Topological Linkage Research Articles

Single-molecule analysis of solvent-responsive mechanically interlocked ring polymers and the effects of nanoconfinement from coarse-grained simulations.

In this study, we simulate mechanically interlocked semiflexible ring polymers inspired by the minicircles of kinetoplast DNA (kDNA) networks. Using coarse-grained molecular dynamics simulations, we investigate the impact of molecular topological linkage and nanoconfinement on the conformational properties of two- and three-ring polymer systems in varying solvent qualities. Under good-quality solvents, for two-ring systems, a higher number of crossing points lead to a more internally constrained structure, reducing their mean radius of gyration. In contrast, three-ring systems, which all had the same crossing number, exhibited more similar sizes. In unfavorable solvents, structures collapse, forming compact configurations with increased contacts. The morphological diversity of structures primarily arises from topological linkage rather than the number of rings. In three-ring systems with different topological conformations, structural uniformity varies based on link types. Extreme confinement induces isotropic and extended conformations for catenated polymers, aligning with experimental results for kDNA networks and influencing the crossing number and overall shape. Finally, the flat-to-collapse transition in extreme confinement occurs earlier (at relatively better solvent conditions) compared to non-confined systems. This study offers valuable insights into the conformational behavior of mechanically interlocked ring polymers, highlighting challenges in extrapolating single-molecule analyses to larger networks such as kDNA.

Topological Ordering of Memory Glass on Extended Length Scales.

Identifying ordering in non-crystalline solids has been a focus of natural science since the publication of Zachariasen's random network theory in 1932, but it still remains as a great challenge of the century. Literature shows that the hierarchical structures, from the short-range order of first-shell polyhedra to the long-range order of translational periodicity, may survive after amorphization. Here, in a piece of AlPO4, or berlinite, we combine X-ray diffraction and stochastic free-energy surface simulations to study its phase transition and structural ordering under pressure. From reversible single crystals to amorphous transitions, we now present an unambiguous view of the topological ordering in the amorphous phase, consisting of a swarm of Carpenter low-symmetry phases with the same topological linkage, trapped in a metastable intermediate stage. We propose that the remaining topological ordering is the origin of the switchable "memory glass" effect. Such topological ordering may hide in many amorphous materials through disordered short atomic displacements.

Topological linkage disequilibrium calculated from coalescent genealogies

We revisit the classical, and introduce a novel, concept of two-locus linkage disequilibrium (LD). In contrast to defining haplotypes as allele combinations at two marker loci, we concentrate on the clustering of a sample of chromosomes induced by their coalescent genealogy. The root of a binary coalescent tree defines two clusters of chromosomes, each one of them containing the left and right descendants of the root. At two different loci this assignment may be different as a result of recombination. We show that the proportion of shared chromosomes among clusters at two different loci, measured by the squared correlation, constitutes a natural measure of LD. We call this topological LD (tLD) since it is induced by the topology of the coalescent tree. We find that it is, on average, larger than classical LD for any given distance between loci. Furthermore, tLD has a smaller coefficient of variation, which should provide an advantage, compared to the use of classical LD, for any kind of mapping purposes. We conclude with a practical application to the LCT region in human populations.

Detecting TF-miRNA-gene network based modules for 5hmC and 5mC brain samples: a intra- and inter-species case-study between human and rhesus

BackgroundStudy of epigenetics is currently a high-impact research topic. Multi stage methylation is also an area of high-dimensional prospect. In this article, we provide a new study (intra and inter-species study) on brain tissue between human and rhesus on two methylation cytosine variants based data-profiles (viz., 5-hydroxymethylcytosine (5hmC) and 5-methylcytosine (5mC) samples) through TF-miRNA-gene network based module detection.ResultsFirst of all, we determine differentially 5hmC methylated genes for human as well as rhesus for intra-species analysis, and differentially multi-stage methylated genes for inter-species analysis. Thereafter, we utilize weighted topological overlap matrix (TOM) measure and average linkage clustering consecutively on these genesets for intra- and inter-species study.We identify co-methylated and multi-stage co-methylated gene modules by using dynamic tree cut, for intra-and inter-species cases, respectively. Each module is represented by individual color in the dendrogram. Gene Ontology and KEGG pathway based analysis are then performed to identify biological functionalities of the identified modules. Finally, top ten regulator TFs and targeter miRNAs that are associated with the maximum number of gene modules, are determined for both intra-and inter-species analysis.ConclusionsThe novel TFs and miRNAs obtained from the analysis are: MYST3 and ZNF771 as TFs (for human intra-species analysis), BAZ2B, RCOR3 and ATF1 as TFs (for rhesus intra-species analysis), and mml-miR-768-3p and mml-miR-561 as miRs (for rhesus intra-species analysis); and MYST3 and ZNF771 as miRs(for inter-species study). Furthermore, the genes/TFs/miRNAs that are already found to be liable for several brain-related dreadful diseases as well as rare neglected diseases (e.g., wolf Hirschhorn syndrome, Joubarts Syndrome, Huntington’s disease, Simian Immunodeficiency Virus(SIV) mediated enchaphilits, Parkinsons Disease, Bipolar disorder and Schizophenia etc.) are mentioned.

