Form factor of helical structures and twisted fibres

A general formalism is presented for the isotropically averaged single-chain scattering function (form factor) of single, double, triple and higher-order helices, as well as twisted fibres consisting of concentric layers of strands. Form factors for double and triple helices with differently sized grooves have also been derived. The formulas include the longitudinal and transverse interference over the pitch and radius of the helices, respectively. The results may be useful for the analysis of small-angle scattering data of (bio)macromolecules or molecular assemblies exhibiting a helical arrangement.

Reconstituted TAD-size chromatin fibers feature heterogeneous nucleosome clusters

Large topologically associated domains (TADs) contain irregularly spaced nucleosome clutches, and interactions between such clutches are thought to aid the compaction of these domains. Here, we reconstituted TAD-sized chromatin fibers containing hundreds of nucleosomes on native source human and lambda-phage DNA and compared their mechanical properties at the single-molecule level with shorter ‘601’ arrays with various nucleosome repeat lengths. Fluorescent imaging showed increased compaction upon saturation of the DNA with histones and increasing magnesium concentration. Nucleosome clusters and their structural fluctuations were visualized in confined nanochannels. Force spectroscopy revealed not only similar mechanical properties of the TAD-sized fibers as shorter fibers but also large rupture events, consistent with breaking the interactions between distant clutches of nucleosomes. Though the arrays of native human DNA, lambda-phage and ‘601’ DNA featured minor differences in reconstitution yield and nucleosome stability, the fibers’ global structural and mechanical properties were similar, including the interactions between nucleosome clutches. These single-molecule experiments quantify the mechanical forces that stabilize large TAD-sized chromatin domains consisting of disordered, dynamically interacting nucleosome clutches and their effect on the condensation of large chromatin domains.

SARS-CoV-2 Spike Protein and Mouse Coronavirus Inhibit Biofilm Formation by Streptococcus pneumoniae and Staphylococcus aureus

The presence of co-infections or superinfections with bacterial pathogens in COVID-19 patients is associated with poor outcomes, including increased morbidity and mortality. We hypothesized that SARS-CoV-2 and its components interact with the biofilms generated by commensal bacteria, which may contribute to co-infections. This study employed crystal violet staining and particle-tracking microrheology to characterize the formation of biofilms by Streptococcus pneumoniae and Staphylococcus aureus that commonly cause secondary bacterial pneumonia. Microrheology analyses suggested that these biofilms were inhomogeneous soft solids, consistent with their dynamic characteristics. Biofilm formation by both bacteria was significantly inhibited by co-incubation with recombinant SARS-CoV-2 spike S1 subunit and both S1 + S2 subunits, but not with S2 extracellular domain nor nucleocapsid protein. Addition of spike S1 and S2 antibodies to spike protein could partially restore bacterial biofilm production. Furthermore, biofilm formation in vitro was also compromised by live murine hepatitis virus, a related beta-coronavirus. Supporting data from LC-MS-based proteomics of spike-biofilm interactions revealed differential expression of proteins involved in quorum sensing and biofilm maturation, such as the AI-2E family transporter and LuxS, a key enzyme for AI-2 biosynthesis. Our findings suggest that these opportunistic pathogens may egress from biofilms to resume a more virulent planktonic lifestyle during coronavirus infections. The dispersion of pathogens from biofilms may culminate in potentially severe secondary infections with poor prognosis. Further detailed investigations are warranted to establish bacterial biofilms as risk factors for secondary pneumonia in COVID-19 patients.

Mobility of Bacterial Protein Hfq on dsDNA: Role of C-Terminus-Mediated Transient Binding

The mobility of protein is fundamental in the machinery of life. Here, we have investigated the effect of DNA binding in conjunction with DNA segmental fluctuation (internal motion) of the bacterial Hfq master regulator devoid of its amyloid C-terminus domain. Hfq is one of the most abundant nucleoid associated proteins that shape the bacterial chromosome and is involved in several aspects of nucleic acid metabolism. Fluorescence microscopy has been used to track a C-terminus domain lacking mutant form of Hfq on double-stranded DNA, which is stretched by confinement to a rectangular nanofluidic channel. The mobility of the mutant is strongly accelerated with respect to the wild-type variant. Furthermore, it shows a reverse dependence on the internal motion of DNA, in that slower motion results in slower protein diffusion. The results demonstrate the subtle role of DNA internal motion in controlling the mobility of a nucleoid associated protein, and, in particular, the importance of transient binding and moving DNA strands out of the way.

Probing Amyloid-DNA Interaction with Nanofluidics

Nanofluidics is an emerging methodology to investigate single biomacromolecules without functionalization and/or attachment of the molecules to a substrate. In conjunction with fluorescence microscopy, it can be used to investigate structural and dynamical aspects of amyloid-DNA interaction. Here, we summarize the methodology for fabricating lab-on-chip devices in relatively cheap polymer resins and featuring quasi one-dimensional nanochannels with a cross-sectional diameter of tens to a few hundred nanometers. Site-specific staining of amyloid-forming protein Hfq with a fluorescence dye is also described. The methodology is illustrated with two application studies. The first study involves assembling bacterial amyloid proteins such as Hfq on double-stranded DNA and monitoring the folding and compaction of DNA in a condensed state. The second study is about the concerted motion of Hfq on DNA and how this is related to DNA's internal motion. Explicit details of procedures and workflows are given throughout.

