The fluorine atom at the 5 position of the pyrimidine ring distinguishes 5-FU from uracil (hydrogen at the 5 position) and thymine (methyl group at the 5 position).

BER is typically initiated by the removal of an inappropriate (e.g. uracil, 8-oxoguanine or certain mismatches) or “false” base, such as 5-fluorouracil, by a lesion specific DNA glycosylase. Following base excision, the resulting abasic site is most often incised by the major AP endonuclease, APE1, to create a strand break with a 5′-deoxyribose phosphate (dRP) residue. At this point, depending on the nature of the 5′-terminal end and other factors (reviewed in [27]), the DNA gap is restored via either short-patch (left) or long-patch (right) BER. In the former situation, the 5′-dRP residue is excised by the lyase activity of DNA POLb and the single nucleotide gap is filled by the same enzyme. Subsequently, a complex of XRCC1 and DNA ligase IIIα (LIG3) seals the remaining nick. In the case of long-patch BER, the 5′-terminal blocking fragment is ultimately removed by a flap endonuclease (FEN1) following strand-displacement synthesis by POLb and/or POLd/e. After excision of the flap DNA structure, the nick is sealed by DNA LIG1. PCNA, RFC and RPA help facilitate the long-patch repair response. See text for additional details.

Enzymes are italicized. TS, thymidylate synthase provides the only de novo source of TMP. dUTPase, dUTP nucleotidohydrolase prevents dUTP and FdUTP accumulation. TK, thymidine kinase salvages thymidine and FdUrd. FdUMP suicide inhibits TS. TMPK, thymidylate kinase, phosphorylates TMP and FdUMP. RNR, ribonucleotide reductase, converts FUDP and UDP to FdUDP and dUDP, respectively.

5-FU:A pairs that arise upon incorporation of FdUTP into the genome during DNA synthesis are recognized and processed by the BER pathway (left; see text and Figure 3 for details). 5-FU:G pairs, however, are recognized by the MMR MutSa complex comprised of MSH2:MHS6 (right). Subsequently, the MutLα heterdimer made up of MLH1:PMS2 associates and either initiates a repair response or triggers apoptotic signaling through ATR/CHK1 activation. A burning question that remains though is “how do 5-FU:G mispairs arise in chromosomal DNA?” See text for further details.