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Title: Necessary Experimental Conditions for Single-Shot Diffraction Imaging of DNA-Based Structures with X-ray Free-Electron Lasers

Abstract

It has been proposed that the radiation damage to biological particles and soft condensed matter can be overcome by ultrafast and ultraintense X-ray free-electron lasers (FELs) with short pulse durations. The successful demonstration of the “diffraction-before-destruction” concept has made single-shot diffraction imaging a promising tool to achieve high resolutions under the native states of samples. However, the resolution is still limited because of the low signal-to-noise ratio, especially for biological specimens such as cells, viruses, and macromolecular particles. Here, we present a demonstration single-shot diffraction imaging experiment of DNA-based structures at SPring-8 Angstrom Compact Free Electron Laser (SACLA), Japan. Through quantitative analysis of the reconstructed images, the scattering abilities of gold and DNA were demonstrated. Suggestions for extracting valid DNA signals from noisy diffraction patterns were also explained and outlined. To sketch out the necessary experimental conditions for the 3D imaging of DNA origami or DNA macromolecular particles, we carried out numerical simulations with practical detector noise and experimental geometry using the Linac Coherent Light Source (LCLS) at the SLAC National Accelerator Laboratory, USA. In conclusion, the simulated results demonstrate that it is possible to capture images of DNA-based structures at high resolutions with the technique development of current andmore » next-generation X-ray FEL facilities.« less

Authors:
 [1];  [2];  [3];  [4];  [5];  [6];  [6];  [7];  [8];  [2];  [5];  [5];  [9];  [10];  [10];  [5]; ORCiD logo [4]; ORCiD logo [2]
  1. Shandong Univ., Jinan (China); SLAC National Accelerator Lab., Menlo Park, CA (United States); ShanghaiTech Univ., Shanghai (China)
  2. ShanghaiTech Univ., Shanghai (China)
  3. SLAC National Accelerator Lab., Menlo Park, CA (United States); Stanford Univ., Stanford, CA (United States)
  4. Chinese Academy of Sciences, Shanghai (China)
  5. Pohang Univ. of Science and Technology, Pohang (Korea)
  6. European XFEL GmbH, Schenefeld (Germany); Gwangju Institute of Science and Technology, Gwangju (Korea)
  7. Chinese Academy of Sciences (CAS), Beijing (China); SLAC National Accelerator Lab., Menlo Park, CA (United States)
  8. Shandong Univ., Jinan (China); ShanghaiTech Univ., Shanghai (China)
  9. Japan Synchrotron Radiation Research Institute, Hyogo (Japan)
  10. RIKEN SPring-8 Center, Hyogo (Japan)
Publication Date:
Research Org.:
SLAC National Accelerator Lab., Menlo Park, CA (United States)
Sponsoring Org.:
USDOE Office of Science (SC), Basic Energy Sciences (BES)
OSTI Identifier:
1476144
Grant/Contract Number:  
2017YFA0504802; 2014CB910401; AC02-76SF00515; 2016R1A2B3010980; 201606220148; 31430031; 21727817
Resource Type:
Accepted Manuscript
Journal Name:
ACS Nano
Additional Journal Information:
Journal Volume: 12; Journal Issue: 8; Journal ID: ISSN 1936-0851
Publisher:
American Chemical Society (ACS)
Country of Publication:
United States
Language:
English
Subject:
59 BASIC BIOLOGICAL SCIENCES; coherent diffraction imaging; DNA origami; single-particle imaging; X-ray diffraction; X-ray free-electron laser

