Table 1.
Summarized biopanning strategies useda for the identification of Integra® (IT) matrix targeting peptides from New England Biolabs libraries
| Protocol | IT1BA | IT6BA | IT6BAS | IT6BGC | IT7BA | IT7BCG | IT8BA | IT8BAS | IT8PA | IT8PAS | IT9MA | IT9PA |
|---|---|---|---|---|---|---|---|---|---|---|---|---|
| Target | Matrix | Sonicated | Sonicated | Sonicated | Sonicated | Sonicated | Sections | Sections | Sections | Sections | Sonicated | Sonicated |
| Library | C7C | C7C | C7C | C7C | PHD12 | PHD12 | C7C | C7C | C7C | C7C | PHD12 | PHD12 |
| Block | BSA | BSA | BSA | BSA | BSA | BSA | BSA | BSA | PO4 | PO4 | NFM | PO4 |
| Elution | Acid | Acid | Acid/salt | GAG | Acid | GAG | Acid | Acid/salt | Acid | Acid/salt | Acid | Acid |
| Selection rounds | 3 to 5 | 3 | 3 | 3 | 3 | 3 | 4 | 3 | 4 | 3 | 3 | 3 |
| Colonies analyzed | 50 | 15 | 15 | 15 | 15 | 15 | 30 | 30 | 30 | 30 | 30 | 30 |
| Peptide ID | Table 2 | Table 2 | Table 2 | Table 2 | Table 2 | Table 2 | Table 3 | Table 3 | Table 3 | Table 3 | Table 3 | Table 3 |
| Phylogeny | Figure 3 | Figure 4A | Figure 4A | Figure 5A | Figure 4B | Figure 5B | Figure 6A,C | Figure 6A | Figure 6B,D | Figure 6B | Figure 7 | Figure 7 |
aFour distinct strategies were evaluated (IT1, IT7, IT8 and IT9), which involved changing the blocking buffer (phosphate-buffered saline with Tween, bovine serum albumin (BSA) and non-fat milk (NFM)), the elution conditions (acid, acid/salt and glaycosaminoglycan), the target (matrix, sonicated samples and thin sections) and the number of rounds (three or four) of biopanning.