Topological Barrier Research Articles

Senataxin RNA/DNA helicase promotes replication restart at co-transcriptional R-loops to prevent MUS81-dependent fork degradation.

Replication forks stalled at co-transcriptional R-loops can be restarted by a mechanism involving fork cleavage-religation cycles mediated by MUS81 endonuclease and DNA ligase IV (LIG4), which presumably relieve the topological barrier generated by the transcription-replication conflict (TRC) and facilitate ELL-dependent reactivation of transcription. Here, we report that the restart of R-loop-stalled replication forks via the MUS81-LIG4-ELL pathway requires senataxin (SETX), a helicase that can unwind RNA:DNA hybrids. We found that SETX promotes replication fork progression by preventing R-loop accumulation during S-phase. Interestingly, loss of SETX helicase activity leads to nascent DNA degradation upon induction of R-loop-mediated fork stalling by hydroxyurea. This fork degradation phenotype is independent of replication fork reversal and results from DNA2-mediated resection of MUS81-cleaved replication forks that accumulate due to defective replication restart. Finally, we demonstrate that SETX acts in a common pathway with the DEAD-box helicase DDX17 to suppress R-loop-mediated replication stress in human cells. A possible cooperation between these RNA/DNA helicases in R-loop unwinding at TRC sites is discussed.

Topological barrier to Cas12a activation by circular DNA nanostructures facilitates autocatalysis and transforms DNA/RNA sensing

Control of CRISPR/Cas12a trans-cleavage is crucial for biosensor development. Here, we show that small circular DNA nanostructures which partially match guide RNA sequences only minimally activate Cas12a ribonucleoproteins. However, linearizing these structures restores activation. Building on this finding, an Autocatalytic Cas12a Circular DNA Amplification Reaction (AutoCAR) system is established which allows a single nucleic acid target to activate multiple ribonucleoproteins, and greatly increases the achievable reporter cleavage rates per target. A rate-equation-based model explains the observed near-exponential rate trends. Autocatalysis is also sustained with DNA nanostructures modified with fluorophore-quencher pairs achieving 1 aM level (<1 copy/μL) DNA detection (106 times improvement), without additional amplification, within 15 min, at room temperature. The detection range is tuneable, spanning 3 to 11 orders of magnitude. We demonstrate 1 aM level detection of SNP mutations in circulating tumor DNA from blood plasma, genomic DNA (H. Pylori) and RNA (SARS-CoV-2) without reverse transcription as well as colorimetric lateral flow tests of cancer mutations with ~100 aM sensitivity.

The local variation of the Gaussian modulus enables different pathways for fluid lipid vesicle fusion

Viral infections, fertilization, neurotransmission, and many other fundamental biological processes rely on membrane fusion. Straightforward calculations based on the celebrated Canham–Helfrich elastic model predict a large topological energy barrier that prevents the fusion process from being thermally activated. While such high energy is in accordance with the physical barrier function of lipid membranes, it is difficult to reconcile with the biological mechanisms involved in fusion processes. In this work, we use a Ginzburg–Landau type of free energy that recovers the Canham–Helfrich model in the limit of small width-to-vesicle-extension ratio, with the additional ability to handle topological transitions. We show that a local modification of the Gaussian modulus in the merging region both dramatically lowers the elastic energy barrier and substantially changes the minimal energy pathway for fusion, in accordance with experimental evidence. Therefore, we discuss biological examples in which such a modification might play a crucial role.

