The i-Motif as a molecular target: More than a complementary DNA secondary structure
The i-motif is a DNA structure formed by C tetrads intercalated with
small loops regions. In vitro this structure is formed at low Ph, since it
requires the protonation of the C’s. However, this structures appear inside the
cell at physiological pH. The present review discuss the functions of i-motifs
as transcription regulators inside the cell and its uses in synthetic biology
and nanotechnology. Special focus is given to the application of i-motifs
knowledge in cancer therapy, since this motif is abundant in tumor cells.
https://www.mdpi.com/1424-8247/14/2/96/htm
In Vitro selection of RNA aptamers binding to nanosized DNA for
constructing artificial riboswitches
The authors present a method to rationally construct artificial
riboswitches using nanosized DNA aptamers. This particular aptamer allowed them
to regulate the internal ribosome entry site-mediated translation in respond to
a ligand (nanosized DNA). They proved that the induction ratio is much higher
than the same type of riboswitch but using a different aptamer. They propose to
use nanosized nucleic acid to build bacterial riboswitches as an alternative
for other regulators such as toehold switches or small transcription activating
RNAs (STARs)
https://pubs.acs.org/doi/pdf/10.1021/acssynbio.0c00384
Behaviour of information flow near criticality
In this paper the mutual information between two
spins in a two-dimensional Ising model are explored. An input spin is chosen,
and its value is set by a random telegraph process with a given timescale. An
output spin, a distance, d, away from the input is then monitored. Two measures
of the mutual information between the input and output spins are then measured:
the instantaneous mutual information of the steady state, and the rate of
increase of mutual information. For a given timescale of the input spin, both
the instantaneous information and information rate were found to express a
maximum close to, but not at, the critical temperature. Furthermore, the
information rate maximum was found to be non-monotonic as a function of the
timescale of the input. These maxima were explained to be due to the balance
between thermal noise, which increases with temperature, and the response time
of the system, which decreases with temperature.
https://journals.aps.org/pre/pdf/10.1103/PhysRevE.103.L010102
Allosteric regulation of DNA circuits enables
minimal and rapid biosensors of small molecules
This paper aimed to detect small molecule
pollutants within environmental water samples, specifically two families of
antibiotics. They employed the corresponding allosteric transcription factor to
initially capture the ligand of interest e.g. TetR (tetracycline repressor).
They exploited the competition between the allosteric transcription factor and
an endonuclease to trigger a TMSD reaction and achieve signal amplification. In
the presence of tetracycline, this can bind to TetR preventing binding of TetR
to tetO (tet operator sequence) allowing the endonuclease to cleave and create
a toehold. This can be accessed by a fluorescence reporter sequence. This is
followed by cleavage cycles in order to get amplification of the signal. This
system gives a broad linear range of detection.
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