Molecular electronics based nanosensors on a viral scaffold

Assembling and interconnecting the building blocks of nanoscale devices and being able to electronically address or measure responses at the molecular level remains an important challenge for nanotechnology. Here we show the usefulness of bottom-up self-assembly for building electronic nanosensors from multiple components that have been designed to interact in a controlled manner. Cowpea mosaic virus was used as a scaffold to control the positions of gold nanoparticles. The nanoparticles were then interconnected using thiol-terminated conjugated organic molecules, resulting in a three-dimensional conductive network. Biotin molecules were attached to the virus scaffold using linkers to act as molecular receptors. We demonstrated that binding avidin to the biotin receptors on the self-assembled nanosensors causes a significant change in the network conductance that is dependent on the charge of the avidin protein.     

Branched nanowire based guanine rich oligonucleotides.

Self-assembly and aggregation of guanine rich sequences can provide useful insights into DNA nanotechnology and telomeric structure and function. In this paper, we designed a guanine rich sequence d(GGCGTTTTGCGG). We found that it can form stable structure in appropriate condition and it exhibits an anomalous CD spectra. This structures can be imaged in ambient environment with a Nanoscope III AFM (Digital Instruments). We found it forms branch structure and long multistrand DNA nanowire after incubation at 37 degrees C for 6-12 hours in 25 mM TE (pH=8.0) + 5 mM Mg2+ + 50 mM K+. The ability to self-assemble into branches and long wires not only clearly demonstrate its potential as scaffold structures for nanotechnology, but also give aids to understand telomeric structure further. We have proposed a model to explain how these structures formed.     

Branched Nanowire Based Guanine Rich Oligonucleotides

Abstract

Self-assembly and aggregation of guanine rich sequences can provide useful insights into DNA nanotechnology and telomeric structure and function. In this paper, we designed a guanine rich sequence d(GGCGTTTTGCGG). We found that it can form stable structure in appropriate condition and it exhibits an anomalous CD spectra. This structures can be imaged in ambient environment with a Nanoscope III AFM (Digital Instruments). We found it forms branch structure and long multistrand DNA nanowire after incubation at 37°C for 612 hours in 25 mM TE (pH=8.0) + 5 mM Mg²⁺ + 50 mM K⁺. The ability to self-assemble into branches and long wires not only clearly demonstrate its potential as scaffold structures for nanotechnology, but also give aids to understand telomeric structure further. We have proposed a model to explain how these structures formed.     

Tissue-engineered bone regeneration

Bone lesions above a critical size become scarred rather than regenerated, leading to nonunion. We have attempted to obtain a greater degree of regeneration by using a resorbable scaffold with regeneration-competent cells to recreate an embryonic environment in injured adult tissues, and thus improve clinical outcome. We have used a combination of a coral scaffold with in vitro-expanded marrow stromal cells (MSC) to increase osteogenesis more than that obtained with the scaffold alone or the scaffold plus fresh bone marrow. The efficiency of the various combinations was assessed in a large segmental defect model in sheep. The tissue-engineered artificial bone underwent morphogenesis leading to complete recorticalization and the formation of a medullary canal with mature lamellar cortical bone in the most favorable cases. Clinical union never occurred when the defects were left empty or filled with the scaffold alone. In contrast, clinical union was obtained in three out of seven operated limbs when the defects were filled with the tissue-engineered bone.     

The construction of DNA molecules of figure-eight structure

Using DNA molecules to construct a structural scaffold for nanotechnology is largely accepted. In this article, we report on two methods for constructing a figure-eight structure of DNA molecules having a relatively high yield that could be used further as a scaffold for nanotechnology applications. In the first method, two plasmids were constructed that, on digestion with a restriction endonuclease producing nicks in the corresponding sites and after heating, produced complementary single-stranded sequences, enabling the plasmids to hybridize to each other and forming a figure-eight structure. The formation of the figure-eight structure was analyzed by restriction analysis and gel electrophoresis as well as by atomic force microscopy. The second method makes use of the bacteriophage M13 that is obtained as either a single- or double-stranded circular DNA molecule. Two M13 molecules harboring complementary sequences were constructed and produced a figure-eight structure on hybridization. The methods described here could be used further for the construction of nanoelectronic devices.     