Topological barriers to defect nucleation generate large mechanical forces in an ordered fluid

Common fluids cannot sustain static mechanical stresses at the macroscopic scale because they lack molecular order. Conversely, crystalline solids exhibit long-range order and mechanical strength at the macroscopic scale. Combining the properties of fluids and solids, liquid crystal films respond to mechanical confinement by both flowing and generating static forces. The elastic response, however, is very weak for film thicknesses exceeding 10 nm. In this study, the mechanical strength of a fluid film was enhanced by introducing topological defects in a cholesteric liquid crystal, producing unique viscoelastic and optomechanical properties. The cholesteric was confined under strong planar anchoring conditions between two curved surfaces with sphere-sphere contact geometry similar to that of large colloidal particles, creating concentric dislocation loops. During surface retraction, the loops shrank and periodically disappeared at the surface contact point, where the cholesteric helix underwent discontinuous twist transitions, producing weak oscillatory surface forces. On the other hand, new loop nucleation was frustrated by a topological barrier during fluid compression, creating a metastable state. This generated exceptionally large forces with a range exceeding 100 nm as well as extended blueshifts of the photonic bandgap. The metastable cholesteric helix eventually collapsed under a high compressive load, triggering a stick-slip-like cascade of defect nucleation and twist reconstruction events. These findings were explained using a simple theoretical model and suggest a general approach to enhance the mechanical strength of one-dimensional periodic materials, particularly cholesteric colloid mixtures.

The overlap gap property: A topological barrier to optimizing over random structures

The problem of optimizing over random structures emerges in many areas of science and engineering, ranging from statistical physics to machine learning and artificial intelligence. For many such structures, finding optimal solutions by means of fast algorithms is not known and often is believed not to be possible. At the same time, the formal hardness of these problems in the form of the complexity-theoretic NP-hardness is lacking. A new approach for algorithmic intractability in random structures is described in this article, which is based on the topological disconnectivity property of the set of pairwise distances of near-optimal solutions, called the Overlap Gap Property. The article demonstrates how this property 1) emerges in most models known to exhibit an apparent algorithmic hardness; 2) is consistent with the hardness/tractability phase transition for many models analyzed to the day; and, importantly, 3) allows to mathematically rigorously rule out a large class of algorithms as potential contenders, specifically the algorithms that exhibit the input stability (insensitivity).

Majorana and non-Majorana modes in a nanowire in partially proximity to a superconductor

We investigate the Majorana and non-Majorana modes in a nanowire in partial proximity to a superconductor, in which the gapped superconductor will play different roles in different topological regimes. In the gapped topological superconducting phase, it plays the role of a topological barrier, which confines some localized edge modes in the quantum dot (QD) region. The probability for the wave function in this region can approach unity by tuning the system parameters. These low-lying localized modes exhibit linear spectra with equal energy level spacing, with eigenvalues εn=vFnπ/(2L), where vF is the Fermi velocity, L is the size of the QD region, and n∈Z. We demonstrate these features using a spinless nanowire in proximity to a p-wave superconductor and a spin–orbit coupled semiconductor nanowire in proximity to a s-wave superconductor. A simple picture is proposed to understand the behavior of these results. However, in the trivial superconducting phase when both bands are occupied in the spin–orbit coupled mode, we observe some non-Majorana modes, with complicated low-lying excited spectra, which resembles that reported in experiments. These differences are rooted deeply in the bulk-edge correspondence. These observations may be able to facilitate the identification of Majorana zero modes in experiments.

Observation of fluctuation-mediated picosecond nucleation of a topological phase.

Topological states of matter exhibit fascinating physics combined with an intrinsic stability. A key challenge is the fast creation of topological phases, which requires massive reorientation of charge or spin degrees of freedom. Here we report the picosecond emergence of an extended topological phase that comprises many magnetic skyrmions. The nucleation of this phase, followed in real time via single-shot soft X-ray scattering after infrared laser excitation, is mediated by a transient topological fluctuation state. This state is enabled by the presence of a time-reversal symmetry-breaking perpendicular magnetic field and exists for less than 300 ps. Atomistic simulations indicate that the fluctuation state largely reduces the topological energy barrier and thereby enables the observed rapid and homogeneous nucleation of the skyrmion phase. These observations provide fundamental insights into the nature of topological phase transitions, and suggest a path towards ultrafast topological switching in a wide variety of materials through intermediate fluctuating states.