Topological Linkage of DNA Tiles Bonded by Paranemic Cohesion.

Catenation is the process by which cyclic strands are combined like the links of a chain, whereas knotting changes the linking properties of a single strand. In the cell, topoisomerases catalyzing strand passage operations enable the knotting and catenation of DNA so that single- or double-stranded segments can be passed through each other. Here, we use a system of closed DNA structures involving a paranemic motif, called PX-DNA, to bind double strands of DNA together. These PX-cohesive closed molecules contain complementary loops whose linking by Escherichia coli topoisomerase 1 (Topo 1) leads to various types of catenated and knotted structures. We were able to obtain specific DNA topological constructs by varying the lengths of the complementary tracts between the complementary loops. The formation of the structures was analyzed by denaturing gel electrophoresis, and the various topologies of the constructs were characterized using the program Knotilus.

Boundary singularities produced by the motion of soap films.

Recent work has shown that a Möbius strip soap film rendered unstable by deforming its frame changes topology to that of a disk through a "neck-pinching" boundary singularity. This behavior is unlike that of the catenoid, which transitions to two disks through a bulk singularity. It is not yet understood whether the type of singularity is generally a consequence of the surface topology, nor how this dependence could arise from an equation of motion for the surface. To address these questions we investigate experimentally, computationally, and theoretically the route to singularities of soap films with different topologies, including a family of punctured Klein bottles. We show that the location of singularities (bulk or boundary) may depend on the path of the boundary deformation. In the unstable regime the driving force for soap-film motion is the mean curvature. Thus, the narrowest part of the neck, associated with the shortest nontrivial closed geodesic of the surface, has the highest curvature and is the fastest moving. Just before onset of the instability there exists on the stable surface the shortest closed geodesic, which is the initial condition for evolution of the neck's geodesics, all of which have the same topological relationship to the frame. We make the plausible conjectures that if the initial geodesic is linked to the boundary, then the singularity will occur at the boundary, whereas if the two are unlinked initially, then the singularity will occur in the bulk. Numerical study of mean curvature flows and experiments support these conjectures.

The Mitochondrial Intermembrane Space Oxireductase Mia40 Funnels the Oxidative Folding Pathway of the Cytochrome c Oxidase Assembly Protein Cox19

Mia40-catalyzed disulfide formation drives the import of many proteins into the mitochondria. Here we characterize the oxidative folding of Cox19, a twin CX9C Mia40 substrate. Cox19 oxidation is extremely slow, explaining the persistence of import-competent reduced species in the cytosol. Mia40 accelerates Cox19 folding through the specific recognition of the third Cys in the second helical CX9C motif and the subsequent oxidation of the inner disulfide bond. This renders a native-like intermediate that oxidizes in a slow uncatalyzed reaction into native Cox19. The same intermediate dominates the pathway in the absence of Mia40, and chemical induction of an α-helical structure by trifluoroethanol suffices to accelerate productive folding and mimic the Mia40 folding template mechanism. The Mia40 role is to funnel a rough folding landscape, skipping the accumulation of kinetic traps, providing a rationale for the promiscuity of Mia40.

