Nucleic acid sequence and repair: role of adduct, neighbor bases and enzyme specificity

B. Singer1 and B. Hang

Donner Laboratory, Life Sciences Division, Lawrence Berkeley National Laboratory, University of California, Berkeley, CA 94720, USA

Abbreviations: AAF, N-acetyl-2-aminofluorene; AF, N-2-aminofluorene; AGT, O6-alkylguanine-DNA alkyltransferase; AP, apurinic/apyrimidinic; APNG, alkylpurine-N-DNA glycosylase; BPDE, benzo[a]pyrene diol epoxide; e6G, O6-ethylguanine; {varepsilon}A, 1,N6-ethenoadenine; m6G, O6-methylguanine; NER, nucleotide excision repair.


    Historical perspective
 Top
 Historical perspective
 Sequence and repair
 Sequence, modification and...
 Sequence, thermodynamic...
 Conclusions
 References
 
The study of the role of sequence in base modification was mainly started in the 1980s in terms of sequence selectivity for mutational events (see for example 1–20). These events were generally roduced by environmental agents, such as UV exposure, alkylating agents and aromatic amines, or spontaneously (21). It has since become clear that such events are not totally random but tend to predominate at specific sites in nucleic acids. This type of investigation led to the idea of `targeted' mutation, which was often related to specific cellular changes in function.

At the onset of the interest in how base sequence affected modification, there was also interest in whether the base sequences flanking damage could also influence replication (see for example 22–25) and repair (see for example 7,8,13,26–28). Significant progress in these research areas was accelerated when it became feasible to design and construct synthetic oligonucleotides with site-directed modified bases (29). In addition, it became generally accepted that nucleic acid sequence and structure are closely linked. Changes in both primary and secondary structures resulting from neighboring bases were presumed to be one of the important factors affecting replication and repair, both qualitatively and quantitatively.

When DNA synthesizers became widely available in the mid 1980s, it was possible to design oligonucleotides of virtually any sequence containing normal or modified bases for which phosphoramidites could be made. With this powerful tool, a new era began in the study of the effect of chemical modification on DNA structure, replication and repair. This Commentary will focus on the relationship between nearest neighbor nucleic acid sequence to damage and its enzymatic repair, with emphasis on oligomer local structure, DNA duplex thermostability and the repair of single site-directed damage. Each of these aspects has been found to depend to varying extents on immediate sequence context.


    Sequence and repair
 Top
 Historical perspective
 Sequence and repair
 Sequence, modification and...
 Sequence, thermodynamic...
 Conclusions
 References
 
One fact that has emerged is that sequence context surrounding a lesion has an influence on the rate and extent of enzymatic repair. The literature on this topic has so far been limited and also diverse in terms of adduct type, base composition and repair systems. Among the lesion types or modifications studied for repair influenced by neighbor sequences were N-acetyl-2-aminofluorene (AAF) (28,3032), N-2-aminofluorene (AF) (32), benzo[a]pyrene diol epoxide (BPDE) (33), UV photoproducts (26,3436), 1,N6-ethenoadenosine ({varepsilon}A) (37), p-benzoquinone derivatives (38), alkyl bases (8,13,3946), base mismatches (27,47,48), uracil (49,50) and apurinic/apyrimidinic (AP) sites (51). The repair systems used for these lesions include enzymes from base excision repair, nucleotide excision repair (NER), mismatch repair, O6-alkylguanine-DNA alkyltransferases (AGT) and photolyase. In addition, the sequence dependence of a special `repair' activity (proofreading) of DNA polymerases was also studied (23,52). Both in vivo and in vitro studies have been reported. We will try to present in this Commentary a basket of data and hypotheses which need to be verified and expanded since, in general, there are few rules or a consensus that at this time can be deduced from this body of work. In defense of this lack of consensus, it should be noted that there are many repair enzymes (5359) and even more modified bases (21,6062), which may indicate that each repair system may have its own requirements regarding the role of sequence.

