Double-Stranded DNA Immobilized in Lying-Flat and Upright Orientation on a PNIPAm-Coated Surface: A Theoretical Study.

Surface-immobilized double-stranded DNA (dsDNA) in upright orientation plays an important role in optimizing and understanding DNA-based nanosensors and nanodevices. However, it is difficult to regulate the surface density of upright DNA due to the fact that DNA usually stands vertically at a high packing density but may lie down at a low packing density. We herein report dsDNA immobilized in upright orientation on a poly(N-isopropylacrylamide) (PNIPAm)-coated surface in theory. The theoretical results reveal that the angle of upright DNA relative to the surface is larger than that of DNA immobilized on the bare surface caused by the lying-flat DNA under proper PNIPAm surface coverage at 45 °C. The surface density of upright DNA is significantly influenced by DNA concentration and DNA length. It is envisioned that the density-regulated DNA molecules immobilized in upright orientation in the present work are well suited to bottom-up construction of complex DNA-based nanostructures and nanodevices.

Correlated Hybrid DNA Structures Explored by the oxDNA Model.

Thermodynamically, perfect DNA hybridization can be formed between probes and their corresponding targets due to the favorable energy. However, this is not the case dynamically. Here, we use molecular dynamics (MD) simulations based on the oxDNA model to investigate the process of DNA microarray hybridization. In general, correlated hybrid DNA structures are formed, including one probe associated with several targets as well as one target hybrid with multiple probes leading to the target-mediated hybridization. The formation of these two types of correlated structures largely depends on the surface coverage of the DNA microarray. Moreover, DNA sequence, DNA length, and spacer length have an impact on the structural formation. Our findings shed light on the dynamics of DNA hybridization, which is important for the application of DNA microarray.

Two Different Ways of Stress Release in Supercoiled DNA Minicircles under DNA Nick.

It is generally believed that DNA nick is an effective way to release stress in supercoiled DNA, resulting from the twisting motion that individual strands rotate around the axis of the DNA helix. Here, we use MD simulations based on the oxDNA model to investigate the relaxation of 336 bp supercoiled minicircular DNA under DNA nick. Our simulations show that stress release, characterized by the abrupt decrease in linking number, may be induced by two types of DNA motion depending on the nick position. Except for the twisting motion, there is a writhing motion, that is, double strands collectively rotating with one plectoneme removal, which may occur in the process of DNA relaxation with the nick position in the loop region. Moreover, the writhing motion is more likely to occur in the DNA with relatively high hardness, such as C-G pairs. Our simulation results uncover the relationship between structural transformation, stress release, and DNA motion during the dynamic process under DNA nick, indicating the influence of nick position on the relaxation of the supercoiled DNA.

Dynamics of protein condensates in weak-binding regime.

Weak complementary interactions between proteins and nucleic acids are the main driving forces of intracellular liquid-liquid phase separation. The sticker-spacer model has emerged as a unifying principle for understanding the phase behavior of these multivalent molecules. It remains elusive how specific interactions mediated by stickers contribute to the rheological properties of the liquid condensates. Previous studies have revealed that for strong binding strength ɛ_{b}, the bulk diffusivity D depends on the effective bond lifetime τ, viz., D∝τ^{-1}. Consequently, equal concentrations of the complementary stickers induce a slow down in the dynamics of the condensates D∝e^{-1.5ɛ_{b}}. However, for weak-binding strength, it is expected that the resulting condensates are dynamic, loose network liquids rather than kinetically arrested, compact clusters. We develop a mean-field theory using the thermodynamics of the associative polymers and perform molecular-dynamics simulations based on the sticker-spacer model to study the controlling factors in the structure and dynamics of such condensates in the weak-binding regime. Through scaling analysis, we delineate how the free sticker fraction W_{f} and the bulk diffusivity D decrease with increasing binding energy and find that the internal dynamics of such network liquids are controlled by the free sticker fraction D∝W_{f}∝e^{-0.5ɛ_{b}} rather than the effective bond lifetime. Referred to as the free-sticker-dominated diffusivity, the microscopic slowdown due to a gradual loss of the free stickers affects the viscosity of the condensates as well, with the scaling of the zero-shear viscosity η∝e^{0.5ɛ_{b}}. Therefore, the way of controlling the structure, diffusivity, and viscosity of the condensates through the binding energy can be tested experimentally.

