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Hot piperidine is often used to cleave abasic and UV-irradiated DNA at the sites of damage. It can inflict non-specific damage on DNA, probably because it is a strong base and creates significant concentrations of hydroxyl ions which can attack purines and pyrimidines. We show that several other amines can cleave abasic DNA at or near neutral pH without non-specific damage. One diamine, N,N'-dimethylethylenediamine, efficiently cleaves abasic DNA at pH 7.4 by either beta- or beta,delta-elimination, depending on temperature. Using end-labelled oligonucleotides we show that cleavage depends mainly on elimination reactions, but that 4',5'-cyclization is also significant. This reagent also cleaves at photoproducts induced by UVC and UVB, producing the same overall pattern as piperidine, but with no non-specific damage. It should prove valuable in locating low levels of photoproducts in DNA, such as those induced by natural sunlight.

Original publication

DOI

10.1093/nar/23.10.1664

Type

Journal article

Journal

Nucleic Acids Res

Publication Date

25/05/1995

Volume

23

Pages

1664 - 1670

Keywords

Base Sequence, DNA, DNA Damage, Hydrogen-Ion Concentration, Indicators and Reagents, Molecular Sequence Data, Oligodeoxyribonucleotides, Piperidines, Purines, Restriction Mapping, Thermodynamics, Ultraviolet Rays