Papers of the week – 4th December 2017

Welcome to our pick of papers and articles from last week. These are a collection of the synthetic biology papers that have captured our attention and that we think you should know about. Maybe you’ve seen some others you’d like to tell us about. Send us a comment or tweet us at @synbiobydesign. See last week’s papers here.

Implementation of a binary calculator using communicating cells

The field of biocomputation advanced following the implementation of a full-adder in mammalian 3D cell culture by Ausländer et al. A full-adder is a binary calculator – it adds 2 binary digits to a number carried on from a previous stage to produce two output values – Sum and Carry, which in this case are reporter proteins human placental secreted alkaline phosphatase and Gaussia Luciferase. The cellular full-adder computational unit consisted of one ANDNOT, four AND ANDNOT, seven OR and ten AND logic gates. Rather than have a single cell containing all the gates, the full-adder was established by 11 different cells types performing one of 11 subprocesses and communicating between each other in cell culture.

https://www.nature.com/articles/nmeth.4505

Large scale DNA origami

DNA origami uses the predictable annealing of nucleic acids to build programmable nano-structures from a template strand and complementary staple strands which bond to form stable, double stranded products. DNA origami has great potential in nanotechnology to build modular, dynamic objects and the possibilities are gradually being realised. This week’s Nature contains FOUR papers on it, and they’re all worth a look:

 

3D DNA structures are becoming more complex. From: https://www.nature.com/articles/nature24648/figures/1
Mass production of DNA origami strands

Bacteriophages have been used previously to produce scaffold strands, however the variable lengths and sequences of scaffold strands are much more costly to produce. This paper utilises bacteriophages in shake flasks for large-scale production of all the single strands from cassettes of target sequences and Zn2+-dependent DNA-cleaving DNA enzymes.

https://www.nature.com/articles/nature24650?sf175705724=1

Giga-dalton structures

In order to mimic the complexity of naturally occurring structures using DNA origami, larger assemblies must be reliably produced. Here we see the start of this with rings of 330 daltons stacked to create micron length tubes with diameters of 350 nanometers.

https://www.nature.com/articles/nature24651

Micro-meter scale fractals

The cover of Nature this week is adorned with a DNA origami representation of the Mona Lisa. Tiles of increasing size and differing patterns can be tessellated to form an image (or ‘fractal’ as the authors have termed it) with up to 8,704 pixels.

https://www.nature.com/articles/nature24655

3D structures from over 10,000 strands

In this paper, 3D structures of up to 30,000 individual DNA strands have been constructed using 13-nucleotide binding domains (typically binding domains are 8-12 nucleotides). Using this method the group assembled a box with defined cavity, a teddy bear and a helicoid among other structures.

https://www.nature.com/articles/nature24648

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