Uncovering the molecular mechanism for dual effect of ATP on phase separation in FUS solution.

Recent studies reported that adenosine triphosphate (ATP) could inhibit and enhance the phase separation in prion-like proteins. The molecular mechanism underlying such a puzzling phenomenon remains elusive. Here, taking the fused in sarcoma (FUS) solution as an example, we comprehensively reveal the underlying mechanism by which ATP regulates phase separation by combining the semiempirical quantum mechanical method, mean-field theory, and molecular simulation. At the microscopic level, ATP acts as a bivalent or trivalent binder; at the macroscopic level, the reentrant phase separation occurs in dilute FUS solutions, resulting from the ATP concentration-dependent binding ability under different conditions. The ATP concentration for dissolving the protein condensates is about 10 mM, agreeing with experimental results. Furthermore, from a dynamic point of view, the effect of ATP on phase separation is also nonmonotonic. This work provides a clear physical description of the microscopic interaction and macroscopic phase diagram of the ATP-modulated phase separation.

pH-Regulated Single and Double Charge Inversions on PEI-Coated Surfaces.

The pH-regulated charge inversions on polyethylenimine (PEI)-coated surfaces are indispensable to their applications in biomaterials and nanomaterials. Various PEI-coated surfaces, where single charge inversion happens, have been extensively investigated, while the surfaces where double charge inversion appears are less reported. Here, using a molecular theory, we systematically study the pH-regulated charge density of PEI-coated surfaces. The results suggest whether single or double charge inversion happens depends on PEI affinity to the surface and the bare surface charge density. The region of double charge inversion is much smaller than that of single charge inversion, revealing the reason why double charge inversion is less observed in experiments. Besides, the charge inversions are significantly influenced by the solution condition. The present work provides a useful guideline to the selection of the coated materials and the parameters of PEI solution in the design of PEI-coated surfaces aiming to promote their applications in multifunctional nanomaterials.

Regulation of oligonucleotide adsorption by a thermo and pH dual-responsive copolymer layer.

Oligonucleotides hold great promise as therapeutic agents to specifically and selectively inhibit gene expression. In order to achieve better targeting efficiency and treatment efficacy, nanocarriers that are dual-responsive to both temperature and pH are more attractive and suitable due to the fact that certain malignancies can cause a slight increase of local temperature and a minor decrease in extracellular pH around the tumor site at the same time. Here, we systematically study oligonucleotide adsorption on the poly(ethyleneimine)-b-poly(N-isopropylacrylamide) (PEI-b-PNIPAm) copolymer layer grafted on a planar surface and nanoparticles with various radii, where the single effect of temperature or pH alone on oligonucleotide adsorption has been extensively investigated, but the combined effect of temperature and pH is less discussed. The theoretical results show that the surface density of the adsorbed oligonucleotides exhibits thermo and pH dual-responsive behavior, in which temperature and pH exhibit a combined effect on the loading capacity of the oligonucleotides. The underlying molecular mechanism of the dual-responsive behavior is revealed. Besides, the effect of important but coupled parameters in nanocarrier design such as polymer surface coverage and length, salt concentration as well as surface curvature (inverse nanoparticle radius) that may influence the dual-responsive behavior of oligonucleotide adsorption is further discussed, which is of great significance to direct the optimal design of PNIPAm/PEI-based nanocarriers to improve the transfection efficiency by achieving the maximal loading capacity of oligonucleotides at different temperatures and pH values.

Self-Assembled Binary Photonic Crystals under the Active Confinement and Their Light Trapping.

