A micropatterned carbohydrate display for tissue engineering by self-assembly of heparin

A novel strategy to construct a fibroblast scaffold on substrates has been demonstrated via top-down photolithography and the subsequent bottom-up processes of molecular self-assembly and molecular recognition. 3-Aminopropyltrimethoxysilane (APS) self-assembled monolayer was micropatterned by photolithography. An anionic polysaccharide heparin was adsorbed selectively on the cationic APS region of the micropatterned substrate. Basic fibroblast growth factor (bFGF) was selectively bound to the displayed heparin region and then micropatterned cultivation of fibroblast cells was successful on the bFGF-heparin-APS substrate.     

Chirality-induced spin-selective properties of self-assembled monolayers of DNA on gold

Here we show that self-assembled monolayers on gold of double-stranded DNA oligomers interact with polarized electrons similarly to a strong and oriented magnetic field. The direction of the field for right-handed DNA is away from the substrate. Moreover, the layer shows very high paramagnetic susceptibility. Interestingly, thiolated single-stranded DNA oligomers on gold do not show this effect. The new findings are rationalized based on recent results in which high paramagnetism was measured for diamagnetic films adsorbed on diamagnetic substrates.     

Raman and point contact current-voltage characterization of laser-induced diffusion in GaAs

Raman scattering and point contact current-voltage (PCIV) measurements were used as characterization tools of tin-diffused GaAs layers. Diffusion was induced by irradiating GaAs substrates covered with thin tin layers single pulses of a ruby laser. Samples processed with the lowest energies show strong damage and incomplete electrical activation as deduced from Raman and PCIV measurements, respectively. Raman microprobe in depth analysis and PCIV profiles also suggest the presence of a damaged region with incomplete electrical activation at the boundary between the molten layer and the solid substrate.     

Organo-silane coated substrates for DNA purification

The use of blood as DNA source to be employed in genetic analysis requires a purification process in order to remove proteins, lipids and any other contaminants, such as hemoglobin, which inhibit PCR. On the other hand, the increasing demand of miniaturized and automated biological tests able to reduce time and cost of analysis, requires the development and the characterization of materials aimed to perform the DNA purification processes in micro-devices. In this work we studied the interaction of DNA molecules with modified silicon based substrates, positively charged after deposition of a (3-aminopropyl)triethoxysilane (APTES) or 3-[2-(2-aminoethylamino)ethylamino]propyl-trimethoxysilane (AEEA) interfacial layer. The evaluation of the DNA adsorption and elution capacity of different substrates (thermally grown silicon oxide, silicon oxide obtained by plasma enhanced chemical vapour deposition, and Pyrex^®) was studied taking into account the nature of the substrate and the effect of DNA length (in the 208-50,000 base pairs range). Main findings are that DNA elution capacity depends both on the utilized substrate and on the choice of the silanizing agent. Higher DNA recovery was obtained from AEEA-modified substrates, but the eluted DNA had different electrophoretic properties from native DNA. DNA with the same electrophoretic behaviour as genomic DNA was instead recovered from APTES-treated surfaces. Furthermore, the length of DNA present in the starting material strongly modulates the elution efficiency, longer DNA being released in a lesser amount, suggesting that opportunely modified surfaces could be used as systems for differential DNA separation.     

Interactions of Pt single atoms with the vitreous silica surface; Adsorption and thermal accommodation

The interaction of platinum single atoms with a pristine vitreous silica substrate was investigated using a molecular dynamics computer simulation technique. The simulation involved a combination of a modified Born-Mayer-Huggins potential and a simple Lennard-Jones (12-6) potential. The parameters used were those established previously for applicability to this system. The Pt adatoms were deposited on substrates held at various temperatures (300–1500 K) as well as on a substrate with artificially immobilized atoms. This allowed a direct evaluation of the thermal accommodation process and its temperature dependence, as well as the overall effect of substrate relaxations on the behavior of the Pt adatoms. The simulations showed rapid thermal accommodation of the Pt adatoms on the 300 K substrates, whereas this effect was lessened considerably on the heated (1500 K) substrates. The inefficient accommodation of the hotter substrate resulted in penetration of the Pt into the subsurface region of the film. In those runs where the substrate atoms were held immobilized, the behavior of the Pt adatoms was significantly different.     