A family of double-layered coordination polymers containing Cd2+, N,O-chelating ligands, and bridging SCN− and Cl−

The syntheses, structures, and characterization (IR, TGA/DTA) of a family of layered coordination polymers containing Cd2+, bridging anions (SCN− and Cl−), and chelating C2H6N2O2 methyl carbazate (mc) and C3H8N2O2 ethyl carbazate (ec) ligands are described, viz: Cd(SCN)2(C2H6N2O2), Cd(SCN)Cl(C2H6N2O2), Cd(SCN)2(C3H8N2O2), and Cd(SCN)Cl(C3H8N2O2). Single-crystal structures show them to contain distorted CdN3OS2 (for the thiocyanate) and CdN2OCl2S (for the thiocyanate/chloride) octahedra, in which the mc and ec ligands adopt an N,O-bidentate coordination mode, and the four anions bridge adjacent metal ions, which leads to polymeric sheets built up from double-octahedral layers propagating in the (1 0 0) plane. The topological linkage of the metal ions, which is the same in each structure, can be described as a distorted hexagonal grid. The crystal structures are completed by weak N–H⋯O, N–H⋯N, N–H⋯Cl, and N–H⋯S hydrogen bonds, which all occur within the (1 0 0) polyhedral layers.

Stimuli-degradable cross-linked polymers synthesized by radical polymerization using a size-complementary [3]rotaxane cross-linker

Stimuli-degradable cross-linked polymers were developed by applying both topological linkage and size complementarity of rotaxane to cross-link their structures. A double vinyl group-tethering [3]rotaxane cross-linker was prepared by reacting the axle ends of sec-ammonium/crown ether-type pseudo[3]rotaxane with a suitably bulky end-cap agent that was as large as the cavity of the wheel. Radical polymerization of a common vinyl monomer in the presence of the [3]rotaxane cross-linker afforded the corresponding stable cross-linked polymer under ambient conditions. An anion exchange reaction with tetra(n-butyl)ammonium chloride caused selective and efficient de-cross-linking of the cross-linked polymers to the vinyl polymer and the axle component of the cross-linker. Stimuli-degradable cross-linked polymers were developed by applying both topological linkage and size-complementarity of rotaxane to cross-link structure. Radical polymerization of a common vinyl monomer in the presence of the [3]rotaxane cross-linker gave the corresponding stable cross-linked polymer under ambient conditions. Anion exchange reaction with tetra(n-butyl)ammonium chloride caused the selective and efficient de-cross-linking of the cross-linked polymers to vinyl polymer and axle component of the cross-linker.

A Single Cohesin Complex Performs Mitotic and Meiotic Functions in the Protist Tetrahymena

The cohesion of sister chromatids in the interval between chromosome replication and anaphase is important for preventing the precocious separation, and hence nondisjunction, of chromatids. Cohesion is accomplished by a ring-shaped protein complex, cohesin; and its release at anaphase occurs when separase cleaves the complex's α-kleisin subunit. Cohesin has additional roles in facilitating DNA damage repair from the sister chromatid and in regulating gene expression. We tested the universality of the present model of cohesion by studying cohesin in the evolutionarily distant protist Tetrahymena thermophila. Localization of tagged cohesin components Smc1p and Rec8p (the α-kleisin) showed that cohesin is abundant in mitotic and meiotic nuclei. RNAi knockdown experiments demonstrated that cohesin is crucial for normal chromosome segregation and meiotic DSB repair. Unexpectedly, cohesin does not detach from chromosome arms in anaphase, yet chromosome segregation depends on the activity of separase (Esp1p). When Esp1p is depleted by RNAi, chromosomes become polytenic as they undergo multiple rounds of replication, but fail to separate. The cohesion of such bundles of numerous chromatids suggests that chromatids may be connected by factors in addition to topological linkage by cohesin rings. Although cohesin is not detected in transcriptionally active somatic nuclei, its loss causes a slight defect in their amitotic division. Notably, Tetrahymena uses a single version of α-kleisin for both mitosis and meiosis. Therefore, we propose that the differentiation of mitotic and meiotic cohesins found in most other model systems is not due to the need of a specialized meiotic cohesin, but due to additional roles of mitotic cohesin.

