Science of Synthesis

Keefe, A. D.; Litovchick, A., Science of Synthesis: DNA-Encoded Libraries, (2024) 1, 504.

Iodo–phosphorothioate ligation occurs between two DNA oligonucleotides, one modified with a 3′-phosphorothioate and the other with a 5′-iodo thymidine (iodo dT). Several vendors are capable of synthesizing such oligonucleotides. For example, the following oligonucleotides were synthesized by TriLink BioTechnologies (San Diego, CA):

MMM MMM MMM MMM MMM MMM MMM/eeeeeeeeeeeee/-8′ (MMM-8)

8′-/eeee eM/MM MMM MMM MMM (MMM-8)

Me eeeeeeeeee MMM eeeeeeeeeeeeeee eee eeee eeeeeeeeeee ee eeeee ee e eeeeee:

MMMMMM MMM MMM MMM MM (MMM-8 ee eeeeee)

Meee eeeeeeeeeeeeeee eee eeeeeee ee eeeeeeeeeeeeeee ee eeee eee 8′-eeeeeeee eeeeee ee MMM-8 eee eee 8′-eeeeeeee eeeeee ee MMM-8.

Meeeeeee Meeeeeee:[‌8‌,‌8‌]

Meeeeeee eeeeeeeee eeee eeeeeeeee eeee 888 µM ee eeee eeeeeeeeeeeeeee (MMM-8, MMM-8, eee MMM-8) ee e eeeeee eeeeeeeeee 88 eM Meee MMe (eM 8.8), 888 eM MeMe, eee 88 eM MeMe8 ee eeee eeeeeeeeeee. Meeeeeee eeeeeeee eeee eeeeeeee ee MMMM, ee eeee ee ee eeeee 8 M eeee/88% eeeeeeeeeeeeee eee eeeeeeeeeeeeeee (MMMM). Me eee eeeeeeee ee eee eeeeee, eeeeeeeeeeeeeee eeeeeeee eeeeeeee eee eeeeeee e eeeee ee 88% eeeeeeee eeeeeee eeeee 88 e ee eeeeeeeeee. Me eee eeeeee eeeeeeeeeeeeeee MMM-8 eee eeeeeeee, ee eeeeeeee eee eeeeeeee, eeee eeeee eeeeeee eeee. Mee eeeeeee eeeeee ee eee eeeeee eee eeeee ee ee 88 ee 88 eeeeeeeeeee, e.e. eeee 8 ee 8 eeeeeeeeeeeee eeeeeeeeeee ee eeee ee eee eeeeeeeee eeeeeeeeeeeeeeee. Mee eeeeeee eeeeeeeee ee e eeeeeeeee eeeeeeeeeeeeeeeeeeee eee eee eeee eeeeeeee ee ee eeeeeee: 8′-eeee eM–eeeeee eeeeeeeeee (8–8 eeeeeeeeeee)–eeeeeeee eeeeeeee (8–88 eeeeeeeeeee)–eeeeee eeeeeeeeee (8–8 eeeeeeeeeee)–eeeeeeeeeeeeeeee-8′. Meee eee eeeeeeeee ee 88–88 eeeeeeeeeee eeee eee eeee eeeeeeee eeee eeeeeeee e 88–88 eee eeeeee eeeeeeeeeeeeeee. Mee eeeeeeeee eeeeeee MMM ee eeeeee-eeeeeeee eeee eee eeeeee eee eeee eeeeeee.

8′-Meee/8′-eeeeeeeeeeeeeeee eeeeeeeeeeeeeeee eee ee eeee ee eeeeeeeeee eeeeee e eeeeeeeeee ee eeee eeee eeeeee e eeeeeeee eeeeeee eeeeeeeeee eeeeeeeee eeee eee 8′-eeeeeeee. Meee eeeeeeee eee ee eeee ee eeeeeeee e MMM ee eeeeee 8′-eeee eM eee 8′-eeeeeeeeeeeeeee eeeeeeeeeeeeeeee eeee eeeee 8′- eee 8′-eeeeee-eeeeeee eee eeeeee-eeeeeee eeeeeeeee ee eeeeeee eeeeeeeeee eee eeeeeeeee. Me eeeeeeee eeeeeeeeee eee eeee-eeeeeeee ee eeee, eeeeeeeeee ee eee 8′-eeeeeeeeeeeeeeee eee eeeeeeeeeee.

Meeeeeee eee Meeeeeeeeeeeeeee Meeeeeeeee:[‌8‌,‌8‌]

Meee 8′-eeee/8′-eeeeeeeeeeeeeeee eee (8 eeeeeeeeee) eee eeeeeeeee ee M8M ee eeee e eeeee eeeeeeeeeeeee ee 8 eM. Meeeeeeeeeee, eeeeee eeeee eeeeeee (88 eeeeeeeeeee) eee eeeee eee eee eeeeeeee eee eeeeeeeee ee eeee eeeeeeeeeee eeeeeeeee. Meee eeeeeeeeee ee eee eeeeeeee, eee eeeeeee eee eeeeeeeeeeee ee eeeeeee.

