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Nucleic Acids Research, 1989, Vol. 17, No. 7 2675-2691
© 1989

CHEMISTRY

The degree of ultraviolet light damage to DNA containing iododeoxyuridine or bromodeoxyuridine is dependent on the DNA sequence

Vincent Murray and Roger F. Martin

Molecular Science Group, Peter MacCallum Cancer Institute 481 Little Lonsdale Street, Melbourne, Victoria 3000, Australia

Received December 13, 1988. Revised February 27, 1989. Accepted February 27, 1989.

The sequence selectivity of 300 nm ultraviolet light damage to DNA containing bromodeoxyuridine or iododeoxyuridine was examined on DNA sequencing gels. This was accomplished using a system where an M13 template was employed to direct synthesis of DNA in which thymidine was fully substituted with bromodeoxyuridine or iododeoxyuridine. The sites of damage corresponded to the positions of analogue incorporation. The extent of damage varied considerably at different sites of cleavage and ranged from the undetectable to over fifteen times the limit of detection (as assessed by laser densitometer scans). Strong damage sites had the "consensus" sequenoe CTT while sites of no detectable damage had the "consensus" sequenoe GTR. Bromodeoxyuridine and iododeoxyuridine had the same sites of damage although the extent of damage varied at different sites and bromodeoxyuridine damage was slightly greater than iododeoxyuridine. DNA containing thymidine was not damaged to any detectable level in this system with 300 nm ultraviolet light. The use of three closely related DNA sequences as targets for damage confirmed that (1) the sites of analogue incorporation are the cause of ultraviolet damage; and (2) that the neigbouring DNA sequence is an important parameter in determining the extent of damage. It is proposed that the microstructure of DNA - in particular the distance between the 5-carbon of the pyrimidine base (which is attached to the halogen) and hydrogen on the 2' carbon of the 5'-deoxyribose - ultimately determines the degree of cleavage with large distances giving a small degree of damage and smaller distances a large degree of damage.


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