Name: DNA Origami Nanoantenna (DONA) Assembly and Gel Electrophoresis
Uploaded: 2023-07-21T12:40:00
Duration: 2 min 22 s
Description: Watch this Scientific Journal Video about DNA Origami Nanoantenna DONA Assembly and Gel Electrophoresis at JoVE.com

The video provides a detailed procedure for assembling and purifying DNA origami nanoantennas (DONAs) using DNA-coated gold nanoparticles. It outlines steps for mixing components, hybridizing with a temperature gradient, and purifying via agarose gel electrophoresis, highlighting the appearance of specific bands corresponding to the DONAs during purification.

dna origami nanoantenna (dona) assembly and gel electrophoresis

通过等离子体 DNA 折纸纳米天线实现单分子 SERS 测量

DNA origami is a nanotechnology technique that involves folding DNA strands into specific shapes and patterns. The ability to create structures with precise control at the nanoscale is one of the key advantages of DNA origami1. The ability to manipulate matter at such a small scale has the potential to revolutionize a wide range of fields, including medicine, electronics, and materials science2. For example, DNA origami structures have been used to deliver drugs directly to cancer cells3,4, create nanoscale sensors for detecting diseases5,6, and create intricate patterns on the surfaces of materials6,7. Furthermore, the ability to use DNA origami to create complex nanoscale structures has created new opportunities for studying fundamental biological processes at the nanoscale8.
Surface enhanced Raman scattering (SERS) is a robust analytical technique that detects and identifies molecules at extremely low concentrations9. It is based on the Raman effect, which is a change in the wavelength of scattered light10. SERS requires a plasmonic metal substrate to enhance the Raman signal of molecules adsorbed onto it. This enhancement can be up to 1011 times greater than the signal obtained from the same molecule measured by conventional Raman spectroscopy, making SERS a highly sensitive method for analyzing trace amounts of substances11.
The Raman signal enhancement of nanoparticles is mostly due to electromagnetic enhancement based on the excitation of localized surface plasmon resonance (LSPR)12. In this phenomenon, electrons within the metal nanoparticle oscillate collectively around the surface of the metal nanoparticle during light incidence. This results in the creation of a standing wave of electrons known as a surface plasmon, which can resonate with the incident light. The LSPR greatly enhances the electric field near the particle&#39;s surface, and the optical absorption of the particle is maximum at the plasmon resonant frequency. The surface plasmon&#39;s energy depends on the shape and size of the metal nanoparticle, as well as the properties of the surrounding medium13. A higher enhancement could be further achieved by plasmonic couplings, such as when two nanoparticles are close to each other at a distance of approximately 2.5 times the diameter length or less14. The proximity causes the LSPR of both nanoparticles to interact with each other, enhancing the electric field in the gap between the particles by several orders of magnitude, far exceeding the enhancement of a single nanoparticle15,16,17. The magnitude of the enhancement is inversely proportional to the distance between the nanoparticles; as the distance decreases, a critical point appears where the enhancement is sufficient to detect single molecules (SMs)18.
DNA origami represents a key technology that can efficiently arrange plasmonic nanoparticles to exploit and optimize the plasmonic coupling19. At the same time, molecules of interest can be placed precisely at the place where optical detection is most efficient. This has been demonstrated with DNA origami-based plasmonic nanoantennas for fluorescence detection20. In contrast to the detection of fluorescent labels, SERS provides the possibility to detect a direct chemical fingerprint of a molecule, making the single-molecule SERS very attractive for sensing as well as monitoring chemical reactions and mechanistic studies. DNA origami can also be used as a mask to fabricate plasmonic nanostructures with well-defined shapes21, although the possibility to position target molecules precisely into the hot spot is then lost.
Using colocalized atomic force microscopy (AFM) and Raman measurements, we can obtain the Raman spectra from a single DNA origami nanoantenna (DONA) and potentially a single molecule if placed at the position of highest signal enhancement. The DONA comprises a DNA origami fork and two precisely positioned nanoparticles, fully coated with DNA complementary to extended staple strands attached to the DNA origami. Upon DNA hybridization, the nanoparticles are bound to the DNA origami fork with a 1.2-2.0 nm gap between the nanoparticle surfaces22. Such assembly creates a hot spot in between the nanoparticles with a signal enhancement of up to 1011-fold, as calculated from finite difference time domain (FDTD) simulations22, thus permitting SM SERS measurements. However, the volume of the highest enhancement is small (in the 1-10 nm3 range), and consequently the target molecules need to be positioned precisely into this hot spot. The DNA origami fork allows the positioning of a single molecule between the two nanoparticles using a DNA fork bridge and suitable coupling chemistry. Nevertheless, observing such SMs in Raman spectra is very challenging22. Alternatively, the nanoparticles can be fully coated with the target molecule, such as a TAMRA dye, to allow for single DONA measurements with a higher SERS intensity21. In this case, the TAMRA is covalently attached to the DNA coating strand (Figure 1).

