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6 protocols using pageblue solution

1

Characterization of Polymer Nanoparticles with Cas9 and gDonor

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PAsp(DET) nanoparticles with gDonor and Cas9 were formulated as described above. The polymer nanoparticles were centrifuged at 17,000 g for 10 min, and the supernatant and pellet were collected. Each sample was mixed with a 100 µg of heparin for particle dissociation. The collected supernatant and pellets were run on a gel, and analyzed for the Cas9 and gDonor content in the polymer nanoparticles. Gel electrophoresis was performed using a 4–20% Mini-PROTEAN TGX Gel (Bio-rad) in Tris/SDS buffer, with a loading dye containing 5% beta-mercaptoethanol. PageBlue solution (Thermo Fisher) staining was conducted and imaged with ChemiDoc MP using ImageLab software (Bio-rad). For particle size measurements, a dynamic light scattering study was conducted using a Zetasizer Nano ZS instrument (Malvern Instruments Ltd., Worcestershire, UK) and a folded capillary cell (DTS 1060, Malvern Instruments). The reported particle size was measured 5 min after particle mixing.
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2

Synthesis and Characterization of Nanoparticles

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Oligonucleotides were purchased from Integrated DNA Technologies (IDT, Coralville, IA). Gold nanoparticles (15 nm) were purchased from BBI solutions. Sodium citrate and 4-(2-hydroxyethyl) piperazine-1-ethanesulfonate (HEPES) were purchased from Mandel Scientific (Guelph, ON). Sodium silicate and cardiotoxin (C9759) were purchased from Sigma Aldrich (St. Louis, MO). Phusion High-fidelity DNA Polymerase was purchased from NEB (Ipswich, MA). The MEGAscript T7 kit, the MEGAclear kit, the PageBlue solution, the propidium iodide, and the PureLink genomic DNA kit were purchased from Thermo Fischer (Waltham, MA). Mini-PROTEAN TGX Gels (4–20%) were purchased from Bio-Rad (Hercules, CA). MTeSR-1 media gentle cell dissociation reagent was purchased from StemCell Technologies (Vancouver, Canada). Matrigel was purchased from BD Biosciences (San Jose, CA). DMEM media, non-essential amino acids, penicillin-streptomycin, DPBS and 0.05% trypsin were purchased from Life Technologies (Carlsbad, CA). EMD Millipore Amicon Ultra-4 100kDa was purchased from Millipore (Germany).
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3

Synthesis and Characterization of Nanoparticles

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Oligonucleotides were purchased from Integrated DNA Technologies (IDT, Coralville, IA). Gold nanoparticles (15 nm) were purchased from BBI solutions. Sodium citrate and 4-(2-hydroxyethyl) piperazine-1-ethanesulfonate (HEPES) were purchased from Mandel Scientific (Guelph, ON). Sodium silicate and cardiotoxin (C9759) were purchased from Sigma Aldrich (St. Louis, MO). Phusion High-fidelity DNA Polymerase was purchased from NEB (Ipswich, MA). The MEGAscript T7 kit, the MEGAclear kit, the PageBlue solution, the propidium iodide, and the PureLink genomic DNA kit were purchased from Thermo Fischer (Waltham, MA). Mini-PROTEAN TGX Gels (4–20%) were purchased from Bio-Rad (Hercules, CA). MTeSR-1 media gentle cell dissociation reagent was purchased from StemCell Technologies (Vancouver, Canada). Matrigel was purchased from BD Biosciences (San Jose, CA). DMEM media, non-essential amino acids, penicillin-streptomycin, DPBS and 0.05% trypsin were purchased from Life Technologies (Carlsbad, CA). EMD Millipore Amicon Ultra-4 100kDa was purchased from Millipore (Germany).
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4