Meeeeeee Meeeeeee eee Meeeeee Meeeeeee:[‌8‌,‌8‌]

Meeee M: Me eeee eeee ee eee eeeee eeeee eee eeeee e 8 eM eeeeeeee ee eeeeee-eeeeeeee MMM eeeeeeeee (8 eeeeeeeeee) ee 888 eM eeeeee eeeeee (eM 8.8), eee eeeeeeeee eeeee M eee (8.8 eeeeeeeeeee), eee eee eeeeee (8.8 eeeeeeeeeee) eee eeee eee eeeeeeee ee eeeeeeeeee ee eeee eeeeeeeeeee eeeeeeeee. Mee Meee-eeeeeeeee eeeee eeee (888 eeeeeeeeeee) eee eeee eeeee ee eeee eeee, eeeeeeee ee 8-(8,8-eeeeeeeee-8,8,8-eeeeeee-8-ee)-8-eeeeeeeeeeeeeeeeee eeeeeeee (MMMMM; 888 eeeeeeeeeee), eeeeeeee ee eeeeeeeeee ee eeee eeeeeeeeeee eeeeeeeee. Mee eeeee eeee eeee eeeeee eee eee eeeeeee eeeeeee eee eeeeeeeeeeee eeee eeeeeee. Mee eeeeee eeeee M eeeeeeee eee eeee eeeeeeee eeeee MM, eeeeeeeeeee ee eeeeeee, eee eeeeeeeee ee M8M ee eeee e eeeee eeeeeeeeeeeee ee 8 eM. Meeeeeeeee (88% e/e) eee eeeee ee eeeeeee eee eeeeeeeeeeee ee eee eeeee M eee (88 °M, 8 e). Mee eeeeeeeeeee eeeeeee eee eeeeeeeeeeee eeeee eeeee eeeeeee.

Meeee M: Mee eeeeeeeeeee, eeeeee eeeee M eeeeeeee eee eeeeeeeee ee 888 eM eeeeee eeeeee (eM 8.8) ee eeee e 8 eM eeeeeeeeeeeee, eee eeee eeeee eeee eeeeeeee eeeeeeee eeeee (8 eeeeeeeeee ee eeeee M eeeeeee ee eeee eeee). Me eeee eeee eee eeeee eee eeeeeeeee eeeee M eee (8.8 eeeeeeeeeee), eee eeeeee (8.8 eeeeeeeeeee), eee eeee eee eeeeeeee ee eeeeeeeeee ee eeee eeeeeeeeeee eeeeeeeee. Me eeee eeee (ee eee eeeee) eee eeeee e eeeeeee ee eee eeeeee eeee (888 eeeeeeeeeee), M,M′-eeeeeeeeeeeeeeeeeeeeeee (MMM; 888 eeeeeeeeeee), eee 8-eeeeeee-8-eeeeeeeeeeeeeeee (MMMe; 888 eeeeeeeeeee), eeeeeeee ee eeeeeeeeee ee eeee eeeeeeeeeee eeeeeeeee. Meee eeeeeeeeee, eee eeeee eeee eeeeee eee eee eeeeeeee eeee eeeeeeeeeeee eeeee eeeeeee. Mee eeeee M eeee eee eeeeeeee eeeee MM, eeeeeeeeeee ee eeeeeee, eee eeeeeeeee ee M8M ee eeee e eeeee eeeeeeeeeeeee ee 8 eM. Meeeeeeeee (88% e/e) eee eeeee ee eeeeeee eee eeeeeeeeeeee ee eee eeeee M eee (88 °M, 8 e). Mee eeeeeeeeeee eeeeeee eee eeeeeeeeeeee eeeee eeeee eeeeeee.

Meeee M: Mee eeeeeeeeeee, eeeeee eeeee M eeeeeeee eee eeeeeeeee ee 888 eM eeeeeeeee eeeeee (eM 8.8) ee eeee e 8 eM eeeeeeeeeeeee, eee eeee eeeee eeee eeeeeeee eeeeeeee eeeee (8 eeeeeeeeee ee eeeee M eeeeeee ee eeee eeee). Me eeee eeee eee eeeee eee eeeee M eee (8.8 eeeeeeeeeee) eee eeeeee (8.8 eeeeeeeeeee), eee eeee eee eeeeeeee ee eeeeeeeeee ee eeee eeeeeeeeeee eeeeeeeee. Me eeee eeee (ee eee eeeee) eee eeeee ee eeeee (88 eeeeeeeeeee) eee MeMM8MM (88 eeeeeeeeeee). Mee eeeeeee eee eeeeeeeee ee 88 °M eeeeeeeee. Meee eeeeeeeeee, eee eeeee eeee eeeeee eee eee eeeeeeee eeeeeeeeeeee eeeee eeeeeee. Mee eeeee M eeee eee eeeeeeee eeeee MM eee eeeeeeeeeee ee eeeeeee.

Meeeeeee eee eMMM-Meeeeeeeee:[‌8‌,‌8‌]

Meeeeeeeeeeee eeeeeeee eee eeee eeeeeee ee eeee-eeee eeeeeeeeeeeeee eeeeeeee eee eee eeeeeeeeee ee eeee eeeeeee, eeeeeeeee Mee eeeeeeeeee eee eeeeeee eeeee MMM eeeeeeeeeee eeee eee MMM eeeeeeeeeeeee. Me eeeeeee eeeeeeee eee eee eeeeeeeeeeeee ee eee eeeeee-eeeeeeee eeeeeee ee eeeeeeeee eeeeeeeee. Me eeeeeee, eee eeeeee eeeeee ee eee eeeeee-eeeeeeee MMM eeeeeee eee ee eeeeeeeee eeeee ee eeeeeeeee eeeee e MMM eeeeeeeeee eeee ee eee Meeeee eeeeeeee ee M. eeee MMM eeeeeeeeee M ee eeeeee eee eeeeeeee MMM eeeeee-eeeeeeee eeeee ee eeeeeeeee.

References