pdU-CE Phosphoramidite

5'-Dimethoxytrityl-5-(1-Propynyl)-2'-deoxyUridine,3'-[(2-cyanoethyl)-(N,N-diisopropyl)]-phosphoramidite
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Product Specifications

Formula:
C42H49N4O8P
M.W.:
768.85
F.W.:
328.22
CAS Number:
198080-43-2
To Retrieve a Catalog Number, Select a Pack Size and Format:
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Technical Documents

Safety Data Sheet

Extinction Table

Glen Report 10.13: Cytofectin GSV Transfection Protocol

Glen Report 11.11: Using Modified Bases to Optimize Hybridization

Glen Report 13.11: C-5 Propynes, Cytofectin and Other Product Updates

Glen Report 17.12: Products for siRNA Research

Glen Report 6.21: C-5 Propyne Derivatives - Antisense Breakthrough

Glen Report 9.11: A Novel Transfection Reagent

Glen Report 33-15: Technical Note - DNA and RNA Nucleoside Numbering System

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: No changes needed from standard method recommended by synthesizer manufacturer.
Specifications
Diluent Anhydrous Acetonitrile
Storage Refrigerated storage, maximum of 2-8°C, dry
Stability Similar to dA,C,G,T-CE Phosphoramidites

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
10-1054-02 0.25 g .25grams 3.25 95 57 35.63 25.91 19 4.75
10-1054-05 0.5 g .5grams 6.5 203.33 122 76.25 55.45 40.67 10.17
10-1054-90 100 µmol .077grams 1 20 12 7.5 5.45 4 1

Expedite

Catalog # Pack Size Grams/Pack Dilution (mL) Approximate Number of Additions
Molarity 50nm 0.2μm 1μm 15μm
10-1054-02 0.25 g .25grams 4.85 0.07 90.6 56.63 41.18 5.66
10-1054-05 0.5 g .5grams 9.71 0.07 187.8 117.38 85.36 11.74
10-1054-90 100 µmol .077grams 1.5 0.07 23.6 14.75 10.73 1.48

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