Biology subjects

Zanchetta, G.

Publications and source records attributed to Zanchetta, G..

5 recordsLinked to original sources

bioRxiv2026

Protoribosomal condensate formation across cationic chemistries

Early ribonucleoprotein systems likely required mechanisms to concentrate and organize RNA. Modern ribosomes use Mg2+ and evolved Lys/Arg-rich protein extensions to stabilize their RNA backbone. Before templated synthesis, however, peptide formation likely generated heterogeneous sequence populations rather than reproducible ribosomal sequences. Here, we compare Mg2+, ribosomal peptides, and statistical peptide libraries in organizing a 136-nucleotide model of the peptidyl transferase center (sPTC). Mg2+ condenses sPTC only at a large excess of positive charge following thermal annealing, producing largely arrested libraries. Acidic conditions further promote condensation. Ribosomal peptides instead promote coacervation near charge stoichiometry and form droplets that readily fuse. Several statistical peptide libraries also coacervate with sPTC, despite comprising heterogenous mixtures rather than a single defined sequence. Increasing mean positive charge favors condensation, but Lys/Arg-containing libraries undergo liquid-liquid phase separation more readily and across broader conditions than matched libraries containing the prebiotically plausible diaminopropionic acid (Dpr) and diaminobutyric acid (Dab). Atomistic computer simulations implicate Arg as a major source of this difference, as it can form more numerous and longer-lived hydrogen bonds with RNA, while competitive partitioning experiments show preferential condensate recruitment in the order Arg > Lys > Dab > Dpr. Together, our findings show that peptide-RNA coacervation can be triggered collectively by statistical peptide ensembles, providing a plausible route to protoribosomal organization without peptide sequence-specific optimization. Cationic chemistry shapes condensate formation and material properties, suggesting that amino acid alphabet formation could have broadened the conditions supporting liquid-like protoribosomal assemblies.

biochemistry↗

bioRxiv2026

SIGHT: an immersive Virtual Reality platform for reinforced learning of optics and functional neuroanatomy of vision

Virtual reality (VR) offers immersive and interactive learning environments that can improve student engagement and 3D visualization. However, its application in medical education is mostly limited to clinical settings and its potential for better understanding complex concepts, or empathy with the patients, remains underexplored. Here, we describe SIGHT (Simulated Immersive Guidance for Human Training), an immersive VR application, designed to teach core concepts in the physics and functional neuroanatomy, or neurophysiology of human vision. Its two integrated learning modules allow first-person experience of normal and pathological conditions: the optics module enables users to manipulate lenses, experience refractive errors such as myopia, presbyopia, and astigmatism and correct them through appropriate lens selection; the neurophysiology module allows learners to navigate the visual pathways from the retina to the visual cortex and to simulate lesions, experiencing the corresponding visual field deficits. User authentication and interactive evaluation steps provide analytical feedback of the experience and learning process. A pilot group of medical students reported high usability, engagement and deeper understanding of the vision-related concepts, showing how the approach of SIGHT can support experiential learning in medical education.

scientific communication and education↗

bioRxiv2025

The Dark Side of Biomolecular Condensates: Quantifying the Role of Nucleic Acids

Liquid-Liquid Phase Separation (LLPS) is being increasingly recognized as a major organizational principle for proteins and nucleic acids (NAs) in cells, as well as a promising strategy for synthetic biology and biomedical applications. Extensive work has explored the role of protein sequence and properties in the regulation of LLPS. On the contrary, the role of nucleic acids has often been overlooked. Here, to fill this gap we focus on model systems made of oligonucleotides with tuned lengths and degree of hybridization, mixed with a moderately charged, disordered peptide. Combining multiple length scales through experiments and molecular dynamics simulations, we unravel the distinct effect of the properties of NAs on the phase behavior and we propose a metric for the stability of biocondensates. We also characterize the conditions for the onset of liquid crystalline order in the droplets and we show that it is associated with a dramatic slowing down of the dynamics of oligonucleotides, while peptides retain high mobility. Our results can be generalized to natural and non-natural NAs of arbitrary structure, providing a guide for the design of synthetic NA-containing coacervates. O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=100 SRC="FIGDIR/small/683552v1_ufig1.gif" ALT="Figure 1"> View larger version (36K): org.highwire.dtl.DTLVardef@179be04org.highwire.dtl.DTLVardef@1aa0192org.highwire.dtl.DTLVardef@4d411aorg.highwire.dtl.DTLVardef@1ed238d_HPS_FORMAT_FIGEXP M_FIG C_FIG

