Mutation Research 485 (2001) 283–307 The major human abasic endonuclease: formation, consequences and repair of abasic lesions in DNA David M. Wilson III ∗ , Daniel Barsky Molecular and Structural Biology Division, Biology and Biotechnology Research Program, L-441, Lawrence Livermore National Laboratory, 7000 East Avenue, Livermore, CA 94551, USA Received 7 September 2000; received in revised form 2 January 2001; accepted 5 January 2001 Abstract DNA continuously suffers the loss of its constituent bases, and thereby, a loss of potentially vital genetic information. Sites of missing bases — termed abasic or apurinic/apyrimidinic (AP) sites — form spontaneously, through damage-induced hydrolytic base release, or by enzyme-catalyzed removal of modified or mismatched bases during base excision repair (BER). In this review, we discuss the structural and biological consequences of abasic lesions in DNA, as well as the multiple repair pathways for such damage, while emphasizing the mechanistic operation of the multi-functional human abasic endonuclease APE1 (or REF-1) and its potential relationship to disease. © 2001 Elsevier Science B.V. All rights reserved. Keywords: APE1; REF-1; Abasic DNA; AP endonuclease; Base excision repair; Apurinic/apyrimidinic site 1. Abasic sites in DNA 1.1. Formation Apurinic/apyrimidinic (AP) sites (Fig. 1) are non- coding lesions that are generated via the spontaneous, chemically-induced, or enzyme-catalyzed hydrolysis of the N-glycosyl bond, severing the information- containing purine or pyrimidine base from the deoxyri- bose sugar of the DNA backbone. In 1972, knowing that bases are released from DNA in detectable amounts [1], Lindahl and Nyberg [2] measured the quantitative release of radiolabeled purine bases from double-stranded DNA as a function of temperature, pH and ionic strength. In a Mg 2+ -containing buffer, they determined the rate constant for spontaneous in ∗ Corresponding author. Tel.: +1-925-423-0695; fax: +1-925-422-2282. E-mail address: wilson61@llnl.gov (D.M. Wilson III). vitro depurination to be 4 × 10 -9 s -1 at 70 ◦ C and physiological pH (7.4). Extrapolating these data to a mammalian cell environment, it was estimated that ∼12,000 purines would be lost spontaneously per genome per cell generation (20 h), in the absence of the protective effects of chromatin packaging. It was subsequently shown that depyrimidination occurs at a rate ∼100 times slower than depurination [3], for reasons that are not obvious. In good agreement with these findings, studies using a biotin-tagged, aldehyde reactive probe (that covalently links to ring-opened AP sites) to monitor in vitro spontaneous AP site for- mation in purified calf thymus DNA projected roughly 9000 AP sites would be generated in each cell per day under normal physiological conditions [4]. To add to the burden of spontaneous AP sites, dam- aging chemicals — e.g. free radicals and alkylating agents — promote base release, often by introduc- ing base modifications that destabilize the N-glycosyl linkage by generating a better leaving group moiety 0921-8777/01/$ – see front matter © 2001 Elsevier Science B.V. All rights reserved. PII:S0921-8777(01)00063-5