Science of Synthesis

Reddavide, F. V.; Heiden, S.; Cui, M.; Lin, W.; Thompson, M.; Zhang, Y., Science of Synthesis: DNA-Encoded Libraries, (2024) 1, 556.

In this section, the materials and the methods to perform DEL selections using the second-generation EDCCL (Y-EDCCL) are described.[‌21‌] The protein target is usually immobilized, via a specific tag, on a suitable solid support. The Y-EDCCL is then exposed to the solid support and, after the washing steps, the coding information of the two sub-libraries are enzymatically joined while the fragments are still bound to the target protein. The elution steps allow the release of the codes, which can undergo the sequencing preparation for the final data analysis.

Meeeeeeee eeee ee eeeeeee MMM eeeeeeeeee eeeee eee eeeeee-eeeeeeeeee MMMMM:[‌88‌]

Mee eeeeeee eee eeeeeeeee eeee eeeeeeee eeeee eeeee-eeee eeeee eee eeeeeeeeee eeeee eeeeeeee. Me ee eeeeeeeee ee eeee eeeeeeeee (e.e., Meeee 88) ee eee eeeeeee ee eeeeeeeee eee Meeeeeeee ee eeeeeeee-eeee eee ee eee eeeeee ee eee eeee eeeee [eeee (e)]. Mee eeeeeee eeeeeee eeee eeeeeeee eeeeeee 8.88-µe eeeeeeeee eeeeeee eeeeeeeee ee eeeeeee eeee eeeeee. Meeeeeee eeeeeee (8.8 eM) eee eeee eeeeee eeee MMM eee-eeeeeee eeeeeeeeee eee MMM eeeeeeeeeee, ee eeeeeee eee-eeeeeee eeeeeeeeee eee eeeeeee eeeeeeeeeeeeee. Mee Meeeeeeee-eeeee eeeeeeeeeeeeee eeeee eeee eeeeeeeee ee 8888 e eee 8 eee, eeeee e eeeee-eeeeee eeeeeeeeee eeeee ee eeeeeeee ee eeee eeeeeeeeeee eeee eee eeee eee ee eeeeeeee. Mee eeeeeeee eeeee, eeeeeeee eeeee eeee eeee ee eeee eeee eee eeee eeee eee 88 e. Meeee eeeeeeeeee eeee eeeeeee ee eee eeeeeeeeee eee eeeeeee eeeee.

• eeeeeee eee eeeeeee eeeeee (MMM-M): 88 eM eeeeee eeeeeeeee, 888 eM MeMe (eM 8.8), 8.88% Meeee 88 (e/e)

• eeeeeeee eeeeee eee eeeeeeeeeeee eeeeeeeeeeee: 888 µM eeeeee ee MMM-M

• MMM eeeeeee eeeeeeee: 8 eM ee eeee eeeeeee eeeeee eee 8.88 ee/eM eeeeeee eeeeeee ee eeeeee eeeee MMM ee MMM-M [eeee (e)]

• eeeeeee eeeeeee (eee eeeeee eeeeeeeeeee eeee eeeeeeeee eeee eeeeeeeee eee eeee):
– eeeeeeeeeeee eeeeeee eeeeee [88 eM Meee (eeee), eM 8.8, 8.88 % Meeee 88 (e/e)]
– Mee-eee eeeeeee eeeeee [888 eM eeeeeeeee, eeeeeeeee ee 88 eM Meee-MMe, eM 8.8, 888 eM MeMe eee 8.88% Meeee-88 (e/e)]
– MMM-eee eeeeeee eeeeee (888 eM Meee eeee, 888 eM MeMe, 8 eM MMM, 88 eM eeeeeee eeeeeeeeeee, 8.8% Meeeee M-888, eM 8.8)

• eeeeeeeeeeee-eeeeee Meeeeeeee (MM Meeeeeeeee Meee Meeeeeee, eeeeeeeeeeee Meeeeeeee Meee Meeeeeeeeee; eeeeeee eeeeeeee: ee. 88 eeee/µM)

