Mechanics of binding of a single integration-host-factor protein to DNA

We report on a single-molecule experiment where we directly observe local bending of a 76 base pair DNA oligomer caused by specific binding of a single integration-host-factor (IHF) protein. The conformational change of the DNA is detected by optically monitoring the displacement of a micron size bead tethered to a surface by the DNA. Since in the bound state the DNA loops around the IHF, a mechanical tension on the DNA tends to eject the protein. We measure how the rate for the protein to fall off the DNA depends on the mechanical tension in the DNA, gaining insight into the energy landscape for this molecular bond. Our method further demonstrates a new paradigm of molecular detection, where ligand binding is detected through the conformational change induced in the probe molecule. Here this allows the detection of single, unlabeled proteins.     

Direct Observation Method of Individual Single-Stranded DNA Molecules Using Fluorescent Replication Protein A

Direct observation studies of single molecules have revealed molecular behaviors usually hidden in the ensemble and time-averaging of bulk experiments. Direct single DNA molecule analysis of DNA metabolism reactions such as DNA replication, repair, and recombination is necessary to fully understand these essential processes. Intercalation of fluorescent dyes such as YOYO-1 and SYTOX Orange has been the standard method for observing single molecules of double-stranded DNA (dsDNA), but effective fluorescent dyes for observing single molecules of single-stranded DNA (ssDNA) have not been found. To facilitate direct single-molecule observations of DNA metabolism reactions, it is necessary to establish methods for discriminating ssDNA and dsDNA. To observe ssDNA directly, we prepared a fusion protein consisting of the 70 kDa DNA-binding domain of replication protein A and enhanced yellow fluorescent protein (RPA-YFP). This fusion protein had ssDNA-binding activity. In our experiments, dsDNA was stained by SYTOX Orange and ssDNA by RPA-YFP, and we succeeded in staining ssDNA and dsDNA by using RPA-YFP and SYTOX Orange simultaneously.     

基于分子内电荷转移的多枝状荧光探针光学性质与响应机理分析

本文采用含时密度泛函理论研究了用于检测生物硫醇的荧光探针分子的光学性质.通过计算探针分子Mol.1、Mol.2和Mol.3与半胱氨酸和同型半胱氨酸反应前后的单光子吸收和发射性质,研究了碳碳三键和苯环结构对荧光探针性质的影响.随着给电子体三苯胺结构的逐渐完善和碳碳三键的加入,探针分子的振子强度逐渐增大,展现出了更好的荧光探针性质.同时,研究了不同侧枝数目对探针分子性质的影响,结果表明,相较于单枝分子Z1和三枝分子Mol.3,两个侧枝的探针分子Z2振子强度更大,检测效果更佳.增加了碳碳三键和苯环后的单枝新型探针分子Mol.4,相较于具有三枝结构的探针分子Mol.3,具有良好的探针性质,且结构更为简单.     

Extension of a DNA molecule by local heating with a laser

Thermal convection and thermophoresis induced by mum-scale local heating are shown to elongate a single DNA molecule. An infrared laser used as a point heat source is converged into a dispersion solution of DNA molecules, which is observed under a fluorescent microscope. The thermal convection around the laser focus manifests as extensional flow for the long DNA chain. A simulation of thermal convection that reproduces the experimental condition provides numerical support for the stretching caused by thermal convection. This DNA elongation technique is a novel method for manipulating the intact single DNA molecules, and it can be applied to a "lab on a chip".     

Automatic analysis for biochip based on macromolecular compound material

This paper illustrates a way of quantifying fluorescent chromogenic information through the image processing and identification, and analyzes the correlations between fluorescent chromogenic reaction and a probe. This analytical method is an important reference for probe development, and also used for analyzing the biochip interaction. The relationship between the same type but differing concentrations of probe and fluorescent images was derived. With light field analysis of probe attachment, we performed numerical analysis of the fluorescent signal in accordance with the method of biological area analysis. Through this method, biochips can simultaneously provide many types of quantitative and qualitative figures for research reference.     

