DNA in self-assembly, chemical reaction networks and more

DNA as a universal substrate for chemical kinetics

This paper discusses development of control circuitry within a chemical system to direct molecular events using strand displacement reactions. The authors show basic methods to construct unimolecular and bimolecular reactions (along with a short kinetic analysis associated with each reaction system). these 2 reaction types can then be used to construct any complex CRN (chemical reaction network). They show this by developing DNA reactions that recreate a Lotka-Volterra chemical oscillator, a limit cycle oscillator, a chaotic system, and a 2-bit pulse counter.

https://www.pnas.org/content/pnas/107/12/5393.full.pdf

Undesired usage and the robust self-assembly of heterogeneous structures

This work introduces a formal description of the “principle of undesired usage”. This principle states that the yield of assembling a structure is not determined by ensuring a perfect stoichiometry between its components but by tuning the reagents chemical potentials, e.g. concentrations, to avoid undesired structures. They demonstrate this principle across several types of assembly processes, with several different modelling techniques.

https://www.nature.com/articles/ncomms7203

SAT-assembly: A new approach for designing self-assembling systems

This paper presents a method of identifying patchy particle assembly components for a given structure. The foundation of the method is based on SAT, a well-known problem in computer science. The SAT problem consists of finding boolean values that solve a given set of boolean equations with a fixed number of variables. The paper goes into great detail on the variables and clauses that characterize patchy particle assembly as SAT problems. The method is performed on a cubic diamond lattice, and the resulting assembly kit is tested using an OxDNA simulation, which found that the correct structure was indeed formed.

https://arxiv.org/pdf/2111.04355.pdf

Local time of random walks on graphs

This paper looks at finding expressions for averages of functions of the local time to be in a given state in a discrete state discrete time Markov process. The local time for a state is the number of times that state is visited in a given time window. The approach taken by the authors here is inspired by path integration techniques from quantum physics. The paper provides a method for finding the z-transform for the average of a given function of the local time. The z-transform is similar to a generating function for the averages of the function of local time in a time window n. Specifically, the average of the function of local time up to time n will be the coefficient of z^-n of the z transform expanded in powers of 1/z. This then does have the limitation, that finding the desired average given the z-transform can be a lot of work. However, overall it was nice to see a more interesting way for finding these functions of local time.

https://journals.aps.org/pre/pdf/10.1103/PhysRevE.104.044302

Imaging RNA polymerase III transcription using a photostable RNA-fluorophore complex.

Quantitative measurement of transcription rates in live cells is important for revealing mechanisms of transcriptional regulation. RNA Pol III is particulary challenging as this RNAP transcribes RNA molecules so it is not possible to use protein reporters. To address this issue, this group developed Corn RNA fluorescent aptamer that resembles the fluorophore found in red fluorescent protein. With this new tool, the authors were able to study and imaging the corn-tagged Pol III transcript levels.

https://www.nature.com/articles/nchembio.2477.pdf

Dissipation bounds the amplification of transition rates far from equilibrium

Kuznets-Speck and Limmer seek to demonstrate an idea that has long been gnawing at people working on the physics of computation. A system with two metastable states is capable of acting a bit. The lifetime of those metastable states determines how long the bit can reliably store information. Another related timescale is the time it takes to switch the bit, when such a switch is required. There is a general feeling that if you want both a long reliability time, and a short switching time, this should be costly (in terms of the energy you have to put in). However, such a tradeoff has not been found, in general, using the tools of modern stochastic thermodynamics. The title of this manuscript suggests that they have been able to identify a hard tradeoff; however, this tradeoff only appears when certain conditions are met. The authors argue that these conditions are quite general, but it is still unclear whether there is a limit on designing a reliable bit that can be switched quickly at low thermodynamic cost.

 https://www.pnas.org/content/118/8/e2020863118

The role of strand displacement: from the origin of life to current perspectives

Rolling-circle and strand-displacement mechanisms for non-enzymatic RNA replication at the time of the origin of life