The self-assembly of oppositely charged colloidal ellipsoids and spheres under active confinement is first proposed to achieve long-range ordered photonic crystals. Compared with the conventional passive confinement, a characteristic of the active confinement is that boundaries are movable. Our Brownian dynamics simulations show that dynamic steady structures, similar to quasi-2D colloidal crystals, can be obtained under the strong confinement when the two boundaries periodically oscillate together. The in-plane structures can be regulated by changing the charge ratio of the two kinds of particles. These dynamic steady structures are determined by the minimum electrostatic energy with the aid of increased mobility of confined particles, which are not available in equilibrium. Numerical simulations verify that light can be perfectly confined in this dielectric binary photonic slab without any radiation, which corresponds to a typical optical bound state with divergent lifetime and ultrasharp spectral profile. Given the changeable geometry of this photonic slab, the trapped optical field might be applicable to enhanced light-matter interactions. In addition, for thicker layers, layer-by-layer ordered structures occur spontaneously, driven by the active confinement, while no global order occurs in the passive confinement. Our results show that the boundary motion can become an important factor affecting self-assembled structure and function.

Temperature-regulated protein adsorption on a PNIPAm layer.

In immunosensors, antibody orientation is a key factor that determines the sensitivity of a device. To date much effort has been devoted to exploring strategies for the direct control of the orientation of antibodies immobilized on a bioactive surface, but less attention has been paid to controlling the orientation of intermediate proteins (though usually used when immobilizing antibodies), which may greatly limit the sensitivity of immunological activities. Therefore, it is of great significance to seek novel methods for controlling protein orientation. Here, we design a new strategy for controlling protein orientation. The main idea is to bind proteins to a ligand-functionalized poly(N-isopropylacrylamide) (PNIPAm) layer, and then the protein orientation can be mediated by environmental temperature. The theory predicts that the protein orientation can show unexpected triple-thermo-responsive behavior. Based on the fraction of ligand adsorbed by the protein, the reponsive behavior can be either complete adsorption or partial adsorption, which is determind by the polymer's surface coverage and the protein's properties. We expect that the present strategy can enrich the methods for controlling intermediate protein orientation and can guide the design of novel immunosensors with superior sensitivity.

Three-Dimensional Non-Close-Packed Structures of Oppositely Charged Colloids Driven by pH Oscillation.

The implementation of non-close-packed structures in colloids is challenging. Using Brownian dynamics simulations, we study the nonequilibrium self-assembly in suspensions of oppositely charged particles, whose charge magnitude is responsive to the pH of the solution. Under the fast pH-oscillating condition, various non-close-packed (e.g., graphitelike and diamondlike) structures are obtained. Here, changing the amplitude of the pH oscillation is an effective way to fabricate colloidal dynamic structures. To clarify the underlying mechanism of the dynamic self-assembly, the analysis of effective potential is adopted. A dimensionless parameter, the ratio of effective repulsion and attraction, is introduced to reflect the subtle interactions in the system. We find that the imbalance between repulsion and attraction is the cause of structural diversity. Madelung energy is used to study the stability of these structures. Our results provide a new way to fabricate non-close-packed structures in colloids, which has potential applications in the synthesis of photonic crystals.

Molecular and Thermodynamic Factors Explain the Passivation Properties of Poly(ethylene glycol)-Coated Substrate Surfaces against Fluorophore-Labeled DNA Oligonucleotides.

Poly(ethylene glycol) (PEG) nanofilms are used to avert the nonspecific binding of biomolecules on substrate surfaces in biomedicine and bioanalysis including modern fluorescence-based DNA sensing and sequencing chips. A fundamental and coherent understanding of the interactions between fluorophore-tagged DNA, PEG-films, and substrates in terms of molecular and energetic factors is, however, missing. Here we explore a large parameter space to elucidate how PEG layers passivate metal oxide surfaces against Cy3-labeled DNA probes. The driving force for probe adsorption is found to be the affinity of the fluorophore to the substrate, while the high-quality PEG films prevent adsorption to bare ITO surfaces. The amount of nonrepelled, surface-bound DNA strongly depends on oligonucleotide size, PEG chain length, and incubation temperature. To explain these observations, we develop an experimentally validated theory to provide a microscopic picture of the PEG layer and show that adsorbed DNA molecules reside within the film by end-tethering the fluorophore to the ITO surface. To compensate for the local accumulation of negatively charged DNA, counterions condense on the adsorbed probes within the layer. The model furthermore explains that surface passivation is governed by the interdependence of molecular size, conformation, charge, ion condensation, and environmental conditions. We finally report for the first time on the detailed thermodynamic values that show how adsorption results from a balance between large opposing energetic factors. The insight of our study can be applied to rationally engineer PEG nanolayers for improved functional performance in DNA analysis schemes and may be expanded to other polymeric thin films.

