近场光学显微术在生物大分子探测与功能研究中的应用

近场光学显微术是唯一一种具有单分子探测灵敏度,且在对生物样品研究时无损伤的一门新兴的高分辨光学显微术,它是根据近场光学理论在扫描探针显微术的基础上发展起来的。它突破了传统光学显微术衍射极限的限制,可在不损伤样品的情况下同时获得其形貌像和光学像,故在探测单个生物分子并研究其结构和功能以及分子间的相互作用等方面具有显著优势。本文主要介绍近几年来近场光学显微术在生物分子探测和功能研究,以及在分子生物学研究中的应用与进展。     

荧光单分子检测技术在生命科学中的应用

荧光单分子检测技术是用荧光标记来显示和追踪单个分子的构象变化、动力学,单分子之间的相互作用以及单分子操纵的研究。过去对于生命科学分子机制的研究,都是对分子群体进行研究,然后平均化来进行单分子估测。因此,单个分子的动态性和独立性也被平均化掉而无法表现出来。荧光单分子检测技术真正实现了对单个分子的实时观测,将过去被平均化并隐藏在群体测量中不能获得的信息显示出来。近几年来,荧光单分子检测技术的飞速发展,为生命科学的发展,开辟了全新的研究领域。现就荧光单分子检测技术在研究动力蛋白、DNA转录、酶反应、蛋白质动态性和细胞信号转导方面的应用进展作一综述。     

快速展示糖苷水解酶活性架构单点突变导致结合力变化的电泳技术

酶分子在长期进化过程中形成一系列氨基酸残基组成的活性架构,参与底物的识别、结合与催化过程,而活性架构中相应氨基酸残基是如何影响酶分子结合底物的能力,进而影响酶分子的催化效率,一直是酶分子理性改造研究的热点.利用亲和电泳技术,可以快速展示内切纤维素酶Tr Cel12A和木聚糖酶Tl Xyn A活性架构中不同突变体的催化活性及其迁移率的变化,进而通过在不同底物浓度凝胶中蛋白质相对迁移率变化程度的定量回归分析,发现由氨基酸单点突变导致蛋白质迁移率的相对变化,可以定量表征酶分子突变前后结合底物能力的变化.亲和电泳测定的有效阻滞常数Kb值与等温滴定量热法和荧光光谱法测定的相关参数比较具有明显相关性.由于亲和电泳技术在测定酶分子与底物的结合能力时具有简便、快速、灵敏的特点,因而可作为常规生化实验室常规普筛技术来检测突变文库中系列突变体导致结合力的变化.     

生物单分子光学探测方法的进展

活细胞中单分子的实时显视是单分子生物学的关键技术,本文针对单分子显视的光学方法做了评述。分别描述了共焦荧光显微术、荧光全内反射显微术以及荧光共振能量转移探测的技术细节,分析了这些技术对于单分子探测所具备的优势和不足。并对单分子方法的未来发展给出预测。指出包括原于力在内的各种探测手段的联合使用和创新荧光染料技术是进一步提高分辨率的突破口。而随着高灵敏和低噪音探测器的发展,各种新方法的出现也有可能突破目前荧光染料尺度给予的分辨极限。     

葡萄糖淀粉酶色氨酸残基及底物结合位点的研究

 本文用N-溴代琥珀酰亚胺(NBS)对葡萄糖淀粉酶进行特异性修饰,当酶分子表面有3个色氨酸残基被修饰后,酶活力完全丧失。用邹氏图解法测得酶活性中心有一个色氨酸残基是必需的。如果在酶液中加入不同的底物再用NBS氧化,用荧光发射和荧光猝灭光谱检测表明,底物对酶分子有不同程度的保护作用。在被测试的三种底物中,这种保护能力依为糊精>淀粉>麦芽糖。     

