基于DNA纳米结构的分子间相互作用研究

研究生物分子间的相互作用是研究生命本质过程中必不可少的环节.近年来,DNA纳米技术在分子间相互作用的研究中发挥了重要作用,取得了一系列进展. DNA纳米结构具有高度的可编程性和可寻址性,可以利用这些性质采取不同的方式将待测体系修饰在DNA纳米结构上,而且可以精确控制分子的排布、种类、数目等,因此可以作为研究分子间相互作用的模板.在此基础上结合单分子技术,如单分子荧光成像(SMF)、原子力显微术等(AFM),可以实现对单个分子的行为观测.本文首先简述了DNA纳米结构作为研究平台的构建,然后对DNA纳米结构在研究分子间相互作用中的应用进行了阐述,包括用作锚定平台、提供具有一定机械性能的支架以及提供纳米级的微环境,最后对DNA纳米技术的发展进行了总结与展望.     

纳米材料的概述、制备及其结构表征

纳米材料在电子、光学、化工、陶瓷、生物和医药等诸多方面的重要应用而引起人们的高度重视。本文从以下3个方面加以论述。 一、纳米材料的概述:从分子识别、分子自组装、吸附分子与基底的相互关系、分子操作与分子器件的构筑,并通过具体的例证加以阐述,包括在STM操作下单分子反应;有机小分子在半导体表面的自指导生长;多肽-半导体表面特异性选择结合;生物分子/无机纳米组装体;光驱动多组分三维结构组装体;DNA分子机器。 二、纳米材料的若干制备方法和结构表征方法:制备方法包括:物理的蒸发冷凝法,分子束外延法(MBE),机械球磨法,扫描探针显微镜法(SPM)。化学的气相沉淀法(VCD),液相沉淀法,溶胶-凝胶法(Sol-gel),L-B膜法,自组装单分子层和表面图案化法,水热/溶剂热法,喷雾热解法,样板合成法或化学环境限制法及自组装法。 三、若干结构表征方法包括:X-射线法(XRD),扩展X射线精细结构吸收谱(EXAFS),X-射线光电子能谱(XPS),光谱法,扫描隧道显微镜/原子力显微镜(STM/AFM)和有机质谱法(OMS)。     

利用DNA折纸术构建功能纳米材料

DNA折纸术(DNA origami)作为一种精确高效的自组装技术,自2006年Rothemund发明以来在生物医药、高灵敏度检测、纳米光电子器件、等离子体光子学等领域展现出巨大的应用潜力,近年来受到广大研究者的高度关注。 利用DNA折纸术构建纳米材料是以DNA origami结构为载体,通过碱基互补配对的原则及三维结构上可程序化设计和可寻址的特点精确地组装很多功能基团如金属及半导体纳米颗粒,蛋白质和单壁碳纳米管等,并应用于研究无标记的RNA杂交检测、单分子的化学反应、检测间距对多价态的配位体-蛋白质之间键合的影响等。本文对近几年来DNA origami构建功能纳米材料的研究进展加以系统综述,并对DNA origami的发展方向和应用前景进行了展望。     

基于氧化石墨烯和DNA量子点组装体的DNA二元逻辑检测及循环可逆设计

制备了水溶性的氧化石墨烯(GO)和以DNA为模板的Cd Te量子点(P1),通过GO与P1的π-π堆积作用组装构建了纳米生物传感器,将其用于双目标DNA分子的逻辑检测,实现了较高的选择性;通过改进DNA序列,实现了该传感器对双目标分子的可逆循环检测及重复利用.利用原子力显微镜(AFM)、透射电子显微镜、电泳和荧光光谱等方法对传感器的构建和检测过程进行了表征.该P1-GO纳米生物传感器在核酸检测等领域具有较大的应用前景.     

利用原子力显微镜研究在单分子水平上DNA与组蛋白的相互作用

核小体是DNA被压缩成染色质的第一级压缩结构. 为了更深刻描述DNA与组蛋白的相互作用,利用透析方法将DNA和组蛋白构建成核小体,并且应用原子力显微镜进行单分子水平上的观察. 实验结果表明利用透析方法得到了核小体的“串珠型排列”,并且对在两种不同的结合条件下DNA与组蛋白的相互作用进行了观察和比较.     