Internal Motion of Chromatin Fibers Is Governed by Dynamics of Uncompressed Linker Strands

Chromatin compaction and internal motion are fundamental aspects of gene expression regulation. Here, we have investigated chromatin fibers comprising recombinant histone octamers reconstituted with double-stranded bacteriophage T4-DNA. The size of the fibers approaches the typical size of genomic topologically associated domains. Atomic force and fluorescence (correlation) microscopy have been used to assess the structural organization, histone-induced compaction, and internal motion. In particular, the fibers are stretched on arrays of nanochannels, each channel with a diameter of 60 or 125 nm. Major intrafiber segregation and fast internal fluctuations are observed. Full compaction was only achieved by triggering an attractive nucleosome interaction through the addition of magnesium cations. Besides compaction, histone complexation results in a dramatic decrease in the fiber's relaxation time. The relaxation times are similar to those of naked DNA with a comparable stretch, which indicates that internal motion is governed by the dynamics of uncompressed linker strands. Furthermore, the main reorganization process is association-dissociation of individually compacted regions. We surmise that the modulation of chromatin's internal motion by histone complexation might have implications for transcriptional bursting.

Role of Internal DNA Motion on the Mobility of a Nucleoid-Associated Protein

Protein transport on DNA is at the core of the machinery of life. Here we investigated the influence of DNA internal motion on the mobility of Hfq, which is involved in several aspects of nucleic acid metabolism and is one of the nucleoid-associated proteins that shape the bacterial chromosome. Fluorescence microscopy was used to follow Hfq on double-stranded DNA that was stretched by confinement to a channel with a diameter of 125 nm. The protein mobility shows a strong dependence on the internal motion of DNA in that slower motion results in faster protein diffusion. A model of released diffusion is proposed that is based on three-dimensional diffusion through the interior of the DNA coil interspersed by periods in which the protein is immobilized in a bound state. We surmise that the coupling between DNA internal motion and protein mobility has important implications for DNA metabolism and protein-binding-related regulation of gene expression.

Interactions between DNA and the Hfq Amyloid-like Region Trigger a Viscoelastic Response

Molecular transport of biomolecules plays a pivotal role in the machinery of life. Yet, this role is poorly understood due the lack of quantitative information. Here, the role and properties of the C-terminal region of Escherichia coli Hfq is reported, involved in controlling the flow of a DNA solution. A combination of experimental methodologies has been used to probe the interaction of Hfq with DNA and to measure the rheological properties of the complex. A physical gel with a temperature reversible elasticity modulus is formed due to the formation of noncovalent cross-links. The mechanical response of the complexes shows that they are inhomogeneous soft solids. Our experiments indicate that the Hfq C-terminal region could contribute to the genome's mechanical response. The reported viscoelasticity of the DNA-protein complex might have implications for cellular processes involving molecular transport of DNA or segments thereof.

Linearization and Labeling of Single-Stranded DNA for Optical Sequence Analysis

Genetic profiling would benefit from linearization of ssDNA through the exposure of the unpaired bases to gene-targeting probes. This is compromised by ssDNA's high flexibility and tendency to form self-annealed structures. Here, we demonstrate that self-annealing can be avoided through controlled coating with a cationic-neutral diblock polypeptide copolymer. Coating does not preclude site-specific binding of fluorescence labeled oligonucleotides. Bottlebrush-coated ssDNA can be linearized by confinement inside a nanochannel or molecular combing. A stretch of 0.32 nm per nucleotide is achieved inside a channel with a cross-section of 100 nm and a 2-fold excess of polypeptide with respect to DNA charge. With combing, the complexes are stretched to a similar extent. Atomic force microscopy of dried complexes on silica revealed that the contour and persistence lengths are close to those of dsDNA in the B-form. Labeling is based on hybridization and not limited by restriction enzymes. Enzyme-free labeling offers new opportunities for the detection of specific sequences.

Effect of HU protein on the conformation and compaction of DNA in a nanochannel

The effect of the heat unstable nucleoid structuring protein HU on the conformation of single DNA molecules confined in a nanochannel was investigated with fluorescence microscopy. Pre-incubated DNA molecules contract in the longitudinal direction of the channel with increasing concentration of HU. This contraction is mainly due to HU-mediated bridging of distal DNA segments and is controlled by channel diameter as well as ionic composition and strength of the buffer. For over-threshold concentrations of HU, the DNA molecules compact into an condensed form. Divalent magnesium ions facilitate, but are not required for bridging nor condensation. The conformational response following exposure to HU was investigated with a nanofluidic device that allows an in situ change in environmental solution conditions. The stretch of the nucleoprotein complex first increases, reaches an apex in ∼20 min, and subsequently decreases to an equilibrium value pertaining to pre-incubated DNA molecules after ∼2 h. This observation is rationalised in terms of a time-dependent bending rigidity by structural rearrangement of bound HU protein followed by compaction through bridging interaction. Results are discussed in regard to previous results obtained for nucleoid associated proteins H-NS and Hfq, with important implications for protein binding related gene regulation.