ZnO homoepitaxy on the O polar face of hydrothermal and melt-grown substrates by pulsed laser deposition

2 cm diameter hydrothermal ZnO crystals were grown and then made into substrates using both mechanical and chemical-mechanical polishing (CMP). CMP polishing showed superior results with an (0002) Ω scan full width half maximum (FWHM) of 67 arcsec and an root mean square (RMS) roughness of 2 Å. In comparison, commercial melt-grown substrates exhibited broader X-ray diffraction (XRD) linewidths with evidence of sub-surface crystal damage due to polishing, including a downward shift of c-lattice parameter. Secondary ion mass spectroscopy revealed strong Li, Fe, Co, Al and Si contamination in the hydrothermal crystals as opposed to the melt-grown substrates, for which glow discharge mass spectroscopy studies had reported high levels of Pb, Fe, Cd and Si. Low temperature photoluminescence (PL) studies indicated that the hydrothermal crystal had high defect and/or impurity concentrations compared with the melt-grown substrate. The dominant bound exciton for the melt-grown substrate was indexed to Al. ZnO films were grown using pulsed laser deposition. The melt-grown substrates gave superior results with XRD (0002) Ω and 2θ/Ω WHM of 124 and 34 arcsec, respectively. Atomic force microscope measurements indicated a low RMS roughness (1.9 nm) as confirmed by fringes in the XRD 2θ/Ω scan. It was suggested that the improvement in XRD response relative to the substrate might be due to “healing” of sub-surface polishing damage due to the elevated T_s used for the growth. Indeed the c-lattice parameter for the homoepitaxial layer on the melt-grown substrate had become that which would be expected for strain-free ZnO. Furthermore, the stability of the PL peak positions relative to bulk ZnO, confirmed that the films appear practically strain free.     

Computational study of the force dependence of phosphoryl transfer during DNA synthesis by a high fidelity polymerase

High fidelity polymerases are efficient catalysts of phosphodiester bond formation during DNA replication or repair. We interpret molecular dynamics simulations of a polymerase bound to its substrate DNA and incoming nucleotide using a quasiharmonic model to study the effect of external forces applied to the bound DNA on the kinetics of phosphoryl transfer. The origin of the force dependence is shown to be an intriguing coupling between slow, delocalized polymerase-DNA modes and fast catalytic site motions. Using noncognate DNA substrates we show that the force dependence is context specific.     

Incorporation of DNA/PEI polyplexes into gelatin/chitosan hydrogel scaffolds: a μ-DSC study

Polyplexes between a double-stranded Salmon DNA and hyperbranched poly(ethyleneimine) (PEI) as well as a maltosylated PEI-Mal were incorporated into a gelatin/chitosan hydrogel scaffold. Calorimetric experiments of the polyplexes show a decrease of the melting temperature in presence of PEI and a peak splitting in presence of PEI-Mal, which can be interpreted to a partial compaction of the DNA strands in presence of PEI-Mal. When the polyplexes are incorporated into a gelatin/chitosan scaffold in the swollen state, the DNA melting peaks at 90 and 93 °C, respectively, indicate in both cases the release of the DNA at the surface of the hydrogel scaffold in a more compact form. Specific interactions between the PEI-Mal shell and gelatin are responsible for the tuning of the release properties in presence of the maltose units in the hyperbranched PEI.     

Fluorescence Turn-On Analysis of Trace Protein Based on Carbon Nanodots and Hybridization Chain Reaction

In this work, an ultrasensitive method for trace protein detection based on fluorescent carbon nanodots and hybridization chain reaction (HCR) is designed. Generally, the synthesized bright carbon nanodots are conjugated with two hairpin-structured DNA probes, respectively, which act as subsequent HCR fuel strands. Since single-stranded parts of DNA probes could be easily absorbed on graphene oxide (GO) nanosheets, fluorescence emission of carbon nanodots is effectively quenched via fluorescence resonance energy transfer. However, in the presence of target protein, the aptamer sequence in another hairpin-structured DNA probe specially interacts with target and the hairpin is opened. A single-stranded region is thus exposed, which initiates HCR by coupling with the DNA fuel strands on carbon nanodots. The formed HCR product displays a rigid, long double-stranded structure, which facilitates the release of carbon nanodots from GO surface. As a result, fluorescence of carbon nanodots is recovered and initial concentration of target protein can be estimated. This protein detection method shows a favorable linear response with a low limit of detection (2.3 fg mL⁻¹). Furthermore, it is highly selective and capable of detecting target in biological fluids like serum samples, which demonstrates the promising applications of this method.     

Topology of protein folding

It is shown that the topological concepts developed previously for the analysis of conformations for strips, double-stranded DNA helices, or elastic thin rods can fruitfully be applied to the study of tertiary folding for complicated protein structures. The topological characteristics determine the integral chirality of proteins and play an important role in the mechanisms of folding and molecular recognition.     

