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Oligo Synthesis

Oligo Synthesis : CEPs

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pdC-CE Phosphoramidite

pdC-CE Phosphoramidite

Glen Research

Catalogue No.DescriptionPack SizePriceQty
10-1014-02pdC-CE Phosphoramidite 0.25g £214.00 Quantity Add to Order
10-1014-05pdC-CE Phosphoramidite 0.5g £427.00 Quantity Add to Order
10-1014-90pdC-CE Phosphoramidite 100µmoles £100.00 Quantity Add to Order

Description

pdC-CE Phosphoramidite

10-1014

Catalog Number: 10-1014-xx

Description: pdC-CE Phosphoramidite

5'-Dimethoxytrityl-N4-diisobutylaminomethylidene-5-(1-Propynyl)-
2'-deoxyCytidine,3'-[(2-cyanoethyl)-(N,N-diisopropyl)]-phosphoramidite
Formula: C51H67N6O7P M.W.: 907.1 F.W.: 327.23
Diluent: Anhydrous Acetonitrile
Coupling: No changes needed from standard method recommended by synthesizer manufacturer.
Deprotection: Deprotection in Ammonium Hydroxide requires a minimum of 12 hours at 55 °C.
Storage: Refrigerated storage, maximum of 2-8°C, dry
Stability in Solution: Similar to dA,C,G,T-CE Phosphoramidites
Please Note: This product is covered by patents or patents pending owned by Isis Pharmaceuticals, Inc. ("Isis"). Purchase of this product includes a limited license to use this product solely for internal research. This license specifically excludes (and you have no right to use this product for): (a) therapeutic or diagnostic applications (including products or services that incorporate this product), (b) any in vivo toxicity/safety study in support of an investigational new drug application (or foreign counterpart), (c) resale (including sale of any products or services that incorporate this product) or (d) gene functionalization activities (including products or services that incorporate data derived from gene functionalization activities) if such activities have commercial application, any and all of which require a separate license from Isis. Neither this product nor any product created through its use may be used in human clinical trials.
Please see Terms and Conditions of Use

C-5 PROPYNE DERIVATIVES AND G-CLAMP

Substitution of C-5 propynyl-dC (pdC) for dC and C-5 propynyl-dU (pdU) for dT are effective strategies to enhance base pairing. Using these base substitutions, duplex stability and melting temperatures are raised by the following amounts: C-5 propynyl-C 2.8° per substitution; C-5 propynyl-U 1.7° per substitution. AP-dC (G-clamp) substitutes for dC and is another very important modified nucleoside that enhances hybridization by 7.5° per substitution. The ability of these modified bases to enhance binding while maintaining specificity has proven useful in antisense research and in the synthesis of high affinity probes. AP-dC is also a fluorescent nucleoside and should find uses in DNA structural research.

 

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Notes

C-5 Propyne and AP-dC Phosphoramidites

This product is covered by patents or patents pending owned by Isis Pharmaceuticals, Inc. (Isis).  Purchase of this product includes a limited licence to use this product solely for internal research.  This licence specifically excludes (an you have no right to use this product for): (a) therapeutic or diagnostic applications (including products or services that incorporate this product), (b) any in vivo toxicity/safety study in support of an investigational new drug application (or foreigh counterpart), (c) resale (including sale of any products or services that incorporate this product), or (d) gene functionalisation activities (including products or services that incorporate data derived from gene functionalisation activities) if such activities have commercial application, any and all of which require a separate licence from Isis.  Neither this product nor any product created through its use may be used in human clinical trials.

A simple agreement must be signed before end-users and custom oligo services amy purchase these products for use as defined above.

FREQUENTLY ASKED TECHNICAL QUESTION

QUESTION: What are the extinction coefficients for propynyl-dC and dU? Also Halogenated dC and dU derivatives? Others?

RESPONSE:See: Table of Extinction Coefficients

REFERENCE(S):
B. Froehler, Gilead
M. Powell
R. Somers

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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)
10-1014 pdC 295 7.7 234 14.7 5.1

 

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
10-1014-02 0.25grams .25grams 2.76 78.67 47.2 29.5 21.45 15.73 3.93
10-1014-05 0.5grams .5grams 5.51 170.33 102.2 63.88 46.45 34.07 8.52
10-1014-90 100µmoles .091grams 1 20 12 7.5 5.45 4 1
Expedite
Cat.No. Pack
Size		 Grams/
Pack		 Dilution
(mL)		 Molarity 50nm 0.2µm 1µm 15µm
Approximate Number of Additions
10-1014-02 0.25grams .25grams 4.11 .07 75.8 47.38 34.45 4.74
10-1014-05 0.5grams .5grams 8.23 .07 158.2 98.88 71.91 9.89
10-1014-90 100µmoles .091grams 1.5 .07 23.6 14.75 10.73 1.48
Beckman
Cat.No. Pack
Size		 Grams/
Pack		 Dilution
(mL)		 Molarity 30nm 200nm 1000nm

Approximate Number of Additions
10-1014-02 0.25grams .25grams 4.11 .07 77.4 48.38 35.18

10-1014-05 0.5grams .5grams 8.23 .07 159.8 99.88 72.64

10-1014-90 100µmoles .091grams 1.5 .07 25.2 15.75 11.45

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