Capacitance DNA bio-chips improved by new probe immobilization strategies

Label-free DNA detection plays a crucial role in developing point-of-care biochips. Capacitance detection is a promising technology for label-free detection. However, data published in literature often show evident time drift, large standard deviation, scattered data points, and poor reproducibility. To address these problems, mercapto-hexanol or similar alkanethiols are usually considered as blocking agents. The aim of the present paper is to investigate new blocking agents to further improve DNA probe surfaces. Data from AFM, SPR, florescence microscopy, and capacitance measurements are used to investigate new lipoate and ethylene-glycol molecules. The new surfaces offer further improvements in terms of diminished detection errors. Film structures are investigated at the nano-scale to justify the detection improvements in terms of probe surface quality. This study demonstrates the superiority of lipoate and ethylene-glycol molecules as blocking candidates when immobilizing molecular probes onto spot surfaces in label-free DNA biochip.     

Identification of durum wheat cultivars and monovarietal semolinas by analysis of DNA microsatellites

 Microsatellites isolated in bread wheat were used to identify 20 Italian durum wheat (Triticum turgidum var. durum L.) cultivars. A total of 15 microsatellite primer pairs were tested against DNA extracted from leaf tissue, single seeds and semolina. Twelve markers showed allelic polymorphism among the 20 cultivars, providing a total of 41 different alleles. Firstly, an analysis of microsatellite informativeness in the chosen set of durum wheat cultivars was made and a set of highly polymorphic microsatellites was established. Secondly, among the most polymorphic cultivars, the minimum number of microsatellites able to distinguish all cultivars was determined. A set of five microsatellites was found sufficient to differentiate the durum wheat cultivars examined. The method is directly applicable to seeds and semolina, and is suitable for detecting seed mixtures in the same seed lot. Received: 22 February 1999 / Revised version: 19 April 1999     

DNA-纳米颗粒共聚体在最大匹配问题中的应用

该文提出一种DNA计算模型,利用DNA-纳米金颗粒共聚体的自组装来解决图论中的一个NP完全问题——最大匹配问题。根据模型该文设计了能够基于一个具体的图进行自组装的特殊的DNA-纳米金颗粒共聚体,然后利用一系列的实验方法来获得最终的解。这种生物化学算法可以极大地降低求解最大匹配问题的复杂度,这将为DNA自组装计算模型提供一种切实可行的方法。     

DNA-CTMA/a-Si:H bio-hybrid photodiode: A light-sensitive photosensor

Recently, considerable interest have occurred in the development of an organic-inorganic-based bio-hybrid photodiodes (Bio-HPDs) with metal-free, eco-friendly, and cost-competitive features for light-sensitive devices. This paper reports a bio-inspired optical absorber material for the fabrication of Bio-HPDs using n-type hydrogenated amorphous silicon (a-Si:H) and a natural deoxyribonucleic acid (DNA)-cetyltrimethylammonium chloride (CTMA) biomaterial. a-Si:H is inexpensive and abundant, and DNA-CTMA is metal-free and eco-friendly. A DNA-CTMA coating on n-type a-Si:H leads to a chemically stable material with increased absorption and effective ties of dangling bonds and interface state density. Analysis results showed that the rectification ratio (RR) of the Bio-HPD is found to be 4 times higher than reference PD. This indicates that the effective RR is improved by the DNA-CTMA layer since it creates molecular charge interactions between DNA-CTMA layer and a-Si:H substrate. Moreover, Bio-HPD shows a light photosensitivity (I_photo/I_dark) of 474 with more reliable and has longer life time. In addition, the formation and feasible charge transport mechanisms are discussed. This biomaterial can be used for the development of commercially viable and environmentally safe large-scale Bio-HPDs applications.     

紫外线诱变固体DNA的拉曼光谱研究

报道了用拉曼光谱法测定紫外线诱变脱氧核糖核酸（ＤＮＡ）前后的拉曼散射结果。实验结果表明,经过紫外线诱变以后,Ａ－ＤＮＡ型结构特征谱线８１０ｃｍ＾－１减弱;分别反应脱氧核糖磷酸盐链振动和Ｃ０Ｏ伸缩振动的谱带８８４ｃｍ＾－１和１０１０ｃｍ＾－１、１０６８ｃｍ＾－１都有不同程度的 减弱;属于脱氧核糖在１４６８ｃｍ＾－１处的谱线显著减弱;还有个别咸基谱带出现（在６７０ｃｍ＾－１处的胸腺嘧啶Ｔ）、增强（在     

Functionalized Nanostructures with Liquid‐Like Behavior: Expanding the Gallery of Available Nanostructures

Recently, we have developed a novel family of functionalized nanostructures that exhibit liquid‐like behavior in the absence of solvents and preserve their nanostructure in the liquid state. The gallery of nanostructures developed so far includes functionalized silica and magnetic iron oxide nanoparticles, layer‐like organosilicate nanoparticles, polyoxometalate clusters, and organic–inorganic hybrid networks. In an effort to demonstrate the wider applicability of this concept and to provide a deeper insight into this class of materials, the present work cites additional paradigms of functionalized nanostructures with similar behavior as above. In one case, surface functionalization of anatase nanoparticles (TiO₂, an inorganic nanostructure) with a quaternary ammonium organosilane leads to ionically modified nanoparticles that, when electrostatically combined with a poly(ethylene glycol) (PEG)‐tailed sulfonate anion, exhibit liquid‐like behavior in the absence of solvents. In a different but quite interesting case of a bionanostructure, ion‐exchange functionalization of a DNA oligonucleotide with a PEG‐tailed quaternary ammonium cation leads to an easily separable liquid derivative with attractive features. These examples show the versatility of this concept over a range of nanostructures.     

