of DNA and could be used to make devices that can be switched between different states using external triggers like changes in pH. Knotted DNA strands are linked to themselves differently from their non-knotted counterparts.

DNA rearrangements play an important role in how this molecule functions in living systems, including how it replicates and recombines. These operations are naturally catalyzed by enzymes called topoisomerases.

Until now, most work on rearranged DNA molecules in the lab has focused on ligating branched DNA species into larger constructs. However, such techniques are often inefficient, explains team leader Nadrian Seeman of NYU.

Topo 1 binds single-stranded DNA

As an alternative, the researchers decided to mimic nature and investigate whether they could link DNA molecules in reactions catalysed by topoisomerases (in their case obtained from the bacterium Escherichia Coli). The topoisomerase they used, known as Topo 1, is the best-studied enzyme among type 1 topoisomerases and is a monomeric metal-binding protein. It works by preferentially binding single-stranded DNA and can cleave single-stranded DNA sites. This cleavage is then followed by re-ligation in a lower-energy form.

The enzyme forms contacts with the so-called 5'- and 3'- terminal regions of the DNA cleavage site and Seeman and colleagues used E. Coli Topo 1 to create a topological bond between DNA constructs and produce interlocked DNA structures. The researchers, reporting their work in ACS Nano DOI: 10.1021/acsnano.5b04333, used a system of closed DNA rings involving a paranemic motif called PX-DNA to bind DNA double strands together. This motif allows the DNA double helices to be coiled together side by side. The closed molecules contain complementary loops that when linked by Topo I can form various types of knotted structures (see figure).

A new tool for the DNA toolbox

“In our work, we have added another tool to the DNA nanotechnology toolbox,” Seeman tells “This toolbox is now available for all investigators in the field to exploit as they see fit.”

The NYU-Western Ontario team says that it can use this type of PX-based system to organise gold nanoparticles, not just DNA strands. A companion paper describing further aspects of this work has also been published in ACS Nano DOI: 10.1021/acsnano.5b04335.