Crystal structures of λ exonuclease in complex with DNA suggest an electrostatic ratchet mechanism for processivity

The λ exonuclease is an ATP-independent enzyme that binds to dsDNA ends and processively digests the 5'-ended strand to form 5' mononucleotides and a long 3' overhang. The crystal structure of λ exonuclease revealed a toroidal homotrimer with a central funnel-shaped channel for tracking along the DNA, and a mechanism for processivity based on topological linkage of the trimer to the DNA was proposed. Here, we have determined the crystal structure of λ exonuclease in complex with DNA at 1.88-Å resolution. The structure reveals that the enzyme unwinds the DNA prior to cleavage, such that two nucleotides of the 5'-ended strand insert into the active site of one subunit of the trimer, while the 3'-ended strand passes through the central channel to emerge out the back of the trimer. Unwinding of the DNA is facilitated by several apolar residues, including Leu78, that wedge into the base pairs at the single/double-strand junction to form favorable hydrophobic interactions. The terminal 5' phosphate of the DNA binds to a positively charged pocket buried at the end of the active site, while the scissile phosphate bridges two active site Mg(2+) ions. Our data suggest a mechanism for processivity in which wedging of Leu78 and other apolar residues into the base pairs of the DNA restricts backward movement, whereas attraction of the 5' phosphate to the positively charged pocket drives forward movement of the enzyme along the DNA at each cycle of the reaction. Thus, processivity of λ exonuclease operates not only at the level of the trimer, but also at the level of the monomer.

The structure of a ring-opened proliferating cell nuclear antigen–replication factor C complex revealed by fluorescence energy transfer

Numerous proteins that function in DNA metabolic pathways are known to interact with the proliferating cell nuclear antigen (PCNA). The important function of PCNA in stimulating various cellular activities requires its topological linkage with DNA. Loading of the circular PCNA onto duplex DNA requires the activity of a clamp-loader [replication factor C (RFC)] complex and the energy derived from ATP hydrolysis. The mechanistic and structural details regarding PCNA loading by the RFC complex are still developing. In particular, the positive identification of a long-hypothesized structure of an open clamp-RFC complex as an intermediate in loading has remained elusive. In this study, we capture an open yeast PCNA clamp in a complex with RFC through fluorescence energy transfer experiments. We also follow the topological transitions of PCNA in the various steps of the clamp-loading pathway through both steady-state and stopped-flow fluorescence studies. We find that ATP effectively drives the clamp-loading process to completion with the formation of the closed PCNA bound to DNA, whereas ATPgammaS cannot. The information derived from this work complements that obtained from previous structural and mechanistic studies and provides a more complete picture of a eukaryotic clamp-loading pathway using yeast as a paradigm.

Targeting of cohesin by transcriptionally silent chromatin

Eukaryotic DNA replication produces sister chromatids that are linked together until anaphase by cohesin, a ring-shaped protein complex that is thought to act by embracing both chromatids. Cohesin is enriched at centromeres, as well as discrete sites along chromosome arms where transcription positions the complex between convergent gene pairs. A relationship between cohesin and Sir-mediated transcriptional silencing has also begun to emerge. Here we used fluorescence microscopy and site-specific recombination to characterize interactions between newly replicated copies of the silent HMR mating-type locus. HMR was tagged with lac-GFP and flanked by binding sites for an inducible site-specific recombinase. Excision of the locus in cells with sister chromatids produced two chromatin circles that remained associated with one another. Pairing of the circles required silent chromatin, cohesin, and the RSC chromatin-remodeling complex. Chromatin immunoprecipitation showed that targeting of cohesin to the locus is Sir-dependent, and functional tests showed that silent chromatin acts in a continuous fashion to maintain cohesion. Remarkably, loss of silencing led to loss of cohesin from linear chromosomal templates but not from excised chromatin circles. The results are consistent with a model in which cohesin binds silent chromatin via topological linkage to individual chromatids.

Earrings and padlocks for the double helix: topological labeling of duplex DNA

Concatenation of hybridization probe with DNA target is crucial for highly localized detection of targeted sequences and might also be used in various gene-therapy applications. Several approaches based on the attachment of a circular oligonucleotide to designated DNA sites have been proposed. Recently, earring-like probes provide a true topological linkage between a probe and the target, thus allowing the DNA labeling by essentially immobile tags. The latest development in this direction takes advantage of oligonucleotide uptake by supercoiled DNA and is an important step forward.

