Production of Purified CasRNPs for Efficacious Genome Editing

Emily Lingeman1, Chris Jeans2, Jacob E. Corn1

1 Innovative Genomics Institute, University of California, Berkeley, California, 2 QB3 MacroLab, University of California, Berkeley, California
Publication Name:  Current Protocols in Molecular Biology
Unit Number:  Unit 31.10
DOI:  10.1002/cpmb.43
Online Posting Date:  October, 2017
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CRISPR‐Cas systems have been harnessed as modular genome editing reagents for functional genomics and show promise to cure genetic diseases. Directed by a guide RNA, a Cas effector introduces a double stranded break in DNA and host cell DNA repair leads to the introduction of errors (e.g., to knockout a gene) or a programmed change. Introduction of a Cas effector and guide RNA as a purified Cas ribonucleoprotein complex (CasRNP) has recently emerged as a powerful approach to alter cell types and organisms. Not only does CasRNP editing exhibit increased efficacy and specificity, it avoids optimization and iteration of species‐specific factors such as codon usage, promoters, and terminators. CasRNP editing has been rapidly adopted for research use in many contexts and is quickly becoming a popular method to edit primary cells for therapeutic application. This article describes how to make a Cas9 RNP and outlines its use for gene editing in human cells. © 2017 by John Wiley & Sons, Inc.

Keywords: Cas9; genome editing; ribonucleoprotein; RNP; CRISPR

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Table of Contents

  • Introduction
  • Strategic Planning
  • Basic Protocol 1: Cas9 Protein Bacterial Expression
  • Basic Protocol 2: Cas9 Purification
  • Basic Protocol 3: gRNA Template Assembly, Amplification, and In Vitro Transcription
  • Basic Protocol 4: gRNA Purification With Magnetic SPRI Beads
  • Alternate Protocol 1: gRNA Purification with RNeasy Spin Columns
  • Support Protocol 1: Production of SPRI Beads and Testing
  • Basic Protocol 5: CasRNP Complex Formation and Electroporation
  • Reagents and Solutions
  • Commentary
  • Literature Cited
  • Figures
  • Tables
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Basic Protocol 1: Cas9 Protein Bacterial Expression

  • Rosetta2(DE3)pLysS competent cells (Novagen, cat. no. 71403)
  • Ice
  • Cas9 expression plasmid: pMJ915, Addgene, plasmid #69090
  • 2×YT liquid medium (without antibiotics)
  • LB‐agar plate containing 100 μg/ml carbenicillin and 33 μg/ml chloramphenicol
  • Sterile glass beads (3 mm)
  • 10% bleach
  • 2×YT liquid media containing 100 μg/ml carbenicillin and 33 μg/ml chloramphenicol.
  • Isopropyl β‐D‐1‐thiogalactopyranoside (IPTG; 1 M in water)
  • Pepstatin A (1 mg/ml in methanol)
  • Leupeptin (1 mg/ml in water)
  • Phenylmethylsulfonyl fluoride (PMSF, 100 mM in 95% ethanol)
  • Nickel Buffer A (ice‐cold, see recipe)
  • Heated water bath (42°C)
  • Incubator (37°C) with rotating platform
  • Sterile pipette tips or toothpicks
  • 250‐ml and 2.5‐liters baffled culture flasks (e.g., Thompson Instrument Company, cat. nos. 931144 and 931136‐B)
  • Refrigerated shaking incubator (e.g., Certomat BS‐1)
  • 25‐ml serological pipette
  • Cell density meter (e.g., GE Lifesciences Ultrospec 10) or UV‐vis spectrometer
  • Centrifuge for 1‐liter bottles (Beckman Coulter Avanti J26‐XP) and 1‐liter bottles (Beckman Coulter, cat. no. 363676)

Basic Protocol 2: Cas9 Purification

  • Cells (from protocol 1)
  • Nickel buffers A and B, Ion‐Exchange Buffers A and B, and Size‐Exclusion Buffer (see reciperecipes)
  • TEV protease (e.g., SelecTEV Protease, Lucigen Corp., cat. no. 30810‐1)
  • 1 M Dithiothreitol (DTT, in water)
  • 0.5 M NaOH
  • Milli‐Q water
  • Liquid nitrogen
  • Sonicator (Sonics VCX 500)
  • Centrifuge and rotor for 30‐ to 40‐ml tubes and up to 30000 × g (e.g., Sorval RC 5C plus, with SS34 rotor)
  • Chromatography columns: all from GE Life Sciences:
    • 5 ml HisTrap FF Crude (17‐5286‐01 pack of 5)
    • HiPrep 26/10 Desalting (17‐5087‐01)
    • 5 ml HiTrap SP HP (17‐1152‐01 pack of 5)
    • Sephacryl S‐300 HR 16/60 (17‐1167‐01)
  • UV/vis spectrometer (e.g., GE Life Sciences NanoVue)
  • Centrifugal concentration units, 10 kDa MWCO (e.g., Millipore, cat. no. UFC901024)
  • 10‐ml and 20‐ml sterile syringes and syringe filters (0.2 μm)
  • FPLC system with gradient‐making capability and fractionation system, with flow rates up to 10 ml/min (e.g., GE Life Sciences AKTA series)
  • Tubes or 96‐well plates for fractionation
  • 1.7‐ml microcentrifuge tubes, certified DNase/RNase‐free

