N4-Et-dC-CE Phosphoramidite

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10-1068
5'-Dimethoxytrityl-N4-ethyl-2'-deoxyCytidine,3'-[(2-cyanoethyl)-(N,N-diisopropyl)]-phosphoramidite

Product Specifications

Formula:
C41H52N5O7P
M.W.:
757.87
F.W.:
317.42
CAS Number:
195535-80-9
Catalog Number: Select Pack Size and Format to Reveal

Description

Sequences with high GC content may contain mismatches and still hybridize because of the high stability of the G-C base pair. The N4-ethyl analogue of dC (N4-Et-dC) hybridizes specifically to natural dG but the stability of the base pair is reduced to about the level of an AT base pair. Coupling N6-Me-dA (10-1003) and N4-Et-dC (10-1068) with 1H-tetrazole leads to a trace of branching at the secondary amine positions, while DCI leads to around 15% branching. In collaboration with Berry and Associates, the acetyl protected monomers were prepared. Acetyl protection was chosen since it would block branching reactions. Oligonucleotides synthesized using these monomers proved to be compatible with all popular deprotection strategies from UltraMild to UltraFast. When the acetyl protected monomers were compared with the unprotected monomers using DCI as activator, branching was reduced from 15% to zero.

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 2-3 days


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
10-1068-02 0.25 g .25grams 3.3 96.67 58 36.25 26.36 19.33 4.83
10-1068-90 100 µmol .076grams 1 20 12 7.5 5.45 4 1
10-1068-95 50 µmol .038grams 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
10-1068-02 0.25 g .25grams 4.92 0.07 92 57.5 41.82 5.75
10-1068-90 100 µmol .076grams 1.5 0.07 23.6 14.75 10.73 1.48
10-1068-95 50 µmol .038grams 0.75 0.07 8.6 5.38 3.91 0.54