原子力显微镜拉伸吸附在金膜表面的短单链DNA分子

对单根DNA分子的操纵和拉伸可以直接研究DNA的弹性等力学性质. 首先通过将金沉积到云母表面制备了表面粗糙度小于0.3 nm的金膜,然后一段硫代的单链DNA (100 bases) 吸附到金膜表面. 利用原子力显微镜观察不同浓度的DNA吸附在金膜上的表面形貌. 进一步用原子力显微镜的力曲线模式拉伸DNA分子,在50％的情况下DNA可以被针尖拉伸,观察到了由于针尖和DNA分子间作用力的不同导致的多种不同力曲线.     

AFM单分子力谱技术及其在活体细胞和菌体表面生物大分子研究中的最新进展

生命活动过程与生物分子内或生物分子间机械力的作用密不可分.原子力显微镜具有极高的力学分辨率,可以在近生理条件下对生物样品进行力学测量,是研究生物体系力学相互作用的理想工具.基于原子力显微镜的单分子力谱(AFM-SMFS)技术可以在单分子、单细胞水平测量生物分子内或生物分子间的相互作用.本文首先扼要介绍了AFM-SMFS技术,包括AFM-SMFS的基本原理、力谱测量及分析方法(蠕虫链模型、自由连接链模型和自由旋转链模型)以及探针的化学修饰方法(硅/氮化硅探针和镀金探针的修饰);重点介绍了利用AFM-SMFS技术对活体细胞表面蛋白(转化生长因子β1、CD20、热休克蛋白以及蛋白酪氨酸激酶)和糖类分子(葡萄糖和甘露糖)的近期研究进展;随后介绍了利用AFM-SMFS技术对活菌体表面蛋白(肝素结合血凝黏附素和Als5p黏附蛋白)和糖类分子(半乳糖、甘露糖、B族碳水化合物、荚膜多糖、α-甘露聚糖、β-甘露聚糖、β-葡聚糖以及几丁质)的近期研究进展;最后对AFM-SMFS技术的缺点和发展前景进行了总结和展望.     

见微知著:单分子力谱技术窥探蛋白质分子动态功能北大核心CSCD

蛋白质的动态功能调控并决定着细胞的生理和病理过程。其不仅受到蛋白质本身生物化学特性的影响,还受到生物体内复杂的生物力学微环境的动态调控。这些生物力因素主要通过耦联生物化学特性来改变蛋白质的动态相互作用、构象变化以及后续的信号传导。近些年来,单分子力谱检测技术突破了传统生物化学技术的限制,在单分子水平有效地研究生物力学——化学耦联调控下的蛋白质动态功能。本文详细介绍了4种代表性的单分子力谱检测技术(原子力显微镜、光镊、生物膜力学探针以及磁镊),着重介绍这些技术在蛋白质动态功能研究方面的典型应用,主要包括蛋白质动态相互作用,蛋白质动态构象变化以及信号传导等。同时,本文还介绍了几种常用的基于上述单分子检测技术的单分子力谱检测方法,主要用于定量检测蛋白质相互作用、构象变化等生物化学过程的分子动力学参数。最后,本文还简要讨论了单分子力谱检测技术的未来发展方向,特别是如何与其他研究手段的有机整合,更全面地研究蛋白质的动态功能。我们希望该综述能够给更多的生物化学家带来新的概念和工具,帮助更全面地研究蛋白质的动态特性。     

原子力显微镜在生物医学上的应用

原子力显微镜(atomic force microscope,AFM)是扫描探针显微镜(SPM)的一种,其分辨率达到纳米级,能对从原子到分子尺度的结构进行三维成像和测量,能观察任何活的生命样品及动态过程。本文概述了AFM的基本工作原理及在生物医学上对DNA、蛋白质、细胞及生物过程等方面进行的研究。     