Designing new strategy for controlling DNA orientation in biosensors.

Orientation controllable DNA biosensors hold great application potentials in recognizing small molecules and detecting DNA hybridization. Though electric field is usually used to control the orientation of DNA molecules, it is also of great importance and significance to seek for other triggered methods to control the DNA orientation. Here, we design a new strategy for controlling DNA orientation in biosensors. The main idea is to copolymerize DNA molecules with responsive polymers that can show swelling/deswelling transitions due to the change of external stimuli, and then graft the copolymers onto an uncharged substrate. In order to highlight the responsive characteristic, we take thermo-responsive polymers as an example, and reveal multi-responsive behavior and the underlying molecular mechanism of the DNA orientation by combining dissipative particle dynamics simulation and molecular theory. Since swelling/deswelling transitions can be also realized by using other stimuli-responsive (like pH and light) polymers, the present strategy is universal, which can enrich the methods of controlling DNA orientation and may assist with the design of the next generation of biosensors.

Crowding-induced cooperativity in DNA surface hybridization.

High density DNA brush is not only used to model cellular crowding, but also has a wide application in DNA-functionalized materials. Experiments have shown complicated cooperative hybridization/melting phenomena in these systems, raising the question that how molecular crowding influences DNA hybridization. In this work, a theoretical modeling including all possible inter and intramolecular interactions, as well as molecular details for different species, is proposed. We find that molecular crowding can lead to two distinct cooperative behaviours: negatively cooperative hybridization marked by a broader transition width, and positively cooperative hybridization with a sharper transition, well reconciling the experimental findings. Moreover, a phase transition as a result of positive cooperativity is also found. Our study provides new insights in crowding and compartmentation in cell, and has the potential value in controlling surface morphologies of DNA functionalized nano-particles.

Modeling Stretching-Induced Immiscibility in Nonmonodisperse Polymer Systems.

The behavior of polymer chains under stretching is a classical problem in polymer science. However, a fundamental question still in mist is how the stretching affects the interactions between polymer chains, especially when the tensions on the chains are unequal. In this work, we combine statistical theory and molecular simulations to study the influence of this tension disparity on the miscibility of athermal polymer systems. Through a minimal model, we demonstrate that when polymer chains of different lengths are under the same stretching disparate tension states among polymer chains can lead to either macroscopic or microscopic phase separation, depending on whether their ending points are mobile or not. Generally, the immiscibility found here is an entropic effect arising from conformational asymmetry between unequally stretched polymer chains. Our findings provide a new mechanism to explain the flow-induced demixing in polymer blends and indicate that heterogeneous structure can occur during stretching, simply as a result of nonmonodispersity in elastic polymer materials.

Pumping of water by rotating chiral carbon nanotube.

Water transportation inside carbon nanotubes is of great importance for designing novel nanodevices. In this article, by using molecular dynamics simulations, we systematically investigate the pumping of water by rotating carbon nanotube (CNT). It is found that the chirality and rotation of the CNT are two preconditions for stable water flux inside it. Besides, we find that the water flux shows an approximately logarithmic dependence on the angular velocity of the rotation, a linear dependence on the radius of the CNT, and interestingly, independence of its length within a certain range of CNT size and angular velocity. Further, we also use a dragging theory which successfully describes the water flux behaviors inside the CNT and can fit well with the results obtained from simulations. The present study provides insight into the designing of nanodevices based on the CNT for real applications.

The coexisting phase behavior of thermo-responsive copolymer solutions.