Basic Protocol 3: gRNA Template Assembly, Amplification, and In Vitro Transcription

  • T7FwdVar oligo (5′‐GGATCCTAATACGACTCACTATAG–protospacer sequence—GTTTTAGAGCTAGAA‐3′)
  • 10 mM dNTPs
  • DEPC‐treated water
  • 5× Phusion HF Buffer
  • RNase Away
  • T7RevAmp primer (5′‐AAAAAAGCACCGACTCGG‐3′)
  • Phusion HF DNA Polymerase
  • Agarose
  • TAE buffer
  • NEB HiScribe T7 High Yield RNA synthesis kit (NEB, cat. no. E2040S) containing:
    • T7 RNA Polymerase Mix
  • RNase‐free DNase
  • Calf intestinal alkaline phosphatase (CIP; NEB, cat. no. M0290)
  • Thermal cycler
  • Agarose gel rig and power source
  • 37°C incubator

Basic Protocol 4: gRNA Purification With Magnetic SPRI Beads

  • SPRI‐beads (see the Support Protocol)
  • IVT reaction (see protocol 4)
  • 80% Ethanol
  • Agarose
  • 10% polyacrylamide TBE‐urea gel
  • Ethanol
  • Pipettes
  • Magnetic stand
  • Qubit or spectrophotometer
  • Polyacrylamide gel rig and power source

Alternate Protocol 1: gRNA Purification with RNeasy Spin Columns

  • IVT Reaction (see protocol 4)
  • Qiagen RNeasy kit containing:
    • RLT Buffer
    • RPE Buffer
    • RNeasy mini spin column
  • 100% ethanol
  • DEPC‐treated water
  • 10% polyacrylamide TBE‐urea gel
  • Benchtop centrifuge
  • 1.5‐ml microcentrifuge

Support Protocol 1: Production of SPRI Beads and Testing

  • 0.5 M EDTA, pH 8.0 (Amresco, cat. no. E177)
  • 1.0 M Tris, pH 8.0 (Amresco, cat. no. E199)
  • Sera‐mag SpeedBeads (Fisher, cat. no. 09‐981‐123)
  • PEG‐8000 (Amresco, cat. no. 0159)
  • 5 M NaCl (Amresco, cat. no. E529)
  • Tween 20 (Amresco, cat. no. 0777)
  • Nuclease‐free water (Amresco, cat. no. E476)
  • Fermentas ladder(s) (Ultra‐low range: Fisher, cat. no. FERSM1211, 50 bp: cat. no. FERSM0371)
  • Ethanol (EtOH)
  • Loading dye (Thermo Fisher, cat. no. R0611)
  • Agarose
  • TAE
  • 50‐ml conical tubes
  • 1.5‐ml microtube
  • Rare‐earth magnet stand (e.g., Ambion, cat. no. AM10055 or NEB, cat. no. S1506S)
  • 200‐μl or 1000‐μl pipettors
  • Aluminum foil
  • Agarose gel rig and power source

Basic Protocol 5: CasRNP Complex Formation and Electroporation

  • Purified Cas9 protein (see protocol 2)
  • Cas9 buffer (see recipe)
  • Purified gRNA ( protocol 5)
  • Single‐stranded DNA (Richardson et al., ; Richardson, Ray, Bray, & Corn, )
  • HEK293Ts or cell line of your choice
  • Trypsin
  • Cell culture medium appropriate for HEK293Ts:
  • DMEM (Thermo Fisher, cat. no. 10566016)
  • 10% Fetal bovine serum (FBS; Seradigm, cat. no. 1500‐500)
  • Nucleofector solution
  • Pipettes and pipette tips
  • Hemacytometer
  • 15‐ml conical tubes
  • Centrifuge
  • 12‐well tissue culture plates
  • Lonza nucleofection cuvetter and solution for your cell type
  • 4D Lonza Nucleofector
  • 200‐μl pipette
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Literature Cited

Literature Cited
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