New methods in DNA folding allows for more complex shapes

What is it about?

DNA origami is a technique that uses one long piece of single stranded DNA (called the scaffold strand), folded in particular ways and held together using small staple strands (these can also be thought of like glue), to make intricate nanostructures. These DNA nanostructures can be made into custom shapes, both in two and three dimensions, and can be made to respond to various stimuli to make functional devices like biosensors. Whilst DNA origami has been revolutionary in the construction of nanostructures, it does have limits. If we wanted to make two interlocking circles of DNA (like the linking rings used by magicians), we would need to first make the scaffold strands, bring them together in the correct orientation, then glue the ends of each strand together to make interlocking circles. This means that the scaffolds are interlinked but not linked together at the scaffold level, much like a paper chain. This chapter explains how we have developed a method called Topogami, to allow us to make two circles looped together at the scaffold level, also known as catenated single stranded DNA. Topogami uses the functionality of an enzyme called Tn3 resolvase and specially designed plasmid called pTopoScaf that act as the starting material. pTopoScaf is a double stranded DNA circle and contains the sequence information for both of the circles we are trying to make and recognition sites for Tn3 resolvase. The Tn3 resolvase can make cuts in the pTopoScaf at the recognition sites, rearrange the DNA, and then rejoin the ends of the DNA without having to use “glue”. We can then use more enzymes to make this double stranded DNA into single stranded DNA. This then produces our truly catenated single stranded DNA.

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Photo by J D on Unsplash

Photo by J D on Unsplash

Why is it important?

DNA circle scaffolds where the ends are joined by “gluing” the ends aren’t as strong as truly catenated DNA circles formed by our Topogami method. This can be a problem, as it could lead to our intricate shapes unravelling in the conditions they are used in. Topogami reduces the chances of this happening because Tn3 resolvases fixes the cuts it makes using very strong covalent bonds, and this is irreversible. Also, this new method can be done in one reaction vessel, much reducing the number of steps required and the potential for one of the steps to go awry.