近场扫描光学成像结合量子点标记的纳米技术在细胞生物学中的应用

近场扫描光学显微镜（NSOM）对传统的光学分辨极限产生了革命性的突破,可在超高光学分辨率下无侵人性和无破坏性地对生物样品进行观测。量子点（QDs）具有极好的光学性能,如荧光寿命长、激发谱宽、生物相容性强、光稳定性好等优点,适合先进的生物成像。NSOM结合QDs标记的纳米技术被应用在细胞生物学中。通过纳米量级NSOM免疫荧光成像（50nm）对特定蛋白分子在细胞表面的动态分布进行可视化研究和数量化分析,阐明了蛋白分子在不同细胞过程中的作用机制。因此,NSOM／QD基成像系统提供了单个蛋白分子最高分辨率的荧光图像,为可视化研究蛋白分子机制的提供了一种强有力的工具。     

单分子免疫检测技术研究进展*

早诊断、早发现、早治疗是提升肿瘤患者生存率的主要手段。临床常用的免疫学检测方法如酶联免疫吸附法、化学发光法等,其检测灵敏度多限制在10^-14~10^-12 mol/L,无法满足早期诊断的需求。单分子免疫检测法,可将待检测分子限制在极小空间范围内(nL以下),对检测信号进行绝对计数,从而实现痕量(可达10^-18 mol/L)标志物的检测。这一超高灵敏度技术实现的关键在于将检测范围限制在极小体积内。经过数十年发展,不论是物理隔离还是利用纳米孔,抑或通过改进显微镜性能,均可在极小体积内(10^-21 L)对信号进行检测。目前基于微阵列的SimoA检测系统已成为单分子免疫检测的金标准,Quanterix公司基于此开发的HD-1分析仪已进入市场应用。基于微液滴的单分子免疫检测技术主要限于实验室,但具有床旁检测的优势。重点介绍了基于物理隔离形式如微阵列和微液滴的单分子免疫检测进展,为进一步开发超高灵敏度检测方法并促进未来临床应用提供理论基础。     

木瓜蛋白酶酶解鱼鳞提取胶原蛋白的工艺研究

用木瓜蛋白酶水解鱼鳞提取胶原蛋白,对影响酶解过程的的主要因素(酶量、温度、底物浓度)分别作为单因素进行了实验。并通过正交实验得到鱼鳞胶原蛋白提取条件的优化组合,同时对提取物进行了分析检测。结果表明,木瓜蛋白酶对鱼鳞有较好的水解效果,酶用量宜采用4g/L,最佳温度为60℃,底物浓度宜选择20%。     

中华仓鼠二氢叶酸还原酶的酶学性质研究

测定中华仓鼠二氢叶酸还原酶（ＤＨＦＲ,Ｅ．Ｃ．１．５．１．３．）催化反应的各个动力学常数,对其反应机制进行了研究。测定了不同浓度脲溶液中酶与底物的解离常数Ｋｄ和表观米氏常数Ｋｍ,结果表明酶与底物二氢叶酸（ＤＨＦ）和还原型尼克酰胺腺嘌呤二核苷酸磷酸（ＮＡＤＰＨ）的结合能力相差很小,都随脲浓度增加而减弱,而且一种底物的结合会削弱酶与另一底物的结合能力。研究了ＤＨＦＲ在脲变性过程中活力和构象的变化,结果表明低浓度脲可使稳态酶活力增强,此时酶的内源荧光发射光谱和ＣＤ谱变化很小;随脲浓度的增加,酶逐渐失活,同时荧光光谱的最大发射峰位红移,荧光强度和椭圆率也明显下降,说明酶活力的变化先于酶分子整体构象的变化,酶活性部位位于比酶分子整体更易受变性剂影响的有限区域,而且酶分子这种相对的和一定限度内的柔性是其表现生物活性所必需的     

单分子光镊技术在生命科学中的应用

单分子光镊技术是近年来发展起来的一种新型的高分辨率光学技术,可以在单分子水平上实时观测并研究生物大分子或复合物相互作用的动态行为。光镊次毫秒级的时间分辨率和皮牛顿的力分辨率可使我们精确获得中间态、折叠速率(两态迁移速率)、作用力、能量、距离等重要的动力学信息;不同于传统的结构生物学方法,光镊实验是在生理条件下进行的,这些优势都使得光镊技术成为生物物理学领域一项不可或缺的技术手段。该文将主要针对这项单分子光学技术的原理及其在生物动力学上的应用和发展前景作简要介绍。     

Zero-mode waveguides: sub-wavelength nanostructures for single molecule studies at high concentrations

