The main aim of our research is to design and construct nanoscale devices using biomolecules DNA, RNA and protein as self-assembling building blocks. The group have been involved in developing the DNA origami method to create 3D nanomechanical devices and have recently invented the single stranded RNA origami method that allows nanostructures to be enzymatically synthesized and expressed in cells.
Our research aims at understanding the fundamental principles for how biomolecules fold into unique and functional shapes and at using this insight to guide the design of novel nanoscale devices for technological applications.
Biomolecules can self-assemble into unique three-dimensional (3D) shapes determined by their sequence of residues. This causal relationship allows us to design the shape of biomolecules by programming their sequence. Our design process starts by investigating the atomic structure of nature's biomolecules from which we extract structural modules and invent new ways of combining them into a defined 3D shape. In a second step, we use computer algorithms that take into account the physical properties and folding kinetics of the molecules to design their sequence. The sequences are then chemically synthesized and used in self-assembly experiments followed by the investigation of their 3D structure and properties by biophysical characterization techniques.
Our research group has been involved in the development of the DNA origami method to create 3D nanomechanical devices such as the DNA origami box, and we are further developing DNA origami devices for applications in biosensing, enzymatic control and drug delivery. Recently, we have invented the RNA origami method that allows nanostructures to be enzymatically synthesized and possibly expressed in cells. We aim to use this new technology for synthetic biology purposes as intracellular sensors and as scaffolds for biosynthesis pathways of relevance to the biotechnology industry.
Biomolecular design is a research area that aims at rationally designing biomolecular structures and devices. One such example is the DNA origami method (Rothemund, Nature 2006). In our lab we have been developing the RNA origami method where RNA nanostructures can be folded during transcription (Geary, Rothemund & Andersen, Science 2014). In this area of research, we are mainly focused on the structure of the biomolecules, and in particular on increasing the size of the structures that can be designed and produced. Therefore, we develop software to aid in the design process as well as practical procedures that efficiently form the structures.
In 2006, Paul Rothemund presented the idea of “scaffolded DNA origami”, in which a long, single-stranded, circular DNA scaffold could be moulded into almost any desired 2-dimensional structure by adding carefully designed “staple strands”. The scaffold usually used is the genomic viral DNA M13, and approximately 200 staple strands are used to form the designed structures. In 2009, a 3-dimensional DNA Origami box was published by Ebbe Sloth Andersen. In this publication, it was also demonstrated that the DNA origami structures could be dynamic by controlling the opening of the box lid through a strand displacement reaction.
In our lab, we have used DNA origami to create complex, 3-dimensional structures with different purposes. One was a DNA origami beacon that was able to function as a very sensitive biosensor responding to specific DNA sequences. Another example is a DNA nanovault that was able to control enzymatic reactions by encapsulating the enzyme in a multi-layered DNA origami structure, thus inhibiting interaction with its substrate.
A main focus of our lab is to use the principles of biomolecular design to create novel nanodevices. One direction that is very important for this goal is to develop biosensor devices. The biosensors that we make are both simple and more complex devices made of DNA or RNA. Our aim is to create nanorobots, which we define as rationally designed autonomous molecular devices that can sense, compute and act functionally. Biosensors are very central to this since they are able to sense, transduce, and report an output.
In 2014, Geary et al introduced a general architecture for rationally designing single-stranded RNA structures of arbitrary shape. In contrast to DNA origami structures, RNA origami structures are designed so that the strand path goes through the whole structure, thus allowing it to fold upon itself co-transcriptionally to form the desired structure without the help of staple strands. The RNA origami structures are stabilised by 180° kissing loops, and tetraloops cap the ends of the helices providing a more thermostable and compact structural fold. Large assemblies forming hexagonal lattices have also been made by connecting monomeric tiles through 120° kissing loops precisely positioned at the corners of the tiles.
In our lab, RNA origami is now mostly used to precisely position aptamers and proteins, e.g. for use as biosensors, or to create larger 2- or 3-dimensinal structures. For example, a small RNA origami structure, called the apta-FRET structure, was used to position the fluorophore-binding aptamers Spinach and Mango to allow Förster Resonance Energy Transfer (FRET) between their fluorophores. This basic structures was then used to design two types of sensors; one responding miRNA sequences and one sensing the small molecule S-adenosine Methionine (SAM).
Synthetic biology is a rigorous engineering discipline that aims to create, control and program biological behaviour. We have recently entered this field with the main goal of using rationally designed molecules to gain better control over biological processes. The RNA origami method can be used to express well-defined nanostructures in cell-like environments, where they can be used to scaffold biological components. By integrating our experience on biomolecular design processes with deep knowledge of biological and biochemical events, we aim to develop valuable tools for the production of complex synthetic nanodevices inside cells.