Tupper and Higgs use basic chemical reasoning illustrated with ODE-level modelling to argue that pre-enzymatic replication of RNA templates would have been most successful in a "rolling circle displacement" mode, wherein a circular template is copied by a product that displaces its own tail as it goes round the template. This tail must eventually be cleaved by some kind of self-cleaving ribozyme, and ligated to form another circular template for the reaction to proceed to another generation. The authors argue that a displacement mechanism is the only way to avoid suppression of the reaction via product inhibition, wherein copies bind strongly to their templates. Going further than previous arguments, they claim that even in systems with time varying external conditions that allow separation and synthesis in different environments, products will still cause inevitable inhibition through rebinding at a critical concentration. This critical concentration is relatively low because pre-enzymatic extension of RNA on a template would have been slow. Moreover, rolling circle displacement is deemed to be better than displacement on a linear template, because linear templates suffer from the fact that the strand that is being synthesised can be easily displaced from the template at each (slow) synthesis step.

https://www.sciencedirect.com/science/article/pii/S0022519321002411

DNA computing: NOT logic gates see the light

This paper describes a NOT gate for DNA computation enabled by optical control of nucleic acid function via light-removable nucleobase caging groups. This temporal precise control using light allowed the authors the introduction of Boolean logic gates into single- and multilayer DNA circuits. The design was successfully integrated within NOT, NOR and NAND circuits demonstrating the potential of DNA circuitry.

https://pubs.acs.org/doi/pdf/10.1021/acssynbio.1c00062

Reactor design for minimizing product inhibition during enzymatic lignocellulose hydrolysis
II. Quantification of inhibition and suitability of membrane reactors

This review discusses the effect of product inhibition in the particular case of lignocellulose hydrolysis. The authors present ways of quantifying and experimentally characterise the inhibition and propose reactor designs that can minimise the product inhibition effect of the enzymatic reaction.

https://www.sciencedirect.com/science/article/pii/S073497501000025X

Perspective: Sloppiness and emergent theories in physics, biology, and beyond

This paper aims to utilise information geometry to simplify models with a large number of parameters. They make the point that in such models with many parameters, there are often multiple combinations of parameters which fit the model and that certain subsets of parameters make little difference to the predictions. This is made more formal by looking at the Fisher Information matrix (FIM) made from the parameters and finding that its eigenvalues have a roughly exponential structure, where the second largest is an order of magnitude smaller than the largest etc. This means only a few eigenvalues are relevant. Information geometry focusses on using the FIM as a Riemannian metric on the manifold of parameters. Due to the exponential structure of the eigenvalues the manifold has a ribbon like structure with boundaries corresponding to simplifications of the model. Certain combinations of parameters having little effect on the predictions translates into certain directions in parameter space being irrelevant. Following these directions to a boundary helps to simplify models. They give the specific example of a metabolic pathway being reduced from 48 parameters to 12.

https://aip.scitation.org/doi/10.1063/1.4923066

Kinetics of heterochiral strand displacement from PNA-DNA heteroduplexes

DNA comes in two distinct enantiomers (L-DNA and D-DNA). These enantiomers can not form base pairs with each other. This paper develops a reaction known as heterochiral strand displacement which allows displacement of one enantiomer by the other using an achiral substrate strand made from PNA. This study undertakes an extensive characterisation of the kinetics of heterochiral strand displacement across a range of toehold lengths and mismatch positions. Heterochiral strand displacement is particularly useful when considering introduction of nanodevices into cells, as L-DNA will not interfere with native cellular molecules or be recognised by nucleases.

https://academic.oup.com/nar/article/49/11/6114/6298617

Room with a Re-view: A series of reviews on nucleic acid nanotechnology

 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. 

https://pubs.acs.org/doi/abs/10.1021/acssynbio.0c00545

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.

https://www.nature.com/articles/s41589-020-00711-4

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.

https://chemistry-europe.onlinelibrary.wiley.com/doi/abs/10.1002/cbic.201700377

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.

https://pubs.acs.org/doi/abs/10.1021/acs.jpcb.9b10131

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.

https://journals.aps.org/pre/abstract/10.1103/PhysRevE.102.062129

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.

https://www.sciencedirect.com/science/article/pii/S0956566315304656

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.

https://onlinelibrary.wiley.com/doi/full/10.1002/adfm.202005940

 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.

https://doi.org/10.1038/s41557-018-0033-8