Repair of aromatic amines by NER
In 1990, Seeberg and Fuchs (28) reported on the efficiency of in vitro excision by Escherichia coli UvrABC excinuclease of 60mers containing an AAF-modified base at different positions within the mutation hot spot NarI sequence, 5'-GGCGCC-3' (63). The extent of repair ranged from 77% in the central sequence, -CxG-, to 12% in -GxC- to 45% in -CxC- (x = AAF-G). Later Mu et al. (30), using the same central sequences and the E.coli repair system, agreed with these data. In addition, they also found that human (A)BC excinuclease had differing neighbor preferences, with nicking efficiencies of 38, 100 and 68% for the same three sequences, respectively (30). In a 1998 paper, Mekhovich et al. (32) used two different 62mer sequences containing -GATxATA- or the NarI sequence -GGCxCC- (x = AAF-G or AF-G) and found 15 and 45% excision of oligomers containing AAF-G by UvrABC excinuclease. Excision of AF-G-containing oligomers showed that the sequence -GGCxCC- was 2-fold better excised than -GATxATA-. These results indicate that efficiency of repair is also adduct dependent. Moreover, these data correlate with the rate of formation of the UvrB– and UvrBC–substrate complexes tested (32), suggesting that the binding efficiency of the enzyme is also dependent on differences in the flanking sequence. Such results illustrate that neighbor sequences can be a major determinant in repair efficiency for this diverse repair system.

Repair of O6-alkylguanine by AGT
The influence of neighbors and opposite bases on formation and repair of a different type of damage, O6-alkylguanine, has been of long-term interest to a number of groups, following the studies of Sukumar, Barbacid and colleagues (4,5), who found that in vivo only the second guanine in codon 12 (GGA) of the H-ras oncogene was modified at the O6 position by N-nitroso-N-methylurea. Other in vitro studies showed that the formation of O6-alkylguanine, a direct mutational event, was also sequence and conformation dependent (8,13,15,22), although the specific requirements are not clear.

There are several possibilities for interpreting the observed sequence-dependent alkylation of guanine in vivo. One of these is the selectivity found for repair of O6-methylguanine (m6G). In several studies using synthetic oligonucleotides, the repair rates by AGT in vitro differ depending on the position or neighbors of m6G. An example was shown by Georgiadis et al. (39), who constructed double-stranded 15mers with a single m6G in a sequence similar to part of the rat H-ras oncogene carrying codon12 (Table IGo). It was found that changes in position (Table IGo, sequence 2 versus 5) and neighbors (5' change in sequence 2 versus 3' change in sequence 3; sequence 4 versus 5) adjacent to m6G affect the rate constant for dealkylation by 7- to 25-fold. The synthetic modified H-ras gene sequence carrying a m6G (second G in GGA sequence) has the lowest repair rate, which is likely to be an important factor contributing to the targeted m6G mutation in vivo (Table IGo). Another factor in repair related to sequence is that the binding affinity of AGT can also be affected, as noted by Fried et al. (42), who reported a dependence of AGT binding activity on base composition. However, studies so far by different research groups have not led to a uniform conclusion on the pattern of sequence and conformation necessary for the observed specificity of alkylation and repair of O6-alkylguanine.


View this table:
[in this window]
[in a new window]
 
Table I. Effect of position and neighbor bases on m6G repair by E.coli AGT (39)
 
A recent paper by Delaney and Essigmann (46) described a new assay to assess the effect of sequence context on the replication and repair of m6G in both repair-deficient (ada, ogt, UvrB) and partially repair-proficient (ogt, UvrB) E.coli cell lines based on construction of a site-specifically adducted viral genome. The Ada protein was twice as efficient acting on m6G when a guanine base rather than an adenine base was 5' to the lesion. In the in vivo system described by these authors (46) it is now possible to separate the effect of the adduct position from that of the nearest neighbors. This type of experiment had only been done in vitro. This approach applied to in vivo repair may open the door to determine the effect of flanking bases on repair of other adducts in vivo.

