Biology subjects

Skoruppa, E.

Publications and source records attributed to Skoruppa, E..

5 recordsLinked to original sources

bioRxiv2025

MDNA: a software module for DNA structure generation and analysis

Exploring the dynamical and structural properties of molecular complexes involving DNA is a fundamentally important aspect of understanding many biological processes. Although tools exist for modeling linear DNA and simple complexes, significant challenges remain in generating intricate biomolecular assemblies and incorporating biologically relevant modifications. These limitations restrict the ability to create accurate starting configurations for advanced molecular simulation studies. Here, we introduce MDNA, a molecular modeling toolkit that bridges these gaps by enabling the construction and analysis of complex DNA structures. MDNA offers a versatile solution to generate DNA shapes using a spline-based mapping technique that enables the construction of DNA configurations with arbitrary shapes. Key features include support for (non-)canonical base modifications, such as Watson-Crick-Franklin to Hoogsteen transitions, DNA methylation, and the ability to refine structures using Monte Carlo minimization. The toolkit also provides geometric analysis tools based on rigid body formalism to evaluate DNA structures and trajectories. Together, these features enable users to model and analyze DNA configurations in high detail with a modular Python interface. By integrating structure generation and analysis into a single workflow, MDNA improves the study of DNA-protein interactions, paving the way for new insights into DNA dynamics and molecular simulations.

biophysics↗

bioRxiv2025

The Effects of DMSO on DNA Conformations and Mechanics

Dimethyl sulfoxide (DMSO) is a polar aprotic solvent used in a wide range of applications, including uses as a drug and in drug delivery, as a solvent for fluorescence dyes, and in enzymatic reactions that process DNA. Consequently, many assays contain low concentrations ([≤] 10%) of DMSO. While it is well known that DMSO lowers the melting temperature of DNA, its effects on DNA conformations and mechanical properties below the melting temperature are unclear. Here we use complementary single-molecule techniques to probe DNA in the presence of 0-60% DMSO. Magnetic tweezers force-extension measurements find that the bending persistence length of DNA decreases moderately and linearly with DMSO concentrations up to 20 vol%, by (0.43 {+/-} 0.02)% per %-DMSO, respectively. Magnetic tweezers twist measurements demonstrate a reduction in melting torque in the presence of DMSO and find that the helical twist of DNA remains largely unchanged up to 20% DMSO, while even higher concentrations slightly unwind the helix. Using AFM imaging, we find a moderate compaction of DNA conformations by DMSO and observe a systematic decrease of the mean squared end-to-end distance by 1.2% per %-DMSO. We use coarse grained Monte Carlo simulations of DNA as a semi-flexible polymer with a variable density of flexible segments or bubbles, representing DMSO-induced local defects or melting, to rationalize the observed behavior. The model quantitates the effects of introducing locally flexible regions into DNA and gives trends in line with the magnetic tweezers and AFM imaging experiments. Our results show that addition of up to 50% DMSO has a gradual effect on DNA structure and mechanics and that for low concentrations ([≤] 20%) the induced changes are relatively minor. Our work provides a baseline to understand and model the effects of DMSO on DNA in a range of biophysical and biochemical assays. STATEMENT OF SIGNIFICANCEDimethyl sulfoxide (DMSO) is a widely used polar aprotic solvent. It is employed e.g. as a drug and in drug delivery, as a solvent for small molecules, and as an additive to enzymatic reactions that process DNA. Despite its wide-spread use, its effects on DNA conformations and properties are not well understood and often neglected. We use single-molecule manipulation with magnetic tweezers and AFM imaging to probe DNA in the presence of 0-60% DMSO. We find that DMSO increases the flexibility of DNA, leading to more compact conformations. Up to 50% DMSO, the induced changes are gradual and approximately linear. Our results provide a quantitative baseline to understand, model, and optimize assays with DNA in the presence of DMSO.