RAS-RAF蛋白相互作用结构域的单分子力谱分析北大核心CSCD

利用自行构建的光镊系统,通过in vitro单分子力谱测量,在单分子水平研究了RAS/RAF/MEK/ERK信号传导通路中的重要信号传导蛋白RAF与其上游G蛋白RAS结合的势垒形态。RAS与野生型RAF的单分子结合力分布情况显示,RAS-RAF结合至少涉及RAS结合区(RAS binding domain,RBD)及半胱氨酸富集区(cysteine rich domain,CRD)两个作用位点。而RAS与RAF突变体RAF(Q257R)的单分子结合力分布,存在两个以上的结合域:最可几力为95 pN的包络对应RAS-RAF[RBD]结合;最可几力为117 pN的包络对应RAS-RAF[CRD]结合;最可几力为159 pN的包络对应RAS-RAF[RBD]和RAS-RAF[CRD]同时存在(叠加)时的相互作用。而且在大于200 pN的范围(光镊有效量程之外),RAS与RAF(Q257R)的结合力仍然有相当的概率分布。这说明,突变体RAF(Q257R)比其野生型更易于与RAS结合,且可能涉及新的结合位点。该发现对解释Q257R的致病机理及设计拮抗剂均有重要指导意义。     

原子力显微镜研究粘附分子与细胞膜上整合素分子的相互作用

目的：研究肝癌细胞弹性变化对其表达的整合素分子与配体分子相互作用的影响。方法：以壳聚糖/ 聚丙烯酰胺水凝胶作为可变基底材料,并将人肝肿瘤细胞（HepG2）接种到不同软硬度壳聚糖/ 聚丙烯酰胺水凝胶基底上,利用原子力显微镜力与距离模式定量测定不同软硬基底上生长的HepG2 肝瘤细胞膜表面整合素分子与层粘连蛋白分子之间相互作用力。结果：功能化的原子力显微镜探针与不同软硬基底上生长的细胞所产生的粘附情况不相同,细胞生长在培养皿的为对照组;细胞生长在硬度为1000Pa 壳聚糖/聚丙烯酰胺水凝胶基底上的为实验组,表达在HepG2 肝瘤细胞膜上的alpha-6-beta-1 整合素与其配体层粘连蛋白相互作用力的大小分别为19± 7 pN和38.85± 19.7 pN。结论：基底软硬度会影响细胞整合素与配体分子间的相互作用。     

核糖体失活蛋白与超螺旋DNA相互作用的原子力显微镜直接观察

运用原子力显微镜研究了核糖体失活蛋白 (RIP)与超螺旋DNA相互作用 ,发现这类毒蛋白 (克木毒蛋白和蓖麻毒蛋白A链 ) ,既能与超螺旋形式的DNA结合 ,又能结合在超螺旋DNA分子中未解旋的双链环区 .在与超螺旋DNA结合后 ,引起超螺旋DNA构象变化以利解旋并与双链DNA结合 ,进而将松弛的DNA双链切成缺口或线性形式 .这说明RIP是一种超螺旋DNA结合蛋白 ,并表现出依赖超螺旋的DNA内切酶活性     

用原子力显微镜研究炎症反应中粘附分子间相互作用

在炎症反应中,白细胞在血液流动动力和粘附分子的作用下在血管内皮上的滚动,是白细胞从流动的血液中浸润、迁移到炎症部位整个过程的第一步。白细胞在内皮细胞上滚动由选择素分子与其配体分子相互作用所导致,其中P选择素分子（P-selectin）与其对应的P-选择素糖蛋白配体-1（PSGL-1）的相互作用起着重要的作用。原子力显微镜技术能定量分析P-seleetin／PSGL-1相互作用的动力学反应。     

原子力显微镜观测紫外线诱导的K562肿瘤细胞DNA损伤

利用彗星电泳检测出UVB、UVC短时间照射会使肿瘤细胞的DNA发生断裂,而长时间照射之后彗星电泳无法检测到碎片,推测可能是由于DNA分子交联的原因[1],国内外尚无定论.为了更直观的研究这种现象,提取了UVB,UVA照射后K562细胞的DNA,并调节到合适的浓度在原子力显微镜下观测.实验结果表明UVB对K562肿瘤细胞DNA损伤的影响呈现时间/剂量效应,较短时间照射主要产生DNA的链断裂,较长时间辐射则主要产生DNA链的交联.UVC对K562肿瘤细胞DNA的损伤大于UVB.UVC短时照射即可引起DNA的断裂和交联,较长时间辐射主要产生交联和一些断裂;长时间照射不但产生大量交联,同时有大量断裂产生,并发生凝缩和缠绕等结构破坏.     