The study of single fluorescent molecules allows individual measurements which can reveal characteristics typically obscured by ensemble averages. Yet, single molecule spectroscopy through traditional optical techniques is hindered by the diffraction limit of light. This restricts the accessible concentrations for single molecule experiments to the nano- to picomolar range. Zero-mode waveguides (ZMWs), optical nanostructures fabricated in a thin aluminum film, confine the observation volume to the range of atto- to zeptoliters. Thus, they extend the accessible concentrations for single molecule spectroscopy to the micro- to millimolar regime. Through the combination of ZMWs and fluorescence correlation spectroscopy, a number of biologically relevant systems have been studied at physiological concentrations. In this review, the concept and implementation of ZMWs is outlined, along with their application to the study of freely diffusing, and membrane-bound fluorescent biomolecules.     

Label-free Single Molecule Detection Using Microtoroid Optical Resonators

Detecting small concentrations of molecules down to the single molecule limit has impact on areas such as early detection of disease, and fundamental studies on the behavior of molecules. Single molecule detection techniques commonly utilize labels such as fluorescent tags or quantum dots, however, labels are not always available, increase cost and complexity, and can perturb the events being studied. Optical resonators have emerged as a promising means to detect single molecules without the use of labels. Currently the smallest particle detected by a non-plasmonically-enhanced bare optical resonator system in solution is a 25 nm polystyrene sphere¹. We have developed a technique known as Frequency Locking Optical Whispering Evanescent Resonator (FLOWER) that can surpass this limit and achieve label-free single molecule detection in aqueous solution². As signal strength scales with particle volume, our work represents a > 100x improvement in the signal to noise ratio (SNR) over the current state of the art. Here the procedures behind FLOWER are presented in an effort to increase its usage in the field.     

High spatial resolution observation of single-molecule dynamics in living cell membranes

Self-organized lipid bilayers together with proteins are the essential building blocks of biological membranes. Membranes are associated with all living systems as they make up cell boundaries and provide basic barriers to cellular organelles. It is of interest to study the dynamics of individual molecules in cell membranes as the mechanism of how biological membranes function at the single molecule remains to be elucidated. In this letter we describe a study in which we incubate rat basophilic leukemia cells with a fluorescently labeled cell membrane component on a surface containing zero-mode waveguides (ZMWs). We used the ZMW to confine fluorescent excitation to an approximately 100-nm region of the membrane to monitor lipid diffusion along the cellular membrane. We showed that confinement with a ZMW largely reduced fluorescent contributions from the cytosolic pool that is present when using a more standard technique such as laser-induced confocal microscopy. We show that optical confinement with ZMWs is a facile way to probe dynamic processes on the membrane surface.     

Zero mode waveguides for single-molecule spectroscopy on lipid membranes

Zero mode waveguides (ZMWs), subwavelength optical nanostructures with dimensions ranging from 50 to 200 nm, have been used to study systems involving ligand-receptor interactions. We show that under proper conditions, lipid membranes will invaginate into the nanostructures, which confine optical excitation to subattoliter volumes. Fluorescence correlation spectroscopy (FCS) was used to characterize the diffusion of fluorescently tagged lipids in liquid-disordered phase 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine (POPC) and gel phase 1,2-distearoyl-sn-glycero-3-phosphocholine (DSPC) membranes incubated on the nanostructured surface. In contrast to the POPC, DSPC membranes did not appear to enter the structures, suggesting that invagination is dependent on membrane rigidity. Although correlation curves obtained from POPC membranes conformed to previously derived models for diffusion in the evanescent field within the nanostructure, the diffusion constants obtained were systematically lower than expected. The validity of the one-dimensional diffusion model for membrane diffusion is discussed and it is concluded that the erroneous diffusion constants are a result of nontrivial membrane conformation within the ZMWs. Additionally, FCS was used to characterize the fraction of fluorescently labeled tetanus toxin C fragment bound to a ganglioside-populated POPC membrane within the ZMWs. This allowed the determination of the toxin's equilibrium binding constant at a concentration of 500 nM; higher than possible with diffraction-limited FCS. To our knowledge, the results presented here are the first reported for supported lipid bilayers in nanostructured devices. Furthermore, they open the possibility of studying membrane imbedded receptors and proteins at physiological concentrations with single-molecule resolution.     