• eeeeeeeeeeee-eeeeee eeeeeeee eeeee (Meeeeeeeee, Meeeeeeee MeMee M-888M8; eeeeeee eeeeeeee: eeeeeeeeeeee eeeeeee 888 eeee/ee eeeee)

• Meeeeeeee Mee-eee Meeeeeeee eee Meeeeeee (Meeeeeeeee, eeeeeeee eee eeeeeeeee 88 µe ee e 88 eMe eeeeeeeee-eeeeee eeeeeee/ee eeeee)

• eeeeeeeeeee eeeeeeee eeeeeee eeeee (Meee Meeeeeeeee; eeeeeee eeeeeeee: 88 ee eeeeeee ee 88 eMe/eM eeeee)

• MMM-eeeeeeeee Meeeeeeee 8 Meee Meee (MM Meeeeeeeee Meee Meeeeeee; eeeeeee eeeeeeee: MMM 888–888 eeee/µM; MMM = M-eeeeeeeeeeeeeeeeee) ee MMMe-Meeeeeeee Meeeeeeee 8 Meee Meee (MM Meeeeeeeee Meee Meeeeeee; eeeeeee eeeeeeee: Meeeeeeeeeeeeeee 88–88 ee/eM)

• Meeeee-MM-MMM eee Meeeeeeee-MMM8-Meeeee (Meeeee Meeeee Meeeeeeeee)

• Mee Meeeeee Meeeee 8.8, eeeeeeeeee eeeeee eee eeeeee eee Meeeee eeeeeeee eeeeee eeeeeeee

• M8 MMM Meeeee (Mee Meeeeee Meeeeee)

• Meeeee eeeeeeee (8′ → 8′ eee-) (Mee Meeeeee Meeeeee)

Meeeeeeee eeee eee MMM eeeee e eeeeee eeeeeee eeee eeeeee Meeeeeeee ee eeeeeeee eeeee:[‌88‌]

Mee eeeee eeeee eeeeeeee e eeeeee eeeeeeee ee eeeeeee eee MMMMM eeeeeeeee. Mee eeeeeeee eee ee eeeeeee ee eeeee eeeeeeeeee, eee eeeeeee eeeee eeeeeeee-eeee eeeeeeeeee.[‌88‌]

 8. Mee eeeeeeeeeeee eeeeeee [eeee (e)] ee eee eeeeeee-eeeeeeee Meeeeeeee [eeee (e)] eeee eeeeeeee eeeeeeeee eee eeeeeeee eeee eee eeeeeeeeeeee ee eee eeeeeeeeeeeee eeeeeee ee eee MMM-eeeeeeeee Meeeeeeee, eeeeeeeeeeee.

 8. Meeeeeeeeeee eeeee ee eeeeeee-eeeeeeee Meeeeeeee, Me-MMM (eeeeee–eeeeeeeeeeeeeeee eeee), ee eeeeeeeeeee eeeee eeee eeeeeeeee [eeee (e)] eeee eeeeeee eee-eeeeeee eeeee eee eeeeee eeeee eeeee eeee eeeeeee eeeeee (8 eM), eeeeeeee ee eeeeeeeeeeeeee ee eeeeeeee eeeeeeeeee, eeeeeeee eee eeeeeeeeeee eeee eeee (eeeeeee eeeeeeee eee eeeee).

 8. Mee eeeeeee eeeee eeeeee ee eeeeee eeeeee eeeeeee [eeee (e)] eee eeeeeee eeeeeee ee eeeeeee eeeeee (888 µM). Mee eeeeeeeeeeee, Me-MMM, ee eeeeeeeeeee eeeee eeee eeee eeeeeeeeeee ee eeeeeeeee ee eee eeee ee eeeeeee eeeeeeee (888 µM) ee eee ee-eeeeeee eeeeeee ee MMM-M (888 µM), eee eeeeeeeee ee ee ee ee eee-eeee-eee eeeee (88 eee; 888° eeeee) eee 88–88 eee. Meeee eeeeeeeeee, eee eeeeeeee eee eeeeeeeeeee ee eeeeeeeeeeee eeeeeeeee, eee eee eeeeeeeeeee eee eeeeeeeee eeeeeee ee eeeeeeeee.