三螺旋脱氧核糖核酸的研究进展

阐述了三螺旋DNA的发展和最新动态,并从3个方面展开评述：(1)三螺旋DNA稳定性的研究。三螺旋DNA的稳定性不仅取决于寡聚核苷酸的内在结构,还受外界环境如溶液的pH值、阳离子的种类和价态、DNA分子嵌入试剂和共聚物等的影响;(2)三螺旋DNA的应用。三螺旋DNA的形成为基因操纵和基因疗法提供了新方法,它在抑制DNA转录、复制、基因定点诱变、定点切割和诱导基因重组等方面有重要的应用前景;(3)三螺旋DNA的检测方法,包括紫外-可见吸收光谱法、荧光分析法、原子力显微术和顺磁共振谱等。     

DNA四面体结构纳米材料及其应用

基于DNA纳米技术自组装的DNA四面体纳米材料,由于结构稳定、机械性能优越、分子修饰位点丰富等特点,逐渐成为DNA纳米材料领域的研究热点。此外,该DNA四面体纳米材料只需一步热变性即可自组装形成,具有合成方法简单、产率高的优点。可通过不同的设计,利用自组装方法将功能分子修饰在DNA四面体的顶点处,包裹在其笼状孔隙结构内,镶嵌或悬挂在双螺旋的边上,甚至通过引入发卡环结构等方式智能控制其结构变化。本文综述了DNA四面体结构纳米材料的设计和自组装原理、功能化修饰方法和结构的智能化,同时介绍了DNA四面体纳米材料在分子诊断、生物成像、分子输送和靶向给药等方面的应用研究,并探讨了此类纳米材料在今后应用研究中应关注的方面。     

双头基两亲分子在气液界面的Langmuir铺展膜结构

用表面压-面积等温线,原子力显微镜（AFM）和X射线衍射（XRD）对两种具有不同取代位置的新型双头基两亲分子（bolaamphiphile）A和B在气液界面形成的Langmuir铺展膜的结构进行了研究,化合物1,20-二十碳二β-萘酯（B）在气液界面形成了拉伸型 Langmuir单分子膜,而化合物1,20-二十碳二α-萘酯（A）在气液界面则形成了具有三层分子厚度的二维结晶膜.     

液体环境单分子免疫球蛋白G的原子力显微镜高分辨成像

原子力显微镜技术( AFM)具有纳米级高分辨成像能力,是研究生物大分子结构和功能的重要工具之一。制备合适的样品是获取高分辨成像的关键要素。本研究结合DNA折纸技术,将抗原分子修饰在DNA折纸上,通过分子识别作用,抗体分子与抗原分子特异性结合,形成由DNA折纸和抗原抗体复合物构成的纳米结构。利用DNA折纸在云母表面上的吸附特点,使得抗体分子选择性地吸附在衬底表面上,由此获得了液体环境中的单个地高辛抗体免疫球蛋白G( IgG)分子的“Y”超微结构形貌。本方法简单、方便,为AFM在单分子水平上检测和表征生物分子结构和功能提供帮助。     

血清对细胞摄取DNA四面体纳米结构行为的影响

研究了细胞培养基中的胎牛血清(FBS)对DNA四面体(Tetrahedral DNA nanostructure,TDNs)进入HeLa细胞的速度和内吞途径的影响.采用自组装技术得到荧光标记的TDNs结构,利用HPLC技术分离得到纯度>95%的TDNs单体,分别采用流式细胞术和共聚焦显微成像等技术比较了在有无血清的情况下,细胞摄取量随时间的变化以及FBS对TDNs摄取途径的影响.实验结果表明,TDNs在培养基和细胞裂解液环境中可以稳定存在12 h以上,培养基中的FBS能够提高HeLa细胞对四面体的摄取量, 但并未改变TDNs进入HeLa细胞的内吞途径.本研究揭示了环境中蛋白质等生物分子对于DNA四面体结构与细胞界面相互作用的影响,为基于DNA纳米材料的细胞学纳米载体的设计和优化提供了新思路.     

A simple DNA Characterization method using fiber-fluorescence in situ hybridization performed without DNA fragmentation

We performed high-resolution fluorescence imaging of lambda phage DNA molecules hybridized with fluorescent-labeled DNA and peptide nucleic acid probes. In this method, the target DNA and probe were mixed, rapidly denatured and then subjected to liquid hybridization conditions. The hybridized DNA sample was then spotted onto a nontreated glass substrate and subjected to molecular combing. The resultant continuous fluorescence signal of intact lambda DNA shows that the fluorescent-labeled probes bound to the predicted sites but in a pattern that was clearly different to the beads-on-a-string pattern typical for fiber-fluorescence in situ hybridization. The key changes to the conventional method are hybridization of the free target DNA in liquid and lowering the denaturation temperature. The method described here allows the rapid and direct visualization of the specific binding sites of intact DNA molecules without damaging the DNA fibers and causing fragmentation of the fluorescence signal. This technique should be a useful tool in studies of genetics and also large-scale DNA sequencing projects.     

