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.
Coupling: 3 minute coupling time is recommended. Due to the steric hindrance at the 5' hydroxyl, the coupling time for the phosphoramidite immediately following the addition of the 8,5'-Cyclo-dA should be increased to 6 minutes.
Deprotection: No changes needed from standard method recommended by synthesizer manufacturer.