 8. Mee eeeeeeeeeeee-eeeeeeeeeeeeee eeeee eeee: Mee eeeee eeee eeeeeeeee eee eeeee eeee eeeeeeee eeeeee (888 µM) [eeee (e)] ee ee eee-ee-eee eeeee (88 eee) ee ee eee 8 eee. Mee eeeeeeee eee eeeeeeeeeee ee eeeeeeeeeeee eeeeeeeee, eee eee eeeeeeeeeee eee eeeeeeeee eeeeeee ee eeeeeeeee.

 8. Mee eee eeee eeeee: Mee eeeee eeee eeeeee eeee eeeeeee eeeeee (888 µM) eeeeeeeeee eeeeeee eeeeee ee eeeeeee eeeee MMM ee ee eee-ee-eee eeeee (88 eee) ee ee eee 8 eee, eee eeee eeeeeeeeeee ee eeeeeeeeeeee eeeeeeeee, eee eee eeeeeeeeeee eee eeeeeeeee. Meee eeee eee eeeeeeee, eeee eee eeeeeeeee eeee eee eeee-eeeeeee eeeeee eeeeeeee eee eeeeeeeeeee eeee e MMM eee-eeeeeee eeee eeeeee eeeeeeee eee eeeeeeeeeee.

 8. Mee MMM eeeeeee eeeeeeee eee eeeeeeee ee eeeeeeeeee eee MMM eeeeee ee MMM-M (888 µM) eee eeeeeeee eeeeeeeeee. Mee MMM eeeeeee eeeeeeee [eeee (e)] eee eeeeeee ee eee eeeeeee-eeeeee eeeee [eeee (e)] eee eeeeeeeee ee ee eee-ee-eee eeeee (88 eee; 888° eeeee) ee ee [eeee (e)] eee 8 e ee eeeeee eee eeeeeee eeeeeee eeeeeee eee eeeeee eeeeeee.

 8. Meeee eeeeeee eeeeeeeeee eeee eee eeeeeee-eeeeeeeeeeeeee eeeee, eee eeeeeeee eee eeeeeeeeeee ee eeeeeeeeeeee eeeeeeeee eee eee eeeeeeeeeee eee eeeeeee (ee eeeeeeeeee eeeeee). Mee eeeee eeee eeeeeeeeeeee eeeeeeeeeee ee eeeeeee eeeeee (888 µM) [eeee (e)] eee eeeeeeeeeee eeee e eee MMM eee-eeeeeee eeee. Mee eeeeeeeeeee eee eeeeeeeee, eee eee eeeeeee eeee eee eeeeeeee eee ee eeee eeeee [eeee (e)].

 8. Meeeee 8: Mee eeeee eeee eeeeeeeeeee ee eee eeeeeeeeeee eeeeeee eeeeee (888 µM); eeeeeeeeeeeee, eee eeeee eeee eeeeeeee eee eeee eeeeeeee eeeeeeee [eeeeee 8 (eeee 88); eeee (e)]. Me eee eeee ee eeeeeeeeeeee eeeee ee eeeeeeeeeee eeeee, eee eeeeeeeeee eee eeeeee ee e eeee eeeee eee 88 eee ee 88 °M [eeee (e)] eeee eeeeeeee eeeeeee, ee eeeeeeeee. Mee Me-MMM eeeee, eee eeeee eeee eeeeeeeeeee eeee eeeeeee eeeeee (ee ee 888 µM, eee e eeeee eeeeeeeee eeeeeeeeeeeee ee 888 eM) eee eeeeeeeee eee 88 eee ee ee eee-ee-eee eeeee (88 eee; 888° eeeee) ee ee.

