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Oligo Synthesis

Oligo Synthesis : CEPs

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4-Thio-dU-CE Phosphoramidite

4-Thio-dU-CE Phosphoramidite

Glen Research

Catalogue No.DescriptionPack SizePriceQty
10-1052-024-Thio-dU-CE Phosphoramidite 0.25g £1,277.00 Quantity Add to Order
10-1052-904-Thio-dU-CE Phosphoramidite 100µmoles £409.00 Quantity Add to Order
10-1052-954-Thio-dU-CE Phosphoramidite 50µmoles £205.00 Quantity Add to Order

Description

4-Thio-dU-CE Phosphoramidite

Structure

Catalog Number: 10-1052-xx

Description: 4-Thio-dU-CE Phosphoramidite

5'-Dimethoxytrityl-2'-deoxy-4-(2-cyanoethylthio)-Uridine,3'-[(2-cyanoethyl)-
(N,N-diisopropyl)]-phosphoramidite
Formula: C42H50N5O7PS M.W.: 799.93 F.W.: 306.23
Diluent: Anhydrous Acetonitrile
Coupling: No changes needed from standard method recommended by synthesizer manufacturer.
Deprotection: Deprotect with1.0M DBU in anhydrous acetonitrile at Room Temperature for 2hrs to remove the cyanoethyl protection. Complete the deprotection with 50mM NaSH in concentrated NH4OH at Room Temperature for 24hrs.
Storage: Refrigerated storage, maximum of 2-8°C, dry
Stability in Solution: 2-3 days

Demand for sulfur modified bases continues to expand for investigations of oligonucleotide structure, but primarily for cross-linking purposes. 6-Thio-dG, 4-Thio-dT and 4-thio-dU are very useful modifications for photo-crosslinking and photoaffinity labelling experiments. Oligos containing 2-thio-dT are useful in examining protein-DNA interaction by acting as photosensitizing probes. The thiocarbonyl group in 2-thio-dT is especially interesting in that it is available to react with compounds associating with the minor groove of DNA. 2-Amino-A forms a very stable base pair with T containing three hydrogen bonds but the stability of the base pair with 2-thio-T is greatly diminished. Due to steric interactions between the 2-thio group of thymidine and the 2-amino group of 2-amino-A, the base pair contains only a single hydrogen bond. Oligos containing 2-amino-dA and 2-thio-dT exhibit high affinity for natural oligonucleotides but show little affinity for other similar oligos even of a complementary sequence.

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Protocols

MSDS

Glen Report 10.1: MORE NOVEL MONOMERS

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Notes

6-Thio-dG, 4-Thio-dT and 4-Thio-dU are protected as the S-cyanoethyl ether which is stable during synthesis and readily removed by ammonium hydroxide.  It is critical to add 50mM sodium hydrosulfide (NaSH) to the ammonium hydroxide used for deprotection.  Especially if room temperature deprotection is carried out, this technique radically reduces the level of ammonolysis which would lead to undesired aminated bases.  Moreover, it is also desirable to remove the cyanoethyl protecting group (1M DBU in acetonitrile, 2-5h/RT) prior to the ammonium hydroxide cleavage and deprotection.

4-Thio-dU-CE Phosphoramidite

5'-Dimethoxytrityl-2'-deoxy-4-(2-cyanoethylthio)-Uridine,3'-[(2-cyanoethyl)-
(N,N-diisopropyl)]-phosphoramidite
Formula: C42H50N5O7PS M.W.: 799.93 F.W.: 306.23
Diluent: Anhydrous Acetonitrile
Coupling: No changes needed from standard method recommended by synthesizer manufacturer.
Deprotection: Deprotect with1.0M DBU in anhydrous acetonitrile at Room Temperature for 2hrs to remove the cyanoethyl protection. Complete the deprotection with 50mM NaSH in concentrated NH4OH at Room Temperature for 24hrs.
Storage: Refrigerated storage, maximum of 2-8°C, dry
Stability in Solution: 2-3 days
  Material Safety Data Sheet