Topologically Non-linked Circular Duplex DNA

The discovery of circular DNA, over 30 years ago, introduced an element of uneasiness in what had been, up to that point, the almost picture-perfect story of the elucidation of the molecular biology of heredity. If DNA indeed has the Watson–Crick right-handed helical secondary structure, then in circular DNA, thousands, or perhaps even millions of twists must be removed in each generation, and re-wound in the next generation. Although enzyme systems adequate for this task have long since been found and characterized, there have nevertheless arisen a number of proposals for alternative DNA structures in which the strands are topologically non-linked, so that they might separate during replication without having to be unwound. These structures have generally been put forth as theory only, and have been largely unaccompanied by experimental evidence to support their applicability to native DNA from living systems. Recently, however, a report has emerged suggesting that it might be possible to separate, intact, the individual single-stranded circular half-chromosomes which constitute the double-stranded circular chromosomes of certain plasmids. This would not be possible unless the chromosomes had one of the alternative, topologically non-linked structures. It is widely believed that after a half-century of worldwide DNA research, any significant change to the Watson–Crick structure is unlikely to stand up to scrutiny. Nevertheless, the present author has found that in many instances in which the behavior of circular duplex DNA is considered to be explicable only in terms of the topologically linked helical model, it is also possible to explain that same behavior in terms of a topologically non-linked model. It is necessary, in these instances, to make certain logical assumptions which cannot be conclusively proven at the present time. The author herein offers an example of one such instance, namely an examination of the behavior of circular duplex DNA in an alkaline titration experiment, where conformational changes in DNA are deduced from changes in its buoyant density at pH’s between 7 and 14. These data have been explained in terms of topological linkage between the DNA strands, but they can also be explained without invoking any such topological linkage, provided that the above-mentioned logical assumptions can be accepted. The principles which emerge from this are applicable to other settings in which knowledge of the topology of DNA is critical to the understanding of observed phenomena.

The Mu Enhancer Is Functionally Asymmetric Both incis and in trans: TOPOLOGICAL SELECTIVITY OF Mu TRANSPOSITION IS ENHANCER-INDEPENDENT

Mu DNA transposition from a negatively supercoiled DNA substrate requires interaction of an enhancer element with the left (attL) and right (attR) ends of Mu. The orientation of the L and R ends with respect to each other (inverted) and with respect to the enhancer is normally inviolate. We show that when the enhancer is provided in trans as a linear fragment, the head to head orientation of the L/R ends is still required. Each functional half of the linear enhancer maintains the same "cross-wise" interaction with the subsites L1 and R1, when present in cis or in trans. In reactions catalyzed by an enhancer-independent variant of the Mu transposase, the need for negative supercoiling of the substrate and the inverted orientation of L and R ends is not relaxed. These results show that the orientation specificity of the enhancer is not determined by its topological linkage to the Mu ends. There is a functional asymmetry inherent to the enhancer. Furthermore, the enhancer does not directly impose topological constraints on the transposition reaction or specify the reactive orientation of the Mu ends.

DNA and RNA Folds in Transcription Complex as Evidenced by Iodine-125 Radioprobing

Folding of the DNA and RNA strands in an arrested T7 RNA polymerase (RNAP) transcription complex was studied by radioprobing, a novel method based on an analysis of the strand breaks produced by decay of the iodine-125 incorporated at the C5 position of cytosine. 125I-labeled cytosines were incorporated into transcripts at different positions relative to the site of the arrest. The intensities of the DNA breaks inversely correlate with the distances from the 125I decay site, so the radioprobing data provide information about the spatial RNA/DNA folding during transcription. We found that the yield of DNA strand breaks is significantly higher in the template than the non-template strand. This is consistent with local opening of the DNA duplex and formation of a hybrid between RNA and the template DNA strand. Our data demonstrate that the RNA-DNA hybrid has a nonuni form A-like structure. When the 125I is incorporatedseven nucleotides from the active center of RNAP, the yield of strand breaks is substantially lower than if 125I is positioned at the ends of the hybrid. Consequently, the DNA and RNA strands are located closer to each other at the ends of the hybrid and somehow separated in the middle. Surprisingly, the 125I-induced breaks were detected in both DNA strands upstream from the transcription “bubble” indicating that DNA and RNA are closely associated outside the RNAP cleft. Thus, radioprobing data imply that the RNA/DNA fold in the complex with T7 RNAP is more complicated than had been anticipated by the existing models. Based on the present data, we suggest a sterically feasible model explaining how formation of the long RNA-DNA hybrid can result in the initiation-to-elongation switch in the T7 transcription complex. According to this model, the topological linkage between the DNA and RNA strands provides the necessary stability for the elongation complex, while permitting movement of the polymerase along the DNA duplex.