PLGA/ECM神经支架性质的体外评价

以赖氨酸、神经生长因子(NGF)、聚乳酸聚羟基乙酸共聚物(PLGA)、猪皮来源的细胞外基质(ECM)为原料制备了一种复合材料;考察其内部三维结构,生物力学性质,降解特性,雪旺氏细胞黏附状况,以及其对NGF的可控释放作用;从而评价其作为促周围神经损伤修复支架的可行性。扫描电子显微镜(SEM)观察显示,PLGA渗透入去细胞猪皮内部固有的蜂窝状孔隙中,并覆盖在孔隙内表面;孔隙率为68.3%～81.2%,密度为0.62～0.68 g/cm3。复合材料的断裂强度为8.308 MPa,断裂伸长率为38.98%,弹性模量为97.27 MPa;在4周的体外降解测试中,其最大失重率为43.3%;赖氨酸在复合材料中的添加对降解液pH的相对稳定具有显著作用;在30 d中,复合材料对NGF的累积释放率为38%;通过雪旺氏细胞与复合材料的共培养,发现雪旺氏细胞能够在其表面及孔隙中黏附。因此表明本复合材料有望成为一种新型的促周围神经损伤修复支架。     

Peptide receptor-based selective dinitrotoluene detection using a microcantilever sensor

We reported that peptide could be utilized as receptor molecule in the gas phase for application in micro/nano sensors by using a specific peptide that recognizes 2,4-dinitrotoluene at room temperature and in an atmospheric environment and measuring changes in the resonant frequency of the peptide immobilized microcantilevers. By using these peptides as receptors on a microcantilever sensor, we were able to experimentally detect 2,4-dinitrotoluene (DNT) vapor at concentrations as low as parts per billion (ppb) in the gas phase. While resonant frequency changes after binding between 2,4-DNT and the specific peptide receptor that was immobilized on microcantilevers were observed, the resonant frequency of DNT nonspecific peptide immobilized microcantilever did not change when exposed to 2,4-DNT vapor. The limit of detection (LOD) was calculated to be 431 ppt of limit of detection is numerically expected by experimental based on an equation that describes the relationship between the noise-equivalent analyte concentration. These results indicate that the peptide receptors hold great promise for use in the development of an artificial olfactory system and electronic nose based on micro/nanotechnology for monitoring various chemical vapors in the gas phase such as explosive mixtures of chemicals and/or volatile organic compounds.     

SAF-Box, a conserved protein domain that specifically recognizes scaffold attachment region DNA

SARs (scaffold attachment regions) are candidate DNA elements for partitioning eukaryotic genomes into independent chromatin loops by attaching DNA to proteins of a nuclear scaffold or matrix. The interaction of SARs with the nuclear scaffold is evolutionarily conserved and appears to be due to specific DNA binding proteins that recognize SARs by a mechanism not yet understood. We describe a novel, evolutionarily conserved protein domain that specifically binds to SARs but is not related to SAR binding motifs of other proteins. This domain was first identified in human scaffold attachment factor A (SAF-A) and was thus designated SAF-Box. The SAF-Box is present in many different proteins ranging from yeast to human in origin and appears to be structurally related to a homeodomain. We show here that SAF-Boxes from four different origins, as well as a synthetic SAF-Box peptide, bind to natural and artificial SARs with high specificity. Specific SAR binding of the novel domain is achieved by an unusual mass binding mode, is sensitive to distamycin but not to chromomycin, and displays a clear preference for long DNA fragments. This is the first characterization of a specific SAR binding domain that is conserved throughout evolution and has DNA binding properties that closely resemble that of the unfractionated nuclear scaffold.     