A Tailored Artificial DNase Blocks Sensor Activation and Prevents Autoimmune and Autoinflammatory Diseases

Excessive self-DNAs recognized by intracellular DNA sensors can initiate innate immunity to express disordered TNF-α or type I IFN resulting in several autoimmune diseases. Cationic polymers have been profoundly proved to alleviate the inflammatory symptoms by removing the debris of cell-free DNA (cfDNA). However, clinical applications of cationic materials have been impeded by concerns of their toxicity and the fate of cfDNA in polymer-cfDNA complex. Herein, it is showed that PEGylated polyimidazoles as a biomimetic DNase potently alleviate pathologic symptoms of self-DNA-associated rheumatoid arthritis (RA) rats and Trex1 (DNase III) deficient Aicardi-Goutiéres syndrome (AGS) mice. The mechanism studies demonstrate that the polyimidazole efficiently attacks the phosphodiester linkages of NAs and cleavages them into small pieces. As imidazole unit is a much weaker organic base that occurs in natural proteins, the polyimidazoles are less toxic to cells and tissues, as manifested by the IC50 values larger than 1000 µg mL⁻¹. This work suggests that synthetic tailored DNase can be a new and safe therapeutic agent to treat chronic autoimmune and refractory inflammatory diseases by degradation of excessive nucleic acids.     

Artificial Intelligence-Assisted Label-Free Spectroscopic Quantification of Global DNA Cytosine Methylation in a Miniature Plasmonic Pickering Emulsion

Epigenetic DNA methylations are early and frequently observed events in a diversity of diseases such as cancer. Despite the considerable clinical values for cancer liquid biopsy, quantitative analysis of DNA methylations remains a major challenge due to the lack of rapid, sensitive detection techniques. Here, an artificial intelligence-assisted label-free surface-enhanced Raman spectroscopy (SERS) (iMeSERS) biosensor is reported for simultaneous quantification of C⁵-methylcytosine (^5mC) level and methylation ratio in DNA samples. This method utilizes the plasmonic Pickering emulsions as the biosensing platform for label-free SERS detection, formed upon the addition of a sub-microliter DNA sample to the hydrophobic Au nanostar-containing n-decane. Distinct spectral signatures of monophosphates of canonical deoxyribonucleotides (dNMPs) and the common methylation modification 5-methyl-2′-deoxycytidine (d^5mCMP) are identified and distinguished by the iMeSERS biosensor. The deep learning algorithms trained with SERS signatures of dNMPs and d^5mCMP are then applied to the quantitative analysis of global DNA methylation. The exceptional capability of the deep learning-driven approach is demonstrated for simultaneous quantification of the methylation ratio and level using a sub-microliter volume of DNA samples. This work shows the power of label-free SERS techniques combined with deep learning algorithms for quantitative analysis of epigenetic DNA modifications with great promises for clinical diagnosis.     

非接触纳米三维表面形貌测量激光与电场在滇稻育种中的微观作用机制分析比较

提出了一种基于激光的Raman -Nath衍射和光干涉进行纳米级测量的光机电一体化的新方法 ,分析了数字鉴相、A/D变换和X/Y驱动的特点 ,并对测量精度进行了扼要地分析用激光加电场进行育种研究 ,发现静电场和激光的作用效果是不相同的。这反映了它们与生物组织的相互作用机制的差异。本文用量子力学对此差异进行了解析分析 ,并与育种试验结果进行印证。得出电场辐照种子 ,可降低蛋白质分子的能级 ,增加种子的生物活性 ;激光辐照种子 ,有可能使DNA的构象发生变化 ,从而引起一定程度上的变异     

Self-Mineralizing Dnazyme Hydrogel as a Multifaceted Bone Microenvironment Amendment for Promoting Osteogenesis in Osteoporosis

The accumulation of reactive oxygen species (ROS) and minimal osteogenic raw material in the osteoporotic bone microenvironment greatly inhibits the activity of osteoblasts. Herein, it is originally proposed to construct a biomatrix multifaceted bone microenvironment amendment -Mineralized zippered G4-Hemin DNAzyme hydrogel (MDH)-to improve osteoporotic osteogenic capacity and promote high-quality bone defect repair. The programmed design of the rolling circle amplified DNA hydrogel synthesis system allows the introduction of massive amounts of zippered G4-Hemin DNAzyme in MDH. The zippered G4-Hemin DNAzyme highly mimics the tight catalytic configuration of horseradish peroxidase and exerts excellent enzyme-like activity with considerable ROS molecule scavenging ability. In addition, the DNA amplification by-product pyrophosphate is ingeniously employed as a sufficient phosphorus source, thus constituting an autonomous mineralization system for waste reuse through the introduction of pyrophosphate hydrolase and calcium ions, which deposits in MDH as an osteogenic raw material and addresses the challenge of DNA hydrogel bio-application stability. The remarkable in vitro and in vivo outcomes demonstrate that MDH can effectively improve the oxidative stress status of osteoblasts, restore the balance of mitochondrial membrane potential, and reduce apoptosis, ultimately demonstrating superior osteogenic capacity.