Exploiting and understanding cellular molecules: nucleic acids and proteins

Strategies for Constructing and Operating DNA Origami Linear Actuators

The authors discuss the protocol optimisation for the fabrication of a DNA origami rotaxane. The objective is to find the protocol that produces the highest yield of working rail/sliders systems to use as linear actuators on the nanometric scale. The use of these sliders, when combined, will allow the fabrication of materials with subnanometer precision using the slider as a “printing head”.

https://onlinelibrary.wiley.com/doi/10.1002/smll.202007704

A tractable genotype–phenotype map modelling the self-assembly of protein quaternary structure

The polyomino model is introduced as a high-level model of assembly of protein sub-domains into larger complexes. The paper introduces the fundamental features of the polyomino model, starting with the genotype to the formation of individual assembly kits and finally the formation of complete structures from assembly kits. The paper investigates polyominos within the wider context of genotype-phenotype maps, with regards to genotype redundancy, phenotype bias, component disconnectivity, shape space covering, as well as phenotypic robustness and its relationship to evolvability, and finds that these are quite similar to the RNA folding GP map. From a GP map perspective, this raises the question of whether these traits are inherent to self-assembling systems. Eventually, the polyomino model could yield insights on artificial systems like DNA tiles.

https://royalsocietypublishing.org/doi/pdf/10.1098/rsif.2014.0249

Paper-based microfluidics for DNA diagnostics of malaria in low resource underserved rural communities

The researchers create a paper based lateral flow devices based on Loop-mediated isothermal amplification (LAMP) of DNA. Although, PCR-based amplification assays remain the gold-standard NAAT, the requirement for trained staff and external power has limited their application in areas with reduced resources. LAMP has recently emerged as easy-to-use alternatives to PCR, owing to greatly simplified hardware requirements.

The paper discusses use of paper origami techniques to prepare blood sample preparation (including magnetic beads on DNA molecules of interest), followed by the LAMP process in a small microfluidic chamber. A hand pressed button initiates lateral flow of the amplified DNA that travels along a small membrane where anti-FITC antibodies and immobilized streptavidin are present as test and control lines. Upon successful attachment of species-specific ligands to anti-FITC antibodies, a positive signal is generated thereby enabling detection of diseases.

https://www.pnas.org/content/116/11/4834

The beauty of nucleic acids and the scope of their application

Continuous Cell-Free Replication and Evolution of Artificial Genomic DNA in a Compartmentalized Gene Expression System

In this study, they coupled DNA replication with gene expression in cell-free system. They performed the experiments in water-in-oil droplets in serial dilution cycles. Circular DNA is replicated through rolling-circle replication followed by homologous recombination catalysed by the proteins, phi29 DNA polymerase, and Cre recombinase expressed from the DNA. Isolated circular DNAs accumulated several common mutations that exhibited higher replication abilities than the original DNA due to its improved ability as a replication template, increased polymerase activity, and a reduced inhibitory effect of polymerization by the recombinase.

https://pubs.acs.org/doi/10.1021/acssynbio.1c00430

Fuel-Driven Dynamic Combinatorial Libraries 

The authors analyse the fuel-driven oligomerisation of isophthalic acid. They determine that while oligomer formation is mainly driven by fuel activation, its relaxation back to equilibrium (isophthalic acid monomers) is not symmetrical. Instead of hydrolysing, the relaxation is produced by the "reshuffling" of the longest oligomers with shorter ones to produce average length oligomers. They also demonstrate that oligomers longer than 3 units can produce some sort of feedback interaction, creating insoluble complexes that resist better the relaxation to equilibrium. Of course, they also have some leak reactions that produce an undesired subproduct with a constant rate. The paper presents an interesting view on a well established far-from-equilibrium assembly reaction as the oligomerisation of isophthalic acid. However, the control over the oligomerisation process is not impressive; the concentration of oligomers decreases exponentially with length.

https://pubs.acs.org/doi/10.1021/jacs.1c01616

A Comparison of Genotype-Phenotype Maps for RNA and Proteins

This paper attempts to identify differences and similarities in the RNA and HP-lattice Protein GP maps. To ensure appropriate comparison, the RNA GP Map has only 2 alphabets. Similarities include the tendency for some simple phenotypes to be highly overrepresented in genotype space. One interesting difference is that whereas most sequences in the RNA GP-Map tend to fold to a unique structure, only a small subset of sequences in the HP GP-Map do so. The average size of genotype sets are much smaller in the HP GP Map, and it takes more mutations from a given sequence to cover the whole phenotype space than in the RNA GP Map.

https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3328697/

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

What are the odds?

Exact face-landing probabilities for bouncing objects: Edge probability in the coin toss and the three-sided die problem

The paper revisits the classical physics problem of what is the probability a thick coin lands on its side. They study the mechanics of a cylinder of a given thickness and radius, being given an initial random angular velocity and linear velocity. The cylinder is then allowed to bounce inelastically until it comes to rest either on one of the faces or on its edge. They then use the areas of phase space which correspond to each of the resting configurations in order to compute the respective probabilities as a function of the thickness to diameter ratio. They find that for example a £1 coin has a probability of landing on its edge of ~1/1000. Comparing to experimental and simulated data they find decent agreement. Further, they calculate the thickness to diameter ratio which would provide a 1/3 probability of landing on the edge. They calculate this to be ~0.831 which is much closer to experimental and numeric studies than previous theoretical suggestions.

https://journals.aps.org/pre/pdf/10.1103/PhysRevE.105.L022201

Hamiltonian memory: An erasable classical bit

The authors consider a model of an information-carrying system in which the information is carried in the phase of a particle moving around a ring. They show that a (magnetic) Hamiltonian can be used to compress a uniform phase distribution to a highly-peaked one, apparently at the cost of no work input. It is unclear to me why this doesn't violate the second law - is this density in phase angle not exploitable as a non-equilibrium store of work? If not, why not?

https://journals.aps.org/prresearch/abstract/10.1103/PhysRevResearch.3.013232

A coarse-grained biophysical model of sequence evolution and the population size dependence

They present a coarse grained model of sequence evolution to ask questions about the speciation rate and how it differs due to effective population size. They rely on a framework analogous to thermodynamics, where the probability of a phenotype is dependent on a balance between its true fitness and the entropy of the phenotype. Using a DNA-protein binding co-evolving system as a framework, they show that, for smaller populations, the most likely phenotype is closer to inviability than for larger populations due to the greater entropic contribution in the former, and hence speciation is faster for smaller populations. This is consistent with experimental evidence, although theirs was a first attempt to explain this occurrence theoretically.

https://www.sciencedirect.com/science/article/pii/S0022519315002039?via%3Dihub