Biology subjects

Wiebeler, C.

Publications and source records attributed to Wiebeler, C..

5 recordsLinked to original sources

bioRxiv2026

Molecular Structure, DNA Binding, and Photophysical Properties of SYTOX Orange and SYTOX Green

Fluorescent dyes are critical to visualizing nucleic acids in many applications. SYTOX Orange and SYTOX Green are cyanine dyes, used in dead cell staining and increasingly in single-molecule assays to probe DNA supercoiling and processing. However, their structures and effects on DNA mechanics are not or only partially known. We determine the structure of SYTOX Orange to be (E)-2-((2-(4 ((diethyl(methyl)ammonio)methyl)phenyl)-6-methoxy-1-methylquinolin-4(1H)-ylidene)methyl)-4-methyloxazolo[4,5-b]pyridin-4-ium, identical to SYBR Gold except for an aza-benzoxazol core that is fundamentally different from other dyes in the SYTOX and SYBR families. We report SYTOX Green to be (Z)-2-(bis(3-(trimethylammonio)propyl)amino)-4-((3-methylbenzo[d]thiazol-2(3H)-ylidene)methyl)-1-phenylquinolin-1-ium, similar to PicoGreen. Using magnetic tweezers, we characterize the effect of SYTOX Orange and SYTOX Green on DNA mechanics. They lengthen and unwind DNA consistent with intercalation and the DNA unwinding angles per dye are 21.1(1){degrees} and 20.5(1){degrees} for SYTOX Orange and Green, respectively. Both dyes leave the DNA bending persistence length and plectoneme size almost unaltered (<10% change up to 1 {micro}M), which is advantageous in assays probing DNA supercoiling. Their photophysical properties reveal close agreement between single-molecule manipulation and optical absorbance and fluorescence spectroscopy. Our comprehensive set of complementary measurements relates mechanical and optical properties to the molecular structures and provides recommendations for their use in applications.

biophysics↗

bioRxiv2026

Transferability of ion force fields to OPC water: Maintaining single-ion and ion-pairing properties

Accurate ion force fields are essential for molecular dynamics simulations of biomolecular systems, particularly in combination with modern water models such as OPC. While OPC water provides an accurate description of key water properties and has been successfully applied in biomolecular simulations, the transferability of existing ion force fields to this model remains an open question. Here, we systematically assess the transferability of monovalent and divalent ion force field parameters (Li+, Na+, K+, Cs+, Mg2+, Ca2+, Sr2+, Ba2+, Cl- and Br-) to OPC water by comparing single-ion and ion-pairing properties with experimental data. Our analysis reveals that no single literature parameter set provides accurate results for all ions when directly transferred to OPC water. We hence introduce the MS/G-LB(OPC) force field, which combines Mamatkulov-Schwierz-Grotz cation parameters with Loche-Bonthuis anion parameters. MS/G-LB(OPC) reproduces hydration free energies, first-shell structural properties and activity derivatives at low salt concentrations. Our results demonstrate that transferring ion parameters to OPC can lead to significant and ion-specific deviations from experimental data, making careful validation essential. At the same time, the systematic transfer and combination of ion parameters from existing force fields can provide a practical and computationally efficient alternative to full reparameterization. MS/G-LB(OPC) is available at https://git.rz.uni-augsburg.de/cbio-gitpub/opcion-force-fields.

biophysics↗

bioRxiv2025

DNA Twist at High Alkaline Ion Concentrations: Evidence against C-Form DNA in Solution

