Parallel Functionalization of DNA Origami

Abstract

DNA origami enables the creation of large supramolecular structures, with precisely defined features at the nanoscale. The concept thus naturally lends itself to the concept of molecular patterning, i.e., the positioning of molecular moieties and functional features. Creation of nanoscale patterns was already disseminated by Rothemund in 2006, in which DNA hairpins were used to produce nanoscale patterns on the flat origami canvases (Rothemund PWK, Nature 440(7082):297-302, 2006). For this type of application, it is often desired to produce multiple different patterns using the same origami canvas by reusing existing origami staple strands, rather than ordering new, custom oligonucleotides for each unique pattern. This chapter presents a method where the enzyme terminal deoxynucleotidyl transferase (TdT) is used in a parallelized reaction to add functional moieties to the end of a selected pool of unmodified staple strand oligonucleotides, which are then incorporated at precisely defined positions in the DNA origami canvas. Introducing arrays of functional features using this enzymatic functionalization of origami staple strands offers a very high degree of flexibility, versatility, and ease of use and can often be obtained faster than custom synthesis. For small synthesis scales, typically employed during initial functional screening of many different molecular patterns, the method also offers a significant advantage in terms of cost. During the past years, we have utilized this to incorporate a large variety of molecules including bulky proteins (Sørensen RS, Okholm AH, Schaffert D, Kodal ALB, Gothelf KV, Kjems J, ACS Nano 7:8098-8104, 2013) in designed patterns from modified nucleotide triphosphate (NTP) building blocks (Jahn K, Tørring T, Voigt NV, Sørensen RS, Kodal ALB, Andersen ES, Bioconjug Chem 22:819-823, 2011). The near-quantitative yields obtained by enzymatic functionalization allow synthesis of a large set of oligonucleotides in a one-pot reaction from commercial starting materials without the need for individual post-purification. Based on the chosen subset of staple strand, it is possible to create any designed functionality, array, or pattern. Here we describe the process going from an idea/design of a DNA origami-specific molecular pattern to nucleotide synthesis and subsequent parallel functionalization of the DNA origami, assembly, and the final characterization.

Keywords: DNA; DNA origami; Enzymatic; Functionalization; Nanotechnology.