Citation Formats

Sun, Zhibin, Fan, Jiadong, Li, Haoyuan, Liu, Huajie, Nam, Daewoong, Kim, Chan, Kim, Yoonhee, Han, Yubo, Zhang, Jianhua, Yao, Shengkun, Park, Jaehyun, Kim, Sunam, Tono, Kensuke, Yabashi, Makina, Ishikawa, Tetsuya, Song, Changyong, Fan, Chunhai, and Jiang, Huaidong. Necessary Experimental Conditions for Single-Shot Diffraction Imaging of DNA-Based Structures with X-ray Free-Electron Lasers. United States: N. p., 2018. Web. doi:10.1021/acsnano.8b01838.
Sun, Zhibin, Fan, Jiadong, Li, Haoyuan, Liu, Huajie, Nam, Daewoong, Kim, Chan, Kim, Yoonhee, Han, Yubo, Zhang, Jianhua, Yao, Shengkun, Park, Jaehyun, Kim, Sunam, Tono, Kensuke, Yabashi, Makina, Ishikawa, Tetsuya, Song, Changyong, Fan, Chunhai, & Jiang, Huaidong. Necessary Experimental Conditions for Single-Shot Diffraction Imaging of DNA-Based Structures with X-ray Free-Electron Lasers. United States. https://doi.org/10.1021/acsnano.8b01838
Sun, Zhibin, Fan, Jiadong, Li, Haoyuan, Liu, Huajie, Nam, Daewoong, Kim, Chan, Kim, Yoonhee, Han, Yubo, Zhang, Jianhua, Yao, Shengkun, Park, Jaehyun, Kim, Sunam, Tono, Kensuke, Yabashi, Makina, Ishikawa, Tetsuya, Song, Changyong, Fan, Chunhai, and Jiang, Huaidong. Mon . "Necessary Experimental Conditions for Single-Shot Diffraction Imaging of DNA-Based Structures with X-ray Free-Electron Lasers". United States. https://doi.org/10.1021/acsnano.8b01838. https://www.osti.gov/servlets/purl/1476144.
@article{osti_1476144,
title = {Necessary Experimental Conditions for Single-Shot Diffraction Imaging of DNA-Based Structures with X-ray Free-Electron Lasers},
author = {Sun, Zhibin and Fan, Jiadong and Li, Haoyuan and Liu, Huajie and Nam, Daewoong and Kim, Chan and Kim, Yoonhee and Han, Yubo and Zhang, Jianhua and Yao, Shengkun and Park, Jaehyun and Kim, Sunam and Tono, Kensuke and Yabashi, Makina and Ishikawa, Tetsuya and Song, Changyong and Fan, Chunhai and Jiang, Huaidong},
abstractNote = {It has been proposed that the radiation damage to biological particles and soft condensed matter can be overcome by ultrafast and ultraintense X-ray free-electron lasers (FELs) with short pulse durations. The successful demonstration of the “diffraction-before-destruction” concept has made single-shot diffraction imaging a promising tool to achieve high resolutions under the native states of samples. However, the resolution is still limited because of the low signal-to-noise ratio, especially for biological specimens such as cells, viruses, and macromolecular particles. Here, we present a demonstration single-shot diffraction imaging experiment of DNA-based structures at SPring-8 Angstrom Compact Free Electron Laser (SACLA), Japan. Through quantitative analysis of the reconstructed images, the scattering abilities of gold and DNA were demonstrated. Suggestions for extracting valid DNA signals from noisy diffraction patterns were also explained and outlined. To sketch out the necessary experimental conditions for the 3D imaging of DNA origami or DNA macromolecular particles, we carried out numerical simulations with practical detector noise and experimental geometry using the Linac Coherent Light Source (LCLS) at the SLAC National Accelerator Laboratory, USA. In conclusion, the simulated results demonstrate that it is possible to capture images of DNA-based structures at high resolutions with the technique development of current and next-generation X-ray FEL facilities.},
doi = {10.1021/acsnano.8b01838},
journal = {ACS Nano},
number = 8,
volume = 12,
place = {United States},
year = {2018},
month = {7}
}

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Figures / Tables:

Figure 1 Figure 1: Schematic of the single-shot diffraction imaging layout with X-ray FELs at SACLA. The X-ray FEL pulses are focused to about 1.5µm by a pair of KB mirrors. After passing througlt the slits, X-ray lasers interact with the DNA-based AuNPs. By demonstrating the zigzag raster scan, fresh samples canmore » be delivered to the X-ray laser beam path.« less

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