arXiv subjects

Saminathan Ramakrishnan

Publications and source records attributed to Saminathan Ramakrishnan.

4 recordsLinked to original sources

arXiv2026

Rheology and Programmable Gelation of DNA Origami Polymer Tadpoles

DNA origami is a powerful method to achieve nanoscale folded structures. Despite rapid improvements in folding and purification methods, DNA origami objects are still often produced in small quantities and studied at single molecule scale. Here, we design simple DNA origami-inspired polymers with complex topologies, and study their rheology and viscoelastic properties in dense conditions. First, we designed and purified topologically distinct DNA nanostructures, linear, circular, and "tadpole" polymers, to evaluate how polymer architecture influences entanglement and rheology. Despite their distinct topologies, we observe that all constructs obeyed universal rheological scalings, likely due to their short length. However, upon thermal annealing in the bulk, the DNA origami-like polymers displayed significantly different behaviours. Our results suggest that DNA origami-like polymers could be used to engineer thermoresponsive behaviours in complex fluids by introducing reversible and topology-dependent crosslinking.

cond-mat.soft↗

arXiv2026

The Integration Host Factor is a pH-responsive protein that switches from DNA bending to DNA bridging in acidic biofilm-like conditions

The Integration Host Factor (IHF) is a nucleoid-associated protein critical for both DNA compaction and biofilm stability. While its role in DNA packaging within the cell is well understood, its structural role in scaffolding biofilms is more puzzling and difficult to reconcile with its known DNA bending activity. Here, we investigated how IHF-DNA interactions are modulated across a pH spectrum mimicking the acidic microenvironments of bacterial biofilms. By performing all-atom calculations we discovered that low pHs lead to a change in protonation of IHF residues, which in turn exposes positively charged patches. We then conjectured that these positively charged residues could lead to intermolecular DNA bridging and tested this hypothesis through single-molecule and bulk assays. We discovered that while at physiological pH IHF mostly bends DNA, at pH < 5 there is clear evidence of IHF-mediated intermolecular crosslinking. Our results demonstrate that pH significantly modulates IHF-DNA interactions and explains the structural role played by IHF in supporting biofilm mechanics through intermolecular crosslinking.

cond-mat.soft↗

arXiv2025

Organisation and dynamics of individual DNA segments in topologically complex genomes

Capturing the physical organisation and dynamics of genomic regions is one of the major open challenges in biology. The kinetoplast DNA (kDNA) is a topologically complex genome, made by thousands of DNA (mini and maxi) circles interlinked into a two-dimensional Olympic network. The organisation and dynamics of these DNA circles are poorly understood. In this paper, we show that dCas9 linked to Quantum Dots can efficiently label different classes of DNA minicircles in kDNA. We use this method to study the distribution and dynamics of different classes of DNA minicircles within the network. We discover that maxicircles display a preference to localise at the periphery of the network and that they undergo subdiffusive dynamics. From the latter, we can also quantify the effective network stiffness, confirming previous indirect estimations via AFM. Our method could be used more generally, to quantify the location, dynamics and material properties of genomic regions in other complex genomes, such as that of bacteria, and to study their behaviour in the presence of DNA-binding proteins.

cond-mat.soft↗

arXiv2023

Single-Molecule Morphology of Topologically Digested Olympic Networks

The kinetoplast DNA (kDNA) is the archetype of a two-dimensional Olympic network, composed of thousands of DNA minicircles and found in the mitochondrion of certain parasites. The evolution, replication and self-assembly of this structure are fascinating open questions in biology that can also inform us how to realise synthetic Olympic networks in vitro. To obtain a deeper understanding of the structure and assembly of kDNA networks, we sequenced the Crithidia fasciculata kDNA genome and performed high-resolution Atomic Force Microscopy (AFM) and analysis of kDNA networks that had been partially digested by selected restriction enzymes. We discovered that these topological perturbations lead to networks with significantly different geometrical features and morphologies with respect to the unperturbed kDNA, and that these changes are strongly dependent on the class of DNA circles targeted by the restriction enzymes. Specifically, cleaving maxicircles leads to a dramatic reduction in network size once adsorbed onto the surface, whilst cleaving both maxicircles and a minor class of minicircles yields non-circular and deformed structures. We argue that our results are a consequence of a precise positioning of the maxicircles at the boundary of the network, and we discuss our findings in the context of kDNA biogenesis, design of artificial Olympic networks and detection of in vivo perturbations.

cond-mat.soft↗