biophysics↗

bioRxiv2021

DNA fluctuations reveal the size and dynamics of topological domains

DNA supercoiling is a key regulatory mechanism that orchestrates DNA readout, recombination, and genome maintenance. DNA-binding proteins often mediate these processes by bringing two distant DNA sites together, thereby inducing (transient) topological domains. In order to understand the dynamics and molecular architecture of protein induced topological domains in DNA, quantitative and time-resolved approaches are required. Here we present a methodology to determine the size and dynamics of topological domains in supercoiled DNA in real-time and at the single molecule level. Our approach is based on quantifying the extension fluctuations - in addition to the mean extension - of supercoiled DNA in magnetic tweezers. Using a combination of high-speed magnetic tweezers experiments, Monte Carlo simulations, and analytical theory, we map out the dependence of DNA extension fluctuations as a function of supercoiling density and external force. We find that in the plectonemic regime the extension variance increases linearly with increasing supercoiling density and show how this enables us to determine the formation and size of topological domains. In addition, we demonstrate how transient (partial) dissociation of DNA bridging proteins results in dynamic sampling of different topological states, which allows us to deduce the torsional stiffness of the plectonemic state and the kinetics of protein-plectoneme interactions. We expect our approach to enable quantification of the dynamics and reaction pathways of DNA processing enzymes and motor proteins, in the context of physiologically relevant forces and supercoiling densities. SignificanceIn the cell, long DNA molecules carry the genetic information and must be stored and maintained, yet remain accessible for read out and processing. DNA supercoiling facilitates compaction of DNA, modulates its accessibility, and spatially juxtaposes DNA sites distant in linear DNA sequence. By binding to two sites in supercoiled DNA, DNA bridging proteins can pinch off topological domains and alter DNA plectoneme dynamics. Here we show how DNA bridging and topological domain dynamics can be detected from changes in the extension fluctuations of supercoiled DNA molecules tethered in magnetic tweezers. Our work highlights how considering DNA extension fluctuations, in addition to the mean extension, provides additional information and enables the investigation of protein-DNA interactions that are otherwise invisible.

biophysics↗

bioRxiv2018

Twist-bend coupling and the statistical mechanics of DNA: perturbation theory and beyond

The simplest model of DNA mechanics describes the double helix as a continuous rod with twist and bend elasticity. Recent work has discussed the relevance of a little-studied coupling G between twisting and bending, known to arise from the groove asymmetry of the DNA double helix. Here, the effect of G on the statistical mechanics of long DNA molecules subject to applied forces and torques is investigated. We present a perturbative calculation of the effective torsional stiffness Ceff for small twist-bend coupling. We find that the \"bare\" G is \"screened\" by thermal fluctuations, in the sense that the low-force, long-molecule effective free energy is that of a model with G = 0, but with long-wavelength bending and twisting rigidities that are shifted by G-dependent amounts. Using results for torsional and bending rigidities for freely-fluctuating DNA, we show how our perturbative results can be extended to a nonperturbative regime. These results are in excellent agreement with numerical calculations for Monte Carlo \"triad\" and molecular dynamics \"oxDNA\" models, characterized by different degrees of coarse-graining, validating the perturbative and non-perturbative analyses. While our theory is in generally-good quantitative agreement with experiment, the predicted torsional stiffness does systematically deviate from experimental data, suggesting that there are as-yet-uncharacterized aspects of DNA twisting-stretching mechanics relevant to low-force, long-molecule mechanical response, which are not captured by widely-used coarse-grained models.

biophysics↗

bioRxiv2018

Bend-Induced Twist Waves and the Structure of Nucleosomal DNA

Recent work indicates that twist-bend coupling plays an important role in DNA micromechanics. Here we show that this coupling induces standing twist waves in bent DNA, and we provide an analytical solution of the minimum-energy shape of a bent double-helical molecule. This solution is in excellent agreement with both coarse-grained simulations of DNA minicircles and experimental structural data for nucleosomal DNA, which is bent and wrapped around histone proteins in a superhelical conformation. Our analysis shows that the observed twist oscillation in nucleosomal DNA, so far attributed to the interaction with the histone proteins, is an intrinsic feature of free bent DNA, and should be observable in other protein-DNA complexes.

biophysics↗