DSAZn与槲皮素的配位结合及对槲皮素的高灵敏度检测

槲皮素为天然黄酮类化合物,可用于高血压、高血脂、心血管疾病、癌症等的预防和治疗;槲皮素的定量检测在生物化学、临床医学等领域尤为重要。利用分子荧光物质(DSAZn)的聚集诱导发光现象(AIE),通过配位作用识别靶标分子槲皮素,结合激发态电子转移原理,提出了一种AIE型荧光分子对槲皮素的高灵敏度、高选择性检测方法。实验研究了pH 7.0的PBS缓冲液中DSAZn的荧光随着五种药物分子（槲皮素、淫羊藿素、异鼠李素、芦丁、多巴胺）加入后的变化情况。采用荧光分光光度计,以415 nm为激发波长,扫描435~680 nm的荧光发射光谱。采用紫外分光光度计,扫描DSAZn 250~750 nm的紫外吸收光谱。紫外检测表明中药分子槲皮素可以与AIE荧光探针形成复合物,因此加入槲皮素后AIE探针的荧光被静态猝灭。荧光检测表明五种药物分子对荧光探针的猝灭强弱有明显差异,槲皮素与DSAZn结合常数为1.34×107 L·mol-1,比其他四种药物分子和DSAZn的结合常数高出一个数量级,显示出DSAZn对槲皮素具有较好的选择性。槲皮素的检测限为3.07 nmol·L-1,低于诸多文献已报道的参考值,表明DSAZn对槲皮素的识别具有较高的灵敏度。由荧光滴定光谱和荧光滴定曲线得到槲皮素对DSAZn的滴定方程为：y=0.013 4x-0.294 82,槲皮素浓度在0~5 μmol·L-1范围内线性关系良好,线性相关系数r=0.994 3。由此构建出一种AIE型荧光分子对槲皮素的高选择性、高灵敏度检测方法,该方法操作简便、重复性好,为具有相似结构药物的检测提供了新的研究思路。     

Physical manipulation of single-molecule DNA using microbead and its application to analysis of DNA-protein interaction

We carried out an individual DNA manipulation using an optical trapping for a microbead. This manipulation system is based on a fluorescent microscopy equipped with an IR laser. Both ends of linear DNA molecule were labeled with a biotin and a thiol group, respectively. Then the biotinylated end was attached to a microbead, and the other was immobilized on a thiol-linkable glass surface. We controlled the form of an individual DNA molecule by moving the focal point of IR laser, which trapped the microbead. In addition, we applied single-molecule approach to analyze DNA hydrolysis. We also used microchannel for single-molecule observation of DNA hydrolysis. The shortening of DNA in length caused by enzymatic hydrolysis was observed in real-time. The single-molecule DNA manipulation should contribute to elucidate detailed mechanisms of DNA-protein interactions.     

Nanostructured Polyelectrolyte-based System as a Toolbox for Metal Ions Detection

The capability of certain heavy metal ions to induce fluorescence decrease by a quenching mechanism suggested us to design and build a sensor potentially tunable for different ions at different concentrations. We propose a quenching-based sensor exploiting a nanostructured architecture in which fluorescent molecules (the sensing probe) are entrapped to recognize a specific analyte (heavy metal ions) through an optical transduction. The polyelectrolyte nanostructured system, named nanocapsule, improves the fluorophore-ion quenching sensitivity allowing a micromolar detection. Furthermore we couple our sensor with an electrical device in order to refine the sensing procedure: the electric field created allows a metal ions spatial gradient, necessary to detect a specific element on a single sample solution, avoiding a comparative analysis with an intensity reference value. Results obtained will show the advantages and the potentialities of our system as a smart toolbox for metal ions detection.     

拉直的单个DNA分子的全内反射荧光实时成像研究

全内反射荧光(TIRF)成像技术利用穿透深度仅200nm左右的隐失波来激发诱导荧光,探测灵敏度和图像信噪比大大提高,成为单分子研究的有力工具。分子梳技术利用DNA末端与固体表面的结合力和周围流体流动产生的侧向力将DNA分子拉伸并平铺在表面上。结合这两种技术,对分子梳拉直的单个DNA分子进行了清晰的实时荧光成像,发现TIRF成像条件下DNA分子与荧光探针YOYO-1组成的复合体可自然避免发生光敏断裂现象;实时监测了单个DNA-YOYO-1复合体的光漂白过程,通过对激发光照射时间与探测器曝光时间进行同步控制,可大幅降低光漂白程度,为拉直的单个DNA分子的长时间实时观察和成像研究优化了实验条件,为实时、可视化地研究其与蛋白质相互作用的动力学过程奠定了基础。     

Parallel confocal detection of single molecules in real time

The confocal detection principle is extended to a highly parallel optical system that continuously analyzes thousands of concurrent sample locations. This is achieved through the use of a holographic laser illumination multiplexer combined with a confocal pinhole array before a prism dispersive element used to provide spectroscopic information from each confocal volume. The system is demonstrated to detect and identify single fluorescent molecules from each of several thousand independent confocal volumes in real time.