Topological energy barrier for skyrmion lattice formation in MnSi

We report the direct measurement of the topological skyrmion energy barrier through a hysteresis of the skyrmion lattice in the chiral magnet MnSi. Measurements were made using small-angle neutron scattering with a custom-built resistive coil to allow for high-precision minor hysteresis loops. The experimental data was analyzed using an adapted Preisach model to quantify the energy barrier for skyrmion formation and corroborated by the minimum-energy path analysis based on atomistic spin simulations. We reveal that the skyrmion lattice in MnSi forms from the conical phase progressively in small domains, each of which consisting of hundreds of skyrmions, and with an activation barrier of several eV.

High transparency Bi2Se3 topological insulator nanoribbon Josephson junctions with low resistive noise properties

Bi2Se3 nanoribbons, grown by catalyst-free Physical Vapor Deposition, have been used to fabricate high quality Josephson junctions with Al superconducting electrodes. The conductance spectra (dI/dV) of the junctions show clear dip-peak structures characteristic of multiple Andreev reflections. The temperature dependence of the dip-peak features reveals a highly transparent Al/Bi2Se3 topological insulator nanoribbon interface and Josephson junction barrier. This is supported by the high values of the Bi2Se3 induced gap and of IcRn (where Ic is the critical current and Rn is the normal resistance of the junction) product both of the order of 160 μeV, a value close to the Al gap. The devices present an extremely low relative resistance noise below 1 × 10−12 μm2/Hz comparable to the best Al tunnel junctions, which indicates a high stability in the transmission coefficients of transport channels. The ideal Al/Bi2Se3 interface properties, perfect transparency for Cooper pair transport in conjunction with low resistive noise, make these junctions a suitable platform for further studies of the induced topological superconductivity and Majorana bound states physics.

Supercoiling in a Protein Increases its Stability.

The supercoiling motif is the most complex type of nontrivial topology found in proteins with at least one disulfide bond and, to the best of our knowledge, it has not been studied before. We show that a protein from extremophilic species with such a motif can fold; however, the supercoiling changes a smooth landscape observed in reduced conditions into a two-state folding process in the oxidative conditions, with a deep intermediate state. The protein takes advantage of the hairpinlike motif to overcome the topological barrier and thus to supercoil. We find that the depth of the supercoiling motif, i.e., the length of the threaded terminus, has a crucial impact on the folding rates of the studied protein. We show that fluctuations of the minimal surface area can be used to measure local stability, and we find that supercoiling introduces stability into the protein. We suggest that the supercoiling motif enables the studied protein to live in physically extreme conditions, which are detrimental to most life on Earth.

Pseudo Klein tunneling induced by zero Chern numbers in multiple-topological barriers silicene junction

We study spin-valley transport property in silicene-based N/TB1/TB2/TB3/N junction where N and TB i(i=1,2,3) are normal regions and topological barriers, respectively. The phase transitions in the TB regions may be controlled by applying perpendicular electric fields, the staggered exchange fields, and the circularly polarized light. When the Fermi level lies inside the gap, the topological phases in the barriers occur and may be classified by spin-valley Chern numbers. We find that the condition to give rise to spin-valley filtering effect satisfies zero values of sum of Chern numbers over all topological barrier regions. Electron with specific spin and valley is allowed to transport when the summation of its spin-valley Chern numbers of all barriers is zero. Despite the system being massive fermions, tunneling without back reflection at zero angle of incidence is found only in the asymmetric junction, predicted at the condition of the zero Chern number. Interestingly, tunneling without back reflection for all angle of incidences, like perfect Klein tunneling, is found in the case of symmetric junction. This anomalous behavior may be called “pseudo Klein tunneling” because it is generated from massive fermions unlike actual Klein tunneling which is generated from massless fermions. The conductance of filtered electron in the symmetric junction cannot be tuned, while in case of asymmetric junction, it is still controllable by external forces. Our investigation reveals the effect of multiple-topological barriers on control of spin-valley filter which may be applicable for spin-valley based electronic devices.

Direct observation of the fast and robust folding of a slipknotted protein by optical tweezers.

