The Highly Conserved Codon following the Slippery Sequence Supports -1 Frameshift Efficiency at the HIV-1 Frameshift Site

Mathew, Suneeth F.; Crowe-McAuliffe, Caillan; Graves, Ryan; Cardno, Tony S.; McKinney, Cushla; Poole, Elizabeth S.; Tate, Warren P.

were subtracted from each measurement. The percentage of readthrough for each sample was calculated using the corresponding readthrough control from each replicate plate. Replicates are from one experiment for UGAAAG samples, and three individual experiments for UGACUG samples. p, pcDNA 3.1(+) with no insert (empty vector); e, pcDNA-eRF1. D. Antizyme frameshifting. Values for Renilla luciferase (Rluc) and firefly luciferase (Luc+) are in relative light units. Background (bkgd) values (cell lysate alone) were subtracted from each measurement. The relative frameshift efficiency for each sample was calculated using the corresponding average readthrough control (RT) from each replicate plate. Replicates are from one experiment. Value in bold italics was omitted as it was greater than two standard deviations below the mean. Az, antizyme; p, pcDNA 3.1(+) with no insert (empty vector); e, pcDNA-eRF1. E: HIV frameshifting. Values for Renilla luciferase (Rluc) and firefly luciferase (Luc+) are in relative light units. Background (bkgd) values (cell lysate alone) were subtracted from each measurement. The relative frameshift efficiency for each sample was calculated using the corresponding readthrough control (RT) from each replicate plate. Replicates are from one experiment. Values in bold italics were not included as they were greater than two standard deviations above or below the mean. Two individual clones, labelled 1 and 2, were used for the UAG reporters. p, pcDNA 3.1(+) with no insert (empty vector); e, pcDNA-eRF1. (XLSX) S7 File. Raw data relating to Fig. 6 . A: Stop codon readthrough. Values for Renilla luciferase (Rluc) and firefly luciferase (Luc+) are in relative light units. Background (bkgd) values (cell lysate alone) were subtracted from each measurement. The percentage of readthrough for each sample was calculated using the corresponding average readthrough control from each replicate plate. Replicates are from one experiment. Values in bold italics were not included as they were greater than two standard deviations above or below the mean. CAG was the UAA readthrough control, UAU the UAG readthrough control, and UGG the UGA readthrough control. ser, serine tRNA; oc, ochre (UAA suppressor tRNA); am, amber (UAG suppressor tRNA); op, opal (UGA suppressor tRNA). B: Antizyme frameshifting. Values for Renilla luciferase (Rluc) and firefly luciferase (Luc+) are in relative light units. Background (bkgd) values (cell lysate alone) were subtracted from each measurement. The relative frameshift efficiency for each sample was calculated using the corresponding average readthrough control (RT) from each replicate plate. Replicates are from one experiment. The value in bold italics was not included as it was greater than two standard deviations above the mean. Az, antizyme; ser, serine tRNA; am, amber (UAG suppressor tRNA); op, opal (UGA suppressor tRNA). C: HIV frameshifting. Values for Renilla luciferase (Rluc) and firefly luciferase (Luc+) are in relative light units. Background (bkgd) values (cell lysate alone) were subtracted from each measurement. The relative frameshift efficiency for each sample was calculated using the corresponding average readthrough control (RT) from each replicate plate. Replicates are from one experiment. The value in bold italics was not included as it was greater than two standard deviations above the mean. ser, serine tRNA; am, amber (UAG suppressor tRNA); op, opal (UGA suppressor tRNA). (XLSX)