First-strand complementary DNA (cDNA) was synthesized from random hexamer primers with a SuperScript III

First-Strand Synthesis System for reverse-transcription polymerase chain reaction (PCR) (Invitrogen Corporation, Carlsbad, CA). The NS5A coding region was amplified with GT-specific primers and Platinum Taq high-fidelity DNA polymerase (Invitrogen). To replace the replicon NS5A with subject sequences, H77c was reconstructed to contain MfeI and SpeI restriction enzyme sites and Con1 was modified to contain Afl2 and Sac2 sites, which frames the NS5A coding region. A recombinant PCR18 was performed on NS5A cDNA generated from specimens using subject-specific primers containing the unique restriction MI-503 manufacturer enzyme sites mentioned above, along with primers specifically designed to change amino-acid residue 232 from serine to isoleucine (S2204I), a replication-enhancing adaptive mutation, into the subject NS5A protein. Finally, the PCR products were digested with the restriction enzymes, MfeI and SpeI, for GT-1a subjects and were ligated into the similarly digested HCV H77c replicon DNA. For GT-1b subjects, the PCR products were infused onto previously

digested Con1 replicon DNA, which was cut with Afl2 and Sac2 restriction enzymes, using the protocol recommended by the manufacture (In-Fusion Cloning Kit; Clontech Laboratories, Mountain View, CA). To replace the N-terminal of NS5A with clinical specimens, NS5A cDNA generated from patient specimens was further GSK-3 activity amplified by PCR using Platinum Taq high-fidelity DNA polymerase (Invitrogen) and forward primer 5′-TCCGGTTCCTGGCTAAGGGAC ATCTGG-3′, which contains an EcoNI site, and reverse primer 5′-CACTACGTATCGGGTATGACTA CTGACAATC-3′, which contains a SnaBI site. These primers were verified by comparison to the coding region of subject-specific NS5A and modified, as necessary, according to the sequence. The PCR product was digested with EcoNI and SnaBI, and the

MCE correct-sized fragments were gel purified and ligated into similarly digested HCV H77c replicon DNA. Clones containing the correct sequence were identified by restriction digestion and confirmed by sequencing analysis. Specific site changes, such as Q30R, E62D, Q30R+E62D, and V75A mutants, were generated in the H77c replicon DNA by using the Agilent Quick-change mutagenesis kit (Agilent Technologies, Inc., Santa Clara, CA), according to the manufacture’s instruction. Transient replication assays and isolation of replicon cell lines have been described previously.13, 15 The EC50 value was calculated as the concentration of inhibitor required for a 50% reduction in luciferase activity. HCV GT 1b (Con1) and 1a (H77c) replicons have been used to evaluate the antiviral profile of NS5A inhibitors, including the clinical lead, BMS-790052.