Saturday 26 December 2020

From monomers to polymers

 Kinetic roughening of the urban skyline

A neat little paper showcasing an application of a statistical mechanical model to city skylines. Kinetic roughening is a nice example of a simple model that showcases some of the main themes of modern statistical mechanics including scaling and continuum limits. These models, in the discrete regime, consist of a lattice of height vectors which evolve in time due to some rules relating them to their neighbours. The roughness is defined as the root mean square of the heights. This roughness displays scaling behaviour, in particular for this paper, the roughness scales as the system size to some power after sufficient time passes. This paper looks at a huge database of 10^7 buildings in the Netherlands and calculates this saturation exponent for many cities. Where there is significant enough data, they find that the cities can be grouped into two sets with different exponents. These exponents correspond to the two main universality classes for roughening models. Finally, they remark that it would be interesting to consider the buildings regulations for each city to explain why they would fall into a given universality class.

https://journals.aps.org/pre/abstract/10.1103/PhysRevE.101.050301

Characterization and mitigation of gene expression burden in mammalian cells

In this work, the authors investigate the burden imposed by synthetic circuits in mammalian cells and study transcriptional and translational burden caused by cellular resource sharing. They were able to mitigate the effects of resource limitations using a microRNA-based incoherent feedforward loop (iFFL) motif. They concluded that using burden-aware designs, synthetic circuits that rely on perturbations will be able to show more accuracy and predictability.

https://www.nature.com/articles/s41467-020-18392-x

A basic introduction to large deviations: Theory, applications, simulations

This approachable set of lecture notes was written following a 2009 paper reviewing the theory of large deviations (or LDT). The techniques of LDT provide a framework for a rigorous formulation of statistical mechanics. Most physicists and engineers have used the techniques of LDT at some point or another, but might not have been aware that this was the case! In essence, LDT is used to quantify the rate at which the probability that the sample mean S (of a set of samples of n independent identically distributed random variables each with mean u) is exponentially suppressed with increasing sample size n, where S is not equal to the mean u. This is a generalisation of the central limit theorem.

https://arxiv.org/pdf/1106.4146.pdf

Programmed spatial organization of biomacromolecules into discrete, coacervate-based protocells

The coacervate created in this work was able to recruit his-tagged enzymes with via interaction with Nickel ion in the protocell. The increased concentration of enzymes led to acceleration in the enzymatic process. The proteins could be released by cleaving specific site as well.

https://www.nature.com/articles/s41467-020-20124-0

DNA programmed chemical synthesis of polymers and inorganic materials 

The present review offers a general perspective on how DNA programmable interactions have been exploited in the field of chemical synthesis, first referring to the possibility of using directed interactions to perform directed polymer synthesis analogously to how copying polymers work in living cells, as well as how DNA can direct the conjugation and directed arrangement of different polymeric materials with aims as diverse as functionalisation for in vivo applications or directed assembly of conducting polymers as well as the assembly of metallic nanoparticles in prescribed arrangements that can have applications for plasmon resonance-based sensor applications. While showing that DNA nanotechnology is a powerful tool for material science-based nanotechnology applications, this review fails to specify which challenges face the field in order to be applied to other other fields (such as MOF, COF or polyoxometalate synthesis) in which the chance to implement programmable interactions could become a paradigm shift.

https://link.springer.com/article/10.1007/s41061-020-0292-x

Emergence of low-symmetry foldamers from single monomers

Molecular self-assembly of simpler components often give rise to complex features in dynamic combinatorial libraries. In this article, the authors describe the emergence of large molecules with low symmetry unlike most previously described systems. When the monomers, capable of forming disulfide bonds among themselves, are equilibrated for several days, different libraries show the formation of predominantly one product, or a very small family of products. In some cases, large molecules were generated with very low symmetry (17 or 23 monomers). Further analysis by ion mobility mass spectrometry, NMR and CD spectroscopy showed that these large molecules are not simple 2D circular molecules, rather they all have unique complex folded structures. This was confirmed by the X-ray crystal structures of the synthesised molecules. The authors conclude that the semi-rigid backbone structures of the molecules, and the presence of several diverse sites for non-covalent interaction, which can overcome the inherent instability of large macrocycles, are crucial for spontaneous formation of newer complex foldamers.

https://www.nature.com/articles/s41557-020-00565-2?utm_source=other&utm_medium=other&utm_content=null&utm_campaign=JRCN_1_DD01_CN_NatureRJ_article_paid_XMOL#Sec8

Fuel-driven transient DNA strand displacement circuitry with self-resetting function

