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Oligo Synthesis

Oligo Synthesis : CEPs

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dK-CE Phosphoramidite

dK-CE Phosphoramidite

Glen Research

Catalogue No.DescriptionPack SizePriceQty
10-1048-02dK-CE Phosphoramidite 0.25g £623.00 Quantity Add to Order
10-1048-90dK-CE Phosphoramidite 100µmoles £214.00 Quantity Add to Order

Description

dK-CE Phosphoramidite

Structure

Catalog Number: 10-1048-xx

Description: dK-CE Phosphoramidite

9-[2'-Deoxy-5'-dimethoxytrityl-Β-D-ribofuranosyl]-2-dimethylaminomethyleneamino-
6-methoxyaminopurine,3'-[(2-cyanoethyl)-(N,N-diisopropyl)]-phosphoramidite
Formula: C44H56N9O7P M.W.: 853.96 F.W.: 358.25
Diluent: Anhydrous Acetonitrile
Coupling: No changes needed from standard method recommended by synthesizer manufacturer.
Deprotection: No changes needed from standard method recommended by synthesizer manufacturer.
Storage: Refrigerated storage, maximum of 2-8°C, dry
Stability in Solution: 24 hours

duplex effects

The design of primers is frequently complicated by the degeneracy of the genetic code. Three strategies are now available to confront this problem. In the first, a mixed base addition (N) is used to form the degenerate site. This approach is best if the number of degenerate sites is small. A second option is the use of 2’-deoxyInosine or 2’-deoxyNebularine which exhibit low, but unequal, hydrogen bonding to the other four bases. The third option is the use of a universal nucleoside. In this strategy, the base analog does not hybridize significantly to the other four bases and makes up some of the duplex destabilization by acting as an intercalating agent. 3-Nitropyrrole 2’-deoxynucleoside (M) is the first example of a set of universal bases. Subsequently, 5-nitroindole was determined to be an effective universal base and to be superior to 3-nitropyrrole, based on duplex melting experiments.

The modified bases designated P and K show considerable promise as degenerate bases. The pyrimidine derivative P, when introduced into oligonucleotides, base pairs with either A or G, while the purine derivative K base pairs with either C or T. A dP dK mix also can serve as a mixed base with much less degeneracy than dA dC dG dT (N).

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Applications & Benefits

The modified bases designated P and K show considerable promise as degenerate bases.  The pyrimidine derivative P, when introduced into oligonucleotides, base pairs with either A or G, while the purine derivative K base pairs with eith C or T.  A dP dK mix can also serve as a mixed base with much less degeneracy than dA dC dG dT (N).

EXTINCTION DATA

Item Nucleoside λMax-1 Emax-1 λMax-2 Emax-2 E260
    (nm) (ml/µmole) nm (ml/µmole) (ml/µmole)
10-1048 dK 279 10.7     7.7

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

 

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
10-1048-02 0.25grams .25grams 2.93 84.33 50.6 31.63 23 16.87 4.22
10-1048-90 100µmoles .085grams 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
10-1048-02 0.25grams .25grams 4.37 .07 81 50.63 36.82 5.06  
10-1048-90 100µmoles .085grams 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
10-1048-02 0.25grams .25grams 4.37 .07 82.6 51.63 37.55    
10-1048-90 100µmoles .085grams 1.5 .07 25.2 15.75 11.45  

If you cannot find the answer to your problem then please contact us or telephone +44 (0)1954 210 200

Related products

If you cannot find the answer to your problem then please contact us or telephone +44 (0)1954 210 200