DNA is highly negatively charged, making its structure strongly dependent on the ionic environment. DNA twist -a central DNA property- varies with ion concentration and identity. Prior studies have focused on salt concentrations below 1 M and it is unclear whether twist trends persist at higher concentrations. It has been proposed that at high salt, DNA transitions from its canonical B-form to C-form, originally observed by fiber diffraction. Here, we use single-molecule magnetic tweezers to measure DNA twist in high concentrations of LiCl, NaCl, KCl, and CsCl. For all salts, twist initially increases approximately as [~][salt]1/2, but plateaus above 3 M. LiCl causes the largest twist increase, by [≤] 0.8{degrees}/bp compared to physiological salt, still far below the suggested C-form values of 2-3{degrees}/bp. We perform all-atom molecular dynamics simulations for DNA in LiCl solutions with different force fields. For parmbsc1, we observe good agreement with experiments when ion activities are taken into account. We find that simulations initiated in the C-form rapidly convert to B-form, while the B-form remains stable. Our results demonstrate ion-specific, systematic changes in DNA twist beyond 1 M salt, but do not support a transition to the C-form for DNA, even at very high salt concentrations.

biophysics↗

bioRxiv2024

Allosteric activation of the SPRTN protease by ubiquitin maintains genome stability

The DNA-dependent protease SPRTN maintains genome stability by degrading toxic DNA-protein crosslinks (DPCs). To understand how SPRTNs promiscuous protease activity is confined to the cleavage of crosslinked proteins, we reconstitute the repair of DPCs including their modification with SUMO and ubiquitin chains, using recombinant human proteins. We discover that DPC ubiquitylation strongly activates SPRTN independently of SPRTNs known ubiquitin-binding domains. Using protein structure prediction, MD simulations and NMR spectroscopy we reveal that ubiquitin binds to an interface at the back of SPRTNs protease domain, promoting an active conformation. Replacing key interfacial residues prevents ubiquitin-dependent activation of SPRTN, which leads to genomic instability and cell cycle defects in cells expressing hypomorphic SPRTN variants that cause premature aging and liver cancer in Ruijs-Aalfs syndrome patients. Collectively, our results demonstrate that SPRTN activation is coupled to the modification of the crosslinked protein, explaining how specificity is achieved during DPC repair.

biochemistry↗

bioRxiv2020

Histidine Protonation Controls Structural Heterogeneity in the Cyanobacteriochrome AnPixJg2

Cyanobacteriochromes are compact and spectrally diverse photoreceptor proteins that bind a linear tetrapyrrole as a chromophore. They show photochromicity by having two stable states that can be interconverted by the photoisomerization of the chromophore. Hence, these photochemical properties make them an attractive target for biotechnological applications. However, their application is impeded by structural heterogeneity that reduces the yield of the photoconversion. The heterogeneity can originate either from the chromophore structure or the protein environment. Here, we study the origin of the heterogeneity in AnPixJg2, a representative member of the red/green cyanobacteriochrome family, that has a red absorbing parental state and a green absorbing photoproduct state. Using molecular dynamics simulations and umbrella sampling we have identified the protonation state of a conserved histidine residue as a trigger for structural heterogeneity. When the histidine is in a neutral form, the chromophore structure is homogenous, while in a positively charged form, the chromophore is heterogeneous with two different conformations. We have identified a correlation between the protonation of the histidine and the structural heterogeneity of the chromophore by detailed characterization of the interactions in the protein binding site. Our findings reconcile seemingly contradicting spectroscopic studies that attribute the heterogeneity to different sources. Furthermore, we predict that circular dichroism can be used as a diagnostic tool to distinguish different substates. Significance statementCyanobacteriochromes are photoreceptor proteins that have attracted attention for their immense potential in bioimaging and optogenetics applications. This is due to their desirable properties such as compactness, photochromicity and diverse spectral tuning. Despite these advantages, nature has set a limitation in the form of structural heterogeneity that presents a drawback for its application in biotechnology. We have identified a histidine residue in the vicinity of the chromophore as the origin of the heterogeneity in red/green CBCRs. The protonation state of this conserved histidine alters an extended network of protein-chromophore interactions and induces heterogeneity. Furthermore, theoretical CD spectroscopy has revealed easy identification of heterogeneity. Hence, our study paves the way for rational design and optimization of protein properties.

biophysics↗