biophysics↗

bioRxiv2024

The interplay between peptides and RNA is critical for protoribosome compartmentalization and stability

The ribosome, owing to its exceptional conservation and biological importance, harbours a remarkable molecular fossil known as the protoribosome. It surrounds the peptidyl transferase center (PTC), responsible for peptide bond formation. While previous studies have demonstrated the PTC activity in RNA alone, our investigation reveals the intricate roles of the ribosomal protein fragments (rPeptides) within the ribosomal core. This research highlights the significance of rPeptides in stability and coacervation of two distinct protoribosomal evolutionary stages. The 617nt "big" protoribosome model which associates with rPeptides specifically, exhibits a structurally defined and rigid nature, further stabilised by the peptides. In contrast, the 136nt "small" model, previously linked to peptidyltransferase activity, displays greater structural flexibility. While this construct interacts with rPeptides with lower specificity, they induce coacervation of the "small" protoribosome across a wide concentration range, which is concomitantly dependent on the RNA sequence and structure. Moreover, these conditions protect RNA from degradation. This phenomenon suggests a significant evolutionary advantage in the RNA-protein interaction at the early stages of ribosome evolution. The distinct properties of the two protoribosomal stages suggest that rPeptides initially provided compartmentalization and prevented RNA degradation, preceding the emergence of specific RNA-protein interactions crucial for the ribosomal structural integrity. 3 keypoints- The most ancient fragments of ribosomal peptides trigger coacervation of protoribosome - The protoribosome coacervation provides protection against RNA degradation - Coacervation is more profound with a smaller and more flexible model of the protoribosome

biophysics↗

bioRxiv2020

Non-Langmuir kinetics of DNA surface hybridization

Hybridization of complementary single strands of DNA represents a very effective natural molecular recognition process widely exploited for diagnostic, biotechnology and nanotechnology applications. A common approach relies on the immobilization on a surface of single stranded DNA probes that bind complementary targets in solution. However, despite the deep knowledge on DNA interactions in bulk solution, the modelling of the same interactions on a surface are still challenging and perceived as strongly system-dependent. Here we show that a two dimensional analysis of the kinetics of hybridization, performed at different target concentration and probe surface density by a label-free optical biosensor, reveals peculiar features inconsistent with an ideal Langmuir-like behaviour. We propose a simple non-Langmuir kinetic model accounting for an enhanced electrostatic repulsion originating from the surface immobilization of nucleic acids and for steric hindrance close to full hybridization of the surface probes. The analysis of the kinetic data by the model enables to quantify the repulsive potential at the surface, as well as to retrieve the kinetic parameters of isolated probes. We show that the strength and the kinetics of hybridization at large probe density can be improved by a 3D immobilization strategy of probe strands with a double stranded linker. Statement of SignificanceHybridization of nucleic acids strands with complementary sequences is a fundamental biological process and is also widely exploited for diagnostic purposes. Despite the availability of effective models for the equilibrium strength of freely diffusing strands, a general predictive model for surface hybridization is still missing. Moreover, the kinetics of hybridization is not fully understood neither in solution nor on a surface. In this work we show that the analysis of the kinetics of hybridization on a surface reveals and enables to quantify two main additional contributions: electrostatic repulsion and steric hindrance. These are general effects expected to occur not only on a surface but in any condition with large density of nucleic acids, comparable to that of the cellular nucleus.

biophysics↗