Compaction and condensation of DNA mediated by the C-terminal domain of Hfq

Hfq is a bacterial protein that is involved in several aspects of nucleic acids metabolism. It has been described as one of the nucleoid associated proteins shaping the bacterial chromosome, although it is better known to influence translation and turnover of cellular RNAs. Here, we explore the role of Escherichia coli Hfq's C-terminal domain in the compaction of double stranded DNA. Various experimental methodologies, including fluorescence microscopy imaging of single DNA molecules confined inside nanofluidic channels, atomic force microscopy, isothermal titration microcalorimetry and electrophoretic mobility assays have been used to follow the assembly of the C-terminal and N-terminal regions of Hfq on DNA. Results highlight the role of Hfq's C-terminal arms in DNA binding, change in mechanical properties of the double helix and compaction of DNA into a condensed form. The propensity for bridging and compaction of DNA by the C-terminal domain might be related to aggregation of bound protein and may have implications for protein binding related gene regulation.

Separation of superparamagnetic particles through ratcheted Brownian motion and periodically switching magnetic fields

Brownian ratchet based particle separation systems for application in lab on chip devices have drawn interest and are subject to ongoing theoretical and experimental investigations. We demonstrate a compact microfluidic particle separation chip, which implements an extended on-off Brownian ratchet scheme that actively separates and sorts particles using periodically switching magnetic fields, asymmetric sawtooth channel sidewalls, and Brownian motion. The microfluidic chip was made with Polydimethylsiloxane (PDMS) soft lithography of SU-8 molds, which in turn was fabricated using Proton Beam Writing. After bonding of the PDMS chip to a glass substrate through surface activation by oxygen plasma treatment, embedded electromagnets were cofabricated by the injection of InSn metal into electrode channels. This fabrication process enables rapid production of high resolution and high aspect ratio features, which results in parallel electrodes accurately aligned with respect to the separation channel. The PDMS devices were tested with mixtures of 1.51 μm, 2.47 μm, and 2.60 μm superparamagnetic particles suspended in water. Experimental results show that the current device design has potential for separating particles with a size difference around 130 nm. Based on the promising results, we will be working towards extending this design for the separation of cells or biomolecules.

Revisiting the Anomalous Bending Elasticity of Sharply Bent DNA

Several recent experiments suggest that sharply bent DNA has a surprisingly high bending flexibility, but the cause of this flexibility is poorly understood. Although excitation of flexible defects can explain these results, whether such excitation can occur with the level of DNA bending in these experiments remains unclear. Intriguingly, the DNA contained preexisting nicks in most of these experiments but whether nicks might play a role in flexibility has never been considered in the interpretation of experimental results. Here, using full-atom molecular dynamics simulations, we show that nicks promote DNA basepair disruption at the nicked sites, which drastically reduces DNA bending energy. In addition, lower temperatures suppress the nick-dependent basepair disruption. In the absence of nicks, basepair disruption can also occur but requires a higher level of DNA bending. Therefore, basepair disruption inside B-form DNA can be suppressed if the DNA contains preexisting nicks. Overall, our results suggest that the reported mechanical anomaly of sharply bent DNA is likely dependent on preexisting nicks, therefore the intrinsic mechanisms of sharply bent nick-free DNA remain an open question.

Structure of the H-NS-DNA nucleoprotein complex

Nucleoid associated proteins (NAPs) play a key role in the compaction and expression of the prokaryotic genome. Here we report the organisation of a major NAP, the protein H-NS on a double stranded DNA fragment. For this purpose we have carried out a small angle neutron scattering study in conjunction with contrast variation to obtain the contributions to the scattering (structure factors) from DNA and H-NS. The H-NS structure factor agrees with a heterogeneous, two-state binding model with sections of the DNA duplex surrounded by protein and other sections having protein bound to the major groove. In the presence of magnesium chloride, we observed a structural rearrangement through a decrease in cross-sectional diameter of the nucleoprotein complex and an increase in fraction of major groove bound H-NS. The two observed binding modes and their modulation by magnesium ions provide a structural basis for H-NS-mediated genome organisation and expression regulation.

Effects of Hfq on the conformation and compaction of DNA

Hfq is a bacterial pleiotropic regulator that mediates several aspects of nucleic acids metabolism. The protein notably influences translation and turnover of cellular RNAs. Although most previous contributions concentrated on Hfq's interaction with RNA, its association to DNA has also been observed in vitro and in vivo. Here, we focus on DNA-compacting properties of Hfq. Various experimental technologies, including fluorescence microscopy imaging of single DNA molecules confined inside nanofluidic channels, atomic force microscopy and small angle neutron scattering have been used to follow the assembly of Hfq on DNA. Our results show that Hfq forms a nucleoprotein complex, changes the mechanical properties of the double helix and compacts DNA into a condensed form. We propose a compaction mechanism based on protein-mediated bridging of DNA segments. The propensity for bridging is presumably related to multi-arm functionality of the Hfq hexamer, resulting from binding of the C-terminal domains to the duplex. Results are discussed in regard to previous results obtained for H-NS, with important implications for protein binding related gene regulation.