原子力及原子力声显微镜应用于生物学领域的回顾与展望

回顾了显微镜的发展史,着重介绍了原子力显微镜的工作原理,工作模式,成像特点及其在生物学领域的应用。对最新的原子力声显微镜的发展做了展望。     

High-speed atomic force microscopy: Imaging and force spectroscopy

Atomic force microscopy (AFM) is the type of scanning probe microscopy that is probably best adapted for imaging biological samples in physiological conditions with submolecular lateral and vertical resolution. In addition, AFM is a method of choice to study the mechanical unfolding of proteins or for cellular force spectroscopy. In spite of 28 years of successful use in biological sciences, AFM is far from enjoying the same popularity as electron and fluorescence microscopy. The advent of high-speed atomic force microscopy (HS-AFM), about 10 years ago, has provided unprecedented insights into the dynamics of membrane proteins and molecular machines from the single-molecule to the cellular level. HS-AFM imaging at nanometer-resolution and sub-second frame rate may open novel research fields depicting dynamic events at the single bio-molecule level. As such, HS-AFM is complementary to other structural and cellular biology techniques, and hopefully will gain acceptance from researchers from various fields. In this review we describe some of the most recent reports of dynamic bio-molecular imaging by HS-AFM, as well as the advent of high-speed force spectroscopy (HS-FS) for single protein unfolding.     

Ultrastable atomic force microscopy: Improved force and positional stability

Atomic force microscopy (AFM) is an exciting technique for biophysical studies of single molecules, but its usefulness is limited by instrumental drift. We dramatically reduced positional drift by adding two lasers to track and thereby actively stabilize the tip and the surface. These lasers also enabled label-free optical images that were spatially aligned to the tip position. Finally, sub-pN force stability over 100 s was achieved by removing the gold coating from soft cantilevers. These enhancements to AFM instrumentation can immediately benefit research in biophysics and nanoscience.     

Characterizing molecular interactions in different bacteriorhodopsin assemblies by single-molecule force spectroscopy

Using single-molecule force spectroscopy we characterized inter- and intramolecular interactions stabilizing structural segments of individual bacteriorhodopsin (BR) molecules assembled into trimers and dimers, and monomers. While the assembly of BR did not vary the location of these structural segments, their intrinsic stability could change up to 70% increasing from monomer to dimer to trimer. Since each stable structural segment established one unfolding barrier, we conclude that the locations of unfolding barriers were determined by intramolecular interactions but that their strengths were strongly influenced by intermolecular interactions. Subtracting the unfolding forces of the BR trimer from that of monomer allowed us to calculate the contribution of inter- and intramolecular interactions to the membrane protein stabilization. Statistical analyses showed that the unfolding pathways of differently assembled BR molecules did not differ in their appearance but in their population. This suggests that in our experiments the membrane protein assembly does not necessarily change the location of unfolding barriers within the protein, but certainly their strengths, and thus alters the probability of a protein to choose certain unfolding pathways.     

Study of interaction between Smad7 and DNA by single-molecule force spectroscopy

Smad7 is an antagonist of TGF-β signaling pathway and the mechanism of its inhibitory effect is of great interest. We recently found that Smad7 could function in the nucleus by binding to the DNA elements containing the minimal Smad binding element CAGA box. In this work, we further applied single-molecule force spectroscopy to study the DNA-binding property of Smad7. Smad7 showed similar binding strength to the oligonucleotides corresponding to the CAGA-containing activin responsive element (ARE) and the PAI-1 promoter, as that of Smad4. However, Smad7 also exhibited a binding activity to the mutant ARE with the CAGA sequence substituted, indicating its DNA-binding specificity is different from other Smads. Moreover, we demonstrated that the MH2 domain of Smad7 had a higher binding affinity to the DNA elements than the full-length Smad7, while the N-terminal domain exhibited an inhibitory effect.     