Probing spatial organization of DNA strands using enzyme-free hairpin assembly circuits

Catalyzed hairpin assembly (CHA) is a robust enzyme-free signal-amplification reaction that has a wide range of potential applications, especially in biosensing. Although most studies of the analytical applications of CHA have focused on the measurement of concentrations of biomolecules, we show here that CHA can also be used to probe the spatial organization of biomolecules such as single-stranded DNA. The basis of such detection is the fact that a DNA structure that brings a toehold and a branch-migration domain into close proximity can catalyze the CHA reaction. We quantitatively studied this phenomenon and applied it to the detection of domain reorganization that occurs during DNA self-assembly processes such as the hybridization chain reaction (HCR). We also show that CHA circuits can be designed to detect certain types of hybridization defects. This principle allowed us to develop a "signal on" assay that can simultaneously respond to multiple types of mutations in a DNA strand in one simple reaction, which is of great interest in genotyping and molecular diagnostics. These findings highlight the potential impacts of DNA circuitry on DNA nanotechnology and provide new tools for further development of these fields.     

Assembly of highly aligned DNA strands onto Si chips

This paper reports a robust and efficient approach to assemble highly aligned DNA strands onto Si chips. The method combines advantages from molecular combing and microcontact printing to realize controlling both the density and direction of DNA strands on the Si chip. In addition, it also can be utilized to prepare stretched DNA structures on solid surfaces. Compared to approaches that use molecular combing directly on silanated surfaces, the stretched single-chain DNA structures are straighter. Furthermore, by exploiting the hydrophobic property of the intrinsic poly(dimethylsiloxane) stamp, this study also describes a simple way to produce straight bundled DNA arrays on Si and other substrates.     

Covalent strategy for immobilization of DNA-microspots suitable for microarrays with label-free and time-resolved optical detection of hybridization

Sequence-specific detection and quantification of nucleic acids are central steps in many molecular biology procedures which have also been transferred to chip-based procedures. Hybridization-based assays can be used to quantify and discriminate between DNA target sequences down to the level of single base mismatches. Arrays of DNA probes immobilized on a support enable simultaneous testing of multiple sequences of a single sample. DNA arrays can be produced either by in-situ synthesis of oligonucleotides or by immobilization of pre-assembled DNA probes. Covalent and directed immobilization improves the reproducibility and stability of DNA arrays. This is especially interesting with repeated use of transducers or chips. Procedures are described for effective covalent immobilization of pre-assembled amino-linked oligonucleotides, by use of ink-jet techniques, on a modified and heated glass surface, with addressable surface areas ranging from 0.01 mm2 to a few mm2. Almost immediate evaporation of the spotted droplets on the heated surfaces leads to very high surface hybridization capacities. The surfaces are suitable for use with a label-free detection method - reflectometric interference spectroscopy (RIfS). It is shown that hybridization capacity and non-specific interaction at these DNA-surfaces can be characterized by use of RIfS. With a consumption of less than 80 ng mm(-2) oligonucleotide and a specific hybridization capacity of more than 300 fmol mm(-2), the activated aminodextran procedure was usually suitable for setting up a DNA array with label-free detection. Non-specific interactions with random oligomers or protein (ovalbumin) were low. Up to 150 repeated regenerations (stripping) of the surfaces by acid treatment and denaturing agents, and 50 days of storage, have been possible without significant loss of hybridization capacity.     

Positioning isolation and biochemical analysis of single DNA molecules based on nanomanipulation and single-molecule PCR

Recently, the isolation and biochemical analysis of DNA at the single-molecule level has been recognized as very important for genetic research and clinical analysis. A unique technique for the positioning, dissection, and isolation of single DNA molecules using atomic force microscopy (AFM) has been demonstrated. Full-length genome DNA molecules were first deposited and stretched by a modified "molecular combing" technique onto a 3-aminopropyl triethoxysilane-coated mica substrate. A single DNA fragment was dissected from one of those genome DNA strands with the AFM tip at the desired position, and then isolated (or picked up) after a special operation called "kneading". All the operations including imaging, dissection, and isolation could be carried out with one tip. The isolated DNA fragment on the AFM tip could be successfully amplified by single-molecule PCR.     

杂交及切断过程的QCM实时检测研究(英文)

采用自组装技术,将 5′端标记有巯基的 20-merODN(oligo 1)以金 硫键形式牢固结合在 7. 995MHz的AT-切石英晶体的镀金表面,然后由石英晶体微天平实时检测了与碱基序列互补的 10 merODN (oligo 2)和 8 merODN(oligo 3)的杂交,同时还研究了稀土金属铈离子在温和条件下对DNA的水解切断作用.结果表明:应用QCM方法可能实时检测DNA的固定和杂交,Ce(IV)能随机切断单链DNA;但不能切断杂交形成的双链DNA,因此可利用杂交保护的方法对单链DNA实行定位切断.     

