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Nucleic Acids Research, Vol 27, Issue 11 2299-2303, Copyright © 1999 by Oxford University Press

ARTICLES

Benzimidazolium triflate-activated synthesis of (6-4) photoproduct- containing oligonucleotides and its application

S Iwai, T Mizukoshi, Y Fujiwara, C Masutani, F Hanaoka and Y Hayakawa
Biomolecular Engineering Research Institute, 6-2-3 Furuedai, Suita, Osaka 565-0874, Japan. iwai@bioorg.beri.co.jp

In the solid-phase synthesis of oligonucleotides containing the pyrimidine(6-4)pyrimidone photoproduct using a dinucleotide building block, considerable amounts of by-products were found as the chain length increased. The by-products were the major product when a 49mer was synthesized on a 40 nmol scale. It was assumed that these by- products were formed by the coupling of phosphoramidites with the N3 imino function of the 5' component of the (6-4) photoproduct. We examined imidazolium triflate and benzimidazolium triflate to find an alternative activator for DNA synthesis. Imidazolium triflate prevented by-product formation to some extent, but the coupling yields were low. Benzimidazolium triflate was comparable to tetrazole in coupling efficiency and reduced by-product formation to a great extent, without modification of the synthesizer program. The obtained 49mer was used to detect proteins that recognize UV-damaged DNA in HeLa cell extracts. Two major protein-DNA complexes were found when a 49mer duplex was used as probe, while a 30mer duplex failed to detect one of them. This application showed the usefulness of long chain 'damaged' oligonucleotides in biochemical studies.
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J. Yamamoto, K. Hitomi, T. Todo, and S. Iwai
Chemical synthesis of oligodeoxyribonucleotides containing the Dewar valence isomer of the (6-4) photoproduct and their use in (6-4) photolyase studies
Nucleic Acids Res., September 11, 2006; 34(16): 4406 - 4415.
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