For both libraries, Vλ and Vκ were independently cloned into phagemid vectors (Fig. S1) creating λ and κ sub-libraries, with XFab1κ (1.1 × 1011) plus XFab1λ (1.4 × 1011) having 2.6 × 1011 total members and XscFv2κ (2.8 × 1011) plus XscFv2λ (8.2 × 1010) having 3.6 × 1011 total members. Both vectors contain an amber stop codon between the antibody fragment and the phage gene 3, enabling soluble expression as well as display. Each antibody

fragment (scFv or Fab VH) is linked to a triple tag (6xHis, c-myc, and V5) to enable detection, capture and purification. selleck The triple tag provides much needed flexibility, since many commercially available antigens utilize one or more of the individual tags above, disallowing their use in an assay with the antigen. Moreover, the V5 tag and 6xHis can be utilized simultaneously to capture and detect the soluble antibody fragment in an ELISA, allowing the determination of soluble antibody expression, as described below. The percentage of clones with full length open reading frame (ORF) ranges from 66% to 85%. Between 58% and 85% of clones express soluble protein as assessed by ELISA (Table 1). Both libraries also have

similar distributions of VH-CDR3 lengths (Fig. 2) each with an average amino acid length of 15.3, which is similar to the distribution of VH-CDR3 lengths of functional antibodies in the IMGT database (Giudicelli et al., 2006). The V-genes from each library were also assessed for amino acid changes from germline sequences for FR1 through FR3 (Fig. 3A). Both libraries have similar find more average amino acid changes from germline sequences of less than two per segment in all but VH-FR3. VH-FR3 has greatest number of amino acid differences, averaging three amino acid differences per sequence. These differences are distributed throughout VH-FR3, with no amino acid position contributing more to the diversity than others. Overall, the percentage of germline representation in the V-genes (FR1–FR3) ranges from 5.6% to 20.7% (Fig. 3B). The difference between the Vλ germline representation in XFab1 and XscFv2 can be accounted for by the difference in primers used to amplify these V-regions. For

XscFv2, thirty-three primers were used to increase Bay 11-7085 the specificity of the priming for each Vλ-gene family and subfamily over the eighteen primers used for Vλ priming for XFab1 (Table S1 and Table S3). Since the primers were designed based on germline sequences, the result of having primers that are more specific is a decrease in natural diversity in FR1. To visualize more clearly the diversity of the libraries from germline sequences, Fig. 3C depicts the distribution of differences from germline sequences for each library. The majority of light chains have 5 or fewer differences from germline and the majority of heavy chains have 8 or fewer differences. For VH, when there are more than twelve differences from germline, most of these differences are in FR3, which is reflected in the data presented in Fig. 3A.