Dynamic remodeling of microbial biofilms by functionally distinct exopolysaccharides

Biofilms are densely populated communities of microbial cells protected and held together by a matrix of extracellular polymeric substances. The structure and rheological properties of the matrix at the microscale influence the retention and transport of molecules and cells in the biofilm, thereby dictating population and community behavior. Despite its importance, quantitative descriptions of the matrix microstructure and microrheology are limited. Here, particle-tracking microrheology in combination with genetic approaches was used to spatially and temporally study the rheological contributions of the major exopolysaccharides Pel and Psl in Pseudomonas aeruginosa biofilms. Psl increased the elasticity and effective cross-linking within the matrix, which strengthened its scaffold and appeared to facilitate the formation of microcolonies. Conversely, Pel reduced effective cross-linking within the matrix. Without Psl, the matrix becomes more viscous, which facilitates biofilm spreading. The wild-type biofilm decreased in effective cross-linking over time, which would be advantageous for the spreading and colonization of new surfaces. This suggests that there are regulatory mechanisms to control production of the exopolysaccharides that serve to remodel the matrix of developing biofilms. The exopolysaccharides were also found to have profound effects on the spatial organization and integration of P. aeruginosa in a mixed-species biofilm model of P. aeruginosa-Staphylococcus aureus. Pel was required for close association of the two species in mixed-species microcolonies. In contrast, Psl was important for P. aeruginosa to form single-species biofilms on top of S. aureus biofilms. Our results demonstrate that Pel and Psl have distinct physical properties and functional roles during biofilm formation. Importance: Most bacteria grow as biofilms in the environment or in association with eukaryotic hosts. Removal of biofilms that form on surfaces is a challenge in clinical and industrial settings. One of the defining features of a biofilm is its extracellular matrix. The matrix has a heterogeneous structure and is formed from a secretion of various biopolymers, including proteins, extracellular DNA, and polysaccharides. It is generally known to interact with biofilm cells, thus affecting cell physiology and cell-cell communication. Despite the fact that the matrix may comprise up to 90% of the biofilm dry weight, how the matrix properties affect biofilm structure, maturation, and interspecies interactions remain largely unexplored. This study reveals that bacteria can use specific extracellular polymers to modulate the physical properties of their microenvironment. This in turn impacts biofilm structure, differentiation, and interspecies interactions.

Buried centimeter-long micro- and nanochannel arrays in porous silicon and glass

We developed a simple process to fabricate deeply buried micro- and nanoscale channels in glass and porous silicon from bulk silicon using a combination of ion beam irradiation, electrochemical anodization and high temperature oxidation. The depth, width and length of these structures can be controllably varied and we successfully fabricated an array of centimeter-long buried micro- and nanochannels. This process allows densely packed, arbitrary-shaped channel geometries with micro- to nanoscale dimensions to be produced in a three-dimensional multilevel architecture, providing a route to fabricate complex devices for use in nanofluidics and lab-on-a-chip systems. We demonstrate the integration of these channels with large reservoirs for DNA linearization in high aspect ratio nanochannels.

Amplified stretch of bottlebrush-coated DNA in nanofluidic channels

The effect of a cationic-neutral diblock polypeptide on the conformation of single DNA molecules confined in rectangular nanochannels is investigated with fluorescence microscopy. An enhanced stretch along the channel is observed with increased binding of the cationic block of the polypeptide to DNA. A maximum stretch of 85% of the contour length can be achieved inside a channel with a cross-sectional diameter of 200 nm and at a 2-fold excess of polypeptide with respect to DNA charge. With site-specific fluorescence labelling, it is demonstrated that this maximum stretch is sufficient to map large-scale genomic organization. Monte Carlo computer simulation shows that the amplification of the stretch inside the nanochannels is owing to an increase in bending rigidity and thickness of bottlebrush-coated DNA. The persistence lengths and widths deduced from the nanochannel data agree with what has been estimated from the analysis of atomic force microscopy images of dried complexes on silica.

Effect of H-NS on the elongation and compaction of single DNA molecules in a nanospace

The effect of the bacterial heat-stable nucleoid-structuring protein (H-NS) on the conformation of single DNA molecules confined in a nanochannel was investigated with fluorescence microscopy. With increasing concentration of H-NS, the DNA molecules either elongate or contract. The conformational response is related to filamentation of H-NS on DNA through oligomerization and H-NS mediated bridging of distal DNA segments and is controlled by the concentration and ionic composition of the buffer. Confinement in a nanochannel also facilitates compaction of DNA into a condensed form for over-threshold concentrations of H-NS. Divalent ions such as magnesium facilitate but are not required for bridging nor condensation. The time scale of the collapse after exposure to H-NS was determined to be on the order of minutes, which is much shorter than the measured time required for filamentation of around one hour. We found that the effect of H-NS is not only related to its binding properties but also the confinement is of paramount importance. The interplay between confinement, H-NS-mediated attraction, and filamentation controls the conformation and compaction of DNA. This finding might have implications for gene silencing and chromosome organisation, because the cross-sectional dimensions of the channels are comparable to those of the bacterial nucleoid.

