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AP-dC-CE Phosphoramidite - (10-1097)

1-[5'-O-(4,4'-Dimethoxytrityl)-β-D-2'-deoxyribofuranosyl]-9-(2-trifluoroacetamidoethoxy)-1,3-diaza-2-oxophenoxazine,3'-[(2-cyanoethyl)-(N,N-diisopropyl)]phosphoramidite

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10-1097

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Product Specifications

Formula:

C₄₉H₅₄F₃N₆O₁₀P

M.W.:

974.97

F.W.:

438.33

CAS Number:

1360536-91-9

1-[5'-O-(4,4'-Dimethoxytrityl)-β-D-2'-deoxyribofuranosyl]-9-(2-trifluoroacetamidoethoxy)-1,3-diaza-2-oxophenoxazine,3'-[(2-cyanoethyl)-(N,N-diisopropyl)]phosphoramidite

Description

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 7-21° per substitution depending upon the sequence and location of the AP-dC. 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.

Details

Usage

Coupling: No changes needed from standard method recommended by synthesizer manufacturer.
Deprotection: AMA (Ammonium hydroxide/40% Methylamine 1:1 v/v) for 10 minutes at 65°C is recommended. (To prevent modification of dC by Methylamine, use Ac-dC (10-1015-xx) during synthesis.)

Specifications
Diluent	Anhydrous Acetonitrile
Recommended Storage	Refrigerated storage, maximum of 2-8°C, dry
Stability In Solution	24 hours

Dilution/Coupling Data

The table below show pack size data and, for solutions, dilution and approximate coupling based on normal priming procedures.

ABI 392/394

Catalog #	Pack Size	Grams/Pack	0.1M Dil. (mL)	Approximate Number of Additions
				LV40	LV200	40nm	0.2μm	1μm	10μm
10-1097-02	0.25 g	.25grams	2.56	72	43.2	27	19.64	14.4	3.6
10-1097-90	100 µmol	.097grams	1	20	12	7.5	5.45	4	1
10-1097-95	50 µmol	.049grams	0.5	3.33	2	1.25	0.91	0.67	0.17

Expedite

Catalog #	Pack Size	Grams/Pack	Dilution (mL)	Approximate Number of Additions
				Molarity	50nm	0.2μm	1μm	15μm
10-1097-02	0.25 g	.25grams	3.83	0.07	70.2	43.88	31.91	4.39
10-1097-90	100 µmol	.097grams	1.5	0.07	23.6	14.75	10.73	1.48
10-1097-95	50 µmol	.049grams	0.75	0.07	8.6	5.38	3.91	0.54