Exploiting cellular machinery for novel applications

Four different mechanisms for switching cell polarity

Cell polarity (asymmetric concentration profiles within the cell) plays a role in migration, division, differentiation, development and signalling. The mechanisms by which polarity is created and maintained is understood, but the dynamics of polarity are less well studied. Here they study a model in which the concentration profile of three interacting molecular species, a polarization marker, an antagonist, and a recruiter, change in response to signals of varying strength and duration. The signalling species either promote or suppress the rate constant for one reaction within the simple reaction network. This leads to altered phase space stability of the system in the presence or absence of a signal. Through phase space stability analysis and simulation, the authors exhaustively identify four distinct ways polarity can switch in response to a signal which could be tested in future experimental studies.

https://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1008587

Recovery of Information Stored in Modified DNA with an Evolved Polymerase

DNA is used for digital information storage, but the potential information loss from degradation and associated issues with error during reading challenge its wide-scale implementation. To address this, the authors propose using degradation-resistant analogues of natural nucleic acids (xNAs) and they used direction evolution to create a polymerase capable of transforming 2’-O-methyl templates into double-stranded DNA with a fully functional proofreading domain to correct mismatches on DNA, RNA and 2’-O-methyl templates. In addition, they implemented a downstream analysis strategy that accommodates deletions to enable the large-scale use of nucleic acids for information storage.

https://pubs.acs.org/doi/pdf/10.1021/acssynbio.1c00575

Stretching of a fractal polymer around a disc reveals KPZ-like statistics

This paper aims to study the directed polymer model around a curved surface. This then has implications in biology for example wrapping DNA up into chromosomes as well as other situations where polymers are wrapped up around rods or similar. They use various scaling techniques to analyse the model around a surface with local radius of curvature R, where the two ends of the polymer are fixed a distance S apart. The key observations of this paper are that the typical distance the polymer goes away from the surface, Δ, scales as R^(1/3) for small radius of curvature and scales as S^α for large radius, with a cross over radius which scales as R^z. This is the same behaviour as surface roughness models mapping Δ to the roughness, R to time and S to the interface size. Further, they note that in a certain limit the exponents tend exactly to the 1+1D KPZ exponents.

https://arxiv.org/pdf/2202.00239.pdf

Cooperative Branch Migration: A Mechanism for Flexible Control of DNA Strand Displacement

They basically demonstrate that if you have a strand that can sequester a displaced domain once it detaches, the reaction will proceed even if it was initially not favoured AG>0. They apply this to increase the rate of strand displacement reactions producing a bulge or a mismatch.

https://pubs.acs.org/doi/10.1021/acsnano.1c10797