(A) Cell lysates expressing SNAP-CA, SNAP-Bcl-xL, and
SNAP-FKBP
were individually labeled with one of three DNA sequences and combined
with a cell lysate expressing SNAP and labeled with 256 DNA sequences.
The pooled lysates were combined with a library of 262 DNA-linked
small molecules, including DNA-linked GLCBS, CBS, Bad, Bak, BakL78A,
and rapamycin, for a model library×library IDUP “selection”.
(B) IDUP using a library of cell lysates expressing SNAP-target fusions
identified all five known target+ligand pairs, including A
- FKBP+rapamycin, B - Bcl-xL+Bad, C - Bcl-xL+Bak,
D - CAII+GLCBS, and E - CAII+CBS, despite having affinities
from 0.2 nM to 3.2 μM. (C) For interactions with Kd = 40 nM–26 μM, we observed a strong relationship
between the log of target–ligand Kd and the number of sequence counts after selection.