Oligo Synthesis : CEPs
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Etheno-dA-CE Phosphoramidite
Etheno-dA-CE Phosphoramidite
Glen Research
| Catalogue No. | Description | Pack Size | Price | Qty |
|
|---|---|---|---|---|---|
| 10-1006-02 | Etheno-dA-CE Phosphoramidite | 0.25g | £212.00£193.80Offer until : 31-Mar-2021Offer Code : GLEN5View Offer | Quantity | Add to Order |
| 10-1006-90 | Etheno-dA-CE Phosphoramidite | 100µmoles | £84.00£79.80Offer until : 31-Mar-2021Offer Code : GLEN5View Offer | Quantity | Add to Order |
Related products
Etheno-dA-CE Phosphoramidite
Etheno-dA-CE Phosphoramidite
Glen Research
| Etheno-dA-CE Phosphoramidite |
Catalog Number: 10-1006-xx
Description: Etheno-dA-CE Phosphoramidite
| 5"-Dimethoxytrityl-etheno-deoxyAdenosine3"-[(2-cyanoethyl)-(N,N-diisopropyl)]-phosphoramidite | ||
| Formula: C42H48N7O6P | 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 |
FLUORESCENT NUCLEOSIDES
Etheno-dA is a fluorescent nucleoside which is especially useful in observing the transition between DNA structural types. It is quite base labile and should be deprotected with ammonium hydroxide at room temperature for 24 hours. Alternatively, UltraMild chemistry can be used. 2-Aminopurine and AP-dC (G-Clamp) are also useful fluorescent nucleosides.
Pyrrolo-dC is a fluorescent deoxycytidine analog that is an ideal probe of DNA structure and dynamics. It base-pairs as a normal dC nucleotide. An oligo fully substituted with pyrrolo-dC has the same Tm as the control dC oligo with the same specificity for dG. Its small size does not perturb the structure of the DNA helix and it is well tolerated by a number of DNA and RNA polymerases. It is highly fluorescent and its excitation and emission are well to the red of most fluorescent nucleotide analogs, which eliminates or reduces background fluorescence from proteins. Pyrrolo-dCTP has potential uses in biological assay development.
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Etheno-dA-CE Phosphoramidite
Etheno-dA-CE Phosphoramidite
Glen Research
Material Safety Data Sheet
Glen Report 6.1: ETHENO-DA AND ETHENO-A* - FLUORESCENT MONOMERS
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Etheno-dA-CE Phosphoramidite
Etheno-dA-CE Phosphoramidite
Glen Research
QUESTION: What are the relative extinction coefficients of 5"-Fluorescein, Hex and Tet etc.. at 260 nm and their Lambda max?
RESPONSE:Please seehttp://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:Please seehttp://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%. The impurity is not detected with AMA at RT for 2 hours.
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Etheno-dA-CE Phosphoramidite
Etheno-dA-CE Phosphoramidite
Glen Research
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.
| Excitation | Emission | |
| Ribo etheno-A | 345 nm | 455 nm |
| Oligo-etheno-dA | 270 nm | 410 nm |
| 300 nm | 410 nm |
REFERENCE(S):1. Srivastava, S.C., et.al., (1994), Nucleic Acids Research, 22, 1296-1304.
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Etheno-dA-CE Phosphoramidite
Etheno-dA-CE Phosphoramidite
Glen Research
EXTINCTION DATA
| Item | Nucleoside | λMax-1 | Emax-1 | λMax-2 | Emax-2 | E260 |
| (nm) | (ml/µmole) | nm | (ml/µmole) | (ml/µmole) | ||
| 10-1006 | Etheno-dA | 295 | 3.4 | 274 | 5.9 | 4.7 |
DILUTION/COUPLING DATA
The table below shows pack size data and, for solutions, dilutions and approximate couplings based on normal priming procedures. Please link formore detailed usage informationwith the various synthesizers.
| ABI 392/394 | |||||||||
| Cat.No. | PackSize | Grams/Pack | 0.1M Dil.(mL) | LV40 | LV200 | 40nm | 0.2µm | 1µm | 10µm |
| Approximate Number of Additions | |||||||||
| 10-1006-02 | 0.25grams | .25grams | 3.21 | 93.67 | 56.2 | 35.13 | 25.55 | 18.73 | 4.68 |
| 10-1006-90 | 100µmoles | .078grams | 1 | 20 | 12 | 7.5 | 5.45 | 4 | 1 |
| Expedite | |||||||||
| Cat.No. | PackSize | Grams/Pack | Dilution(mL) | Molarity | 50nm | 0.2µm | 1µm | 15µm | |
| Approximate Number of Additions | |||||||||
| 10-1006-02 | 0.25grams | .25grams | 4.8 | .07 | 89.6 | 56 | 40.73 | 5.6 | |
| 10-1006-90 | 100µmoles | .078grams | 1.5 | .07 | 23.6 | 14.75 | 10.73 | 1.48 | |
| Beckman | |||||||||
| Cat.No. | PackSize | Grams/Pack | Dilution(mL) | Molarity | 30nm | 200nm | 1000nm | ||
| Approximate Number of Additions | |||||||||
| 10-1006-02 | 0.25grams | .25grams | 4.8 | .07 | 91.2 | 57 | 41.45 | ||
| 10-1006-90 | 100µmoles | .078grams | 1.5 | .07 | 25.2 | 15.75 | 11.45 | ||
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