EXTINCTION DATA

Item Nucleoside λMax-1 Emax-1 λMax-2 Emax-2 E260
    (nm) (ml/µmole) nm (ml/µmole) (ml/µmole)
10-1052 4-thio-dU 330 30.4     3.6

Literature Highlights

Glen Report 10.1: MORE NOVEL MONOMERS

DILUTION/COUPLING DATA

The table below shows pack size data and, for solutions, dilutions and approximate couplings based on normal priming procedures. Please link for more detailed usage information with the various synthesizers.

ABI 392/394
Cat.No. Pack
Size		 Grams/
Pack		 0.1M Dil.
(mL)		 LV40 LV200 40nm 0.2µm 1µm 10µm
Approximate Number of Additions
10-1052-02 0.25grams .25grams 3.13 91 54.6 34.13 24.82 18.2 4.55
10-1052-90 100µmoles .08grams 1 20 12 7.5 5.45 4 1
10-1052-95 50µmoles .04grams .5 3.33 2 1.25 .91 .67 .17
Expedite
Cat.No. Pack
Size		 Grams/
Pack		 Dilution
(mL)		 Molarity 50nm 0.2µm 1µm 15µm  
Approximate Number of Additions
10-1052-02 0.25grams .25grams 4.66 .067 86.8 54.25 39.45 5.43  
10-1052-90 100µmoles .08grams 1.5 .067 23.6 14.75 10.73 1.48  
10-1052-95 50µmoles .04grams .75 .067 8.6 5.38 3.91 .54  
Beckman
Cat.No. Pack
Size		 Grams/
Pack		 Dilution
(mL)		 Molarity 30nm 200nm 1000nm    
Approximate Number of Additions
10-1052-02 0.25grams .25grams 4.66 .067 88.4 55.25 40.18    
10-1052-90 100µmoles .08grams 1.5 .067 25.2 15.75 11.45    
10-1052-95 50µmoles .04grams .75 .067 10.2 6.38 4.64

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Applications & Benefits

EXTINCTION DATA

Item Nucleoside λMax-1 Emax-1 λMax-2 Emax-2 E260


(nm) (ml/µmole) nm (ml/µmole) (ml/µmole)
10-1052 4-thio-dU 330 30.4

3.6

DILUTION/COUPLING DATA

The table below shows pack size data and, for solutions, dilutions and approximate couplings based on normal priming procedures.

ABI 392/394
Cat.No. Pack
Size		 Grams/
Pack		 0.1M Dil.
(mL)		 LV40 LV200 40nm 0.2µm 1µm 10µm
Approximate Number of Additions
10-1052-02 0.25grams .25grams 3.13 91 54.6 34.13 24.82 18.2 4.55
10-1052-90 100µmoles .08grams 1 20 12 7.5 5.45 4 1
10-1052-95 50µmoles .04grams .5 3.33 2 1.25 .91 .67 .17
Expedite
Cat.No. Pack
Size		 Grams/
Pack		 Dilution
(mL)		 Molarity 50nm 0.2µm 1µm 15µm
Approximate Number of Additions
10-1052-02 0.25grams .25grams 4.66 .07 86.8 54.25 39.45 5.43
10-1052-90 100µmoles .08grams 1.5 .07 23.6 14.75 10.73 1.48
10-1052-95 50µmoles .04grams .75 .07 8.6 5.38 3.91 .54
Beckman
Cat.No. Pack
Size		 Grams/
Pack		 Dilution
(mL)		 Molarity 30nm 200nm 1000nm

Approximate Number of Additions
10-1052-02 0.25grams .25grams 4.66 .07 88.4 55.25 40.18

10-1052-90 100µmoles .08grams 1.5 .07 25.2 15.75 11.45

10-1052-95 50µmoles .04grams .75 .07 10.2 6.38 4.64

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Related products

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