 8. Meeeeee, eee eeeee eeee eeeeee eeee ee e eeeeeeeeee ee eeeeeeee eeee eee eee eeeeeeeeeee, eeeeeeeeee eee MMM-eeee, eee eeeeeeeeeee eeee e eee MMM eee-eeeeeee eeee. Mee eeeeeee eee eee ee eeeeee ee e eeeeeee eee eeeeeee eeeeeeeeee [eeee (e)].

88. Meeeee 8: M eeeeeeee eeeeeee [eeee (e)] eee eeeeeeee ee eeeeee M8 MMM eeeeee (888 eeeee eeeee) eeee 8 eM MMM eee MMM8 eeeeee ee e eeeee eeeeee ee 88 µM. Meeee eeeeeeeee eeeeeeeeeeee eee eeeee, eeeeeeee eee eeeeeee eee eeeeeeeee ee 88 °M eeee eeeeee eeeeeee ee e eeeee (888 eee, eeeeeee).

88. Meeeee eeeeeeee, eeeeeee eeee 8′ → 8′ eee 8′ → 8′ eeeeeeeeeee eeeeeeee, ee e eeeee eeeeee ee 88 eeeee eee eMMMe (eeeeeeeeeeeeeee eeeeeeeeeeeee) ee e eeeee eeeeeeeeeeeee ee 888 µM, eeee eeeee ee eee eeeeeeee eee eee eee eeeeeee eee eeeeeeeee eee 8 e ee 88 °M ee e eeeee, eeee eeeeee eeeeeee.

88. Mee eeeee eeee eeeeeeeeeeee eeee eee eeeeeeeeeee eeeeeee eeeeee (888 µM; eee Meee 8) ee eeeeeee eee eeeee eeeeeeeee.

Meeee eeee eeeee eeee ee eee eeee ee ee-MMMMM:[‌88‌]

Me eeeee eeeee eee eeeeeeeeeee MMMMM eee e eeeeeeeeeeeee eeeeee eeee ee eeeeee ee eeee eeeeeeeeeee, eeee eee ee ee eeee ee eeeeeee eeee eeeeeeeeeee eee, eeeeeee, eee eeeeeee eeeeeee ee eee eeeeeee. Mee eeee-eeeeeee MMMMM (ee-MMMMM) eeeeeeee eee eeeeeee ee eee eeeeeeeeeeeee eeeeee ee eee eeeeeee eeeeeee, eeeeeeee ee e eeeeeeeeeee ee eee eee eee-eeeeeeeee, eeee eeeeeeee eee eeeeeee ee eeee eeeeeeeeeee.[‌88‌] Me eee eeeeeeeee eeeee, eee eeeeee eeeeeeeee ee eeeeeeeee; e eeeee ee eeeeeee eeeee e eeeeeeeeeeee eeeeee eee eeeeeeee eeeeeeeeee.[‌88‌]

8. Mee MMM eeeeeee eeeeeeee eeeeeeeeeee eee eee eeeeeeeee, eee eeeeeee eeeeeeeee eee eeee eeeeeeeeeee: eee eeeeeeee eee eeeee ee e 8.8-eM MMM eee-eeeeeee eeee eeeee e eee-eeeeeee eee [eeee (e)].

8. Mee eeeee ee eeee eeeeeeeeeee eeeeeeeee ee e eeee ee eeee eeeeeeeeeee eee 8 eee ee e eeee eeeee (88–88 °M, eeeeeeeee ee eee eeeeeee eeeeeeeeeee ee eee eeeeeeeeeeeee eeeeee), eee eee eeee ee eee eeeeeeeee eeeeeeeeeee eee 88 eee, eee eeee eee eeee eee eeee ee eeee ee ee eee 88 eee [eeee (e)].

8. Mee eeee eee eeeeeeeeeee ee eeeeeee eeeee eee 8 eee, eee eee eeeeeeee eee ee-eeeeeeeee ee eee eeeee eee 8–8 e [eeee (e)], eeeeeeee ee eee eeeee-eeeeeeeee eeeeeee eeeee (Meee 8 eeeee).

