Robust direct digital-to-biological data storage in living cells
This paper describes an engineered redox-responsive CRISPR adaptation
system for direct storage of digital data in living cells. They encoded binary
data in 3-bit units into CRISPR arrays using SoxRS system and proved that it
can be maintained over many generations. This DNA-based cellular memory device
can be used not only in digital data storage but also in other biological
recording applications.
https://www.nature.com/articles/s41589-020-00711-4
How we make DNA origami
A practical guide on making a DNA origami object. From designing a 3D
objects, ordering to folding, purification and quantification.
https://chemistry-europe.onlinelibrary.wiley.com/doi/abs/10.1002/cbic.201700377
DNA hairpin hybridization under extreme pressures: A single-molecule
FRET study
The authors test the stability of small hairpins of DNA as a function of
temperature, pressure (1-3000 bar) and stem length. The overall results show
that, due to the increase in free volume of the hairpin, an increase in the
media pressure destabilises the hairpins. In addition, it is shown that the thermodynamic
parameters of the hairpin can be easily modelled by dividing the contribution
of the stem and loop.
https://pubs.acs.org/doi/abs/10.1021/acs.jpcb.9b10131
First-passage probabilities and mean number of sites visited by a
persistent random walker in one- and two-dimensional lattices
This paper looks to solve for a few relevant statistics for persistent
random walker models in 1 and 2 dimensions. A persistent random walk is a
discrete time stochastic process and a simple example of a random walker with
memory. The walker moves in a certain direction, one step per time and at any
time has a certain probability to change direction. This paper utilises various
methods, primarily generating functions and transforms of them, to calculate
the first passage probability for a site, that is the probability that the
walker reaches a certain site for the first time at a certain time; and the
mean number of sites visited by the walker as a function of time. However, most
of the equations required to solve to find analytic solutions were not soluble,
so, instead the limiting behaviours were found. Further, the continuum limit of
these were also found to be in agreement with previous calculations. This
somewhat technical paper showcases various methods and theorems useful for
studying random walk models.
https://journals.aps.org/pre/abstract/10.1103/PhysRevE.102.062129
An enzyme-free surface plasmon resonance biosensor for real-time
detecting microRNA based on allosteric effect of mismatched catalytic hairpin
assembly
This paper presents an alternative approach for miRNA detection with a
potential diagnostic outlook. This particular study aimed to achieve
enzyme-free and label-free detection. They made use of catalytic hairpin
assembly to facilitate enzyme-free amplification, and surface plasmon resonance
for label-free detection. This system realised a picomolar limit of detection,
even in the presence of total cellular RNA. This platform also shows good reusability.
https://www.sciencedirect.com/science/article/pii/S0956566315304656
DNA-based stategies for site-specific doping
In the present paper the authors propose two different strategies with
which DNA origami could be used as a tool for doping in Silicon lithography. In
the first one the adsorption of DNA constructs over the surface at high
temperature results on the deposition of phosphate groups over the surface
resulting in n-type doping, whereas in the second one, the DNA origami acts as
a passive masking element that gets modified with functional groups and acts as
mask element prior to the etching process. The authors demonstrate the
viability of the process to build FET devices with the technique, but, although
the technique presents advantages such as low cost, the minimum width of the
device built is equivalent to fabrication standards from 12 years ago.
https://onlinelibrary.wiley.com/doi/full/10.1002/adfm.202005940
Second-generation DNA-templated macrocycle libraries for the
discovery of bioactive small molecules
Here the authors improve upon an earlier method in which DNA templated
chemical synthesis is used to generate diverse DNA-tagged libraries of
bioactive molecules from a few DNA-tagged building blocks. First, a library of
20x20x20x32=256000 DNA templates with orthogonal codons is generated. Then
reagents, which have DNA tags complementary to the codons on the template,
combine to generate the macrocycle molecule encoded by the DNA template.
Effective molecules can be identified by selection (increased binding affinity
to a target molecule and filtering) and then reading the DNA templates by dna
sequencing.
https://doi.org/10.1038/s41557-018-0033-8
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