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6 protocols using cleancap reagent ag 3 ome

1

Synthetic mRNA Production and Purification

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Template DNAs were prepared by PCR using PrimeSTAR Max DNA Polymerase (Takara Bio) and the primers listed in Table S1, and the Monarch PCR & DNA Cleanup Kit (New England BioLabs Japan Inc.) was used to purify the PCR products. Template DNA sequences used in this study are shown in Table S2. The MEGAscript T7 Transcription Kit (Thermo Fisher Scientific K.K.) was used to transcribe mRNAs from the template DNAs. Additionally, 6 mM GTP, 6 mM CTP, and 6 mM ATP were used from the MEGAscript T7 Transcription Kit (Thermo Fisher Scientific) with 6 mM N1-methyl-pseudoUTP (TriLink Biotechnologies, San Diego, CA, USA) and 4.8 mM CleanCap Reagent AG (3′ OMe) (TriLink Biotechnologies). After transcription, template DNAs were digested using TURBO Dnase (Thermo Fisher Scientific), and transcribed mRNAs were purified using Agencourt RNAClean XP (Agencourt Bioscience Corporation, Beverly, MA, USA). Next, the mRNAs were dephosphorylated using Quick CIP (New England BioLabs Japan) and purified using the RNeasy Mini Kit (Qiagen K.K., Tokyo, Japan). The mRNAs were quantified using NanoDrop One (ThermoFisher Scientific K.K.), and their sizes were confirmed using the Agilent RNA 6000 Nano Assay and the Agilent 2100 Bioanalyzer (Agilent Technologies Japan Ltd., Tokyo, Japan).
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2

Poly(A) RNA Quantification Protocol

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1,1,1,3,3,3-Hexafluoro-2-propanol,
acetonitrile, ethanol (LC/MS grade), formic acid, methanol (LC/MS
grade), triethylamine, triethylammonium acetate, phenol:chloroform,
water (LC/MS grade), and isopropanol were all obtained from Sigma-Aldrich
(MO). Custom oligonucleotides were obtained from IDT. (IA) Custom
poly(A) standards were obtained from the Horizon Discovery (CO) DNAPac
RP 4 μm × 2.1 mm × 100 mm HPLC column, 7.5 M LiCl
solution, nuclease-free water, RNase T1, DNase I, PCR strip tubes,
and glass HPLC vials with caps were all obtained from ThermoFisher
Scientific (NJ). RNase H, RNase H buffer, Cutsmart buffer, and HiScribeT7
High Yield RNA Synthesis Kit were obtained from New England Biolabs
(MA). QIAprep Miniprep kit was obtained from QIAgen (MD). CleanCap
Reagent AG and CleanCap Reagent AG (3′ OMe) were purchased
from TriLink Biotechnologies (CA).
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3

Synthesis of mCherry IVT-mRNA

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The DNA coding sequence for mCherry fluorescent protein was sourced from SnapGene (www.snapgene.com/resources) software and then codon optimized. The mCherry sequence was then cloned into an in vitro transcribed mRNA (IVT-mRNA) production template plasmid carrying a T7 promoter, 5′ and 3′ UTR elements, Kozak consensus sequence, and 101 poly(A) tail. DNA synthesis, cloning, and industrial grade endotoxin-free plasmid preparation service was provided by GenScript. IVT-mRNA (in vitro transcribed mRNA) was synthesized on linearized plasmid using the T7 MEGAScript (Thermo Fisher). Nucleoside-modified N1-Methylpseudouridine-5’-Triphosphate (TriLink, N-1081) was incorporated into the IVT-mRNA reaction. 5′ Capping of the IVT-mRNA was included in the reaction using the trinucleotide cap1 analog, CleanCap® Reagent AG (3′ OMe) (TriLink, N-7413). Single-stranded IVT-mRNA was purified by cellulose purification, as previously described (45 (link)). The mRNA was analyzed by agarose gel electrophoresis and was stored at −20 °C.
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4

Synthesis and Characterization of Modified mRNA

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RNA ranging in size from 100 nt to 9.4 kb was synthesized using the MEGAscript T7 transcription kit (Thermo Fisher Scientific, Invitrogen, Waltham, MA, USA). The reaction included UTP for generating standard IVT mRNA or N1-methylpseudouridine 5′-triphosphate (m1ΨTP) (TriLink) for nucleoside modified mRNA, in which 100% of uridine was substituted with m1Ψ. In a subset of RNAs, the sequences of the first three transcribed nucleotides were GCG, GGA, AGC, AGG or AGA. Cap analog, ARCA-G (TriLink, N-7003), beta-S-ARCA (D1, BioNTech SE) [17 (link)] or CleanCap® Reagent AG (3′ OMe) (TriLink, N-7413) were added to the transcription reaction to generate mRNA with cap0 (A0), cap0 (D1) or cap1 (CC1), respectively. Vaccinia virus capping enzymes (New England Biolabs) were used according to the manufacturer’s instructions to enzymatically cap the synthesized mRNA and generate RNA with cap0 (E0) or cap1 (E1). RNA quality was tested using 1.4% agarose gel electrophoresis [18 (link)], and RNA concentration was measured using a NanoDrop spectrophotometer (Thermo Fisher Scientific).
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5

Efficient mRNA Synthesis for SARS-CoV-2

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mRNA was synthesized following standard procedures (Baronti et al., 2018 (link); Beckert and Masquida, 2011 (link); Whitley et al., 2021 (link)). Namely, we used T7 RNA polymerase in the presence of a CleanCap Reagent AG (3’ OMe) (TriLink) on linearized plasmids encoding codon-optimized SARS-CoV-2 gene. After transcription, the mRNA was purified by magnetic particles, flash frozen, and stored at −80 °C until further use.
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6

Optimized mRNA Production for COVID-19 Variants

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DNA templates, which incorporated 5′ untranslated regions (UTR) (GGGAAAUAAGAGAGAAAAGAAGAGUAAGAAGAAAUAUAAGAGCCACC), signal peptide sequences from Igκ (ATGGAGACAGACACACTCCTGCTATGGGTACTGCTGCTCTGGGTTCCAGGTTCCACCGGTGAC), codon optimized wild-type (Wuhan-Hu-1, GenBank YP_009724390.1), Delta, Omicron, and Omicron with additional L452R mutation (Hybrid) RBD sequence, 3′ UTR (UGAUAAUAGGCUGGAGCCUCGGUGGCCAUGCUUCUUGCCCCUUGGGCCUCCCCCCAGCCCCUCCUCCCCUUCCUGCACCCGUACCCCCGUGGUCUUUGAAUAAAGUCUGA), and a poly-A tail were constructed. Before subjected to in vitro transcription reaction to synthesize mRNA with T7 RNA polymerase (NEB, MA, USA), the DNA template was linearized with EcoRV (NEB, MA, USA). The in vitro transcription reaction included CleanCap®Reagent AG (3′ OMe) (Trilink, CA, USA) for co-transcriptional capping of mRNA and complete replacement of uridine by N1-methyl-pseudouridine (Trilink, CA, USA). The mRNA was purified by LiCl (Invitrogen, MA, USA) precipitation and dsRNA was depleted by cellulose (Sigma-Aldrich, MA, USA). Purified RNA was kept frozen at − 80 °C until further use.
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