A nanofluidic device for single molecule studies with in situ control of environmental solution conditions

We report an approach to study the in situ conformational response of single biomolecules such as DNA to a change in environmental solution conditions. These conditions are, for example, the composition of the buffer or the presence of protein. For this purpose, we designed and fabricated a nanofluidic device featuring two arrays of parallel nanochannels in a perpendicular configuration. The cross-sections of the channels are rectangular with a diameter down to 175 nm. These lab-on-a-chip devices were made of polydimethylsiloxane (PDMS) cast on a high quality master stamp, obtained by proton beam writing and UV lithography. Biomolecules can be inserted into the device through the array of channels in one direction, whereas the buffer can be exchanged through the intersecting array of channels in the other direction. A buffer exchange time inside the grid of nanochannels of less than one second was measured by monitoring the conductivity of salt solutions. The exchange time of a protein was typically a few seconds, as determined by imaging the influx of fluorescence labelled protamine. We demonstrate the functionality of the device by investigating the compaction of DNA by protamine and the unpacking of pre-compacted DNA through an increase in the concentration of salt.

Time-dependent bending rigidity and helical twist of DNA by rearrangement of bound HU protein

HU is a protein that plays a role in various bacterial processes including compaction, transcription and replication of the genome. Here, we use atomic force microscopy to study the effect of HU on the stiffness and supercoiling of double-stranded DNA. First, we measured the persistence length, height profile, contour length and bending angle distribution of the DNA-HU complex after different incubation times of HU with linear DNA. We found that the persistence and contour length depend on the incubation time. At high concentrations of HU, DNA molecules first become stiff with a larger value of the persistence length. The persistence length then decreases over time and the molecules regain the flexibility of bare DNA after ∼2 h. Concurrently, the contour length shows a slight increase. Second, we measured the change in topology of closed circular relaxed DNA following binding of HU. Here, we observed that HU induces supercoiling over a similar time span as the measured change in persistence length. Our observations can be rationalized in terms of the formation of a nucleoprotein filament followed by a structural rearrangement of the bound HU on DNA. The rearrangement results in a change in topology, an increase in bending flexibility and an increase in contour length through a decrease in helical pitch of the duplex.

Revisiting blob theory for DNA diffusivity in slitlike confinement

Blob theory has been widely applied to describe polymer conformations and dynamics in nanoconfinement. In slit confinement, blob theory predicts a scaling exponent of 2/3 for polymer diffusivity as a function of slit height, yet a large body of experimental studies using DNA produce a scaling exponent significantly less than 2/3. In this work, we develop a theory that predicts that this discrepancy occurs because the segment correlation function for a semiflexible chain such as DNA does not follow the Flory exponent for length scales smaller than the persistence length. We show that these short length scale effects contribute significantly to the scaling for the DNA diffusivity, but do not appreciably affect the scalings for static properties. Our theory is fully supported by Monte Carlo simulations, quantitative agreement with DNA experiments, and the results reconcile this outstanding problem for confined polymers.

Intrachain dynamics of large dsDNA confined to slitlike channels

Exploration of intrachain hydrodynamics of dsDNA within channels has been limited to indirect analysis of global coil dynamics. In this Letter, we isolate hydrodynamic interactions within single molecules of dsDNA confined to slitlike channels by making use of density covariance measurements. We show that the strength of hydrodynamic interactions in DNA is dependent on the intrachain correlation length and that screening by symmetry in slitlike confinement results in a screening length that is proportional channel height. Moreover, we directly show the partial draining nature of the blobs formed by dsDNA in slits and predict under what conditions a dsDNA blob should obey nondraining Zimm behavior.

Bipedal nanowalker by pure physical mechanisms

Artificial nanowalkers are inspired by biomolecular counterparts from living cells, but remain far from comparable to the latter in design principles. The walkers reported to date mostly rely on chemical mechanisms to gain a direction; they all produce chemical wastes. Here we report a light-powered DNA bipedal walker based on a design principle derived from cellular walkers. The walker has two identical feet and the track has equal binding sites; yet the walker gains a direction by pure physical mechanisms that autonomously amplify an intrasite asymmetry into a ratchet effect. The nanowalker is free of any chemical waste. It has a distinct thermodynamic feature that it possesses the same equilibrium before and after operation, but generates a truly nonequilibrium distribution during operation. The demonstrated design principle exploits mechanical effects and is adaptable for use in other nanomachines.

