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.     

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.     

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.     

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200 nm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.     

水溶性苝系衍生物荧光探针识别金属离子的光物理机制计算研究

随着人们对荧光化合物电子光谱和光物理行为的深入研究,在利用荧光分子作为探针,检测各种不同体系的状态及其变化等方面都有了巨大的进展。其中,N,N′-二天冬氨酸铵盐-3,4,9,10-四羧酸二酰亚胺(PTCDA)是一种水体环境中选择性好灵敏度高的典型荧光分子探针。本文用密度泛函理论对PTCDA的光物理机制进行研究。计算了PTCDA分子在理想状态下的最优构型,电荷布居和激发光谱。根据计算结果,拟合此苝系衍生物激发态与Cu2+结合前后的吸收光谱,与Cu2+结合前后,吸收光谱峰形相似,加铜后整体吸收峰位发生了红移,有猝灭变色现象。通过与实验值的对比,计算所得分子构型合理有效,激发光谱谱峰位置切合实际。分析得出：PTCDA分子对二价铜离子有较好荧光探测活性,其光信号响应机制属于分子内电荷转移(ICT)机制。当分子接收二价铜离子时,吸收光谱谱峰位置红移,分子内电荷转移方向和强度均发生变化,既有猝灭信号,也有光的颜色变化信号,是一种具有猝灭与变色双信号的荧光探针材料,具有很大的开发潜力。所做工作只是用量子化学计算方法在分子荧光探针领域进行光物理响应机制分析的初步探索,可以为该领域提供系统而有价值的理论参考。     

Submillisecond detection of single rhodamine molecules in water

Using a modified confocal fluorescence microscope and a CW argon laser, we have measured fluorescence bursts from diffusing single Rh6G molecules that clearly exceed the background intensity. The exact average number of molecules in the observable volume elements was measured directly via the fluorescence intensity autocorrelation function. This allowed us to estimate the probability of finding several molecules simultaneously in the volume element. A tradeoff between the number of detected fluorescence photons and the signal-to-background ratio was observed. In a volume element of 0.24 fl, 4 photoelectrons on average were detected from a molecule of Rh6G with a fluorescence-to-background ratio of 1000, while the volume element of 60 fl yielded on average 100 photoelectrons with a background of 25 counts. In fast single-molecule detection the intersystem crossing into the triplet state plays an important role, affecting the maximum emission rate from the molecule.This is a peer-reviewed conference proceeding article from the Third Conference on Methods and Applications of Fluorescence Spectroscopy, Prague, Czech Republic, October 18–21, 1993.     

Quantification of fluorescent molecules in heterogeneous media by use of the fluorescence decay amplitude analysis

In heterogeneous media, including biological objects, fluorescent molecules of one kind often exist as a mixture of species with different fluorescence parameters. Fractional concentrations of these species can be measured by analyzing their fluorescence decay amplitudes. The amplitudes are linear functions of concentrations of actually fluorescent molecules, i.e., molecules whose fluorescence decay can be measured. Other (quenched) molecules do not influence these amplitudes. The other parameter that has to be measured to calculate these concentrations is the radiative rate constant. The parameter can be excluded by comparison of decay amplitudes of the sample studied and a standard. The comparison should be made taking into account the dependence of the radiation rates on emision wavelength. The method has been tested in experiments with the fluorescent probe 3-methoxybenzanthrone (MBA) bound with phosphatidylcholine bilayer membranes. The probe has a complex fluorescence decay in these membranes. The decay can be described as two exponentials, with decay times of 2 and 12 ns and a blue-shifted fluorescence spectrum of the short-life component as compared with long-life one. The shift was used to correct calculated radiative rate values. After this, about 100% of the MBA molecules were found to be fluorescent in these membranes. Thus, this approach can be used to measure absolute concentrations of subpopulations of fluorescent molecules in heterogeneous biological objects.     

