Saturday, 21 November 2020

From membrane to cytoplasm: cellular applications of nucleic acid nanotechnology

Unzipping of a double stranded block copolymer DNA by a periodic force

In this paper, a simple model for mechanical unzipping of double stranded DNA (dsDNA) is explored using Monte Carlo simulations. Block copolymer DNA is considered, consisting of repeated units of different length each having two hydrogen bond monomers and three hydrogen bond monomers. Results for a static force applied to the tip of the dsDNA are reproduced displaying a first order transition from zipped to unzipped states and is independent of sequence. Simulations for a periodic force are also made and these are found to depend greatly on the sequence. Hysteresis curves are obtained for different sequences and the scaling of their area with frequency and amplitude of the periodic force is studied.

https://arxiv.org/abs/2010.13367

Genetic circuit characterization by inferring RNA polymerase movement and ribosome usage

This paper focuses on the analysis of complete genetic circuits using -omics tools (RNA sequencing and ribosome profiling) with pre-characterized genetic parts. They characterized the performance of each part of the circuit as well as the impact of the genomic context. These characterization results were used to understand the circuit dynamics and to analyse the circuit impact on the host cell (genetic burden).

https://www.nature.com/articles/s41467-020-18630-2

Noise-induced symmetry breaking far from equilibrium and the emergence of biological homochirality

All biological molecules, like amino acids and sugars, are mostly found with a single chirality i.e. the spatial arrangement of its atoms. A specular arrangement of the molecule (enantiomer) would be equally stable; however, they are significantly scarcer. A mechanism to explain this asymmetry is still unknown, but some reactions networks have been proposed to explain the homochirality of biological molecules. Previous models assumed that homochirality is an equilibrium state. These models rely on an opposite enantiomers annihilation reaction, which doesn't correspond with the real dynamics of living systems.

The authors of this paper propose a new model that can explain homochirality with non-equilibrium dynamics. In the model, a single enantiomer can be randomly formed due to the system noise. If the autocatalytic formation of that enantiomer is faster than its degradation, it can keep replicating itself if the system is continuously fed with the enantiomer precursor. Next steps will validate these results in an experimental system, like Joyce's self-replicative ribozyme.

https://journals.aps.org/pre/abstract/10.1103/PhysRevE.95.032407

Signalling-based neural networks for cellular computation

Samaniego et al. point out that the kinase/phosphatase signal transduction networks have properties that lend themselves towards imitating neural networks built of molecular perceptrons. In particular, the antagonistic nature of the phosphatase/kinase push-pull motif naturally allows the output level of a substrate to incorporate a weighted sum over inputs with positive and negative contributions. Moreover, mechanisms such as zero-order ultrasensitivity allow the activity level of the substrate to show almost switch-like behaviour relative to a threshold in this weighted sum. The authors prove certain properties of cellular neural nets constructed in this way, demonstrating the possibility of encoding non-linear functions in multi-layer networks. The question of how practical this would be - particularly due to the peculiar properties of zero-order ultrasensitivity - remains an open question.

https://www.biorxiv.org/content/10.1101/2020.11.10.377077v1

Functional and morphological adaptation in DNA protocells via signal processing prompted by artificial metalloenzymes

A protocell made of pure DNA. This protocell is constructed by annealing two types of ssDNAs produced by rolling circle polymerization from circular DNA templates. The protocell encapsulates artificial metallozymes that produces DNA-intercalating chemical. As the intercalating molecule gets produced, the protocell undergoes morphological changes such as expansion.

https://www.nature.com/articles/s41565-020-0761-y

A DNA-nanoassembly-based approach to map membrane protein nanoenvironments

Mapping the nano-environment and the expression levels of extracellular proteins can reveal a lot of details about the cellular conditions associated with particular diseases. Different cancer states have shown different levels of EGFR family proteins and their dimerization states, especially the formation of heterodimers with Her2 protein. In this article the researchers have devised an approach to hybridize affibody (small, engineered proteins for high target specificity)-oligomer conjugates with a nanocomb (a long DNA strand partially hybridized with shorter DNA oligomers with overhangs). This nanocomb contains a Her2 binding affibody anti-Her2 attached to one end as a reference. The other overhangs encode information of their relative position to the reference, and a common binding domain for the oligos conjugated with the protein-binding affibodies. The affibody-oligo conjugates library is added to the concerned protein, and the nanocomb then binds to the conjugates which are close to the bound reference. These partially hybridised overhang-oligo complexes are then polymerised and nicked by enzymes, and the resulting double stranded DNAs are analysed by NGS. This analysis provides information about which affibodies are bound relatively close to the reference, and the distance between them. The group has shown that this approach can distinguish between different cells with different expression levels and dimerization state of Her2 as a proof of principle.

https://www.nature.com/articles/s41565-020-00785-0

Nucleic acid strand displacement with synthetic mRNA inputs in living mammalian cells

In this paper, the authors investigated the efficiency of a basic strand displacement reaction within living mammalian cells. Probes were designed and modified in order to minimise the egration of nucleases and to ensure that the probes localise to the cytoplasm. The cells are engineered to express a target mRNA with the probe target sequence. In the 3’ UTR. Detection of the target mRNA results in detectable fluorescence and estimation of the number of mRNA molecules per cell. Moreover, this system can be used to follow target mRNA localisation in real-time.

https://pubs.acs.org/doi/pdf/10.1021/acssynbio.8b0028

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