High throughput fabrication of disposable nanofluidic lab-on-chip devices for single molecule studies

An easy method is introduced allowing fast polydimethylsiloxane (PDMS) replication of nanofluidic lab-on-chip devices using accurately fabricated molds featuring cross-sections down to 60 nm. A high quality master is obtained through proton beam writing and UV lithography. This master can be used more than 200 times to replicate nanofluidic devices capable of handling single DNA molecules. This method allows to fabricate nanofluidic devices through simple PDMS casting. The extensions of YOYO-1 stained bacteriophage T4 and λ-DNA inside these nanochannels have been investigated using fluorescence microscopy and follow the scaling prediction of a large, locally coiled polymer chain confined in nanochannels.

Conformation Model of Back-Folding and Looping of a Single DNA Molecule Confined Inside a Nanochannel

Currently, no theory is available to describe the conformation of DNA confined in a channel when the nanochannel diameter is around the persistence length. Back-folded hairpins in the undulating wormlike chain conformation result in the formation of loops, which reduces the stretch of the molecule in the longitudinal direction of the channel. A cooperativity model is used to quantify the frequency and size of the loop domains. The predictions agree with results from the Monte Carlo simulation.

Effect of Nanoslit Confinement on the Knotting Probability of Circular DNA

Monte Carlo simulations are used to study the knotting probability of circular DNA confined in a slit. We systematically vary the slit height, the width, and the contour length of the DNA molecule. We find that the trend in knotting probability with respect to slit height can be monotonic or nonmonotonic, depending on the width and contour length. The nonmonotonic trend is caused by two competing factors: the increase of the effective persistence length and the increase of segment density by slit confinement. These factors are antagonistic, in the sense that the increase in effective persistence length disfavors knot formation, whereas the increase in segment density favors the knotting probability. Our simulation results bring to light the importance of both chain length and width for slit-confined circular DNA and can be used to guide future experiments which aim to produce populations of knotted DNA through cyclization or catalyzed double-strand passage reactions in confinement.

A single-channel microparticle sieve based on Brownian ratchets

We present a novel device for the separation of microparticles in a single channel, which is made of inversely asymmetric Brownian ratchets. It enables separation into two different fractions with an adjustable threshold and can be modeled with good agreement. This device serves as proof of concept for an extremely compact class of microsieves.

MRP14 (S100A9) protein interacts with Alzheimer beta-amyloid peptide and induces its fibrillization

Increasing evidence supports the contribution of local inflammation to the development of Alzheimer's disease (AD) pathology, although the precise mechanisms are not clear. In this study, we demonstrate that the pro-inflammatory protein S100A9 interacts with the Aβ1-40 peptide and promotes the formation of fibrillar β-amyloid structures. This interaction also results in reduced S100A9 cytotoxicity by the binding of S100A9 toxic species to Aβ1-40 amyloid structures. These results suggest that secretion of S100A9 during inflammation promotes the formation of amyloid plaques. By acting as a sink for toxic species, plaque formation may be the result of a protective response within the brain of AD patients, in part mediated by S100A9.

Effect of nanochannel geometry on DNA structure in the presence of macromolecular crowding agent

We experimentally and numerically study the effects of macromolecular crowding agents on DNA structure when confined to a nanochannel. Curiously, DNA response to crowding is significantly different between bulk phase, nanoslit confinement, and nanotube confinement. Coarse grained Brownian dynamics simulations reproduce trends seen in the experiments and allow us to develop a deeper understanding of the key physics at play in these systems. It is proposed that the occupancy of free volume next to the channel wall by crowders causes an effective reduction in confining dimensions of the channel that initially swells DNA in nanoconfinement.

Control of the flow properties of DNA by topoisomerase II and its targeting inhibitor

The flow properties of DNA are important for understanding cell division and, indirectly, cancer therapy. DNA topology controlling enzymes such as topoisomerase II are thought to play an essential role. We report experiments showing how double-strand passage facilitated by topoisomerase II controls DNA rheology. For this purpose, we have measured the elastic storage and viscous loss moduli of a model system comprising bacteriophage λ-DNA and human topoisomerase IIα using video tracking of the Brownian motion of colloidal probe particles. We found that the rheology is critically dependent on the formation of temporal entanglements among the DNA molecules with a relaxation time of ∼1 s. We observed that topoisomerase II effectively removes these entanglements and transforms the solution from an elastic physical gel to a viscous fluid depending on the consumption of ATP. A second aspect of this study is the effect of the generic topoisomerase II inhibitor adenylyl-imidodiphosphate (AMP-PNP). In mixtures of AMP-PNP and ATP, the double-strand passage reaction gets blocked and progressively fewer entanglements are relaxed. A total replacement of ATP by AMP-PNP results in a temporal increase in elasticity at higher frequencies, but no transition to an elastic gel with fixed cross-links.

