List of Publications
Computer-Aided Production of Scaffolded DNA Nanostructures from Flat Sheet Meshes
Building on our earlier work on polyhedral shapes (see below) we are now using a similar technique to render flat sheets in DNA. Interestingly, the original algorithm handled 3D objects much better than flat sheets using some mathematical tricks and lots of AFM imaging Erik and Melik were able to demonstrate how the technique can render some stunning flat sheet shapes that are larger (per base-pair) than the original flat sheets by Rothemund, and that fold without magnesium!
Angew. Chem. Int. Ed., p. DOI:10.1002/anie.201602446 (2016)
DNA rendering of polyhedral meshes at the nanoscale
Wouldn't it be nice to be able to just draw an nanostructure shape using conventional 3D graphics software? In this paper we show that this is now possible! Using a routing of the DNA scaffold that is derived from graph theory, we can automate the entire DNA-nanostructure design process and Erik used this to fold some pretty interesting shapes. Including a well known computer-graphics bunny...
523, p. 441–444 (2015)
Purification of Functionalized DNA Origami Nanostructures
Using nanocalipers we can tinker with cell communication (see 'Spatial Control ...'-paper below). Now, how do you actually produce nanocalipers in the most efficient, purest way? In this paper Alan shows you how it is done for a wide range of purification methods using 3 different molecules that we like to put on our nanocalipers. And, introducing two new ways to purify DNA origami!
9, p. 4968-4975 (2015)
Rolling circle replication requires single-stranded DNA binding protein to avoid termination and production of double-stranded DNA
Rolling circle amplification (RCA), maybe not so rolling after all? We have found that Phi29 polymerase is not always following the right template when making new DNA in RCA. Sometimes the polymerase flips and starts to backtrack. This leads to an unexpected amount of double-stranded DNA where we initially expected to find only single-stranded DNA.
Nucleic Acids Research
42, p. 10596-10604 (2014)
Spatial control of membrane receptor function using ligand nanocalipers
How do cells feel their environment? Can they sense nanoscale distribution of ligands at the surface of neighboring cells? Using DNA origami, we were able to show together with Ana’s lab that indeed it seems like cells do have some kind of blind-reading alphabet that they use to communicate.
11, p. 841-846 (2014)
DNA Origami Structures Directly Assembled from Intact Bacteriophages
An origami design intended to fold the entire Lambda genome using 3000 oligonucleotides. We noticed that Lambda DNA that you buy is full of nicks and very unsuitable for use as an origami scaffold. So we made our own Lambda DNA from phage. And then Philipp just made phage and added the oligos directly to that...
10, p. 1765-1769 (2014)
Enzymatic production of 'monoclonal stoichiometric' single-stranded DNA oligonucleotides
Everyone needs DNA oligos. Well, maybe not everyone, but everyone who does some kind of biotechnical research at least. Solid-phase synthesis is great, but biological nanomachines (enzymes) kick-ass when it comes to producing long, sequence controlled polymers. Here, Cosimo and the lab show you how to make single-stranded DNA oligos enzymatically, and how this can be used in for example DNA nanotechnology. Check our 'software' section for a tool to calculate the pseudogenes!
10, p. 647-652 (2013)
A DNA Origami Delivery System for Cancer Therapy with Tunable Release Properties
DNA Origami can be used to deliver anti-cancer drugs! In fact, we found that by tuning the DNA twist density, we could create structures that really like to hold on to its Doxorubicin. The slow release allowed us to use less Dox than usual to get a therapeutic effect. More treatment with less is of course extra good when dealing with cardiotoxic drugs like Dox.
6, p. 8684-8691 (2012)
Self-assembly of three-dimensional prestressed tensegrity structures from DNA
By using DNA origami, Tim was able produce nanoscale tensegrity structures. The structures are composed of rigid rods and flexible bands. The rods were made from DNA origami bundles, and the bands were just single stranded DNA! It turns out that single stranded DNA makes perfect nanoscopic rubber bands. The tensegrity devices could be used to amplify small mechanical signals into large conformational changes: cutting one of the rubber bands will make the entire structure blow up.
