Biophysics Reports

2023 Vol. 9, No. 4

Cover Story

DNA-based point accumulation in nanoscale topography (DNA-PAINT) is a well-established technique for single-molecule localization microscopy (SMLM), enabling resolution of up to a few nanometers. Traditionally, DNA-PAINT involves the utilization of tens of thousands of single-molecule flu-orescent images to generate a single super-resolution image. This process can be time-consuming, which makes it unfeasible for many researchers. Here, the authors propose a simplified DNA-PAINT labeling method and a deep learning-enabled fast DNA-PAINT imaging strategy for subcellu-lar structures, such as microtubules. By employing the method, super-resolution reconstruction can be achieved with only one-tenth of the raw data previously needed, along with the option of acquiring the widefield image. As a result, DNA-PAINT imaging is significantly accelerated, making it more accessible to a wider range of biological researchers.

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PROTOCOL

Deep learning-enabled fast DNA-PAINT imaging in cells

Min Zhu, Luhao Zhang, Luhong Jin, Yunyue Chen, Haixu Yang, Baohua Ji, Yingke Xu

2023, 9(4): 177-187. doi: 10.52601/bpr.2023.230014

Abstract(210)

PDF(20)

Abstract:
DNA-based point accumulation in nanoscale topography (DNA-PAINT) is a well-established technique for single-molecule localization microscopy (SMLM), enabling resolution of up to a few nanometers. Traditionally, DNA-PAINT involves the utilization of tens of thousands of single-molecule fluorescent images to generate a single super-resolution image. This process can be time-consuming, which makes it unfeasible for many researchers. Here, we propose a simplified DNA-PAINT labeling method and a deep learning-enabled fast DNA-PAINT imaging strategy for subcellular structures, such as microtubules. By employing our method, super-resolution reconstruction can be achieved with only one-tenth of the raw data previously needed, along with the option of acquiring the widefield image. As a result, DNA-PAINT imaging is significantly accelerated, making it more accessible to a wider range of biological researchers.

Reconstitution of membrane contact by unilamellar vesicles

Shulin Li, Min Zhang, Liang Ge

2023, 9(4): 188-194. doi: 10.52601/bpr.2023.230011

Abstract(616)

PDF(43)

Abstract:
Eukaryotic cells compartmentalize diverse biochemical functions within organelles defined by intracellular membranes. Recent focus has intensified on studying the interactions among organelles and the role of membrane contacts in maintaining cellular balance. While analyzing these contacts mainly involves fluorescence and electron microscopy, as well as biochemical cell fractionation, understanding their mechanisms and responses to genetic and environmental changes remains challenging. Here we describe an approach employing in vitro reconstitution of membrane contacts using unilamellar vesicles. This technique offers insights into contact mechanisms when combined with established methods like fluorescence imaging and mass spectrometry, potentially deepening our understanding of membrane contacts and organelle networks.

REVIEW

Xenopus cell-free extracts and their applications in cell biology study

Junjun Liu, Chuanmao Zhang

2023, 9(4): 195-205. doi: 10.52601/bpr.2023.230016

Abstract(186)

PDF(12)

Abstract:
Xenopus has proven to be a remarkably versatile model organism in the realm of biological research for numerous years, owing to its straightforward maintenance in laboratory settings and its abundant provision of ample-sized oocytes, eggs, and embryos. The cell cycle of these oocytes, eggs, and early embryos exhibits synchrony, and extracts derived from these cells serve various research purposes. Many fundamental concepts in biochemistry, cell biology, and development have been elucidated through the use of cell-free extracts derived from Xenopus cells. Over the past few decades, a wide array of cell-free extracts has been prepared from oocytes, eggs, and early embryos of different Xenopus species at varying cell cycle stages. Each of these extracts possesses distinct characteristics. This review provides a concise overview of the Xenopus species employed in laboratory research, the diverse types of cell-free extracts available, and their respective properties. Furthermore, this review delves into the extensive investigation of spindle assembly in Xenopus egg extracts, underscoring the versatility and potency of these cell-free systems in the realm of cell biology.

RESEARCH ARTICLE

Live-cell super-resolution imaging unconventional dynamics and assemblies of nuclear pore complexes

Xianxin Ye, Minzhu Guan, Yaorong Guo, Xiang Liu, Kunhao Wang, Tongsheng Chen, Shiqun Zhao, Liangyi Chen

2023, 9(4): 206-214. doi: 10.52601/bpr.2023.230010

Abstract(396)

PDF(45)

Abstract:
Super-resolution microscopy has promoted the development of cell biology, but imaging proteins with low copy numbers in cellular structures remains challenging. The limited number of designated proteins within nuclear pore complexes (NPCs) impedes continuous observation in live cells, although they are often used as a standard for evaluating various SR methods. To address this issue, we tagged POM121 with Halo-SiR and imaged it using structured illumination microscopy with sparse deconvolution (Sparse-SIM). Remarkably, POM121-SiR exhibited more than six-fold fluorescence intensity and four-fold enhanced contrast compared to the same protein labeled with tandem-linked mCherry, while showing negligible photo-bleaching during SR imaging for 200 frames. Using this technique, we discovered various types of NPCs, including ring-like and cluster-like structures, and observed dynamic remodeling along with the sequential appearance of different Nup compositions. Overall, Halo-SiR with Sparse-SIM is a potent tool for extended SR imaging of dynamic structures of NPCs in live cells, and it may also help visualize proteins with limited numbers in general.

Theoretical framework and experimental solution for the air−water interface adsorption problem in cryoEM

Joon S. Kang, Xueting Zhou, Yun-Tao Liu, Kaituo Wang, Z. Hong Zhou

2023, 9(4): 215-229. doi: 10.52601/bpr.2023.230008

Abstract(514)

PDF(63)

Abstract:
As cryogenic electron microscopy (cryoEM) gains traction in the structural biology community as a method of choice for determining atomic structures of biological complexes, it has been increasingly recognized that many complexes that behave well under conventional negative-stain electron microscopy tend to have preferential orientation, aggregate or simply mysteriously “disappear” on cryoEM grids. However, the reasons for such misbehavior are not well understood, which limits systematic approaches to solving the problem. Here, we have developed a theoretical formulation that explains these observations. Our formulation predicts that all particles migrate to the air–water interface (AWI) to lower the total potential surface energy-rationalizing the use of surfactant, which is a direct solution to reduce the surface tension of the aqueous solution. By performing cryogenic electron tomography (cryoET) on the widely-tested sample, GroEL, we demonstrate that, in a standard buffer solution, nearly all particles migrate to the AWI. Gradually reducing the surface tension by introducing surfactants decreased the percentage of particles exposed to the surface. By conducting single-particle cryoEM, we confirm that suitable surfactants do not damage the biological complex, thus suggesting that they might provide a practical, simple, and general solution to the problem for high-resolution cryoEM. Applying this solution to a real-world AWI adsorption problem involving a more challenging membrane protein, namely, the ClC-1 channel, has resulted in its near-atomic structure determination using cryoEM.