Effect of crowding on the conformation of interwound DNA strands from neutron scattering measurements and Monte Carlo simulations

With a view to determining the distance between the two opposing duplexes in supercoiled DNA, we have measured small angle neutron scattering from pHSG298 plasmid (2675 base pairs) dispersed in saline solutions. Experiments were carried out under full and zero average DNA neutron scattering contrast using hydrogenated plasmid and a 1:1 mixture of hydrogenated and perdeuterated plasmid, respectively. In the condition of zero average contrast, the scattering intensity is directly proportional to the single DNA molecule scattering function (form factor), irrespective of the DNA concentration and without complications from intermolecular interference. The form factors are interpreted with Monte Carlo computer simulation. For this purpose, the many body problem of a dense DNA solution was reduced to the one of a single DNA molecule in a congested state by confinement in a cylindrical potential. It was observed that the interduplex distance decreases with increasing concentration of salt as well as plasmid. Therefore, besides ionic strength, DNA crowding is shown to be important in controlling the interwound structure and site juxtaposition of distal segments of supercoiled DNA. This first study exploiting zero average DNA contrast has been made possible by the availability of perdeuterated plasmid.

Model for a Brownian ratchet with improved characteristics for particle separation

We introduce an extension of the simple on-off ratchet by including a second asymmetric sawtooth potential with half the periodicity and inverse asymmetry in the ratchet cycle. As a result of this additional potential, the Brownian particles exhibit reversal of the direction of their mean displacement when relevant parameters such as the on time of the potentials are varied. This direction reversal offers new opportunities for microfluidic particle separation in sieve devices. Based on the results of our extended ratchet model, we propose two designs. Compared to the classical microfluidic sieve, the proposed devices can be made of significantly smaller sizes without sacrificing the resolution of the separation process. In fact, one of our devices can be reduced to a single channel. We study our extended ratchet model by Brownian dynamics simulations and derive analytical and approximative expressions for the mean displacement using an extension of the method of discrete steps. We show that these expressions are valid in relevant regions of the parameter space and that they can be used to predict the occurrence of direction reversal.

Viscoelasticity of entangled lambda-phage DNA solutions

The viscoelastic moduli of lambda-phage DNA through the entanglement transition were obtained with particle tracking microrheology. With increasing frequency, the viscous loss modulus first increases, then levels off, and eventually increases again. Concurrently, the elastic storage modulus monotonously increases and eventually levels off to a constant high frequency plateau value. Once the DNA molecules become entangled at about ten times the overlap concentration, the elastic storage modulus becomes larger than the viscous loss modulus in an intermediate frequency range. The number of entanglements per chain is obtained from the plateau value of the elasticity modulus. The longest, global relaxation time pertaining to the motion of the DNA molecules is obtained from the low shear viscosity as well as from the lowest crossover frequency of the viscous loss and elastic storage moduli. The concentration dependencies of the low shear viscosity, the number of entanglements per chain, and the relaxation time agree with the relevant scaling laws for reptation dynamics of entangled polyelectrolytes in an excess of simple, low molecular weight salt with screened electrostatic interactions.

Conformational response of supercoiled DNA to confinement in a nanochannel

Monte Carlo simulations were done to study the conformation of supercoiled DNA confined in a nanochannel. The molecule has a superhelical density of around -0.05 and is bathed in a monovalent salt solution with an ionic strength of 2, 10, or 150 mM. The cross-sectional diameter of the circular shaped nanochannel was varied in the range of 10 to 80 nm. The conformational properties were characterized by the writhing number and the distribution in the distance between the two opposing strands of the superhelix. With increasing confinement, as set by a smaller tube diameter and/or decreased screening of the Coulomb interaction, the supercoil becomes more tightly interwound and long-range structural features such as branching and the formation of hairpins are progressively suppressed. Analysis of the energetics shows a concurrent increase in electrostatic energy and energy of interaction of the supercoil with the wall, but the elastic twisting energy decreases. Confinement in a nanochannel or otherwise hence results in a decrease in the absolute value of the twist exerted on the duplex. The bending energy remains approximately constant, which means that there are no significant deflections from the wall. The simulation results are interpreted with theory based on the wormlike chain model, including the effects of the wall, charge, elasticity, and configurational entropy. It was found that the theory is reasonably successful in predicting the structural response to the confinement at the local level of the diameter and pitch of the supercoil.

Molecular dynamics simulation of multivalent-ion mediated attraction between DNA molecules

All atom molecular dynamics simulations with explicit water were done to study the interaction between two parallel double-stranded DNA molecules in the presence of the multivalent counterions putrescine (2+), spermidine (3+), spermine (4+) and cobalt hexamine (3+). The inter-DNA interaction potential is obtained with the umbrella sampling technique. The attractive force is rationalized in terms of the formation of ion bridges, i.e., multivalent ions which are simultaneously bound to the two opposing DNA molecules. The lifetime of the ion bridges is short on the order of a few nanoseconds.

