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Based on prior studies, the G11C/U27Δ double mutant was prepared.
The EfFICH111A mutant was prepared by an institutional cloning facility, which closed in the meantime and we therefore have no means to recover primer information.
To weaken this structure (by ΔG of about 20 kJ/mol) the same double mutant was prepared using another mutagenic oligonucleotide with silent mutations in the Ala1 (GCU) and Leu2 (UUG) codons.
The FYVE-CENT R1945Q mutant was prepared by PCR site-directed mutagenesis.
A G27 ΔHP0723::KanSacB, KanR, Sucrose Sensitive mutant was prepared using the primers of Supplementary Table S1.
Total RNA from wild type and mutant was prepared for small RNA Sequencing-by-Synthesis according to the prescribed procedure and standards of the Illumina Sample Preparation Protocol.
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The full-length HIV-1 WT IN, the 50-212 corelytic core domain (CC), the 1-212 two-domain protein (ΔC) and the E152A point mutant were prepared as previously described [21].
Probes of the sequences 5'-tttcttgggcttccttgttttgacttgtaaccataaat-3' and 5'- tttcttgggcttccttggggtgacttgtaaccataaat-3' (mutant) were prepared by end labeling annealed oligos with γ32P-ATP using T4 Polynucleotide Kinase (Promega) and purification with MicroSpin™ G-50 Sephadex columns (Amersham Biosciences).
The recombinant HA-Wss1 protein and HA-Wss1-AQA mutant were prepared similarly except that the Ni-NTA purification step was omitted.
Heat inactivated bacteria of wild-type and ΔSPI-1 mutant were prepared by heating the culture to 65 °C for 30 min.
To further demonstrate the biological effect of G and GA KRAS mutants, NIH3T3 cells which stably transfected with empty vector, KRAS-WT, KRAS-G12V, G or GA mutant were prepared.
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