作者聚焦：通过等离子体 DNA 折纸纳米天线实现单分子表面增强拉曼散射测量  

等离子体DNA折纸纳米天线实现的单分子表面增强拉曼散射测量

Our research aims to develop new tools to detect single molecules by surface-enhanced Raman scattering or source. This is the only technique that provides a chemical fingerprint of a molecule and is sensitive enough to detect single molecules. In this way, detailed mechanistic information about chemical reactions can be obtained.DNA origami nanostructures have been used to precisely position both plasmonic nanoparticles and target molecules. And this is required because the enhanced Raman scattering originates from a small nanometric volume between the nanoparticles which we call hotspots. And we have now created new plasmonic DNA origami nanoantenna, exactly for this purpose.The main challenge is to place target molecules in such hotspots between two nanoparticles and collect Raman data from exactly one nanoantenna structure. To collect large amounts of data and efficient correlation between atomic force microscopy an Raman spectroscopy needs to be done. The plasmonic DNA origami nanoantennas allow for a reproducible production of a large number of plasmonic dimers in which the target molecule is precisely positioned in between the nanoparticles in the hotspot.And through a correlation of the AFM and Raman data, we can now make sure that there's only a single molecule that is detected. Now we can track single molecules such as dye molecules or proteins in real time, and their behavior in the hotspots and their reactions to chemical changes in the environment. For example, the change of the spin state of single human molecules was recently monitored.In the future, we aim to monitor chemical reactions at the single molecular level and to study their reaction mechanisms. In addition, we can use this technology to detect medically-relevant biomolecules with very high sensitivity.

Watch this Scientific Journal Video about DNA Origami Nanoantenna DONA Assembly and Gel Electrophoresis at JoVE.com

DNA Origami Nanoantenna (DONA) Assembly and Gel Electrophoresis  

DNA折纸纳米天线（DONA）组装和凝胶电泳

为了组装DNA折纸纳米天线或DONAs，请使用DNA涂层的金纳米颗粒和已经组装的DNA折纸叉。将纳米叉溶液加入到包覆的金纳米颗粒溶液中，保持最终摩尔浓度比为1.5比1。向混合物中加入来自50毫摩尔储备溶液的氯化镁，以达到4毫摩尔的最终氯化镁浓度。使用超纯水将最终体积调节至 20 微升。使用热循环仪中的温度梯度杂交 DONA。从快速加热到40摄氏度开始，按照显示的温度梯度程序逐步进行。为了纯化DONAs，通过将0.8克琼脂糖溶解在补充有5毫摩尔氯化镁的80毫升T A E中来制备1%琼脂糖凝胶。将含有30%甘油和13毫摩尔氯化镁的2.25微升上样缓冲液加入18微升DONA溶液中。在冰水浴中以 70 伏电运行凝胶 60 分钟。切下感兴趣的带并将其放在用石蜡塑料薄膜包裹的显微镜载玻片上。然后使用第二张石蜡薄膜包裹的显微镜载玻片挤出溶液。使用移液管将挤压的液体收集到500微升管中。在琼脂糖凝胶纯化过程中，与DONAs相对应的二聚体条带出现在游离金纳米颗粒条带（样品中运行最快的条带）上方。

Research

JoVE Journal

Chemistry

DNA Origami Nanoantenna (DONA) Assembly and Gel Electrophoresis

Single-Molecule Surface-Enhanced Raman Scattering Measurements Enabled by Plasmonic DNA Origami Nanoantennas

Surface-enhanced Raman scattering (SERS) has the capability to detect single molecules for which high field enhancement is required. Single-molecule (SM) ...