单分子技术研究T7解旋酶的解旋与换链

单分子荧光共振能量转移(smFRET)和磁镊(MT)技术目前广泛应用于研究分子马达.相较于常规技术,其具有高精度及动态观测的优点.本文研究对象为T7解旋酶,是六聚体解旋酶的典型代表.研究表明,这种解旋酶主要消耗脱氧胸苷三磷酸(dTTP)提供能量,且仅能沿着5′-3′单向进行行走和解旋工作.目前对于六聚体解旋酶的解旋和换链机制的认知仍然存在着诸多问题,因此本文主要以此作为切入点开展研究.首先通过运用smFRET技术研究T7解旋酶在不同DNA底物上的解旋现象,发现其需要3′-尾链参与到解旋工作中,但其为单链或双链结构并无明显区别;通过改变脱氧核糖核酸(DNA)序列中的GC含量,发现T7解旋酶随着序列中GC含量的升高会更容易在解旋过程中发生回退现象,导致解旋长度明显缩短;通过进一步分析发生回退先的实验数据,发现T7解旋酶除了可以瞬时回退到叉形DNA岔口或脱落外,还可以缓慢回退到叉形DNA岔口;运用MT技术研究该解旋酶,同样发现这种缓慢回退现象的存在.根据T7解旋酶解旋DNA遵循的单向性和极性,其只能沿着5′到3′方向进行行走和解旋.因此,本文推测这种缓慢回退的现象可能是解旋酶从5′-链转移至3′-链上,即发生换链过程;最后,本文提出了T7解旋酶在解旋过程中进行换链的模型,将有助于进一步理解环状六聚体解旋酶行使其功能的分子机制.     

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.     

Research on the Raman properties of NiFe/cicada wing composite SERS platform modified by silver nanoparticles

Composite structures have been widely concerned in the preparation of surface enhanced Raman scattering (SERS) substrates. In this paper, by solving the problem that the magnetic material was difficult to glow in magnetron sputtering, ferro-nickel (NiFe) alloy was deposited on the cicada wing (CW) and the NiFe/CW substrate was obtained. The results of sliver nanoparticles (Ag NPs) modified on the substrate were subsequently compared, and the SERS properties of the new Ag/NiFe/CW substrate were analyzed. Obviously, the intensity of SERS signals has been greatly improved after the modification of Ag NPs, and the substrate exhibits excellent reproducibility. The Ag NPs modified substrates were also applied to the detection of toxic crystal violet (CV) solution, which showed remarkable SERS activity. It has been proved that the strategy of modifying Ag NPs on the substrate to form a composite structure has great potential for improving the SERS performance of the substrate.     

衬底材料对制备立方氮化硼薄膜的影响

较系统地研究了不同衬底材料对制备氮化硼薄膜的影响。用热丝增强射频等离子体CVD法,以NH3,B2H6和H2为反应气体,在Si,Ni,Co和不锈钢等衬底材料上,成功生长出高质量的立方氮化硼薄膜,还用13.56MHz的射频溅射系统将c-BN薄膜沉积在Si衬底上,靶材为h-BN(纯度为99.99％）,溅射气体为氩气和氮气的混合气体,所得到的氮化硼薄膜中立方相含量高于90%,用X射线衍射谱和傅里叶变换红谱对样品进行了分析表明,衬底材料与c-BN的晶格匹配情况,对于CVD生长立方氮化硼薄膜影响很大,而对溅射生长立方氮化硼薄膜影响不大。     

Automatic recognition and evaluation of micro-contaminant particles on ultra-smooth optical substrates using image analysis method

Micro-contaminant particles on surface of optical substrate have unfavorable influence on light characteristics and instability of optical devices. Proper recognition and evaluation of micro-contaminant particles on post-cleaning substrate are important in fabricating high-performance optical substrates. Based on image analysis and difference of gray scale threshold in image zones, this paper presents a technique for automatically recognizing micro-contamination, and the relevant software developed for on-line evaluation of the level of cleanliness on ultra-smooth optical substrate. Using the self-developed software incorporating high-resolution microscope, optical yttrium iron garnet (YIG) and K8 substrate surfaces of post-chemical mechanical polishing (CMP) were investigated. Results from analyzing the YIG and K8 optical substrates before-and-after laser cleaning illustrated the success of the developed automatic recognition and on-line evaluation system in identifying the micro-contaminant particles on the ultra-smooth substrate surface.     

Artificial allosteric control of maltose binding protein

We demonstrate the allosteric control of a protein based on mechanical tension. When substrate binding is accompanied by a significant change of conformation of the protein, a mechanical tension favoring one or the other conformation will alter the binding affinity for the substrate. We have constructed a chimera where the two lobes of the maltose-binding protein are covalently coupled to the ends of a DNA oligomer. The mechanical tension on the protein is controlled externally by exploiting the difference in stiffness between single stranded and double stranded DNA. We report that the binding affinity of the protein for its substrates is significantly altered by the tension.     