Understanding the folding mechanism of knotted and slipknotted proteins has attracted considerable interest. Due to their topological complexity, knotted and slipknotted proteins are predicted to fold slowly and involve large topological barriers. Molecular dynamics simulation studies suggest that a slipknotted conformation can serve as an important intermediate to help greatly reduce the topological difficulty during the folding of some knotted proteins. Here we use a single molecule optical tweezers technique to directly probe the folding of a small slipknotted protein AFV3-109. We found that stretching AFV3-109 can lead to the untying of the slipknot and complete unfolding of AFV3-109. Upon relaxation, AFV3-109 can readily refold back to its native slipknot conformation with high fidelity when the stretching force is lower than 6 pN. The refolding of AFV3-109 occurs in a sharp two-state like transition. Our results indicate that, different from knotted proteins, the folding of a slipknotted protein like AFV3-109 can be fast, and may not necessarily involve a high topological barrier.

Deep Intraspecific Divergence in the Endemic Herb Lancea tibetica (Mazaceae) Distributed Over the Qinghai-Tibetan Plateau.

Qinghai-Tibetan Plateau (QTP) is an important biodiversity hub, which is very sensitive to climate change. Here in this study, we investigated genetic diversity and past population dynamics of Lancea tibetica (Mazaceae), an endemic herb to QTP and adjacent highlands. We sequenced chloroplast and nuclear ribosomal DNA fragments for 429 individuals, collected from 29 localities, covering their major distribution range at the QTP. A total of 19 chloroplast haplotypes and 13 nuclear genotypes in two well-differentiated lineages, corresponding to populations into two groups isolated by Tanggula and Bayangela Mountains. Meanwhile, significant phylogeographical structure was detected among sampling range of L. tibetica, and 61.50% of genetic variations was partitioned between groups. Gene flow across the whole region appears to be restricted by high mountains, suggesting a significant role of geography in the genetic differences between the two groups. Divergence time between the two lineages dated to 8.63 million years ago, which corresponded to the uplifting of QTP during the late Miocene and Pliocene. Ecological differences were found between both the lineages represent species-specific characteristics, sufficient to keep the lineages separated to a high degree. The simulated distribution from the last interglacial period to the current period showed that the distribution of L. tibetica experienced shrinkage and expansion. Climate changes during the Pleistocene glacial-interglacial cycles had a dramatic effect on L. tibetica distribution ranges. Multiple refugia of L. tibetica might have remained during the species history, to south of the Tanggula and north of Bayangela Mountains, both appeared as topological barrier and contributed to restricting gene flow between the two lineages. Together, geographic isolation and climatic factors have played a fundamental role in promoting diversification and evolution of L. tibetica.

Spin-valley and layer polarizations induced by topological phase transitions in bilayer silicene

We study spin-valley transport property in a single barrier bilayer silicene junction, where the barrier is under topological phase and controllable by electric field, staggered exchange field and off-resonant circularly polarized light. The tight binding model is adopted to describe the Hamiltonian. The ballistic transport through a topological barrier is investigated using the standard Landauer's formalism. The topological phases in bilayer silicene may be classified by spin-valley Chern numbers which is twice that in monolayer silicene. It is found that the four species of electron, two valley and two spin degrees of freedom, may be perfectly filtered. Electron having zero Chern number may allow to tunnel through the barrier, while the others are completely suppressed. This perfect spin-valley filter is due directly to topological phase transitions when staggered exchange field or off-resonant circularly polarized light is applied into the barrier. The perfect switching of layer (or pseudospin) polarization is predicted, allowed to control 100% carrier flowing only in top (or bottom) layer by electric field. The perfect switching from 100% to −100% of spin and valley polarizations is also found due to topological phase transition in the barrier. The result is quite different form transport property in bilayer graphene which lacks spin-orbit interaction and is planar atomic structure. This work reveals the potential of bilayer silicene as a topological material for spin-valleytronics.

