Inflammation-mediated reactive molecules can damage
DNA by oxidation and chlorination. The
biological consequences of this damage are as yet incompletely understood. In this paper, we have constructed
oligonucleotides containing
5-chlorouracil (ClU), one of the known
inflammation damage products. The thermodynamic stability, base pairing configuration, and duplex conformation of
oligonucleotides containing ClU paired opposite
adenine have been examined. NMR spectra reveal that the ClU-A base pair adopts a geometry similar to that of the T-A base pair, and the ClU-A base pair-containing duplex adopts a normal B-form conformation. The line width of the imino
proton of the ClU residue is substantially greater than that of the corresponding T imino
proton; however, this difference is not attributed to a reduced thermal or thermodynamic stability or to an increased level of
proton exchange with
solvent. While the NMR studies reveal an increased level of chemical exchange for the ClU imino
proton of the ClU-A base pair, the ClU residue is not a target for removal by the Escherichia coli mispaired
uracil glycosylase, which senses damage-related helix instability. The results of this study are consistent with previous reports indicating that the
DNA of replicating cells can tolerate substantial substitution with ClU. The fraudulent, pseudo-Watson-Crick ClU-A base pair is sufficiently stable to avoid glycosylase removal and, therefore, might constitute a persistent form of cellular DNA damage.