Cis-syn Thymine Dimer Phosphoramidite

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11-1330
5'-Dimethoxytrityl-2'-deoxy-5,6-dihydro-Thymidine-(cis-syn-cyclobutanyl)-5'->3'-(methyl-phosphoryl)-2'-deoxy-5,6-dihydro-Thymidine-3'-[methyl-(N,N-diisopropyl)]-phosphoramidite

Product Specifications

Formula:
C49H63N5O15P2
M.W.:
1024.01
F.W.:
608.39
CAS Number:
118187-67-0
Catalog Number: Select Pack Size and Format to Reveal

Description

One of the major sources of DNA damage in all organisms is the UV component of sunlight. The predominant reaction induced by UV light on DNA is dimerization of adjacent pyrimidine bases leading to cyclobutane dimers (CPDs). The dimers formed in the most significant quantity are the cis-syn cyclobutane dimer of two thymine bases. Although formed routinely, these dimer products are efficiently excised and repaired enzymatically by nucleotide excision repair (NER) or the dimerization is reversed by photolase enzymes. A further mode of oxidative damage is radiation-induced damage of DNA, which has been shown to lead to bridged cyclonucleosides. The purines, cyclo-dA and cyclo-dG, are predominantly formed, although the cyclo pyrimidines have also been detected. Cyclo-dA is doubly intriguing since it contains both damaged base and damaged sugar residues and, as such, should have a considerable biological impact. In a manner analogous to thymine dimer, cyclo purines cause significant distortion of the regular DNA helix and these lesions are repaired not by base excision repair (BER) but by NER.

Details

Usage

  • Coupling: 10 minute coupling recommended.
  • Deprotection: |1. Remove the methyl phosphate groups by treating the support with thiophenol/triethylamine/THF (1:2:2) v/v/v for 45 minutes at room temperature. Wash the support with THF 1X, methanol 5X, acetonitrile 3X and dry with air or argon.|2. Cleave and deprotect the oligo in the dark with ammonium hydroxide at room temperature under conditions appropriate to remove the protecting groups on the nucleobases.
Specifications
Diluent Anhydrous Acetonitrile
Storage Freezer storage, -10 to -30°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
11-1330-02 0.25 g .25grams 2.44 68 40.8 25.5 18.55 13.6 3.4
11-1330-90 100 µmol .102grams 1 20 12 7.5 5.45 4 1
11-1330-95 50 µmol .051grams 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
11-1330-02 0.25 g .25grams 3.64 0.07 66.4 41.5 30.18 4.15
11-1330-90 100 µmol .102grams 1.5 0.07 23.6 14.75 10.73 1.48
11-1330-95 50 µmol .051grams 0.75 0.07 8.6 5.38 3.91 0.54