Thymine glycol (5,6-dihydroxy-5,6-dihydrothymine) is formed when thymine is subjected to oxidative stress, including ionizing radiation. Oxidation of the 5,6 double bond of Thymidine generates two chiral centers at C5 and C6. The cis-5R,6S form is generated as the predominant product along with the other diastereomer, the cis-5S,6R form. The presence of thymidine glycol in DNA has significant biological consequences and many organisms possess specific repair enzymes for the excision of this lesion.
Coupling: 3 minute coupling time is recommended. Monomers that allow for UltraMILD deprotection must be used. (Catalog Numbers: dA: 10-1601-xx, dC: 10-1015-xx, dG: 10-1621-xx, dT: 10-1030-xx.). To avoid any exchange of the iPr-Pac group on the dG with acetyl, use the UltraMild Cap Mix A (40-4210-xx/ 40-4212-xx).
Deprotection: Cleave and deprotect the oligonucleotide in 30% Ammonium Hydroxide for 2 hours at Room Temperature. Dry down and dissolve the residue in 0.5 mL of TEA.3HF and keep at 40° C overnight to remove the TBDMS protecting groups. Add an equal volume of dH2O and desalt on a Glen Gel-Pak™ column or equivalent.