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Research

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. 


Biomolecular design

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.

DNA origami method

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.

RNA origami method

 

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).

Biosensors and nanorobots

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.

Synthetic biology

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.

Scientific visualization

We offer a research programme for optimizing scientific data design and scientific imagery in contemporary bio- and nanoscience. The rapid increase of molecular and nanoscale data in contemporary science has produced an urgent need for developing new visual frameworks and tools to explore, analyze and communicate data. We aim at developing innovative visual solutions for contemporary scientific imagery, creates integrated visual systems based on graphic design and animation, and develops educational strategies in science visualization for scientists.

Research news

2018.02.13 | Awards

Funding: New European network on DNA-based nanorobotics

News on the iNANO website about the DNA-Robotics PhD school that we are part of. The PhD school is organized by Kurt Gothelf and funded by the European Commission – Marie Skłodowska-Curie Actions.

2018.01.24 | Research news

Highlight: RNA-Based FRET Sensors for Use In Vivo

Mette D. E. Jepsen gives a short introduction to her study on RNA-based apta-FRET devices and their potential future applications. The highlight is published in Cell Systems Calls.

2017.12.20 | Research news

News story: Nanorobot controls enzymes (in Danish)

News story about the DNA vault paper by Peter Gammelby published in Rømer.

2017.12.05 | Research news

Blog: Illustrating Streptococcus pneumoniae

Ditte Høyer Engholm is blogging about how to illustrate science.

2017.08.29 | Awards

Funding: Grant from Novo Nordisk Foundation for RNA biosensors

The lab received a grant from the Novo Nordisk Foundation to work on genetically encoded RNA-based FRET biosensors.

2016.12.01 | Research news

Inauguration - First Danish Cryo-EM Facility

The facility is centered on a flagship Titan Krios microscope with post-Quantum Gatan K2 detector and screening microscopes.

2016.02.29 | Research news

News story: EUR 2 million grant to RNA origami research

News from the Faculty of Science and Technology about the ERC consolidator grant that was awarded to Ebbe S. Andersen to conduct research on RNA origami for synthetic biology applications.

2016.01.01 | Awards

Funding: ERC Consolidator Grant

The ERC Consolidator Grant was awarded to Ebbe S. Andersen to work on RNA origami for synthetic biology applications.