Fast and sensitive DNA analysis using changes in the FRET signals of molecular beacons in a PDMS microfluidic channel

A new DNA hybridization analytical method using a microfluidic channel and a molecular beacon-based probe (MB-probe) is described. A stem-loop DNA oligonucleotide labeled with two fluorophores at the 5′ and 3′ termini (a donor dye, TET, and an acceptor dye, TAMRA, respectively) was used to carry out a fast and sensitive DNA analysis. The MB-probe utilized the specificity and selectivity of the DNA hairpin-type probe DNA to detect a specific target DNA of interest. The quenching of the fluorescence resonance energy transfer (FRET) signal between the two fluorophores, caused by the sequence-specific hybridization of the MB-probe and the target DNA, was used to detect a DNA hybridization reaction in a poly(dimethylsiloxane) (PDMS) microfluidic channel. The azoospermia gene, DYS 209, was used as the target DNA to demonstrate the applicability of the method. A simple syringe pumping system was used for quick and accurate analysis. The laminar flow along the channel could be easily controlled by the 3-D channel structure and flow speed. By injecting the MB-probe and target DNA solutions into a zigzag-shaped PDMS microfluidic channel, it was possible to detect their sequence-specific hybridization. Surface-enhanced Raman spectroscopy (SERS) was also used to provide complementary evidence of the DNA hybridization. Our data show that this technique is a promising real-time detection method for label-free DNA targets in the solution phase. Figure FRET-based DNA hybridization detection using a molecular beacon in a zigzag-shaped PDMS microfluidic channel     

DNA molecular motor driven micromechanical cantilever arrays

The unique ability of living systems to translate biochemical reactions into mechanical work has inspired the design of synthetic DNA motors which generate nanoscale motion via controlled conformational change. However, while Nature has evolved intricate mechanisms to convert molecular shape change into specific micrometer-scale mechanical cellular responses, the integration of artificial DNA motors with mechanical devices presents a major challenge. Here we report the direct integration between an ensemble of DNA motors and an array of microfabricated silicon cantilevers. The forces exerted by the precise duplex to nonclassical i-motif conformational change were probed via differential measurements using an in-situ reference cantilever coated with a nonspecific sequence of DNA. Fueled by the addition of protons, the open to close stroke of the motor induced 32 +/- 3 mN/m compressive surface stress, which corresponds to a single motor force of approximately 11 pN/m, an order of magnitude larger than previous classical hybridization studies. Furthermore, the surface-tethered conformational change was found to be highly reversible, in contrast to classical DNA motors which typically suffer rapid system poisoning. The direction and amplitude of motor-induced cantilever motion was tuneable via control of buffer pH and ionic strength, indicating that electrostatic forces play an important role in stress generation. Hybrid devices which directly harness the multiple accessible conformational states of dynamic oligonucleotides and aptamers, translating biochemical energy into micromechanical work, present a radical new approach to the construction of "smart" nanoscale machinery and mechano-biosensors.     

电化学石英晶体微天平研究界面电场对DNA杂交的影响

采用电化学石英晶体微天平, 现场监测不同界面电场下完全匹配的靶标DNA和不完全匹配的靶标DNA分别与寡聚核苷酸探针分子杂交的过程. 结果表明, 电极表面荷正电时DNA表观杂交效率比电极表面荷负电时高, 但假阳性比较显著; 而电极表面荷负电时能有效地抑制错配杂交. 探讨了引入界面电场后探针分子取向和微观作用力对DNA杂交的影响.     

<Emphasis Type="Italic">Escherichia coli</Emphasis> single-strand binding protein–DNA interactions on carbon nanotube-modified electrodes from a label-free electrochemical hybridization sensor

An electrochemical hybridization biosensor based on the intrinsic oxidation signals of nucleic acids and proteins has been designed, that makes use of the unique binding event between Escherichia coli single-strand binding protein (SSB) and single-stranded DNA (ssDNA). The voltammetric signal from guanine oxidation significantly decreased upon binding of SSB to single-stranded oligonucleotides (probe), anchored on a single-walled carbon nanotube (SWCNT) -modified screen-printed carbon electrode (SPE). Simultaneously, oxidation of the tyrosine (Tyr) and tryptophan (Trp) residues of the SSB protein increased upon binding of the SSB protein to ssDNA and ss-oligonucleotides. After the hybridization, SSB did not bind to the double helix form, and the guanine signal could be observed along with the disappearance of the oxidation signal of the protein. The amplification of intrinsic guanine and protein oxidation signals by SWCNT, and a washing step with sodium dodecylsulfate, enabled the specific detection of a point mutation. Monitoring the changes in the guanine and protein signals upon hybridization greatly simplified the detection procedure. The detection limit of 0.15 g/ml target DNA can be applied to genetic assays. To the best of our knowledge, this is the first work that utilizes the monitoring of SSB–DNA interactions on a solid transducer for the electrochemical detection of DNA hybridization by using intrinsic oxidation signals.