5, p. 520 (2010)
Folding DNA Origami from a Double-Stranded Source of Scaffold
For DNA origami we need scaffolds, long single stranded DNA that can be folded with the help of short, synthetic DNA oligonucleotides. These long scaffold strands had up until this publication been limited to the genome of a single stranded DNA virus, the M13 virus. In this paper we show that using a few tricks you can actually use double stranded DNA and fold each of the two strands into separate structures! This will open the door to using a much broader variety of DNA samples for DNA origami.
131, p. 9154 (2009)
Self-assembly of DNA into nanoscale three-dimensional shapes
DNA origami, now in 3D! It turns out that Paul Rothemunds DNA origamis can be folded like real origamis into thick multi-layered object. We show off some pretty complex structures and try to explain the design process and experimental tricks in depth. Each of us contributed with a design that exemplifies different aspects of the technology. We had to do the design the hard way: writing scripts in python to generate the staple sequences. Fortunately for future users of this technology, Shawn's software caDNAno, nowdays makes the process a little less tedious.
459, p. 414 (2009)
Anisotropically Functionalized Nanoparticle Dimers
Building blocks for self-assembly need to have a minimal structural complexity, they can't look the same all around. They need to have an _up_ and a _down_, i.e. they must be anisotropic. Usually gold particles are pretty symmetric but in this paper we show that the trick to break the symmetry that we described in earlier papers is working in the lab.
Eur. Phys. J. D
43, p. 299 (2007)
DNA-Mediated Self-Assembly of Nanostructures - Theory and Experiments
This thesis summarizes the work Björn performed during the last years of his PhD at Mid Sweden University. Its an easy-to-read text with technical stuff mostly in the appended papers. Should be simple to follow even for those of you that are not familiar with nano self-assembly.
DNA Scaffolded Nanoparticle Structures
This paper describes some of our efforts to attach nanoparticles on DNA-origami. We reproduce Rothemunds original experiment and try to extend the concept by attaching proteins and metals to the origamis. Proteins are OK, attaching metal nanoparticles seems harder...
J. of Physics Conf. Ser.
61, p. 458 (2007)
Programmable Self-Assembly - Unique Structures and Bond Uniqueness
If one wants to self-assemble a complex nanostructure, what are the basic requirements for the constituting building blocks? In this paper we try to look at the design level tradeoffs between making a few quite simple building blocks with few types of bonds, or a lot of building blocks with highly specific bonds. Surely the first alternative must be better?
J. Comp. and Theor. Nanosci.
3, p. 391 (2006)
Study of DNA coated nanoparticles as possible self-assembly building blocks
This paper describes our idea of how to make building blocks for algorithmic assembly from DNA-coated gold particles. If you coat a gold particle with DNA you will get a completely symmetric building block. Here we were one of the first to show a feasible way to break the symmetry and a path to build complex DNA-gold assemblies.
Appl. Surface. Sci.
252, p. 5538 (2006)
Novel in-situ Fabricated Josephson Junctions: Trilayer on a Substrate Slope
Back in the day when top-down fabrication was still a-la-mode, Bjorn put together a new approach for fabrication of superconducting Josephson-junctions. Thin films of YBaCuO were fabricated and processed in a cleanroom. Electronic measurements at 4 degrees Kelvin revealed that the junctions were working, sort of.
IEEE Trans. Appl. Supercond.
13, p. 794 (2003)
Submicron YBa2Cu3Ox ramp Josephson Junctions
Using electron beam lithography and state of the art technology for fabricating high temperature superconductors we managed to make functional Josephson junctions that were really small. Some interesting voltage - current characteristics were observed and discussed.
Applied Physics Letters
80, p. 1022 (2002)