Extended Data Fig. 5: DEL selection against HeLa cells labelled with the tags with different lengths of complementary bases.
From: Selection of DNA-encoded chemical libraries against endogenous membrane proteins on live cells
a) The 4,802-member DEL was selected against the DNA-tagged FR on HeLa cells with different lengths of complementary bases in the tag. Two cell batches (P1 and P4) were used in the selections. The selection procedure and data processing method were the same as in Figs. 5–6. b) The effects of different DNA tag lengths were calculated and summarized in the table; key parameters include: ΔH, ΔS, ΔG, fold of affinity increase, and Kd of the DNA tag/library DNA duplex. c)–d) Column graph and the table summarizing the selection results; EF: enrichment factor. The tag lengths from 6 to 10 bases corresponded to a free energy gain from 5.65 to 9.70 kcal/mol and an affinity increase of ~11,000 to 9-million folds. At 6- and 7-nt, the tag hybridized with library DNA at µM affinity; at 9- and 10-nt, the tag and the library DNA formed stable duplexes, which would increase the affinity of all library compounds to nM binders (Kd: 285 nM and 103 nM, respectively). The results also showed that the enrichment fold of FA and MTX dropped with the 10-nt tag, but many other library compounds were enriched. We reasoned this might be because the 10-nt tag formed stable DNA duplex with all library compounds and resulted in the enrichment of many low-affinity binders. DNA tag shorter than 6-base was not tested because it would have hybridization specificity issue at such a short length; the tag may hybridize with the other regions of the library DNA, instead of the primer-binding site.