The authors present an enzyme-driven mechanism to allow continuous cycling of nucleic acid strand displacement circuits. The basic idea is to have strands that are uncompetitive on their own at displacing an output from a complex, but which can be ligated to a helper duplex which in turn can be ligated to the complex, allowing displacement to proceed. The ligation is performed by specific ligase enzymes, and consumes ATP. Subsequently, restriction enzymes can cut the strands, allowing the system to revert back to its initial condition. In principle, such a system could maintain a dynamic steady state of constantly cycled outputs, but the evidence for that in this manuscript is limited. Rather, transient spikes are observed in response to a signal, since there is apparently not enough ATP to sustain the output for a long period. An interesting question to ask is whether the scheme presented can be generalised to a large strand displacement network.

https://pubs.acs.org/doi/abs/10.1021/jacs.0c09681

Feedback regulation of crystal growth by buffering monomer concentration

Many reactions, like crystallisation, need to operate at a very specific reagent concentration regime. However, even if the concentration requisites are met, as the reaction proceeds, the reagents get consumed and the reaction regime will change. The authors propose a method for maintaining constant reagent concentration by using buffering species. The mechanism consists of a pool of inactive DNA bricks that are in equilibrium with its active form thanks to a toehold exchange reaction. This mechanism is then used to grow a population of DNA nanotubes of regular sizes. When the active bricks are consumed, the equilibrium is displaced to the formation of new active bricks. However, the buffering power of this method is still limited, and the desired concentration can only be maintained for a few hours. Further increments of the buffering species concentration would block the reaction sites of the active monomers, hindering nanotube formation.

https://www.nature.com/articles/s41467-020-19882-8

Thursday 3 December 2020

A communication problem: cellular signalling networks

Do we understand the mechanisms used by biological systems to correct their errors?

This paper is a review of kinetic proofreading in biological systems, presented in a mostly historical fashion. The original concept of kinetic proofreading as introduced by Hopfield and Ninio is recounted. Following this, the concept of trade-offs between speed, energy dissipation and accuracy is introduced. The key results that biological systems tend to get accuracy to within acceptable levels, then prioritise maximising speed, followed by minimising energy dissipation is presented. In the process of explaining this, a number of methods utilised are briefly mentioned including: first passage time analysis, asymptotic analysis, and thermodynamic uncertainty relations. Finally, the concept of energetic vs kinetic discrimination is briefly introduced.

https://pubs.acs.org/doi/10.1021/acs.jpcb.0c06180

A biomimetic DNA‐based membrane gate for protein‐controlled transport of cytotoxic drugs

The ability to design membrane nanopores with controllable channel opening has the potential to have many applications in biomedicine, biosensing and artificial cells. In this paper, the researchers have shown the design and synthesis of a membrane nanopore constructed of only seven oligonucleotides where the lid of the nanopore is a thrombin/binding aptamer (TBA). Therefore, passage of small molecules through the nanopore is only allowed in presence of thrombin. It is shown that the nanopores can be incorporated in lipid vesicles. Nanopore-incorporated vesicles containing fluorescent dye are observed to release the dye only in presence of thrombin which proves that the channel opening is tightly controlled. This approach is applied to release biologically relevant molecules for controlled killing of cells. Cytotoxic drug topotecan is filled in vesicles containing the nanopores on the membrane; and these vesicles are added to HeLa cervical cancer cells. Upon addition of thrombin, the drug is released to the cells, and cell viability drops to 20% after three days compared to 95% when no thrombin is added. This paper thus shows a simple approach for biocompatible membrane nanopore design which can be opened by the presence of a biologically relevant substance.

https://onlinelibrary.wiley.com/doi/full/10.1002/anie.202011583

DNA origami guided self-assembly of plasmonic polymers with robust long-range plasmonic resonance

The production of 1D chains by assembling DNA origami tiles have been widely used in nanofabrication. The defined geometry of the DNA tiles is harnessed to control the distance between DNA-bound metallic nanoparticles, producing nanowires used for plasmon propagation. However, regular origami tile assemblies are flawed by its flexibility, which leads to defects in plasmon signal propagation due to the variable distance between nanoparticles. The authors of this paper optimise the rigidity of the DNA origami chains by exchanging the classical tile for a hashtag-shaped structure. The proposed hashtag-structure can be functionalised with nanoparticles in several ways, while increasing the persistence length of the produced nanowires by one order of magnitude.

https://pubs.acs.org/doi/abs/10.1021/acs.nanolett.0c04055

Combinatorial signal perception in the BMP pathway

Cells can sense ligands in their environment which bind to receptors on their surface, and trigger a response through intra-cellular signalling pathways. There are many types of type 1 and type 2 receptors in the bone morphogen pathway (BMP) that a cell could express, even more types of dimeric ligands that could be sensed. Through a combination of an in vivo search and the construction of a minimal mathematical model, Antebi et al. create a framework through which we can understand the multifarious signal processing operations that occur at the boundaries of cells. Crucially, the concentration of ligands (which is assumed to greatly exceed the number of available receptors) and the affinities between receptors and ligands determine the equilibrium distribution of ligand-receptor configurations, but the activity (the strength with which a ligand receptor combo can catalyse a signal) of the configuration does not need correlate with its probability of occurrence. Therefore, in a system with two types of surface receptors and two types of ligands (each with an affinity and activity with each receptor), the signal transduced can quantitatively differ when the ligands are presented alone or in combination.

