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Oligo Synthesis

Oligo Synthesis : CEPs

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2-Aminopurine-CE Phosphoramidite

2-Aminopurine-CE Phosphoramidite

Glen Research

Catalogue No.DescriptionPack SizePriceQty
10-1046-022-Aminopurine-CE Phosphoramidite 0.25g £355.00 Quantity Add to Order
10-1046-902-Aminopurine-CE Phosphoramidite 100µmoles £127.00 Quantity Add to Order

Description

2-Aminopurine-CE Phosphoramidite

Structure

Catalog Number: 10-1046-xx

Description: 2-Aminopurine-CE Phosphoramidite

5'-Dimethoxytrityl-N2-(dimethylaminomethylidene)-2'-deoxypurine
riboside,3'-[(2-cyanoethyl)-(N,N-diisopropyl)]-phosphoramidite
Formula: C43H53N8O6P M.W.: 809.01 F.W.: 313.21
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: 2-3 days

The C-nucleoside 2’-deoxypseudouridine, in contrast to dU, forms stable C:pseudoU-A triplets. 2-Aminopurine lacks groups critical for hydrogen bonding and is a mildly fluorescent base.

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 cross-linking 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 6.2

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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)
10-1046 2-Aminopurine 303 6.8 243 5.7 1

 

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

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:Please see 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%. The impurity is not detected with AMA at RT for 2 hours.

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
10-1046-02 0.25grams .25grams 3.09 89.67 53.8 33.63 24.45 17.93 4.48
10-1046-90 100µmoles .081grams 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
10-1046-02 0.25grams .25grams 4.61 .07 85.8 53.63 39 5.36
10-1046-90 100µmoles .081grams 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
10-1046-02 0.25grams .25grams 4.61 .07 87.4 54.63 39.73

10-1046-90 100µmoles .081grams 1.5 .07 25.2 15.75 11.45

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Related products

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