Automated cryo-EM sample preparation by pin-printing and jet vitrification

The increasing demand for cryo-electron microscopy (cryo-EM) reveals drawbacks in current sample preparation protocols, such as sample waste and lack of reproducibility. Here, we present several technical developments that provide controlled and efficient sample preparation for cryo-EM studies. Pin printing substantially reduces sample waste by depositing only a sub-nanoliter volume of sample on the carrier surface. Sample evaporation is mitigated by dewpoint control feedback loops. The deposited sample is vitrified by jets of cryogen followed by submersion into a cryogen bath. Because the cryogen jets cool the sample from the center, premounted autogrids can be used and loaded directly into automated cryo-EMs. We integrated these steps into a single device, named VitroJet. The device’s performance was validated by resolving 4 standard proteins (apoferritin, GroEL, worm hemoglobin, beta-galactosidase) to ~3 Å resolution using a 200-kV electron microscope. The VitroJet offers a promising solution for improved automated sample preparation in cryo-EM studies.

[1]  A. Bartesaghi,et al.  2.2 Å resolution cryo-EM structure of β-galactosidase in complex with a cell-permeant inhibitor , 2015, Science.

[2]  F. Sun Orienting the future of bio-macromolecular electron microscopy , 2018, Chinese Physics B.

[3]  B. Carragher,et al.  Spotiton: a prototype for an integrated inkjet dispense and vitrification system for cryo-TEM. , 2012, Journal of structural biology.

[4]  P. Emsley,et al.  Features and development of Coot , 2010, Acta crystallographica. Section D, Biological crystallography.

[5]  D. Lohse,et al.  Maximal air bubble entrainment at liquid-drop impact. , 2012, Physical review letters.

[6]  W. Xu,et al.  An improved cryo-FIB method for fabrication of frozen hydrated lamella. , 2016, Journal of structural biology.

[7]  J. Dubochet,et al.  Electron microscopy of frozen water and aqueous solutions , 1982 .

[8]  N. Unwin,et al.  Analysis of transient structures by cryo-microscopy combined with rapid mixing of spray droplets. , 1994, Ultramicroscopy.

[9]  Kai Zhang,et al.  Gctf: Real-time CTF determination and correction , 2015, bioRxiv.

[10]  Michael Schatz,et al.  Single-particle cryo-EM using alignment by classification (ABC): the structure of Lumbricus terrestris haemoglobin , 2017, IUCrJ.

[11]  C. Russo,et al.  Specimen Preparation for High-Resolution Cryo-EM. , 2016, Methods in enzymology.

[12]  Martin Grininger,et al.  The deadly touch: protein denaturation at the water-air interface and how to prevent it , 2018, bioRxiv.

[13]  A. Hyman,et al.  Visualizing the molecular sociology at the HeLa cell nuclear periphery , 2016, Science.

[14]  Lori A. Passmore,et al.  Controlling protein adsorption on graphene for cryo-EM using low-energy hydrogen plasmas , 2014, Nature Methods.

[15]  Sjors H.W. Scheres,et al.  RELION: Implementation of a Bayesian approach to cryo-EM structure determination , 2012, Journal of structural biology.

[16]  A. Verkleij,et al.  Intermediary structures during membrane fusion as observed by cryo-electron microscopy. , 1989, Biochimica et biophysica acta.

[17]  Shaoxia Chen,et al.  Prevention of overfitting in cryo-EM structure determination , 2012, Nature Methods.

[18]  Sjors H.W. Scheres,et al.  A Bayesian View on Cryo-EM Structure Determination , 2012, 2012 9th IEEE International Symposium on Biomedical Imaging (ISBI).

[19]  Thomas C Terwilliger,et al.  New tools for the analysis and validation of cryo-EM maps and atomic models , 2018, bioRxiv.

[20]  Clinton S Potter,et al.  Spotiton: New features and applications. , 2018, Journal of structural biology.

[21]  C. Russo,et al.  Measuring the effects of particle orientation to improve the efficiency of electron cryomicroscopy , 2017, Nature Communications.

[22]  R. Wepf,et al.  Robust workflow and instrumentation for cryo-focused ion beam milling of samples for electron cryotomography. , 2018, Ultramicroscopy.

[23]  Joachim Frank,et al.  Preparation of macromolecular complexes for cryo-electron microscopy , 2007, Nature Protocols.

[24]  T. Creighton Methods in Enzymology , 1968, The Yale Journal of Biology and Medicine.

[25]  Andrej Bieri,et al.  Blotting-free and lossless cryo-electron microscopy grid preparation from nanoliter-sized protein samples and single-cell extracts. , 2017, Journal of structural biology.

[26]  Clinton S Potter,et al.  Optimizing "self-wicking" nanowire grids. , 2018, Journal of structural biology.

[27]  Toh-Ming Lu,et al.  Structural dynamics of ribosome subunit association studied by mixing-spraying time-resolved cryogenic electron microscopy. , 2015, Structure.

[28]  Diana C. F. Monteiro,et al.  A cryo-EM grid preparation device for time-resolved structural studies , 2019, bioRxiv.

[29]  Lori A. Passmore,et al.  Ultrastable gold substrates for electron cryomicroscopy , 2014, Science.

[30]  W. Kühlbrandt The Resolution Revolution , 2014, Science.

[31]  L E Scriven,et al.  Controlled environment vitrification system: an improved sample preparation technique. , 1988, Journal of electron microscopy technique.

[32]  Christopher J. Williams,et al.  MolProbity: More and better reference data for improved all‐atom structure validation , 2018, Protein science : a publication of the Protein Society.

[33]  D. Maurice,et al.  Cryofixation of tissue surfaces by a propane jet for electron microscopy , 1978 .

[34]  T. N. Stevenson,et al.  Fluid Mechanics , 2021, Nature.

[35]  Joachim Frank,et al.  A Fast and Effective Microfluidic Spraying-Plunging Method for High-Resolution Single-Particle Cryo-EM. , 2017, Structure.

[36]  Yong Zi Tan,et al.  Routine single particle CryoEM sample and grid characterization by tomography , 2017, bioRxiv.

[37]  R. Glaeser,et al.  Opinion: hazards faced by macromolecules when confined to thin aqueous films , 2016, Biophysics reports.

[38]  Jasenko Zivanov,et al.  A Bayesian Approach to Beam-Induced Motion Correction in Cryo-EM Single-Particle Analysis , 2018 .

[39]  Eugen Ermantraut,et al.  Perforated support foils with pre-defined hole size, shape and arrangement , 1998 .

[40]  Monya Baker,et al.  Cryo-electron microscopy shapes up , 2018, Nature.

[41]  J. Dubochet,et al.  Cryo-electron microscopy of vitrified specimens , 1988, Quarterly Reviews of Biophysics.

[42]  P. Gennes,et al.  Capillarity and Wetting Phenomena , 2004 .

[43]  B. Widom Capillarity and Wetting Phenomena: Drops, Bubbles, Pearls, Waves , 2003 .

[44]  P. Frederik,et al.  Cryoelectron microscopy of liposomes. , 2005, Methods in enzymology.

[45]  Clinton S Potter,et al.  An Improved Holey Carbon Film for Cryo-Electron Microscopy , 2007, Microscopy and Microanalysis.

[46]  Marin van Heel,et al.  Similarity measures between images , 1987 .

[47]  Robert M Glaeser,et al.  How good can cryo-EM become? , 2015, Nature Methods.

[48]  A. Neild,et al.  Delivery of femtolitre droplets using surface acoustic wave based atomisation for cryo-EM grid preparation. , 2018, Journal of structural biology.