https://doi.org/10.1016/j.cell.2017.08.015

3D engine in DNA code

Turing-completeness of Chemical Reaction Networks as well as the capability to be mapped into DNA Strand Displacement systems is always brought up as a proof of their versatility. However, most of the academic literature focuses on the implementation of CRNs in the context of building controllers, cellular automata or other sorts of computer science model problems rather than software applications that are found in our daily life. The present work presents how to encode a rudimentary 3D shader engine into a CRN and how to emulate and execute it, the most interesting part being how does it display a mapping between a high level standard abstraction language (Like JavaScript and CRNs). While still being impractical when compared to silicon-based devices, it's easy to see how a bridge between regular coding skills and molecular programming can be built. But it also must be said that in terms of software conservation, being able to engineer a sort of CRN/DNA-based assembler code that an be retroengineered into a high level language can be a promising technology to preserve software in a format with a longer life than optical or magnetic devices.

https://observablehq.com/@pallada-92/3d-engine-in-dna-code 

Computing signal transduction in signaling networks modeled as Boolean Networks, Petri Nets and hypergraphs 

Transduction networks are known for being the regular architecture used bicellular systems to perform signal processing and decision making. Back from the foundational work by Dennis Bray they have been described as distributed network computing elements and mappings with computational models (mainly neural networks) have been drawn. But alternative mappings with other computing models can be drawn. In this paper, the authors explore other networks computing models that can be used to model transduction such as graphs, hypergraphs, Boolean Networks or Petri Nets, establishing the conditions in which a model is isomorphic to another and highlighting the strengths and weaknesses of each one. However, some of the strengths attributed to the Boolean Network model are rarely found in a biological context and none of the models take into account explicitly the catalytic nature of the network elements and the implications of the system, thus leaving room to potential new formalisms.

https://www.biorxiv.org/content/10.1101/272344v2.full

Self-limiting polymerization of DNA origami subunits with strain accumulation

The polymerization of DNA origami was controlled by accumulated strain during the growth process. The DNA origami consist of three domains with the middle domain being shorter than others. As the three domains are connected by linkers, they can deform while they grow, accumulating the strain coming from short middle domain. By controlling the length of the middle domain, the authors precisely controlled the growth of the DNA origami objects without any external control.

https://pubs.acs.org/doi/10.1021/acsnano.0c07696

Single cell characterization of a synthetic bacterial clock with a hybrid feedback loop containing dCas9-sgRNA

Oscillatory dynamics facilitates the temporal orchestration of metabolic and growth processes inside cells and organisms. In this work, they present a synthetic oscillator gene circuit (repressilator) in which one of the repressors was replaced by CRISPRi system and they monitored the oscillations in microfluidic reacts using single cell experiments. They found that the period of the oscillator is much slower since it depends on the irreversible binding of the CRISPR system that prolongs its dilution phase. They propose to use RNA aptamers and use CRISPRa (activation) to improve the dynamics of the oscillator and explore the potential applications.

https://pubs.acs.org/doi/pdf/10.1021/acssynbio.0c00438

A ratiometric electrochemical biosensor for the exosomal microRNAs detection based on bipedal DNA walkers propelled by locked nucleic acid modified toehold mediate strand displacement reaction

In this paper, the researchers attempted to develop a novel biosensor for exosomal miRNAs, which achieved high sensitivity, high specificity and high reproducibility, such that the biosensor could be used multiple times. Their system involved locked nucleic acid capture probe associated with a bipedal DNA walker. The presence of the target miRNA led to release of the bipedal DNA walker by toehold-mediated strand displacement. The DNA walker walking over the electrode surface facilitated amplification of the electrochemical signal, allowing a low signal-to-background ratio.

https://www.sciencedirect.com/science/article/pii/S0956566317307170

Reciprocal coupling in chemically fueled assembly: A reaction cycle regulates self-assembly and vice versa

The authors seek to develop a synthetic system that replicates the behaviour of natural biopolymers such as actin, in which the constituent monomers can adopt two states, one of which is favourable for polymerisation ("active") and the other of which is less so. Moreover, the environment of the polymer catalyses the deactivation of the monomers, leading to non-equilibrium "living" polymerisation. The resultant dynamics are essential to cytoskeletal mechanics and motion. In this paper, the assembling monomers are short peptides with a switachble chemical moiety which can be charged (inactive) or neutral (active). Differential assembly in the two regimes is demonstrated, as is a catalytic effect on activation/deactivation rates of the polymer environment. However, the paper doesn't demonstrate preferential deactivation in the polymer state, as is seen in the natural counterpart.

https://pubs.acs.org/doi/10.1021/jacs.0c10486