Transcription profiling suggests that mitochondrial topoisomerase IB acts as a topological barrier and regulator of mitochondrial DNA transcription

Mitochondrial DNA (mtDNA) is essential for cell viability because it encodes subunits of the respiratory chain complexes. Mitochondrial topoisomerase IB (TOP1MT) facilitates mtDNA replication by removing DNA topological tensions produced during mtDNA transcription, but it appears to be dispensable. To test whether cells lacking TOP1MT have aberrant mtDNA transcription, we performed mitochondrial transcriptome profiling. To that end, we designed and implemented a customized tiling array, which enabled genome-wide, strand-specific, and simultaneous detection of all mitochondrial transcripts. Our technique revealed that Top1mt KO mouse cells process the mitochondrial transcripts normally but that protein-coding mitochondrial transcripts are elevated. Moreover, we found discrete long noncoding RNAs produced by H-strand transcription and encompassing the noncoding regulatory region of mtDNA in human and murine cells and tissues. Of note, these noncoding RNAs were strongly up-regulated in the absence of TOP1MT. In contrast, 7S DNA, produced by mtDNA replication, was reduced in the Top1mt KO cells. We propose that the long noncoding RNA species in the D-loop region are generated by the extension of H-strand transcripts beyond their canonical stop site and that TOP1MT acts as a topological barrier and regulator for mtDNA transcription and D-loop formation.

Entropic Interactions between Two Knots on a Semiflexible Polymer.

Two knots on a string can either be separated or intertwined, and may even pass through each other. At the microscopic scale, such transitions may occur spontaneously, driven by thermal fluctuations, and can be associated with a topological free energy barrier. In this manuscript, we study the respective location of a trefoil () and a figure-eight () knot on a semiflexible polymer, which is parameterized to model dsDNA in physiological conditions. Two cases are considered: first, end monomers are grafted to two confining walls of varying distance. Free energy profiles and transition barriers are then compared to a subset of free chains, which contain exactly one and one knot. For the latter, we observe a small preference to form an intertwined state, which can be associated with an effective entropic attraction. However, the respective free energy barrier is so small that we expect transition events to occur spontaneously and frequently in polymers and DNA, which are highly knotted for sufficient strain lengths.

Protein-induced DNA linking number change by sequence-specific DNA binding proteins and its biological effects.

Sequence-specific DNA-binding proteins play essential roles in many fundamental biological events such as DNA replication, recombination, and transcription. One common feature of sequence-specific DNA-binding proteins is to introduce structural changes to their DNA recognition sites including DNA-bending and DNA linking number change (ΔLk). In this article, I review recent progress in studying protein-induced ΔLk by several sequence-specific DNA-binding proteins, such as E. coli cAMP receptor protein (CRP) and lactose repressor (LacI). It was demonstrated recently that protein-induced ΔLk is an intrinsic property for sequence-specific DNA-binding proteins and does not correlate to protein-induced other structural changes, such as DNA bending. For instance, although CRP bends its DNA recognition site by 90°, it was not able to introduce a ΔLk to it. However, LacI was able to simultaneously bend and introduce a ΔLk to its DNA binding sites. Intriguingly, LacI also constrained superhelicity within LacI-lac O1 complexes if (-) supercoiled DNA templates were provided. I also discuss how protein-induced ΔLk help sequence-specific DNA-binding proteins regulate their biological functions. For example, it was shown recently that LacI utilizes the constrained superhelicity (ΔLk) in LacI-lac O1 complexes and serves as a topological barrier to constrain free, unconstrained (-) supercoils within the 401-bp DNA loop. These constrained (-) supercoils enhance LacI's binding affinity and therefore the repression of the lac promoter. Other biological functions include how DNA replication initiators λ O and DnaA use the induced ΔLk to open/melt bacterial DNA replication origins.

Protein-induced DNA linking number change by sequence-specific DNA binding proteins and its biological effects.

