https://onlinelibrary.wiley.com/doi/abs/10.1002/smll.201902979
DNA nanostructures can be formed of several different DNA origami units that bind between themselves with complementary extended strands. However, the binding reaction between two origamis doesn't have a perfect yield (80~90%), which decreases exponentially with the number of origami units added.
The paper demonstrates that the source of imperfect yield when binding origamis is not due to the stability of the binding, but all the possible competing reactions. Proper purification of each origami piece, especially with an agarose gel in low salt conditions, removes the excess of DNA strands used to build these origamis. The removal of excess strands helps to reduce the homodimers and other large structures, increasing binding yield up to 99%.
Coupling of DNA Circuit and Templated Reactions for Quadratic Amplification and Release of Functional Molecules
https://pubs.acs.org/doi/abs/10.1021/jacs.9b05688
By putting a four base-pair overhang with a photocatalysis modification onto the final product of catalysed hairpin assembly, the response to the presence of an initiating strand was further amplified, resulting in quadratic amplification.
Nucleobase-Templated Polymerization: Copying the Chain Length and Polydispersity of Living Polymers into Conjugated Polymers.
https://doi.org/10.1021/ja809613n
In the absence of a template, step polymerisation processes often offer little control over the average average length and width of the distribution of polymers produced. The average molecular weight and the spread of the molecular weight distribution of an ensemble of polymers have significant effects on the macroscopic properties, such as viscosity, of the polymer bulk.
Living systems use templates to direct the synthesis of polymers. The template functions as a guide for information transfer, but also fixes the polymer length and narrows the length distribution.
In this work, a thymine block template polymer was used to direct the synthesis of another polymer. To achieve a narrow polymer length distribution, the templates must also have a narrow length distribution. The template was created by 'living polymerisation'. Living polymerisation is a catch-all for polymerisation processes in which termination is prohibited and the initiation rate is much faster than the elongation rate, leading to a smaller variance in polymer length.
Once the templates were assembled, they could be used to grow templated polymers. After the templated polymers were elongated, they were non-autonomously separated from the template, which did not cause the polymers to fragment. The distribution of templated polymer lengths had an average close that of the templates and a narrow spread. By contrast, polymerisation with incompatible templates and in the absence of templates resulted in short polymers with broad length distributions.
This is experimental confirmation that templates, regardless of informational content, are unsurprisingly effective in narrowing and controlling polymer length distributions.
De novo design of protein logic gates
https://science.sciencemag.org/content/368/6486/78
In the present work, the lab of David Baker demonstrate that they can design and create different alpha helical bundle motifs with tunable binding affinities. These motifs bind orthogonally only to programmed domains. With these domains, incorporated into transcription factors via fusion proteins, the authors are able to implement the six basic Boolean Logic Gate functions in genetic circuits that work independently of the type of host cell.
DNA origami cryptography for secure communication
Biomolecular cryptography exploits theromdynamically controlled biomolecular interactions instead of typical computational schemes for the same level of encryption. This paper suggests a DNA origami-based encryption method with a key size of 700 bits (for comparison, typical RSA key length is 1024 bits to ensure day-to-day web browsing security).
Alice wants to pass a secret message to Bob. Alice converts the message to a spot pattern (based on binary conversion of alphabets in the message and their positions). A custom DNA scaffold sequence is routed through a defined geometry covering this spot pattern. M-strands (biotinylated message strands), corresponding to the spot patterns, are hybridized onto the scaffold strand.
The scaffold is now passed onto Bob. Bob holds the staples to fold the DNA origami structures to reveal the biotin patterns. He then uses streptavidin to make the biotin patterns recognizable and obtain the hidden secret message. The security is maintained by unpredictability of the sequence, length and folding of the scaffold strand.
A blueprint for a synthetic genetic feedback controller to reprogram cell fate
The paper considers the problem of controlling cell phenotypes by manipulating the concentration of transcription factors in the underlying gene-regulatory networks. To this end, a fast-slow/high-gain feedback controller is developed, consisting of fast production and degradation of the transcription factors, which, for suitable multi-stable (multi-phenotypic) gene-regulatory networks, destroys all but one stable equilibrium and achieves desired uni-stability (uni-phenotype). The controller is mathematically justified at the deterministic level using suitable perturbation methods. Furthermore, an experimental implementation of the controller is also proposed, based on an intracellular integration of suitable synthetic genes which can be controlled by inducible promoters.
Nicking-Assisted Reactant Recycle To Implement Entropy-Driven DNA Circuit
Molecular circuits implemented using nucleic acid nanotechnology typically produce double-stranded waste complexes when they run. In this work, the authors propose that these waste complexes can be reconverted into active reaction-ready multi-stranded "gates" through the action of a nicking enzyme that cleaves the backbone of one of the fuel strands. This approach means that, in the simplest of settings, only a supply of single-stranded molecules (rather than harder-to-produce gate complexes) is required to sustain circuit function.
Although impressive, these circuits show a fairly high level of unwanted leak reactions. Moreover, the recycling of waste does not occur indefinitely, and complex cascaded circuits cannot be produced due to sequence constraints. The article really emphasizes the need for in situ production of nucleic acid complexes.
The Protection Role of Magnesium Ions on Coupled Transcription and Translation in Lyophilized Cell-Free System
The storage of a cell-free protein synthesis platform usually involves lyophilization that decreases or even inactivates transcription/translation machinery due to conformational damage of the involved enzymes. The authors proposed that two-metal-ion regulation by magnesium provides protection and regulation of the enzymes and they are essential to preserving the activity of the cell-free protein synthesis systems. This work has important implications for maximizing protein yields in cell-free systems.
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