High-Speed Atomic Force Microscopy Revealing Contamination in DNA Purification Systems

In-site electrophoretic elution of excessive fluorescein isothiocyanate from fluorescent particles in gel for image analysis

去除荧光标记后残余荧光染料可以提高荧光颗粒检测的灵敏度、准确度和效率。该文发展了一种原位电泳洗脱(electrophoretic elution, EE)模型,用于在荧光标记后快速去除多余的荧光探针,实现荧光颗粒的灵敏检测。将牛血清蛋白(BSA)和磁珠(MBs)作为模式蛋白和微颗粒,混合孵育获得MBs-BSA,用异硫氰酸荧光素(FITC)对MBs-BSA标记,得到MBs-BSA_FITC复合物。将含有多余FITC的MBs-BSA_FITC溶液与低凝聚温度琼脂糖凝胶溶液按1:5的体积比混合,并将混合物凝胶和纯琼脂糖凝胶分段填充到电泳通道中。电泳过程中,利用颗粒尺寸与凝胶孔径的差异来保留MBs-BSA_FITC,同时将游离的FITC洗脱。经过30 min的电泳洗脱,通道内多余的FITC清除率达到97.6%,同时目标颗粒荧光信号保留了27.8%。成像系统曝光时间为1.35 s时,电泳洗脱将颗粒与背景的荧光信号比(P/B ratio, PBr)从1.08增加到12.2。CCD相机的曝光时间增加到2.35 s,可以将PBr提高到15.5,可进一步实现对微弱荧光亮点的高灵敏检测。该模型有以下优点:(1)能对颗粒表面非特异性吸附的FITC实现有效洗脱,提高了检测的特异性;(2)能够将97%以上的游离FITC清除;(3) 30 min内能够使凝胶内的背景荧光大幅降低,提高了PBr和检测灵敏度。因此,该方法具有在凝胶中进行基于磁珠/荧光颗粒点的免疫检测、在免疫电泳或凝胶电泳中对蛋白质/核酸条带进行荧光染色等领域的应用潜力。

Algal Viruses: The (Atomic) Shape of Things to Come

Visualization of algal viruses has been paramount to their study and understanding. The direct observation of the morphological dynamics of infection is a highly desired capability and the focus of instrument development across a variety of microscopy technologies. However, the high temporal (ms) and spatial resolution (nm) required, combined with the need to operate in physiologically relevant conditions presents a significant challenge. Here we present a short history of virus structure study and its relation to algal viruses and highlight current work, concentrating on electron microscopy and atomic force microscopy, towards the direct observation of individual algae⁻virus interactions. Finally, we make predictions towards future algal virus study direction with particular focus on the exciting opportunities offered by modern high-speed atomic force microscopy methods and instrumentation.

[Progress in the applications of high-speed atomic force microscopy in cell biology]

Without losing its high resolution, high-speed atomic force microscope (HS-AFM) represents a perfect combinationof scanning speed and precision and allows real-time and in situ observation of the dynamic processes in a biological system atboth the cellular and molecular levels. By combining the extremely high temporal resolution with the spatial resolution andcoupling with other advanced technologies, HS-AFM shows promising prospects for applications in life sciences such as cellbiology. In this review, we summarize the latest progress of HS-AFM in the field of cell biology, and discuss the impact ofenvironmental factors on conformation dynamics of DNA, the binding processes between DNA and protein, the domainchanges of membrane proteins, motility of myosin, and surface structure changes of living cells.

DNA nanomapping using CRISPR-Cas9 as a programmable nanoparticle

Progress in whole-genome sequencing using short-read (e.g., <150 bp), next-generation sequencing technologies has reinvigorated interest in high-resolution physical mapping to fill technical gaps that are not well addressed by sequencing. Here, we report two technical advances in DNA nanotechnology and single-molecule genomics: (1) we describe a labeling technique (CRISPR-Cas9 nanoparticles) for high-speed AFM-based physical mapping of DNA and (2) the first successful demonstration of using DVD optics to image DNA molecules with high-speed AFM. As a proof of principle, we used this new “nanomapping” method to detect and map precisely BCL2–IGH translocations present in lymph node biopsies of follicular lymphoma patents. This HS-AFM “nanomapping” technique can be complementary to both sequencing and other physical mapping approaches.

Physical mapping of DNA can be used to detect structural variants and for whole-genome haplotype assembly. Here, the authors use CRISPR-Cas9 and high-speed atomic force microscopy to ‘nanomap’ single molecules of DNA.