8. Meeeeee, eee eeeee eeee eeeeeeeeeee ee eeeeeee eeeeee (888 µM) eee eeeeeeeee eeeeeeeee ee eee eeee eeee (Meee 8 eeeee). Mee eeee eee eeeeeeeeeee, eee eee eeeeeeeeeee eee eeeeeeeee eeeeeee eee eeeeee ee e eee eeee eee eeeeeeee eee eeeeeee.

Meeee

(e) Mee eee ee e eeeeeeeee ee eee eeeeeee ee eeeeee eeeeeeeeeee ee eeeeeee eee Meeeeeeee eeee eeeeeeee ee eee eeeeeee eee ee eeeeee eeeeeeeeeee eeeeeeeeeeee eee eeeeeeeeee eeee eee eeeeeee.

(e) Meeeeee ee eeeeee MMM ee eeee ee e eeeeeeee eeeee ee eeeeee eee eee-eeeeeeee eeeeeee ee eee MMM eeeeeee ee eee eeeeeee ee eee Meeeeeeee eeeee.

(e) Meeee eeeeeeee, ee ee eeeeeeeeee ee eeeeeee eeeeeeee eee eeeeeeeeee eeeeeee eeeeeeeeeeeee e.e. eeeeeeeee eeeeeeee eeeeeeee eeeee eeeeeeeee-eeeeeeee eeeeeeeeeeeee eeeeeee. Me ee eeeeeeeeeee, e eeeeee eeeeeeeeeeeee eeeee MMM-eeeeeeee eeeeee eeeeeeeeeee ee MMM-eeeeeeeee eeeee eee ee eeee.

(e) Meee eeeee MMM-eeeeeeeee eeeee, eeeeeee ee eeee eeeee eeeeeeeeee eee eeeee eeee eee eeeeeee ee eeeeee eeeeeeeee MMM. Mee eeeeeeee eeeeee ee eeeeeee eeeee eeeeee eeeeeeeeee eeeeeeeeeeee eeeeeee eee MMM-eee eee eee eeeee eeeeeee.

(e) Mee eeeee eeee eeeeeeeee eee eeeeee ee 8 °M; eeeeee eeeeeeeeee e eeeeeee eeeeee ee eeeee eeee eee eeeeeeee eeeeeee, eee eeeee eeeeeeeee eee eeeeeeeeee eee eeeeee eeeee.

(e) Meee eeeee eee eeeeeeeeeeee-eeeeeeeeeeeeee eeeee, ee eeeeee eee eeeeeeeeee eeeee eee ee eee eeeeeee ee eee eeeeeeeeeeee eeeeeee, ee eeeeee ee eeeeeeeeeeee eeeeeee eeeeee eeee eee eeeeeee eeeeeeee ee eee eeeee ee eeee, eeeeeeeeee ee eeeee 8.8 eeeee eee eeeeeee eeeeeeee.

(e) Mee eeeeee eeeeee eeeee ee ee eeeeeeee eeeeeee eeee e eee 88 eM eeeee eeeeeeee ee eeeeee ee MMMM ee eeeeee eeee eeeeeeeeee ee eeeeee. Mee eee ee eee eeeeee eeeeee eeeeee eee eeeeeeeee ee eeeeeeeee eeeeeeeeeeee eeeeeee ee eee eeeeee eeeeee.

(e) Meee eeeeeeee, eee eee eeeeeee ee eeeeeeeeee eee eeeeeee eeeeeeeee eee eeeeeeeeeeeee, ee eeee ee eee eeeeeee MMM eeeeeeeee eeeeeeee, eee eee ee e eeeeeeee eeeeeee eee eeeeeee (ee eeeeeeeeee ee e MMM eeeeeee) ee eeeeeeeeeee. Mee eeeeeeeeee ee eee eeeeeeee eeeeeee ee eee eeeeeee-eeeeeeeeeeeeee eeeee eee ee eeeeeeee ee ee e eeeeeeeeeeee MMM eeeee eee eeeeeeeeeeeeeeee eeeee ee eeeeeee. Meeeeeeeeeeee, eeeeeeeee eeeee eeee eeeeeeeeeee eeeeeee eee ee eeee ee eeeee eee eeeeeee eeeeeeee.

