Thymidine Glycol CE Phosphoramidite

5'-Dimethoxytrityl-2'-deoxy-(5R,6S)-5,6-bis(t-butyldimethylsilyloxy)-5,6-dihydroThymidine,3'-[(2-cyanoethyl)-(N,N-diisopropyl)]-phosphoramidite
main product photo

Product Specifications

Formula:
C52H79N4O10PSi2
M.W.:
1007.36
F.W.:
338.21
CAS Number:
318497-58-4
To Retrieve a Catalog Number, Select a Pack Size and Format:
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Technical Documents

Safety Data Sheet

Glen Report 16.13: Minor Base and Related Novel Phosphoramidites

Glen Report 29.13: Studying DNA Repair Pathways Using Site-Specifically Modified Oligonucleotides

Glen Report 33-15: Technical Note - DNA and RNA Nucleoside Numbering System

Description

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.

Details

Usage

  • 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.
Specifications
Diluent Anhydrous Acetonitrile
Storage Freezer storage, -10 to -30°C, dry
Stability 2-3 days

Dilution/Coupling Data

The table below show pack size data and, for solutions, dilution and approximate coupling based on normal priming procedures.

ABI 392/394

Catalog # Pack Size Grams/Pack 0.1M Dil. (mL) Approximate Number of Additions
LV40 LV200 40nm 0.2μm 1μm 10μm
10-1096-02 0.25 g .25grams 2.48 69.33 41.6 26 18.91 13.87 3.47
10-1096-90 100 µmol .101grams 1 20 12 7.5 5.45 4 1
10-1096-95 50 µmol .05grams 0.5 3.33 2 1.25 0.91 0.67 0.17

Expedite

Catalog # Pack Size Grams/Pack Dilution (mL) Approximate Number of Additions
Molarity 50nm 0.2μm 1μm 15μm
10-1096-02 0.25 g .25grams 3.7 0.07 67.6 42.25 30.73 4.23
10-1096-90 100 µmol .101grams 1.5 0.07 23.6 14.75 10.73 1.48
10-1096-95 50 µmol .05grams 0.75 0.07 8.6 5.38 3.91 0.54

References

1 K. Groebke, and C.J. Leumann, Helv Chim Acta, 1990, 73, 608-617.

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