Role of an adenylyl cyclase isoform in ethanol's effect on cAMP regulated gene expression in NIH 3T3 cells

Previous research has indicated that the cyclic AMP (cAMP) signal transduction system plays an important role in the predisposition to and development of ethanol abuse in humans. Our laboratory has demonstrated that ethanol is capable of enhancing adenylyl cyclase (AC) activity. This effect is AC isoform-specific; type 7 AC (AC7) is most enhanced by ethanol. Therefore, we hypothesized that the expression of a specific AC isoform will play a role on the effect of ethanol on cAMP regulated gene expression. We employed NIH 3T3 cells transfected with AC7 or AC3 as a model system. To evaluate ethanol's effects on cAMP regulated gene expression, a luciferase reporter gene driven by a cAMP inducing artificial promoter was utilized. Stimulation of AC activity leads to an increase in the reporter gene activity. This increase was enhanced in the presence of ethanol in cells expressing AC7, while cells expressing AC3 did not respond to ethanol. cAMP reporter gene expression was increased in the presence of 8-bromo-cAMP; this expression was not enhanced by ethanol. These observations are consistent with our hypothesis. The basal level of CREB phosphorylation was high and did not change by cAMP stimulation or in the presence of ethanol. However, there were significant changes in the TORC3 amount in nuclei depending on stimulation conditions. The results suggest that nuclear translocation of TORC3 plays a more important role than CREB phosphorylation in the observed changes in the cAMP driven reporter gene activity.     

6-Amino-chrysene, a potent inhibitor of transferase activity in single living RTG2 cells

Previous reports on the inhibitory effect of 6-amino-chrysene (6AC) on benzo(a)pyrene (BP) metabolism using single living cells have suggested that aryl hydrocarbon hydroxylase (AHH) is not the only pathway for 6AC metabolism. We present here results demonstrating that direct glucuronidation may constitute an alternative pathway for 6AC elimination. First, we describe the conjugate of 6AC to UDP-glucuronic acid (UDPGA) in solution. We performed competition experiments between 6AC and monohydroxy BP, which are known to be good substrates for glucuronic transferase (GT), in RTG2 cells, using microspectrofluorimetry. Because of intracellular accumulation of fluorescent metabolites during BP metabolism, RTG2 cells can be used as a tool for simultaneous study of AHH and GT activities. When RTG2 cells have been simultaneously treated with BP and 6AC, GT appeared to be a more specific target for 6AC than AHH in these cells. Therefore, 6AC can be expected to act as a more specific inhibitor for GT than for AHH activity.     

Development of plants resistant to tomato geminiviruses using artificial trans‐acting small interfering RNA

RNA interference (RNAi), a conserved RNA‐mediated gene regulatory mechanism in eukaryotes, plays an important role in plant growth and development, and as an antiviral defence system in plants. As a counter‐strategy, plant viruses encode RNAi suppressors to suppress the RNAi pathways and consequently down‐regulate plant defence. In geminiviruses, the proteins AC2, AC4 and AV2 are known to act as RNAi suppressors. In this study, we have designed a gene silencing vector using the features of trans‐acting small interfering RNA (tasiRNA), which is simple and can be used to target multiple genes at a time employing a single‐step cloning procedure. This vector was used to target two RNAi suppressor proteins (AC2 and AC4) of the geminivirus, Tomato leaf curl New Delhi virus (ToLCNDV). The vector containing fragments of ToLCNDV AC2 and AC4 genes, on agro‐infiltration, produced copious quantities of AC2 and AC4 specific siRNA in both tobacco and tomato plants. On challenge inoculation of the agro‐infiltrated plants with ToLCNDV, most plants showed an absence of symptoms and low accumulation of viral DNA. Transgenic tobacco plants were raised using the AC2 and AC4 tasiRNA‐generating constructs, and T₁ plants, obtained from the primary transgenic plants, were tested for resistance separately against ToLCNDV and Tomato leaf curl Gujarat virus. Most plants showed an absence of symptoms and low accumulation of the corresponding viruses, the resistance being generally proportional to the amounts of siRNA produced against AC2 and AC4 genes. This is the first report of the use of artificial tasiRNA to generate resistance against an important plant virus.     