Fluorescence correlation spectroscopy. II. An experimental realization

This paper describes the first experimental application of fluorescence correlation spectroscopy, a new method for determining chemical kinetic constants and diffusion coefficients. These quantities are measured by observing the time behaviour of the tiny concentration fluctuations which occur spontaneously in the reaction system even when it is in equilibrium. The equilibrium of the system is not disturbed during the experiment. The diffusion coefficients and chemical rate constants which determine the average time behaviour of these spontaneous fluctuations are the same as those sought by more conventional methods including temperature-jump or other perturbation techniques. The experiment consists essentially in measuring the variation with time of the number of molecules of specified reactants in a defined open volume of solution. The concentration of a reactant is measured by its fluorescence; the sample volume is defined by a focused laser beam which excites the fluorescence. The fluorescent emission fluctuates in proportion with the changes in the number of fluorescent molecules as they diffuse into and out of the sample volume and as they are created or eliminated by the chemical reactions. The number of these reactant molecules must be small to permit detection of the concentration fluctuations. Hence the sample volume is small (10^?8 ml) and the concentration of the solutes is low (～ 10^?9 M). We have applied this technique to the study of two prototype systems: the simple example of pure diffusion of a single fluorescent species, rhodamine 6G, and the more interesting but more challenging example of the reaction of macromolecular DNA with the drug ethidium bromide to form a fluorescent complex. The increase of the fluorescence of the ethidium bromide upon formation of the complex permits the observation of the decay of concentration fluctuations via the chemical reaction and consequently the determination of chemical rate constants.     

Near-field fluorescence microscopy

The ability to study the structure and function of cell membranes and membrane components is fundamental to understanding cellular processes. This requires the use of methods capable of resolving structures with nanometer-scale resolution in intact or living cells. Although fluorescence microscopy has proven to be an extremely versatile tool in cell biology, its diffraction-limited resolution prevents the investigation of membrane compartmentalization at the nanometer scale. Near-field scanning optical microscopy (NSOM) is a relatively unexplored technique that combines both enhanced spatial resolution of probing microscopes and simultaneous measurement of topographic and optical signals. Because of the very small nearfield excitation volume, background fluorescence from the cytoplasm is effectively reduced, enabling the visualization of nano-scale domains on the cell membrane with single molecule detection sensitivity at physiologically relevant packing densities. In this article we discuss technological aspects concerning the implementation of NSOM for cell membrane studies and illustrate its unique advantages in terms of spatial resolution, background suppression, sensitivity, and surface specificity for the study of protein clustering at the cell membrane. Furthermore, we demonstrate reliable operation under physiological conditions, without compromising resolution or sensitivity, opening the road toward truly live cell imaging with unprecedented detail and accuracy.     

Cylindrical illumination confocal spectroscopy: rectifying the limitations of confocal single molecule spectroscopy through one-dimensional beam shaping

Cylindrical illumination confocal spectroscopy (CICS) is a new implementation of single molecule detection that can be generically incorporated into any microfluidic system and allows highly quantitative and accurate analysis of single fluorescent molecules. Through theoretical modeling of confocal optics and Monte Carlo simulations, one-dimensional beam shaping is used to create a highly uniform sheet-like observation volume that enables the detection of digital fluorescence bursts while retaining single fluorophore sensitivity. First, we theoretically show that when used to detect single molecules in a microchannel, CICS can be optimized to obtain near 100% mass detection efficiency, <10% relative SD in burst heights, and a high signal/noise ratio. As a result, CICS is far less sensitive to thresholding artifacts than traditional single molecule detection and significantly more accurate at determining both burst rate and burst parameters. CICS is then experimentally implemented, optically characterized, and integrated into separate two microfluidic devices for the analysis of fluorescently stained plasmid DNA and single Cy5 labeled oligonucleotides. CICS rectifies the limitations of traditional confocal spectroscopy-based single molecule detection without the significant operational complications of competing technologies.     

