Uracil residues incorporated into DNA
Uracil residues incorporated into DNA exist transiently since they are subject to removal by the multi-step uracil-initiated DNA Schaftoside excision repair (BER) process , . In E. coli, uracil-DNA BER is initiated by uracil-DNA glycosylase (Ung), which catalyzes the hydrolytic cleavage of the N-glycosylic bond linking the uracil base to its cognate deoxyribose phosphate . Under some conditions, E. coli double-strand uracil-DNA glycosylase (Dug), also called Mug, appears to serve as a backup activity for uracil excision . Dug/Mug has been reported to play an anti-mutator role in stationary-phase cells . In extracts of E. coli ung dug mutant cells, uracil-initiated BER was abolished . Following uracil excision, the resultant baseless site can be cleaved by a class II apurinic/apyrimidinic (AP) endonuclease to generate a terminal 3′-hydroxyl and a deoxyribose 5′-phosphate (dRP) residue . The dRP residue, together with one or more nucleotides, may be removed by the 5′–3′-exonuclease activity of DNA polymerase I (Pol I)  or by the deoxyribophosphodiesterase (dRPase) activity of Fpg protein . A DNA repair patch, characterized as short (one nucleotide) or long (>1 nucleotide) is synthesized by DNA Pol I, and NAD+-dependent DNA ligase (Lig) catalyzes phosphodiester bond formation to seal the DNA chain . E. coli defective in uracil-DNA BER exhibit a mutator phenotype characterized by a predisposition towards C to T base substitutions, presumably from an accumulation of unrepaired deaminated cytosine residues in DNA . Mutations in the E. coli dUTPase gene (dut) were shown to cause a large increase in dUMP incorporation into the genome . Subsequently, it was found that while some dut mutations were lethal, their lethality could be suppressed by null mutations in the dcd gene which, presumably, reduced the accumulation of dUTP and, hence, uracil in DNA . Interestingly, dut insertion mutations (null mutations) were found to be lethal, regardless of compensatory mutations such as ung or dcd, suggesting that dUTP pyrophosphatase might serve a essential function apart from its nucleotidylhydrolase activity . In Saccharomyces cerevisiae, the DUT1 gene is also required for viability . Guillet et al.  isolated a viable dut(1-1) allele of the S. cerevisiae DUT1 gene with compromised activity. The phenotype of the dut1-1 single mutant included growth delay, cell cycle abnormalities, and a high spontaneous mutation rate inferred to result from accumulation of AP-sites cause by excision of incorporated dUMP . Several different methods have been reported for detecting uracil residues in DNA, including acid hydrolysis of DNA followed by gas chromatography/mass spectrometry (GC/MS) of the derivatized nucleobases , in vivo DNA labeling with [6-3H]dUrd , 32P-postlabeling of DNA 2′-deoxynucleoside 3′-monophosphates , and single cell gel electrophoresis . In some cases, uracil-DNA glycosylase was used to selectively excise the uracil base from the DNA and create a uracil-excision-mediated apyrimidinic site. In order to monitor uracil excision, HPLC-tandem mass spectrometry  and GC/MS  techniques were developed to measure the free uracil released following the reaction with Ung. An alternative approach was developed based on the detection of the uracil-excision-mediated AP-site using covalent modification with [14C]methoxyamine . In this method, [14C]methoxyamine reacted with the aldehydic sugar moiety of the AP-site and uracil detection was inferred from the formation of acid-insoluble [14C]DNA . While each technique may offer particular advantages, in vivo and in vitro radioactive labeling methods reportedly lack specificity and sensitivity , while methods involving mass spectrometry have yielded variable results , , and may be more cumbersome as they require costly, specialized equipment.