Tuesday, 2 February 2021

Under pressure: DNA origami, hairpins and the effect of extreme pressure

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.


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.


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.


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.


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.


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.


 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.


No comments:

Post a Comment