天然高分子复合人工肌腱组织细胞外基质的构建与表征

胶原与壳聚糖是2种具有较好生物相容性和一定力学强度的天然高分子,可在肌腱组织工程中用于细胞外基质的构建,但二者单独使用时各有不足.本研究利用二者性能上的互补,在一定的外力场作用下,采用EDC/NHS对2种天然高分子材料进行共价交联,获得具有一定空间取向和力学强度的多孔支架,然后引入细胞黏附因子RGD进行表面修饰,构建了具有较好组织相容性和细胞亲和性及适当降解速率的人工肌腱组织细胞外基质.对基质材料的力学性能、亲水性、体外降解速率等的检测和显微观察,结果显示:所构建的多孔支架材料柔软富有弹性,抗拉强度达:15.0Mpa,相应形变为:7.33%;孔隙率:79.4%;吸水率:772%;保水率:206%;在RPM1640培养液(含10%胎牛血清)和人血清中,3周总降解率分别为4.13%和37.2%,其降解速率可与肌腱修复周期相吻合,RGD修饰后材料对3T3-L1细胞具有较好的亲和性.有望成为理想的人工肌腱组织和人造皮肤细胞外基质,或整形手术的软组织填充材料.     

Evidence for intramolecular disulfide bond shuffling in the folding of mutant human lysozyme

Our previous results using the Saccharomyces cerevisiae secretion system suggest that intramolecular exchange of disulfide bonds occurs in the folding pathway of human lysozyme in vivo (Taniyama, Y., Yamamoto, Y., Kuroki, R., and Kikuchi, M. (1990) J. Biol. Chem. 265, 7570-7575). Here we report on the results of introducing an artificial disulfide bond in mutants with 2 cysteine residues substituting for Ala83 and Asp91. The mutant (C83/91) protein was not detected in the culture medium of the yeast, probably because of incorrect folding. Thereupon, 2 cysteine residues Cys77 and Cys95 were replaced with Ala in the mutant C83/91, because a native disulfide bond Cys77-Cys95 was found not necessary for correct folding in vivo (Taniyama, Y., Yamamoto, Y., Nakao, M., Kikuchi, M., and Ikehara, M. (1988) Biochem. Biophys. Res. Commun. 152, 962-967). The resultant mutant (AC83/91) was secreted as two proteins (AC83/91-a and AC83/91-b) with different specific activities. Amino acid and peptide mapping analyses showed that two glutathiones appeared to be attached to the thiol groups of the cysteine residues introduced into AC83/91-a and that four disulfide bonds including an artificial disulfide bond existed in the AC83/91-b molecule. The presence of cysteine residues modified with glutathione may indicate that the non-native disulfide bond Cys83-Cys91 is not so easily formed as a native disulfide bond. These results suggest that the introduction of Cys83 and Cys91 may act to suppress the process of native disulfide bond formation through disulfide bond interchange in the folding of human lysozyme.     

Thermostability and molecular encapsulation within an engineered caged protein scaffold