Sequence-specific DNA-binding proteins play essential roles in many fundamental biological events such as DNA replication, recombination, and transcription. One common feature of sequence-specific DNA-binding proteins is to introduce structural changes to their DNA recognition sites including DNA-bending and DNA linking number change (ΔLk). In this article, I review recent progress in studying protein-induced ΔLk by several sequence-specific DNA-binding proteins, such as E. coli cAMP receptor protein (CRP) and lactose repressor (LacI). It was demonstrated recently that protein-induced ΔLk is an intrinsic property for sequence-specific DNA-binding proteins and does not correlate to protein-induced other structural changes, such as DNA bending. For instance, although CRP bends its DNA recognition site by 90°, it was not able to introduce a ΔLk to it. However, LacI was able to simultaneously bend and introduce a ΔLk to its DNA binding sites. Intriguingly, LacI also constrained superhelicity within LacI-lac O1 complexes if (-) supercoiled DNA templates were provided. I also discuss how protein-induced ΔLk help sequence-specific DNA-binding proteins regulate their biological functions. For example, it was shown recently that LacI utilizes the constrained superhelicity (ΔLk) in LacI-lac O1 complexes and serves as a topological barrier to constrain free, unconstrained (-) supercoils within the 401-bp DNA loop. These constrained (-) supercoils enhance LacI's binding affinity and therefore the repression of the lac promoter. Other biological functions include how DNA replication initiators λ O and DnaA use the induced ΔLk to open/melt bacterial DNA replication origins.

Direct Observation of the Folding Trajectory of a Slipknotted Protein

Over the last two decades, as a surprising feature for proteins, knotted/slipknotted topology has been found in certain proteins. Such knotted/slipknotted proteins need to overcome the topological difficulty in order to reach their functional native states. It is challenging to understand the folding mechanism of such proteins. AFV3-109 is a small alpha/beta protein containing a slipknot. In our previous studies, we have shown that stretching AFV3-109 from its N-C termini can readily lead to the unfolding of AFV3-109 and untying the slipknotted structure. However, it has been challenging to monitor the folding process of AFV3-109 from its unfolded conformation enroute to its slipknotted native state. Here use single molecule optical tweezers to investigate the folding process of AFV3-109. Using constant velocity mode, we found that unfolded AFV3-109, which was prepared by mechanically stretching from its both termini, can readily refold at a force of ∼4 pN or lower to its native state with the slipknot conformation. The refolding of most AFV3-109 occurs in a sharp transition (with a time resolution of ∼50 us), indicative of a two-state like transition without the accumulation of intermediate states. The apparent ease of such a folding into the slipknotted conformation for most AFV3019 suggests the topological barrier is not high for forming a protein slipknot under the experimental setting. Moreover, we observed that a small fraction of unfolded AFV3-109 molecules refold into the native state via a continuous folding trajectory, suggesting a more complex refolding pathway. These results open the avenue towards understanding of the folding mechanism of slipknotted and knotted proteins.

DNA supercoiling, a critical signal regulating the basal expression of the lac operon in Escherichia coli.

Escherichia coli lac repressor (LacI) is a paradigmatic transcriptional factor that controls the expression of lacZYA in the lac operon. This tetrameric protein specifically binds to the O1, O2 and O3 operators of the lac operon and forms a DNA loop to repress transcription from the adjacent lac promoter. In this article, we demonstrate that upon binding to the O1 and O2 operators at their native positions LacI constrains three (−) supercoils within the 401-bp DNA loop of the lac promoter and forms a topological barrier. The stability of LacI-mediated DNA topological barriers is directly proportional to its DNA binding affinity. However, we find that DNA supercoiling modulates the basal expression from the lac operon in E. coli. Our results are consistent with the hypothesis that LacI functions as a topological barrier to constrain free, unconstrained (−) supercoils within the 401-bp DNA loop of the lac promoter. These constrained (−) supercoils enhance LacI’s DNA-binding affinity and thereby the repression of the promoter. Thus, LacI binding is superhelically modulated to control the expression of lacZYA in the lac operon under varying growth conditions.