Accessing molecular dynamics in cells by fluorescence correlation spectroscopy

Fluorescence correlation spectroscopy (FCS) analyzes spontaneous fluctuations in the fluorescence emission of small molecular ensembles, thus providing information about a multitude of parameters, such as concentrations, molecular mobility and dynamics of fluorescently labeled molecules. Performed within diffraction-limited confocal volume elements, FCS provides an attractive alternative to photobleaching recovery methods for determining intracellular mobility parameters of very low quantities of fluorophores. Due to its high sensitivity sufficient for single molecule detection, the method is subject to certain artifact hazards that must be carefully controlled, such as photobleaching and intramolecular dynamics, which introduce fluorescence flickering. Furthermore, if molecular mobility is to be probed, nonspecific interactions of the labeling dye with cellular structures can introduce systematic errors. In cytosolic measurements, lipophilic dyes, such as certain rhodamines that bind to intracellular membranes, should be avoided. To study free diffusion, genetically encoded fluorescent labels such as green fluorescent protein (GFP) or DsRed are preferable since they are less likely to nonspecifically interact with cellular substructures.     

207 Nanopore immobilization of DNA polymerase enhances single-molecule sequencing

A zero-mode waveguide (ZMW) is a nanoscale optical waveguide driven at a frequency below its cut-off. In this mode, the electric field, instead of traveling down the axis of the conducting cavity, decays exponentially. By fabricating waveguides with sub-wavelength diameters and illuminating them with laser light, the electric field in the waveguide is confined enough to enable single-molecule optical detection at micromolar concentration [1]. Immobilizing single DNA polymerases in ZMWs and using special phosphate-fluorescently labeled dNTPs form the basis for single-molecule real-time DNA sequencing, one of the most promising next-generation sequencing platforms [2]. In this method, the polymerase replicates the sample DNA, and as it incorporates new bases into the product strand, the labeled dNTPs emit a burst of light before the phosphate is cleaved off. The sequence of colors corresponds to the DNA sequence (see Figure 1 below from Eid et al., 2009). Because the ZMW aperture’s diameter is sub-diffraction-limit, it is impossible to optically distinguish one polymerase in a ZMW from two. Having only one polymerase in each waveguide is critical to sequencing accuracy. In its present state, experimenters use diffusion to fill ZMWs with polymerases, resulting in a Poisson distribution for filling ZMWs, and consequently a theoretical limit of 36.8% of ZMWs having only one polymerase [2]. We achieve full polymerase occupancy of ZMWs by fabricating the structures on an ultrathin silicon nitride membrane and drilling a nanopore at the base of each waveguide with an ion beam. A short DNA fragment with biotin on either end is conjugated to a streptavidin and then drawn into the nanopore with a voltage bias. There is then a free biotin at the base of the ZMW. A polymerase–streptavidin complex can diffuse into the ZMW and bind to the exposed biotin. Because the nanopore is too small to fit more than one molecule, only one ZMW will bind to a biotin in the nanopore. Upon flushing the ZMW chamber, the biotin-bound polymerase will remain trapped in the pore, and only a single polymerase will remain at the base of each waveguide.      

Triple-Color Coincidence Analysis: One Step Further in Following Higher Order Molecular Complex Formation

Confocal fluorescence spectroscopy is a versatile method for studying dynamics and interactions of biomolecules in their native environment with minimal interference with the observed system. Analyzing coincident fluctuations induced by single molecule movement in spectrally distinct detection channels, dual-color fluorescence cross-correlation, and coincidence analysis have proven most powerful for probing the formation or cleavage of molecular bonds in real time. The similarity of the optical setup with those used for laser scanning microscopy, as well as the non-invasiveness of the methods, make them easily adaptive for intracellular measurements, to observe the association and dissociation of biomolecules in situ. However, in contrast to standard fluorescence microscopy, where multiple fluorophores can be spectrally resolved, single molecule detection has so far been limited to dual-color detection systems due to the harsh requirements on detection sensitivity. In this study, we show that under certain experimental conditions, employing simultaneous two-photon excitation of three distinct dye species, their successful discrimination indeed becomes possible even on a single molecule level. This enables the direct observation of higher order molecular complex formation in the confocal volume. The theoretical concept of triple-color coincidence analysis is outlined in detail, along with an experimental demonstration of its principles utilizing a simple nucleic acid reaction system.