Nanopore translocation of topologically linked DNA catenanes

Amplification-Free Quantification of Endogenous Mitochondrial DNA Copy Number Using Solid-State Nanopores

Mitochondrial DNA (mtDNA) quantification is crucial in understanding mitochondrial dysfunction, which is linked to a variety of diseases, including cancer and neurodegenerative disorders. Traditional methods often rely on amplification-based techniques, which can introduce bias and lack the precision needed for clinical diagnostics. Solid-state nanopores, an emerging biosensing platform, have the advantage of offering single-molecule and label-free approaches by enabling the direct counting of DNA molecules without amplification. The ion-current signatures obtained from each DNA molecule contain rich information on the molecules' lengths and origin. In this study, we present an amplification-free method for mtDNA quantification using solid-state nanopores and machine learning. Intriguingly, we find that native (unamplified) mtDNA translocations harbor structurally distinctive features that can be exploited to specifically detect and quantify mtDNA copies over the background of genomic DNA fragments. By combining selective degradation of linear genomic DNA (gDNA) via exonuclease V with a support vector machine (SVM)-based model, we isolate and quantify mtDNA directly from biological samples. We validate our method using plasmids or isolated mtDNAs by spiking in predetermined quantities. We then quantify endogenous mtDNAs in a cancer cell line and in blood cells and compare our results with qPCR-based quantification of the mtDNA/nuclear DNA ratios. To elucidate the source of the ion-current signatures from the native mtDNA molecules, we perform synchronous electro-optical sensing of mtDNAs during passage through the nanopore after NHS ester reaction with fluorophore compounds. Our results show correlated electro-optical events, indicating that the mtDNA is complexed with packaging proteins. Our assay is robust, with a high classification accuracy and is capable of detecting mtDNA at picomolar levels, making it suitable for low-abundance samples. This technique requires minimal sample preparation and eliminates the need for amplification or purification steps. The developed approach has significant potential for point-of-care applications, offering a low-cost and scalable solution for accurate mtDNA quantification in clinical settings.

Translation as a Biosignature

Life on Earth relies on mechanisms to store heritable information and translate this information into cellular machinery required for biological activity. In all known life, storage, regulation, and translation are provided by DNA, RNA, and ribosomes. Life beyond Earth, even if ancestrally or chemically distinct from life as we know it, may utilize similar structures: it has been proposed that charged linear polymers analogous to nucleic acids may be responsible for storage and regulation of genetic information in nonterran biochemical systems. We further propose that a ribosome-like structure may also exist in such a system, due to the evolutionary advantages of separating heritability from cellular machinery. In this study, we use a solid-state nanopore to detect DNA, RNA, and ribosomes, and we demonstrate that machine learning can distinguish between biomolecule samples and accurately classify new data. This work is intended to serve as a proof of principal that such biosignatures (i.e., informational polymers or translation apparatuses) could be detected, for example, as part of future missions targeting extant life on Ocean Worlds. A negative detection does not imply the absence of life; however, the detection of ribosome-like structures could provide a robust and sensitive method to seek extant life in combination with other methods. Key Words: RNA world-Darwinian evolution-Nucleic acids-Agnostic life detection. Astrobiology 24, 1257-1274.

Unraveling the Influence of Topology and Spatial Confinement on Equilibrium and Relaxation Properties of Interlocked Ring Polymers

We use Langevin dynamics simulations to study linked ring polymers in channel confinement. We address the in- and out-of-equilibrium behavior of the systems for varying degrees of confinement and increasing topological and geometrical complexity of the interlocking. The main findings are three. First, metric observables of different link topologies collapse onto the same master curve when plotted against the crossing number, revealing a universal response to confinement. Second, the relaxation process from initially stretched states is faster for more complex links. We ascribe these properties to the interplay of several effects, including the dependence of topological friction on the link complexity. Finally, we show that transient forms of geometrical entanglement purposely added to the initial stressed state can leave distinctive signatures in force-spectroscopy curves. The insight provided by the findings could be leveraged in single-molecule nanochannel experiments to identify geometric entanglement within topologically linked rings.

Topological Entanglement of Linear Catenanes: Knots and Threadings

We used molecular dynamics simulations to investigate the self-entanglements of the collapsed linear catenanes. We found two different types of topologically complex states. First, we observed numerous long-lived knotting events of the catenane backbone. However, comparison with conventional polymers reveals that knots are suppressed in catenanes. Next, we observed topologically complex states with no analogue in polymers, where a concatenated ring was threaded by other near or distal rings sliding through it. Differently from knots, these threaded states can disentangle by becoming fully tightened. A detailed thermodynamic and microscopic analysis is employed to rationalize the persistence of threaded states, which can survive significant internal reorganizations of the entire catenane. We finally discuss the broader implications of these previously unreported types of entanglements for other systems, such as noncollapsed and interacting catenanes.

Constraints on Knot Insertion, Not Internal Jamming, Control Polycatenane Translocation Dynamics through Crystalline Pores

The translocation of polymers through pores and channels is an archetypal process in biology and is widely studied and exploited for applications in bio- and nanotechnology. In recent times, the translocation of polymers of various different topologies has been studied both experimentally and by computer simulation. However, in some cases, a clear understanding of the precise mechanisms that drive their translocation dynamics can be challenging to derive. Experimental methods are able to provide statistical details of polymer translocation, but computer simulations are uniquely placed to uncover a finer level of mechanistic understanding. In this work, we use high-throughput molecular simulations to reveal the importance that knot insertion rates play in controlling translocation dynamics in the small pore limit, where unexpected nonpower law behavior emerges. This work both provides new predictive understanding of polycatenane translocation and shows the importance of carefully considering the role of the definition of translocation itself.