An Earring for the Double Helix: Assembly of Topological Links Comprising Duplex DNA and a Circular Oligodeoxynucleotide

Novel DNA nanostructures, locked pseudorotaxane and locked catenane were assembled through topological linkage of a double-stranded target to a circular oligodeoxyribonucleotide (cODN)+. The formation of these supramolecular complexes occurs with remarkable sequence specificity and is accomplished via local opening of duplex DNA by a pair of homopyrimidine bis-PNAs. The obtained cODN label, resembling an earring, forms a true topological link with the linear or closed circular (cc) target DNA and occupies a fixed position along the double helix. The PNA directed assembly described here introduces PNA oligomers into the repertoire of DNA nanotechnological tools.

Outside-in: an alternative approach to forest map digitizing

ABSTRACT Abstract. This paper examines the problem of polygon digitizing, and suggests an inversion of the traditional approach for polygons of the environmental type, where each individual polygon, rather than its boundaries, is of primary interest. Many workers in geology, forestry, soil science, etc. have found the tedious specification of boundary arcs and their topological linkage and editing to be a major block to productivity. An alternative digitizing approach is described using Thiessen/Voronoi polygons to generate topology automatically and to reduce map digitizing times significantly. The digitizing of representative points within each polygon is performed using the GIS. The stand-alone Voronoi polygon building and boundary extraction module then generates linked arcs that are returned to the GIS for further analysis. Examples of the productivity enhancement in a production environment are given, along with the algorithms used.

The Genealogy of GIS Studies and the Concept of Topological Space

1. GIS studies and the quantitative revolution in geographyThe early development of GIS studies originated at the University of Washington in which the quantitative revolution in geography took place in the late 1950's. Garrison's students including Bunge, W., Tobler, W. R. and Marble, D. F. had the original leadership in GIS study and have driven the top level initiatives for GIS development. The Garrison School was divided into two parties by different analytical concepts and approaches. One was a quantitative statistical geography whose conceptual keywords were spatial structure, spatial process and spatial interaction in Newtonian space, and the other was GIS studies based on topological space concepts.By the early 1970's, GIS studies were not dominant when compared with statistical analysis in geography because of the lack of technology in graphical facilities. But from the late 1970's GIS studies have been increasing by the development of some computer graphics technologies.2. GIS studies in the 1960's and 1970'sIn the late 1960's, the development of DIME files had a special influence in terms of topological data structure, geocoding and addressmatching. Fisher, H. made an important contribution to GIS study from the late 1960's to the middle 1970's and established the Harverd Laboratory for Computer Graphics and Spatial Analysis in which ODES-SEY as Vector GIS was desigend. A significant symposium about topological data structure was held in 1977 at this laboratory. The results of the symposium were published as Harvard Papers on Geographic Information System edited by Dutton, G. in 1978.A vector GIS model was traced to CGIS (Canada Geographic Information System) which Tomlinson, H. R. designed in the early 1960's. This vector model means that the space was defined by the set of spatial objects such as points, lines, and polygons with topological linkage and connection.A Raster GIS model also was developed in the 1970's in the field of grobal environmental studies such as environmental monitoring systems and resource management using remote sensing technology and Landsat data in large national projects.3. Systematization of GIS studies in the 1980's and 1990's and the concept of topological spaceWe can recognize the spatial patterns and shapes of geographic entities on a map which represents what we see and know about the real world as one of models of the surface of the earth. The nature of a map as a model of the real world that depends on the concept of space demonstrates a variety of underlying conceptual frameworks. Geographical spatial models are based on the concepts of absolute space or Newtonian space. In particular, since quantitative geography was advocated, it has been important to measure distance between geographical entities and to make a distance based spatial model using Euclidean geometry.But with the progress in GIS studies, spatial data structure stored as a database in a computer has been drastically shifted from a Euclidean space concept to a topological space concept. The concepts of topological space and topologically spatial analysis were made clear in the context of GIS Spatial Data Models in the 1980's and 1990's.