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

Product Specifications

Formula:

C₅₂H₇₉N₄O₁₀PSi₂

M.W.:

1007.36

F.W.:

338.21

CAS Number:

318497-58-4

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Technical Documents

Description

Details

Dilution/Coupling Data

References

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