Assessing the flexibility of intermediate filaments by atomic force microscopy

Eukaryotic cells contain three cytoskeletal filament systems that exhibit very distinct assembly properties, supramolecular architectures, dynamic behaviour and mechanical properties. Microtubules and microfilaments are relatively stiff polar structures whose assembly is modulated by the state of hydrolysis of the bound nucleotide. In contrast, intermediate filaments (IFs) are more flexible apolar structures assembled from a approximately 45 nm long coiled-coil dimer as the elementary building block. The differences in flexibility that exist among the three filament systems have been described qualitatively by comparing electron micrographs of negatively stained dehydrated filaments and by directly measuring the persistence length of F-actin filaments (approximately 3-10 microm) and microtubules (approximately 1-8 mm) by various physical methods. However, quantitative data on the persistence length of IFs are still missing. Toward this goal, we have carried out atomic force microscopy (AFM) in physiological buffer to characterise the morphology of individual vimentin IFs adsorbed to different solid supports. In addition, we compared these images with those obtained by transmission electron microscopy (TEM) of negatively stained dehydrated filaments. For each support, we could accurately measure the apparent persistence length of the filaments, yielding values ranging between 0.3 microm and 1 microm. Making simple assumptions concerning the adsorption mechanism, we could estimate the persistence length of an IF in a dilute solution to be approximately 1 microm, indicating that the lower measured values reflect constraints induced by the adsorption process of the filaments on the corresponding support. Based on our knowledge of the structural organisation and mechanical properties of IFs, we reason that the lower persistence length of IFs compared to that of F-actin filaments is caused by the presence of flexible linker regions within the coiled-coil dimer and by postulating the occurrence of axial slipping between dimers within IFs.     

Functionalization of amino-modified probes for atomic force microscopy

The probes for atomic force microscopy (AFM) functionalized with bovine serum albumin (BSA) were obtained; they can be used for molecular recognition studies. The procedure of modification and functionalization of the AFM probe included three stages. First, amino probes were obtained by modification in vapors of an amino silane derivative. Then, a covalent bond was formed between the surface amino groups of the probe and a homobifunctional aminoreactive crosslinker. Finally, the probe with a covalently attached crosslinker was functionalized with BSA molecules. The AFM probes were characterized by force measurements at different stages of the modification; the adhesion force and the work of adhesion force were determined. The modification process was confirmed by visualization of BSA and supercoiled pGEMEX DNA molecules immobilized on the standard amino mica and on amino mica modified with a crosslinker.     

原子力显微技术在酶学研究中的应用

酶在生物体的生命活动中占有及其重要的地位,机体功能的和谐统一有赖于酶的作用。原子力显微技术(AFM)作为一门新发展起来的技术,为人们认识酶的结构与功能提供了又一新的窗口。AFM能够在生理条件下对生物样品进行三维成像,在分子水平上实时监测生理生化反应。AFM还能够在皮牛顿精度上测定分子间作用力。目前,AFM已用于单分子酶的化学性质及其作用原理的研究。本简述AFM在酶学中的应用情况。     

原子力显微技术成像在生物医学中的应用

原子力显微技术利用探针尖端与标本之间相互作用的力场对标本进行三维成像。这种成像可在生理条件下进行 ,可进行动态观察和标本容易制备是有别于其它成像技术如电子显微镜成像等的特点。对于细胞和生物大分子 ,能够在生理条件下成像具有重要意义。它意味着人们在认识生命本质的方法学方面 ,又向前迈出了新的一步。本文简要综述对细胞和生物大分子的成像在生物医学方面的应用。     

Atomic force microscope-based single-molecule force spectroscopy of RNA unfolding

Single-molecule force spectroscopy (SMFS) using the atomic force microscope (AFM) has emerged as an important tool for probing biomolecular interaction and exploring the forces, dynamics, and energy landscapes that underlie function and specificity of molecular interaction. These studies require attaching biomolecules on solid supports and AFM tips to measure unbinding forces between individual binding partners. Herein we describe efficient and robust protocols for probing RNA interaction by AFM and show their value on two well-known RNA regulators, the Rev-responsive element (RRE) from the HIV-1 genome and an adenine-sensing riboswitch. The results show the great potential of AFM–SMFS in the investigation of RNA molecular interactions, which will contribute to the development of bionanodevices sensing single RNA molecules.     

Observation of single-stranded DNA on mica and highly oriented pyrolytic graphite by atomic force microscopy

Atomic force microscopy was used to image single-stranded DNA (ssDNA) adsorbed on mica modified by Mg(2+), by 3-aminopropyltriethoxysilane or on modified highly oriented pyrolytic graphite (HOPG). ssDNA molecules on mica have compact structures with lumps, loops and super twisting, while on modified HOPG graphite ssDNA molecules adopt a conformation without secondary structures. We have shown that the immobilization of ssDNA under standard conditions on modified HOPG eliminates intramolecular base-pairing, thus this method could be important for studying certain processes involving ssDNA in more details.