(e) Meeee eee eeeeeee ee eeeeeeeee eee eeeee ee eee eeeeeeee eeeeeee eeeeee eeeeeeee eeeeeeeeee eeeee ee eeeee ee eeeeeeee eeeee eeeeeeeeeeeeee eee eee eeeeeeeeeeee ee eeeee ee eee eee ee eee eeeeeeee eeeeee.

(e) Me ee eeeeeeeee ee eeeeeeee eee eeeee eeeeeee ee e eee 8.8-eM eeee eeeee MMM eeeeeeeeee eee eeeeeee eeeeeee eeeee ee eeeeeeee eee eeeee-eeee ee eee-eeeeeee eeeeeee eeeeeee eeee eee ee eeeeeeee ee eee eeee ee eee eeee.

(e) Me eeeeeee eeeee eeee eeee eeee eeeeeeeeeeeeee eee eeeeeeee, eeee eee ee eeeeeeeee eeeee eee eeeeeee eeeeeeeeee eee eeeeee eee eeeeeee eeee.

(e) Me ee eeeeeeeee ee eee eee-eeeeeee eeeee eee eeee; eeee ee eeeeeee ee eeeeee eee eeee ee eeeeee eeeeeee eee eeeeeeeee eeeeee.

(e) Meee eeeee e eeee-eeeeeeee eeeeeeee eeeeeeee, eeee eeeeee ee eeeee eeee eee eeeeeeee eeeeee eee ee eeeeee eeeeee eeee 8 eeeeee eee eeeeee ee eeeeeee eeeeee eeeeeeeeeee.

(e) Meeeeee ee eeee eeeeeeeeeee eeeee ee eeeeeeeeeeee ee eee eeeeeee eeeeeee ee eee eeeeeeee eee eeeeeee ee eeeee eeeeeee eeeeeee.

(e) Mee eeeeeee ee eeeeee eee eeeeeee eeeeeeeeee ee −88 °M. Mee eeeeeee eeeeeee eee eee ee eeeeeeeeee, e.e. ee eeeee ee eeeeeeeeeeee MMM (eeeeeeee eeeeeeee) eee Meeeeeee eeeeeeeeee eeeee MMM eeeeeeeee-eeeeeeee eeeeeee.

(e) Mee eeeeeee eeeeeee eee eeeeeee ee eee MMM eeeeeeeeeeeee eee-eeeeeeeee. Me eeeeee eeee eee eeeeee eeeeeee eee ee eeeeeeee eeeee ee eee Meeeeeee eeeeeeeeee, e eeeeeeee eeee ee eeeeeeeee.

(e) Me eeeeeeee eee eeee eeeeeeeeeee eeeeeee, eee eeee-eeeeeeeeeee eeee ee eeeeeeeee 88 °M eeeee eee eeeeeee eeeeeeeeeee, eeeee eee eeeeeeeee eeeeeee ee eeeeeee eee ee 8 °M eeeee eee eeeeeee eeeeeeeeeee ee eee eeeeeeeeeeeee eeeeee.

(e) Meee ee eee eeeeee ee eeee eeeeeeeeeee eee eeeeeeee eee eeeeeeeeee ee eee eeeeeee eeee ee eeeeeeeee ee ee eeeee 8–8 eeeee. Me eeeeeee eeee eeeeee, eee eee ee eeeeeeeeee eee ee eeeeeeee ee eeeeeeeeee ee eee eeeeeeeeeee eeeeeee eee eeeeee eeeeeeee ee eeeeeeee.

References