基于无标记荧光共振能量转移的microRNA检测方法研究

利用以阳离子共轭聚合物为能量供体的荧光共振能量转移(FRET)策略和滚环扩增放大技术,建立了一种新型的microRNA(miRNA)检测方法。阳离子共轭聚合物采用聚[(9,9-双(6’-N,N,N-三乙基铵)己基)亚芴基亚苯基二溴化物](PFP)。PFP是一种由大量吸光单元共轭而成的阳离子聚合物,具有独特的光捕获和荧光增强性能,可以和带有负电荷的DNA通过静电作用相互结合。SG是一种能够结合于所有双链DNA双螺旋小沟区域的染料,其在游离状态下,荧光微弱,但一旦与双链DNA结合后,荧光会大大的增强。首先,设计了一条可与目标分子特异性杂交的锁式探针和与RCA产物序列互补的DNA链。当体系中存在miRNA时,在T4 DNA连接酶作用下,锁式探针连接成环;随后,在phi29 DNA聚合酶和dNTPs共同作用下,在miRNA的3’端滚环扩增出一条与锁式探针序列互补的长单链DNA,所得产物与互补DNA链杂交形成双链DNA(dsDNA)。此时SG作为FRET受体掺入其中,形成SG-dsDNA共同体。随后, SG-dsDNA与PFP因静电相互作用而紧密接近,由于PFP的发射光谱与SG的激发光谱有重叠,因此二者之间可以发生FRET现象。反之,当体系中不存在miRNA时,挂锁探针则无法连接成环,阻止了扩增反应的进行及其产物与互补DNA链的杂交反应。加入SG后,由于SG与单链DNA的结合能力很弱, SG则游离于溶液中,不会与PFP发生有效的FRET。因此目标分子的浓度与体系的FRET效率直接相关。以let 7a作为待测miRNA分子,在0.05~5 nmol·L-1的范围内, let 7a的浓度与从反应体系测得的FRET效率(I520/I423)成正比。同时以无PFP参加的检测方案作为对比实验,证明了PFP确实具有提高灵敏度的作用。另外,以四种同族miRNA分子及两种其他miRNA分子作为干扰物质对方法的特异性进行了考察,发现除了两种与目标分子序列高度相似的物质存在干扰外,其他物质几乎不产生信号。利用该方法对细胞总RNA提取液中let 7a的含量及其加标含量进行了检测,测量所得回收率基本令人满意。所建立的方案不需要荧光标记探针,有效降低了检测成本,简化了操作步骤,在与miRNA相关的疾病诊断领域具有一定的应用前景。     

Investigation and Development of Quantum Dot-Encoded Microsphere Bioconjugates for DNA Detection by Flow Cytometry

The development of screening assays continues to be an active area of research in molecular diagnostics. Fluorescent microspheres conjugated to biomarkers (nucleic acids, proteins, lipids, carbohydrates) and analyzed on flow cytometer instruments offered a new approach for multiplexed detection platform in a suspension format. Quantum dots encoded into synthetic microspheres have the potentials to improve current screening bioassays and specifically suspension array technology. In this paper, commercialized quantum dot-encoded microsphere were evaluated and optimized as fluorescent probes to address some of the limitations of suspension array technologies. A comprehensive study was undertaken to adapt the bioconjugation procedure to the quantum dot-encoded microsphere structural and optical properties. Both the leaching-out of quantum dots and microspheres degradation under bioconjugation experimental conditions were minimized. A rapid, efficient and reproducible conjugation method was developed for the detection of single-stranded DNA with the commercialized quantum dot-encoded microsphere. Approximately ten thousand microspheres were conjugated to short amino-modified DNA sequences in one hour with high efficiency. The bioconjugated microspheres acting as fluorescent probes successfully detected a DNA target in suspension with high specificity. Quantum dot-encoded microsphere commercial products are limited which strongly prevents reproducible and comparative studies between laboratories. The method developed here contributes to the understanding of quantum dot-encoded microsphere reactivity, and to the optimization of adapted experimental procedure. This step is essential in the development of this new fluorescent probe technology for multiplex genotyping assay and molecular diagnostic applications.     

超衍射极限相干反斯托克斯拉曼散射显微成像技术及其探测极限分析

理论上提出一种突破衍射极限限制的相干反斯托克斯拉曼散射显微成像方法, 并对其探测极限进行分析.通过引入环形附加探测光与艾里斑周边的声子作用, 实现点扩展函数的改造, 提高相干反斯托克斯拉曼散射显微成像系统的横向空间分辨率. 随着分辨率的提高, 信号强度也随之降低, 尤其当应用于生物学、医学研究时, 样品分子数密度通常很低, 这将导致信号探测更加困难. 因此分析系统的探测极限, 确定超分辨体积元内的最小可探测分子数是展开超衍射极限相干反斯 托克斯拉曼散射显微成像实验研究的重要前提. 当泵浦光、斯托克斯光、探测光光强均达到极大值, 分辨率约40 nm三维空间内, 超衍射极限相干反斯托克斯拉曼散射显微成像系统的散粒噪声信噪比由曝 光时间与样品分子数密度决定. 曝光时间若取20 ms, 探测极限约为10³, 样品分子数目只有大于探测极限, 才能保证信号可以从噪声背景中提取出来. 关键词： 突破衍射极限 相干反斯托克斯拉曼散射 非线性光学 探测极限     