Using a molecular theory for dilute PEO-b-PNIPAm solutions, we first take the formation of hydrogen bonds between copolymer monomers and water molecules into account, which enables us to study the impact of temperature on PEO-b-PNIPAm self-assembly effectively by quantitatively describing the different changes in water affinities of two blocks. With the increase of temperature, hydrogen bonds between PNIPAm and water break down dramatically, resulting in the hydrophobic character of PNIPAm while PEO remains hydrophilic. Amphiphilic copolymers in the aqueous surrounding can aggregate into various structures: micelles and vesicles. According to the equilibrium criterion of the excess grand potential under the conditions of the grand canonical ensemble, we find that both structures are stable and can coexist. Theoretically calculated potentials of mean force of aggregates further verify the coexistence of micelles and vesicles, although the low critical solution temperatures of different aggregates are different under these conditions. A phase diagram as functions of temperature and the weight fraction of PEO (fPEO) is obtained, which shows different regions of micelles, vesicles and their coexistence. It implies the appearance of two types of micelle-vesicle transition: spontaneous and temperature-induced. Since PEO-b-PNIPAm as a thermoresponsive material has a broad range of applications, a systematic investigation of the phase behavior is very useful not only for the scientific interest but also for the practical applications.

Time dependence of lysozyme adsorption on end-grafted polymer layers of variable grafting density and length.

A combined experimental and theoretical approach establishes the long-lived nature of protein adsorption on surfaces coated with chemically grafted macromolecules. Specifically, we monitor the time dependence of adsorption of lysozyme on surfaces comprising polymer assemblies made of poly(2-hydroxyethyl methacrylate) brushes grafted onto flat silica surfaces such that they produce patterns featuring orthogonal and gradual variation of the chain length (N) and grafting density (σ). We show that in the kinetically controlled regime, the amount of adsorbed protein scales universally with the product σN, while at equilibrium the amount of adsorbed protein is governed solely by σ. Surprisingly, for moderate concentrations of protein in solution, adsorption takes more than 72 h to reach an equilibrium, or steady state. Our experimental findings are corroborated with predictions using molecular theory that provides further insight into the protein adsorption phenomenon. The theory predicts that the universal behavior observed experimentally should be applicable to polymers in poor and theta solvents and to a limited extent also to good solvent conditions. Our combined experimental and theoretical findings reveal that protein adsorption is a long-lived phenomenon, much longer than generally assumed. Our studies confirm the previously predicted important differences in behavior for the kinetic versus thermodynamic control of protein adsorption.

Application of a narcotrend-assisted anesthesia in-depth monitor in the microwave coagulation for liver cancer during total intravenous anesthesia with propofol and fentanyl / 癌症

<p><b>BACKGROUND AND OBJECTIVE</b>CT-guided microwave coagulation is a minimally invasive surgery for patients with liver cancer. Total intravenous anesthesia with propofol and fentanyl is commonly used. The depth of anesthesia during microwave coagulation for liver cancer is still monitored by clinical signs. There are few subjective and effective indicators. This study explored the application of Narcotrend-assisted "depth of anesthesia" monitoring on microwave coagulation for patients with liver cancer during total intravenous anesthesia with propofol and fentanyl.</p><p><b>METHODS</b>Forty liver cancer patients underwent CT-guided microwave coagulation were randomly assigned to receive Narcotrend index monitoring or standard clinical monitoring for depth of anesthesia with 20 patients in each group. All patients received total intravenous anesthesia with propofol and fentanyl. The depth of anesthesia for patients in the Narcotrend group was measured according to a Narcotrend index, which was maintained between D2 and E0. The depth of anesthesia for those in the standard clinical practice group was measured according to heart rate, mean arterial pressure, and patient movement. Changes of hemodynamics, the duration of the emergence from anesthesia, and the recovery of orientation were recorded. The doses of propofol and fentanyl, postoperative visual analogue scores (VAS), and the incidence of postoperative nausea and vomiting were also recorded.</p><p><b>RESULTS</b>There was no significant alteration in heart rate or mean arterial pressure between the two groups. Compared with other anesthetic stages, both heart rate and mean arterial pressure decreased during the induction of the anesthesia in the two groups(P<0.05). The doses of propofol were higher in the standard clinical practice group than in the Narcotrend group [(460+/-30) mg vs. (380+/-35) mg, P<0.01]. The duration of emergence and orientation were longer in the standard clinical practice group than in the Narcotrend group [(9.5+/-2.9) min vs. (4.9+/-2.2) min, P<0.01; (12.2+/-3.5) min vs. (6.6+/-3.2) min, P<0.01, respectively]. There was no difference in the dosage of fentanyl, VAS, or the incidence of postoperative nausea or vomiting between the two groups (P>0.05).</p><p><b>CONCLUSION</b>For patients with liver cancer, monitoring the depth of anesthesia with Narcotrend on microwave coagulation can contribute to lower dosage of propofol and shorten duration of recovery during total intravenous anesthesia with propofol and fentanyl.</p>