Charge structure and counterion distribution in hexagonal DNA liquid crystal

A hexagonal liquid crystal of DNA fragments (double-stranded, 150 basepairs) with tetramethylammonium (TMA) counterions was investigated with small angle neutron scattering (SANS). We obtained the structure factors pertaining to the DNA and counterion density correlations with contrast matching in the water. Molecular dynamics (MD) computer simulation of a hexagonal assembly of nine DNA molecules showed that the inter-DNA distance fluctuates with a correlation time around 2 ns and a standard deviation of 8.5% of the interaxial spacing. The MD simulation also showed a minimal effect of the fluctuations in inter-DNA distance on the radial counterion density profile and significant penetration of the grooves by TMA. The radial density profile of the counterions was also obtained from a Monte Carlo (MC) computer simulation of a hexagonal array of charged rods with fixed interaxial spacing. Strong ordering of the counterions between the DNA molecules and the absence of charge fluctuations at longer wavelengths was shown by the SANS number and charge structure factors. The DNA-counterion and counterion structure factors are interpreted with the correlation functions derived from the Poisson-Boltzmann equation, MD, and MC simulation. Best agreement is observed between the experimental structure factors and the prediction based on the Poisson-Boltzmann equation and/or MC simulation. The SANS results show that TMA is too large to penetrate the grooves to a significant extent, in contrast to what is shown by MD simulation.

Binding of Mg2+, Cd2+, and Ni2+ to Liquid Crystalline NaDNA: Polarized Light Microscopy and NMR Investigations

The interaction of the divalent metal ions Mg(2+), Cd(2+), and Ni(2+) with liquid crystalline NaDNA solutions (molar ratios Me(2+)/DNA-phosphate </=0.050) was investigated by polarized light microscopy and multinuclear (31)P, (2)H, and (23)Na NMR. Our findings show that the state of the cholesteric NaDNA phase at equal MgCl(2), CdCl(2), or NiCl(2) concentration is affected in a different way and to a different extent by the nature of the divalent cation. Indeed, we found that the occurrence of an isotropic phase is markedly favored by Mg(2+), and to a lower extent by Cd(2+), and that the pitch of the cholesteric phase decreases in the presence of Cd(2+) or Ni(2+). (23)Na NMR spectroscopy also shows differences between the binding behavior of Mg(2+) and the transition metal ions in the counterion atmosphere around DNA. The results are discussed in terms of different binding modes of the metal ions.

Liquid crystal formation in supercoiled DNA solutions

The critical concentrations pertaining to the liquid crystal formation of pUC18 plasmid in saline solutions were obtained from (31)P nuclear magnetic resonance, polarized light microscopy, and phase equilibrium experiments. The transition is strongly first order with a broad gap between the isotropic and anisotropic phase. The critical boundaries are strongly and reversibly dependent on temperature and weakly dependent on ionic strength. With polarized light microscopy on magnetically oriented samples, the liquid crystalline phase is assigned cholesteric with a pitch on the order of 4 microm. Preliminary results show that at higher concentrations a true crystal is formed. The isotropic-cholesteric transition is interpreted with lyotropic liquid crystal theory including the effects of charge, orientation entropy, and excluded volume effects. It was found that the molecular free energy associated with the topology of the superhelix is of paramount importance in controlling the width of the phase gap. The theoretical results compare favorably with the critical boundary pertaining to the disappearance of the isotropic phase, but they fail to predict the low concentration at which the anisotropic phase first appears.

Dimensions of plectonemically supercoiled DNA

With a view to determine the configuration and regularity of plectonemically supercoiled DNA, we have measured the small angle neutron scattering from pUC18 plasmid in saline solutions. Furthermore, we have derived the mathematical expression for the single chain scattering function (form factor) of a superhelical structure, including the longitudinal and transverse interference over the plectonemic pitch and radius, respectively. It was found that an interwound configuration describes the data well, provided interactions among supercoils are accounted for in the second virial approximation. The opening angle was observed to be relatively constant and close to 58 degrees, but it was necessary to include a significant distribution in radius and pitch. For diluted supercoils with vanishing mutual interaction, the derived structural results agree with independent measurements, including the distribution in linking number deficit as determined by gel electrophoresis. With increasing plasmid concentration, prior and covering the transition to the liquid-crystalline phase, the radius and pitch are seen to decrease significantly. The latter observation shows that compaction of negatively supercoiled DNA by confinement results in a decrease in writhing number at the cost of a positive twist exerted on the DNA duplex. It is our conjecture that the free energy associated with this excess twist is of paramount importance in controlling the critical boundaries pertaining to the transition to the anisotropic, liquid-crystalline phase.

Detection of sodium ions in anisotropic environments through spin-lock NMR

A new method for selectively detecting sodium ions in anisotropic environments is presented. A spin-lock (SL) sequence, followed by a coherence transfer pulse, generates rank-two zero-quantum coherences, and converts them into observable transverse magnetization. The quadrupolar polarization is only generated when there are residual quadrupolar couplings in the sample, and provided the SL field strength is comparable to these couplings. This filter has proved to be more efficient than a double-quantum magic-angle (DQ-MA) filter in generating observable signal from ions in anisotropic media in both a nasal bovine cartilage sample and a liquid crystalline DNA sample. Finally, the SL filtering technique does not rely on a flip angle effect for the selection of the desired signal component, as does a DQ-MA filter, and may therefore prove desirable in an imaging experiment, due to its better tolerance to phase and flip angle imperfections.