CRISPR Reagent Preparation Protocol

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Unmodified crRNA, 5’ Amine-crRNA, 5’ Azide-crRNA, 5’ Thiol-crRNA, 3’ Amine-crRNA, 5’ Amine-Donor, 3’ Amine-Donor, 5’ Azide-Donor, and various DNA sequences were purchased from Integrated DNA Technology (IDT). Phusion High-fidelity DNA Polymerase was purchased from NEB (Ipswich, MA). The Megascript T7 kit, the Megaclear kit, the PageBlue solution, the propidium iodide, and the PureLink genomic DNA kit were purchased from Thermo Fisher (Waltham, MA). Mini-PROTEAN TGX Gels (4–20%) were purchased from Bio-Rad (Hercules, CA). 4-(2-hydroxyethyl) piperazine-1-ethanesulfonate (HEPES) were purchased from Mandel Scientific (Guelph, ON). Sodium silicate was purchased from Sigma Aldrich (St. Louis, MO). Matrigel was purchased from BD Biosciences (San Jose, CA). DMEM media, non-essential amino acids, penicillin-streptomycin, DPBS and 0.05% trypsin were purchased from Life Technologies (Carlsbad, CA). EMD Millipore Amicon Ultra-4 100 kDa and 300 kDa were purchased from Millipore (Germany). Streptococcus pyogenes Cas9 (spCas9) and Acidaminococcus sp. Cpf1 (AsCpf1) were purchased from the QB3 Macrolab from UC Berkeley. PAsp(DET) polymer was a generous gift from Dr. Kataoka’s group (Miyata et al., 2008 (link); Kim et al., 2010 (link), 2014 (link)).
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5

Purification and Storage of SpCas9 and AsCpf1

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SpCas9 and AsCpf1 were purchased from the MacroLab in UC Berkeley. Proteins were stored in 50 mM HEPES (4-(2-hydroxyethyl)-1-piperazineethanesulfonic acid) at pH 7.5 with 300 mM NaCl, 10% glycerol, and 100 μM tris(2-carboxyethyl) phosphine at −80 °C. PAsp(DET) polymer was synthesized using the following literature references46 (link),60 (link),61 (link). Phusion High-fidelity DNA Polymerase was purchased from NEB (Ipswich, MA, USA). The MEGAscript T7 kit, the MEGAclear kit, the PageBlue solution, the propidium iodide, and the PureLink genomic DNA kit were purchased from Thermo Fisher (Waltham, MA, USA). Mini-PROTEAN TGX (Tris-Glycine eXtended) gels (4–20%) were purchased from Bio-Rad (Hercules, CA, USA). Dulbecco’s modified Eagle's medium (DMEM), non-essential amino acids, penicillin–streptomycin, Dulbecco's phosphate-buffered saline (PBS), and 0.05% trypsin were purchased from Life Technologies (Carlsbad, CA, USA).
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6

Nanoparticle-Mediated CRISPR Delivery

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Oligonucleotides were purchased from Integrated DNA Technologies. GNPs (60 nm) were purchased from BBI Solutions. Sodium citrate and HEPES were purchased from Mandel Scientific. Sodium silicate was purchased from Sigma-Aldrich. Phusion High-Fidelity DNA Polymerase was purchased from NEB. The MEGAscript T7 kit, the MEGAclear kit, the PageBlue solution, the propidium iodide and the PureLink Genomic DNA kit were purchased from ThermoFisher. Mini-PROTEAN TGX Gels (4–20%) were purchased from Bio-Rad. DMEM media, non-essential amino acids, penicillin-streptomycin, Dulbecco’s PBS and 0.05% trypsin were purchased from Life Technologies. Amicon Ultra-4 30 kDa was purchased from EMD Millipore. Cas9 proteins with an amino-terminal 6xHis-tag and two SV40 NLS peptides at the carboxyl terminus and Cpf1 proteins were purchased from Macrolab UC Berkeley. The Poly (PAsp(DET)) was a gift from Kazunori Kataoka’s group43 (link),44 (link). The SYTOX Red Dead Cell Stain (excitation/emission of 640/658 nm) and the SuperScript III First-Strand Synthesis kit were purchased from Invitrogen.
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