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Oligo Synthesis

Oligo Synthesis : Supports,CPGs

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5-Br-dU-CPG

5-Br-dU-CPG

Glen Research

Catalogue No.DescriptionPack SizePriceQty
20-2090-015-Br-dU-CPG 0.1g £40.00£36.80Offer until : 31-Dec-2019Offer Code : GLEN88% off all Glen Research products View Offer Quantity Add to Order
20-2090-415-Br-dU-CPG 4x1.0µm £160.00£147.20Offer until : 31-Dec-2019Offer Code : GLEN88% off all Glen Research products View Offer Quantity Add to Order
20-2090-425-Br-dU-CPG 4x0.2µm £96.00£88.32Offer until : 31-Dec-2019Offer Code : GLEN88% off all Glen Research products View Offer Quantity Add to Order

5-Br-dU-CPG

5-Br-dU-CPG

Glen Research

5-Br-dU-CPG

Catalog Number: 10-1090-xx

Description: 5-Br-dU-CE Phosphoramidite

5'-Dimethoxytrityl-5-bromo-2'-deoxyUridine,3'-[(2-cyanoethyl)-
(N,N-diisopropyl)]-phosphoramidite
Formula: C39H46BrN4O8P M.W.: 809.69 F.W.: 369.07

Diluent: Anhydrous Acetonitrile
Coupling: No changes needed from standard method recommended by synthesizer manufacturer.
Deprotection: Ammonium Hydroxide: room temperature as required by nucleobases.
Storage: Refrigerated storage, maximum of 2-8°C, dry
Stability in Solution: 2-3 days

Structure

HALOGENATED NUCLEOSIDES

Brominated and iodinated nucleosides are used in crystallography studies of oligonucleotide structure. They are also photolabile and are used for cross-linking studies to probe the structure of protein-DNA complexes. Antibodies exist to Br-dU and oligonucleotides containing Br-dU can be used as probes.

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5-Br-dU-CPG

5-Br-dU-CPG

Glen Research

MSDS

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5-Br-dU-CPG

5-Br-dU-CPG

Glen Research

EXTINCTION DATA

Item Nucleoside λMax-1 Emax-1 λMax-2 Emax-2 E260


(nm) (ml/µmole) nm (ml/µmole) (ml/µmole)
10-1090 5-Br-dU 278 9.7

5

Frequently Asked Technical Question

QUESTION: What methods are available for crosslinking DNA with DNA, RNA, proteins?

RESPONSE:The most widely used method seems to be using Br-dU and, more recently, I-dU (1). The substitution of photoreactive Br and I for the 5-Me group of thymidine is attractive since their radii are similar to that of the methyl group. These modifications do not significantly affect the binding of oligonucleotides with proteins. Br-dU is irradiated at 308nm and crosslinking is typically not greater than 40%. Crosslinking of I-dU at 308nm is higher but is optimal at 325nm. Laser excitation is preferred.

After the synthesis of oligonucleotides containing Br-dU or I-dU, care must be taken to avoid loss of the halogens. Even though both modifications are quite stable to ammonium hydroxide, it is sensible to play safe and carry out the deprotection at room temperature for 24 hours. Even better, use the UltraMild monomers and deprotect with potassium carbonate in methanol at room temeperature. The oligonucleotide products should be protected from light - plastic tubes and amber vials are safe. Gel electrophoresis should be carried out protected from light.

REFERENCE(S):
(1) M.C. Willis, B.J. Hicke, O.C. Uhlenbeck, T.R. Cech and T.H. Koch, Science, 1993, 262, 1255.


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
10-1090-02 0.25grams .25grams 3.09 89.67 53.8 33.63 24.45 17.93 4.48
10-1090-90 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
10-1090-02 0.25grams .25grams 4.61 .07 85.8 53.63 39 5.36
10-1090-90 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
10-1090-02 0.25grams .25grams 4.61 .07 87.4 54.63 39.73

10-1090-90 100µmoles .081grams 1.5 .07 25.2 15.75 11.45

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