Thermal stress reduction of GaAs epitaxial growth on V-groove patterned Si substrates

We investigate the thermal stresses for GaAs layers grown on V-groove patterned Si substrates by the finite-element method. The results show that the thermal stress distribution near the interface in a patterned substrate is nonuniform,which is far different from that in a planar substrate. Comparing with the planar substrate, the thermal stress is significantly reduced for the Ga As layer on the patterned substrate. The effects of the width of the V-groove, the thickness, and the width of the SiO₂ mask on the thermal stress are studied. It is found that the SiO₂ mask and V-groove play a crucial role in the stress of the Ga As layer on Si substrate. The results indicate that when the width of V-groove is 50 nm, the width and the thickness of the SiO₂ mask are both 100 nm, the Ga As layer is subjected to the minimum stress. Furthermore,Comparing with the planar substrate, the average stress of the Ga As epitaxial layer in the growth window region of the patterned substrate is reduced by 90%. These findings are useful in the optimal designing of growing high-quality Ga As films on patterned Si substrates.     

Observation of single- and double-stranded DNA using non-contact atomic force microscopy

Non-contact atomic force microscopy (NC-AFM) has been applied to observe single- and double-stranded DNA. For the wet processes used to prepare the sample, a strong adhesion force at the surface is observed even in vacuum conditions. Despite the presence of this adhesion force, single- and double-stranded DNA images can be obtained by NC-AFM. Because of the high sensitivity of the tip-sample interaction, NC-AFM images provide stronger contrast than tapping mode (TM)-AFM images. NC-AFM images reveal detailed structures of single- and double-stranded DNA which are not revealed by TM-AFM. In addition, several NC-AFM images show contrast artifacts, which might provide information on the detailed structure of DNA.     

基于近红外光谱的柔性基底紫外臭氧改性效果表征研究

近年来,随着纳米科技、聚合物材料和先进制造技术的发展,以柔性传感器为代表的新兴柔性电子器件在可穿戴、健康医疗、物联网终端等领域发挥着越来越重要的作用。作为柔性电子器件的载体,柔性基底对传感器的机械可靠性和电学传感性能等方面有着重要的意义。但由于其表面非极性键造成的高疏水性限制了功能性材料在其表面的沉积,常常造成柔性基底层与电极层/敏感层之间不稳定的界面结合。因此,利用紫外臭氧处理对柔性基底表面改性受到了广泛的关注。利用近红外光谱技术对柔性基底的紫外臭氧处理效果进行快速精准评估,旨在从基团分子层面探究其改性效果,在实际应用中是对传统依靠接触角测量评估方法的有效补充。具体而言,对四种常见的柔性基底材料聚二甲基硅氧烷(PDMS)、聚萘二甲酸乙二醇酯（PEN）、聚对苯二甲酸乙二醇酯（PET）和聚酰亚胺（PI）进行了1/2/5/10 min不同时长的紫外臭氧（UVO）改性处理,并利用近红外光谱对其改性效果进行表征研究,最后利用接触角测量方法对上述的表征结果进行了验证分析。近红外光谱分析表明：对于柔性PDMS基底,紫外光能量不足以切断其中的甲基（—CH₃）官能团和（—C—Si—）等化学键,无法引入羟基、羧基等亲水性基团。对于柔性PEN和PET基底而言,紫外臭氧处理的效果要优于柔性PDMS基底,且对柔性PET基底的处理效果要优于柔性PEN基底,其原因可能是PEN基底材料中萘环的双环结构具有很强的紫外光吸收能力,阻隔了380 nm以下的大部分紫外线能量。对于柔性PI基底,紫外臭氧处理可以有效引入羟基（—OH）和羧基（—COOH）等活性基团,且这些官能团的强度和数量随着处理时间的增加而增加,从而在短时间内使得PI基底表面能增大、接触角减小、湿润性提高。接触角测试结果验证：紫外臭氧处理对于柔性PDMS基底处理效果不明显（接触角下降幅度为8.4%）;对柔性PET基底处理的效果（接触角下降幅度为39.6%）要优于柔性PEN基底的处理效果（接触角下降幅度为9.4%）;紫外臭氧处理的效果对柔性PI基底处理效果最佳,接触角下降幅度达到了62.7%。     

Ultraviolet laser-induced damage on fused silica substrate and its sol-gel coating

A comparative study of the laser-induced damage thresholds (LIDTs) of fused silica substrates and their sol-gel silica coatings was carried out with 355 nm laser irradiation. Chemical etching and superpolishing were employed in different ways to improve the substrate. The laser damage tests showed that the coated substrate was no more susceptible to laser damage than the bare substrate, showing that the substrate quality was the dominant factor limiting the LIDT for UV irradiation. In addition, it was found that high value of substrate microroughness was more harmful to the LIDT of the coated than the bare substrate, and that a proper combination of etching and superpolishing can optimize the LIDT.