Streptavidin-biotin binding in the presence of a polymer spacer. A theoretical description.

The binding of streptavidin to biotin located at the terminal ends of poly(ethylene oxide) tethered to a planar surface is studied using molecular theory. The theoretical model is applied to mimic experiments (Langmuir 2008, 24, 2472) performed using drop-shape analysis to study receptor-ligand binding at the oil/water interface. Our theoretical predictions show very good agreements with the experimental results. Furthermore, the theory enables us to study the thermodynamic and structural behavior of the PEO-biotin + streptavidin layer. The interfacial structure, shown by the volume fraction profiles of bound proteins and polymers, indicates that the proteins form a thick layer supported by stretched polymers, where the thickness of the layer is greater than the height of the protein. When the polymer spacer is composed of PEO (3000), a thick layer with multilayers of proteins is formed, supported by the stretched polymer chains. It was found that thick multilayers of proteins are formed when long spacers are present or at very high protein surface coverages on short spacers. This shows that the flexibility of the polymer spacer plays an important role in determining the structure of the bound proteins due to their ability to accommodate highly distorted conformations to optimize binding and protein interactions. Protein domains are predicted when the amount of bound proteins is small due to the existence of streptavidin-streptavidin attractive interactions. As the number of proteins is increased, the competition between attractive interactions and steric repulsions determines the stability and structure of the bound layer. The theory predicts that the competition between these two forces leads to a phase separation at higher protein concentrations. The point where this transition happens depends on both spacer length and protein surface coverage and is an important consideration for practical applications of these and other similar systems. If the goal is to maximize protein binding, it is favorable to be above the layer transition, as multiple layers can accommodate greater bound protein densities. On the other hand, if the goal is to use these bound proteins as a linker group to build more complex structures, such as when avidin or streptavidin serves as a linker between two biotinylated polymers or proteins, the optimum is to be below the layer transition such that all bound linker proteins are available for further binding.

Structure and organization of nanosized-inclusion-containing bilayer membranes.

Based on a considerable amount of experimental evidence for lateral organization of lipid membranes which share astonishingly similar features in the presence of different inclusions, we use a hybrid self-consistent field theory (SCFT)/density-functional theory (DFT) approach to deal with bilayer membranes embedded by nanosized inclusions and explain experimental findings. Here, the hydrophobic inclusions are simple models of hydrophobic drugs or other nanoparticles for biomedical applications. It is found that lipid/inclusion-rich domains are formed at moderate inclusion concentrations and disappear with the increase in the concentration of inclusions. At high inclusion content, chaining of inclusions occurs due to the effective depletion attraction between inclusions mediated by lipids. Meanwhile, the increase in the concentration of inclusions can also cause thickening of the membrane and the distribution of inclusions undergoes a layering transition from one-layer structure located in the bilayer midplane to two-layer structure arranged into the two leaflets of a bilayer. Our theoretical predictions address the complex interactions between membranes and inclusions suggesting a unifying mechanism which reflects the competition between the conformational entropy of lipids favoring the formation of lipid- and inclusion-rich domains in lipids and the steric repulsion of inclusions leading to the uniform dispersion.