Self-assembling biological complexes such as viral capsids have been manipulated to function in innovative nanotechnology applications. The E2 component of pyruvate dehydrogenase from Bacillus stearothermophilus forms a dodecahedral complex and potentially provides another platform for these purposes. In this investigation, we show that this protein assembly exhibits unusual stability and can be modified to encapsulate model drug molecules. To distill the E2 protein down to its structural scaffold core, we synthesized a truncated gene optimized for expression in Escherichia coli. The correct assembly and dodecahedral structure of the resulting scaffold was confirmed with dynamic light scattering and transmission electron microscopy. Using circular dichroism and differential scanning calorimetry, we found the thermostability of the complex to be unusually high, with an onset temperature of unfolding at 81.1 +/- 0.9 degrees C and an apparent midpoint unfolding temperature of 91.4 +/- 1.4 degrees C. To evaluate the potential of this scaffold for encapsulation of guest molecules, we made variants at residues 381 and 239 which altered the physicochemical properties of the hollow internal cavity. These mutants, yielding 60 and 120 mutations within this cavity, assembled into the correct architecture and exhibited high thermostability that was comparable to the wild-type scaffold. To show the applicability of this scaffold, two different fluorescent dye molecules were covalently coupled to the cysteine mutant at site 381. We demonstrate that these mutations can introduce non-native functionality and enable molecular encapsulation within the cavity while still retaining the dodecahedral structure. The unusually robust nature of this scaffold and its amenability to internal changes reveal its potential for nanoscale applications.     

Optimal design of bio-hybrid systems with a hollow fiber scaffold: model analysis of oxygen diffusion/consumption

The oxygen distribution in various bio-hybrid systems composed of cellular tissue on an artificial scaffold was estimated by mathematically modeling the oxygen consumption and diffusion. Mathematical models were established for practical systems such as bio-hybrid artificial liver (BAL) and bio-hybrid blood vessels, and the calculated results were compared with corresponding experimental data. Analysis of a spherical organoid (“spheroid”) composed of hepatic cells suggested that the oxygen consumption rate in hepatocyte spheroids incubated in a BAL is one or two orders of magnitude larger than the total average value that had been calculated for various organs. A model was established for a BAL system on a scaffold of commercially available hollow fiber (typical inner and outer radii of 150 and 200 μm) to determine the optimal conditions under which the hepatocytes can be packed as closely as possible into the hollow fiber lumen while still maintaining viability without falling into oxygen deficiency. A model of bio-hybrid blood vessels formed by vascular endothelial cells incubated on the inner wall of a hollow fiber scaffold was used to estimate the maximum thickness of viable endothelial tissue under various conditions of outer partial oxygen pressure and different sizes and permeabilities of the hollow fiber scaffold. The model suggested that the oxygen supply becomes quite restricted when the hollow fiber membrane is thicker than 100 μm; the thickness of the endothelium in a 500 μm-thick hollow fiber membrane was estimated to be 7 μm at most, even when the membrane permeability was as large as that of the culture medium.     

Permeability analysis of scaffolds for bone tissue engineering

Porous artificial bone substitutes, especially bone scaffolds coupled with osteobiologics, have been developed as an alternative to the traditional bone grafts. The bone scaffold should have a set of properties to provide mechanical support and simultaneously promote tissue regeneration. Among these properties, scaffold permeability is a determinant factor as it plays a major role in the ability for cells to penetrate the porous media and for nutrients to diffuse. Thus, the aim of this work is to characterize the permeability of the scaffold microstructure, using both computational and experimental methods. Computationally, permeability was estimated by homogenization methods applied to the problem of a fluid flow through a porous media. These homogenized permeability properties are compared with those obtained experimentally. For this purpose a simple experimental setup was used to test scaffolds built using Solid Free Form techniques. The obtained results show a linear correlation between the computational and the experimental permeability. Also, this study showed that permeability encompasses the influence of both porosity and pore size on mass transport, thus indicating its importance as a design parameter. This work indicates that the mathematical approach used to determine permeability may be useful as a scaffold design tool.     

Atomic force microscope investigation of large-circle DNA molecules

A circular bacterial artificial chromosome of 148.9kbp on human chromosome 3 has been extended and fixed on bare mica substrates using a developed fluid capillary flow method in evaporating liquid drops. Extended circular DNA molecules were imaged with an atomic force microscope (AFM) under ambient conditions. The measured total lengths of the whole DNA molecules were in agreement with sequencing analysis data with an error range of +/-3.6%. This work is important groundwork for probing single nucleotide polymorphisms in the human genome, mapping genomic DNA, manipulating biomolecular nanotechnology, and studying the interaction of DNA-protein complexes investigated by AFM.