Glen Research Product Information

Catalog Number: 10-1006-xx
Description: Etheno-dA-CE Phosphoramidite

5'-Dimethoxytrityl-etheno-deoxyAdenosine,3'-[(2-cyanoethyl)- (N,N-diisopropyl)]-phosphoramidite

Formula: C42H48N7O6
M.W.: 777.86 
F.W.: 337.23 

Diluent: Anhydrous Acetonitrile

Coupling: No changes needed from standard method recommended by synthesizer manufacturer. The use of UltraMILD monomers are preferred. (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: If UltraMILD reagents were used, deprotect in 0.05M Potassium Carbonate in Methanol for 4 hours at Room Temperature OR for 2 hours at hours in 30% Ammonium Hydroxide. If standard bases were used, deprotection in Ammonium Hydroxide at Room Temperature for 24-36 hours will give acceptable yields.

Storage: Refrigerated storage, maximum of 2-8°C, dry

Stability in Solution: 1-2days

   

Pricing Information

Catalog Number

Pack Size

Price (US$)


10-1006-90
100µm
105.00
10-1006-02
0.25g
255.00

Related Document(s)

  

Literature Highlight(s)

FREQUENTLY ASKED TECHNICAL QUESTION

QUESTION: Can Etheno-dA be substituted for dA in a sequencing or PCR primer . What is the best method for cleavage/deprotection of oligos containing Etheno-dA. What are the excitation/emmision wavelengths for oligos containing etheno-dA.?

RESPONSE:Due to the structure of the 1, N6 etheno structure etheno dA will not base-pair with T or dU. For this reason oligonucleotides with etheno-dA in the middle or 3'-end will not act as PCR or sequencing primers. However if located at or near the 5''-end etheno-dA can be incorporated one or more times and still act as an effective sequencing or PCR primer (1).

Etheno-dA is somewhat labile to NH4OH so it is best to use base labile protecting groups such as Pac dA, isopropyl-Pac-dG and Ac-dC and either deprotect with K2CO3:MeOH, 4 hr. at RT. or NH4OH 4 hr. at RT.. If using standard protecting groups use mild deprotection conditions (0.4 M Methanolic NaOH; MeOH:H2O, 4:1) 17 hr. at room temperature.

ExcitationEmission

Ribo etheno-A345 nm455 nm
Oligo-etheno-dA 270 nm410 nm
300 nm410 nm

REFERENCE(S):
1. Srivastava, S.C., et.al., (1994), Nucleic Acids Research, 22, 1296-1304.


QUESTION: What are the relative extinction coefficients of 5'-Fluorescein, Hex and Tet etc.. at 260 nm and their Lambda max?

RESPONSE:Please see http://www.glenresearch.com/Technical/Extinctions.html

REFERENCE(S):
Oligonucleotide Properties Calculator; http://www.basic.northwestern.edu/biotools/oligocalc.html


QUESTION: What are the relative extinction coefficients of various dyes?

RESPONSE:http://www.glenres.com/Technical/Extinctions.html#dyes


QUESTION: Does AMA or methylamine cause any degradation to fluorescein or fluorescein-type dyes such as FAM or FITC?

RESPONSE:Response: While AMA (Ammonium hydroxide/40% Methylamine 1:1 v/v) is considered compatible with fluorescein, the use of methylamine when deprotecting a Fluorescein-labeled oligo does lead to a small amount of degradation, which is characterized by a the appearance of a late-eluting peak by RP HPLC that shows no visible fluorescein absorbance. With standard deprotection conditions (AMA 10 minutes at 65 C) the amount of degradation is approximately 5%


EXTINCTION DATA

ItemNucleosideλMax-1Emax-1λMax-2Emax-2E260
(nm)(ml/µmole)nm(ml/µmole)(ml/µmole)
10-1006Etheno-dA2953.42745.94.7

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)
LV40LV20040nm0.2µm1µm10µm
Approximate Number of Additions
10-1006-020.25grams.25grams3.2193.6756.235.1325.5518.734.68
10-1006-90100µmoles.078grams120127.55.4541
Expedite
Cat.No.Pack
Size
Grams/
Pack
Dilution
(mL)
Molarity50nm0.2µm1µm15µm
Approximate Number of Additions
10-1006-020.25grams.25grams4.8.0789.65640.735.6
10-1006-90100µmoles.078grams1.5.0723.614.7510.731.48

 

 

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01/19/2019

 

 

 

 

 

 

 

 

 

 

 

 

 

 


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