Biology subjects

Ameta, S.

Publications and source records attributed to Ameta, S..

4 recordsLinked to original sources

bioRxiv2026

Phase composition-specific behaviour of functional RNAs in liquid-liquid phase-separated microenvironment

The internal dynamics of liquid-liquid phase-separated systems are governed primarily by polymer packing, excluded-volume effect, and interactions between polymers and encapsulated macro-molecules. Although one immediate effect of such a constrained microenvironment is diffusion limitation, it remains unclear whether encapsulated macromolecules can also exhibit phase composition-specific functional behaviour that is not observable in a well-mixed aqueous environment. In this regard, different phases in a phase-separated environment can be accessed via a phase diagram that demarcates the region between two-phase (droplets) and one-phase (polymer-rich, no droplets) regimes. While the two-phase region is heterogeneous, most previous work on encapsulating functional macromolecules in phase-separated droplets uses a single point from the phase diagram. This leaves a clear gap in understanding on how the function scales across this landscape of droplets and identifying regions advantageous for the encapsulated macromolecule and its function. Here, using the Spinach light-up RNA aptamer, we show that RNA function does not scale uniformly across the phase diagram. We show that RNA can exhibit phase composition-specific functional behaviour due to constraints imposed by the internal microenvironment of phase-separated droplets. Furthermore, using variants of the Spinach aptamer, we show that fluorescence activity differences among the variants vary differently with phase-separation regimes across the phase map, suggesting that some regions of the phase diagram can confer a selective advantage. Our results highlight the potential of liquid-liquid phase-separated internal microenvironments in guiding the differentiation of functional RNA variants, which could serve as a physical selection pressure in pre-cellular evolution.

evolutionary biology↗

bioRxiv2023

Constrained dynamics of oligonucleotides in the phase-separated droplets

Phase-separated droplets are excellent means of compartmentalizing functional molecules and have been shown as excellent models for protocells. Although complex functions based on oligonucleotides have been studied, we still lack an understanding of how the oligonucleotide dynamics are affected by the condensed internal environment of these droplets. Particularly, we lack high-resolution experimental measurements of the dynamical parameters that control oligonucleotide diffusion inside the phase-separated droplets. In addition, there is no clarity on how these dynamical parameters differ in the charged (coacervates) vs non-charged (aqueous two-phase system, ATPS) environment of these droplets. In this study, using fluorescence correlation spectroscopy (FCS), we demonstrate the constrained dynamics of oligonucleotides inside membraneless phase-separated droplets at an unprecedented resolution. We further compare transport properties at different lengths of oligonucleotides as well as salt concentrations. We observe that among all the parameters the oligonucleotides caging (spatial restriction in the movement) inside the matrix has a considerable impact on the diffusive dynamics. Our study provides a way of unravelling, quantifying and understanding physical parameters governing the polymer transport dynamics inside the phase-separated droplets.

biophysics↗

bioRxiv2022

Multispecies autocatalytic RNA reaction networks in coacervates

Robust and dynamic localization of self-reproducing autocatalytic chemistries is a key step in the realization of heritable and evolvable chemical systems. While autocatalytic chemical reaction networks already possess attributes such as heritable self-reproduction and evolvability, localizing functional multispecies networks within complex primitive phases, such as coacervates, has remained unexplored. Here, we show the self-reproduction of an RNA system within charge-rich coacervates where catalytic RNAs are produced by the autocatalytic assembly of constituent smaller RNA fragments. We systematically demonstrate the catalytic assembly of active ribozymes within phase-separated coacervates -- both in micron sized droplets as well as a coalesced macrophase, underscoring the facility of the complex, charge-rich phase to support these reactions in multiple configurations. By constructing multispecies reaction networks, we show that these newly assembled molecules are active, participating both in self- and cross-catalysis within the coacervates. Finally, these collectively autocatalytic reaction networks endow unique compositional identities to the coacervates which in turn transiently protect the identity against external perturbations, due to differential molecular transport and reaction rates. Our results establish a compartmentalised chemical system possessing a compositional identity possessing a balance between robustness and variability required for chemical evolution.

evolutionary biology↗

bioRxiv2019

Darwinian properties and their trade-offs in autocatalytic RNA networks

Discovering autocatalytic chemistries that can evolve is a major goal in systems chemistry and a critical step towards understanding the origin of life. Autocatalytic networks have been discovered in various chemistries, but we lack a general understanding of how network topology controls the Darwinian properties of variation, differential reproduction, and heredity, which are mediated by the chemical composition. Using barcoded sequencing and droplet microfluidics, we establish a landscape of thousands of networks of RNAs that catalyze their own formation from fragments, and derive relationships between network topology and chemical composition. We find that strong variations arise from catalytic innovations perturbing weakly connected networks, and that reproduction increases with global connectivity. These rules imply trade-offs between reproduction and variation, and between compositional persistence and variation along trajectories of network complexification. Overall, connectivity in reaction networks provides a lever to balance variation (to explore chemical states) with reproduction and heredity (persistence being necessary for selection to act), as required for chemical evolution.

evolutionary biology↗