用于大景深单分子定位显微的多功能全息相位片的设计及数值模拟

发展具有大轴向定位范围的单分子定位技术对于实现厚样品的超分辨成像具有重要的价值.基于波前编码技术,将变形多值纯相位光栅与双螺旋点扩散函数相位片相结合,提出一种可以通过空间光调制器实现的具有高衍射效率的新型全息相位片的设计方法.这种全息相位片可以将样品内多个层面的分子信息以双螺旋的形式成像在同一个探测面的不同位置,在无需扫描的情况下提高双螺旋点扩散函数工程的轴向定位范围和分辨率,解决活细胞内单分子定位和示踪技术中的大景深探测难题.数值模拟表明,设计的5×5全息相位片可以将样品内25个层面上的分子信息以双螺旋的形式成像在同一探测面上的不同位置,相邻两个层面的间隔为0.5μm,实现了轴向12μm的探测范围,证明了设计的可行性.     

Nanoscale resolution in the focal plane of an optical microscope

Utilizing single fluorescent molecules as probes, we prove the ability of a far-field microscope to attain spatial resolution down to 16 nm in the focal plane, corresponding to about 1/50 of the employed wavelength. The optical bandwidth expansion by nearly an order of magnitude is realized by a saturated depletion through stimulated emission of the molecular fluorescent state. We demonstrate that en route to the molecular scale, the resolving power increases with the square root of the saturation level, which constitutes a new law regarding the resolution of an emerging class of far-field light microscopes that are not limited by diffraction.     

一种改进型单分子操纵装置及其应用

改进了单分子横向磁镊装置,可以直接用于观察单个DNA分子的伸长和扭转并随时更换样品池内的溶液,还可以同时操纵多个DNA分子,大大提高实验效率.此方法可以提供01到40pN范围的拉力,足以满足大部分单分子DNA实验的要求.用该装置实时观测到了DNA分子在拉力作用下的伸长以及在旋转磁场作用下的扭转,并成功地观察到了分子马达拉动DNA的动力学过程,从而验证了该装置的实用性. 关键词： 横向磁镊 单分子操纵 DNA拉伸 DNA扭转     

一种快速测量共聚焦X射线分析装置探测微元尺寸方法

共聚焦X射线荧光技术是一种无损的三维光谱分析技术,在材料,生物,矿物样品分析,考古,证物溯源等领域具有广泛应用。共聚焦X射线荧光谱仪的核心部件为两个多毛细管X光透镜。一个为多毛细管X光会聚透镜（PFXRL）,其存在一后焦点,作用是把X光管所发出的发散X射线会聚成几十微米大小的高增益焦斑。另一透镜为多毛细管X光平行束透镜（PPXRL）,其存在一几十微米大小前焦点,置于X射线能量探测器前端,其作用是接收特定区域的X射线荧光信号。在共聚焦Ｘ射线荧光谱仪中,PFXRL的后焦点与PPXRL的前焦点重合,所形成的区域称作探测微元。只有置于探测微元区域的样品能够被谱仪检测到,使样品与探测微元相对移动,逐点扫描,便能够对样品进行三维无损的X射线分析。探测微元的尺寸决定共聚焦X射线荧光谱仪的空间分辨率,因此精确测量谱仪的探测微元的尺寸是非常重要的。如图1所示,谱仪探测微元可以近似为椭球体,其尺寸可以用水平方向分辨率X, Y,和深度分辨率Z表示。目前,常采用金属细丝或金属薄膜通过刀口扫描的方法测量谱仪探测微元尺寸。为了精确的从三个维度测量探测微元尺寸,金属细丝直径要小于探测微元尺寸。金属细丝和探测微元都是数十微米级别的尺寸大小,很难把金属靠近探测微元。为了得到探测微元在不同X射线能量下尺寸变化曲线,要采用多种金属细丝测量。采用单个金属细丝依次测量比较耗费时间。采用金属薄膜可以很方便地测量探测微元的深度分辨率Z,但是当测量水平分辨率X, Y时,难以准确测量。为了解决以上谱仪探测微元测量中存在的问题,本文提出采用多种金属丝平行粘贴在硬纸片上作为样品用于快速测量探测微元尺寸。附有金属细丝的硬纸片靠近谱仪探测微元,可以将探测微元置于硬纸片所在平面。由于硬纸片与金属细丝在同一水平面,在谱仪摄像头的协助下,可以把金属细丝迅速的靠近探测微元。靠近探测微元后,在全自动三维样品台的协助下,金属细丝沿两个方向对探测微元分别进行一次二维扫描。通过对二维扫描数据的处理便可以获得探测微元尺寸随入射X射线能量变化曲线。采用此方法对实验室所搭建的共聚焦X射线荧光谱仪的探测微元进行了测量。