In contrast to the above data on neighbor effects for repair of m6G, Rajewsky's laboratory found that human AGT repair of O6-ethylguanine (e6G) in a 29mer double-stranded sequence is not significantly affected by 3' and 5' neighbor changes (43). This may be attributed to the structural changes induced in the oligomer by differential steric effects conferred by the ethyl versus the methyl group. Preliminary work suggests that the ethyl group in e6G apparently causes greater distortion in the backbone compared with the methyl group as modeled in the authors' laboratory (unpublished data). In this case, is it possible that the size of the ethyl group is large enough, compared to a methyl group, to affect base pairing of the nearest neighbors so that all neighbors tested appear to allow a similar extent of dealkylation?

Repair of base mismatches
Mismatch repair is central to preservation of the integrity of the genome. Over a period of about 20 years, enzymes have been isolated and characterized as specifically restoring one of two opposite bases when they are not Watson–Crick paired (53,54,64). A generally used example is the G·T mismatch resulting from deamination of 5-methylcytosine paired with G. In this case, the repaired base is the opposite T. Over a period of time, a number of mismatches have been found in DNA in vivo and studied in terms of their effect on DNA structure and repair. Mismatch repair is more complex than the name indicates. For example, the G·T mismatch can be repaired by two different pathways: short patch repair (G·T mismatch DNA glycosylase) and long patch mismatch repair (53,54). The G·T mismatch glycosylase (6567) can also repair G·U (65,67), m6G·T, 2-aminopurine·T (47) and 3,N4-ethenocytosine·G mismatches (68,69).

Ullah et al. (47) found that, in in vitro experiments using recombinant G·T mismatch glycosylase, the nature of the 5'-flanking bases to a G·T mismatch has a marked effect on efficiency of repair in the following order: C (64%) > T (21%) {approx} G (19%) > A (5%). The G·T mismatch glycosylase also excises a m6G·T pair, but only when preceded by a 5' pyrimidine (47). There appears to be no clear structural reason for this strong 5'-flanking effect, but it could be anticipated since the G·T mismatch is formed predominantly in CpG sequences. More recently, Saparbaev and Laval (48) also reported an effect of sequence context in repair of a G·T mismatch by both human and E.coli repair enzymes. With 5'-G·C adjacent to a G·T mismatch, using both human G·T mismatch glycosylase and its E.coli homolog, double-stranded uracil glycosylase, repair efficiency ranged from 27 to 100%. However, changing the 5'-flanking base pair from G·C to A·T almost abolished the activity (0–4%). In general, regardless of the details of each experimental system studied, there was a dramatic change in extent of G·T repair depending on the 5'-flanking base. Whether this is due to G·C versus A·T 5'-flanking pairs or the effect of purines versus pyrimidines is not evident. The data discussed above have practical relevence and indicate that enzyme/substrate identification or efficiency cannot be judged by a single sequence in which the data could be dependent on unknown factors.

Radman and co-workers (27) have shown, using an in vivo E.coli transfection system, that increasing the number of G·C pairs flanking either transition (G·T and A·C) or transversion (G·A and C·T) mismatches increased the extent of repair to various extents as measured by percent mixed infective centers. For example, for the C·T mismatch, changing the number of G·C flanking bases either 5' or 3' from one to four increased repair 2-fold. It should be noted that in vivo both long and short patch mismatch repair occurs and the overall results cannot be separated in these terms.

3'-Exonuclease activity of T4 DNA polymerase
This type of repair is commonly called `proofreading' and is the result of 3'-exonuclease activity of a DNA polymerase. As with other repair systems discussed, as well as replication with polymerases (2325,7077), there is also a sequence dependence reported for the proofreading activity. Goodman and colleagues have investigated the influence of neighbor bases on proofreading efficiency and fidelity (23,52). One system studied by these investigators contained a single aminopurine paired to a T in a 17mer primer annealed to a 30mer template. The pre-steady-state kinetics for excision of aminopurine with different neighbor base pairs 5' to aminopurine on the primer showed that the rate of removal of aminopurine by T4 DNA polymerase varied in the order: C·G << G·C < T·A < A·T (Figure 1Go). Thus, it was presumed that the flanking G·C stabilized the region around the primer terminus, as compared to flanking A·T, which may make melting more difficult, as suggested by the authors (52). Structural studies indicated that the accessibility of the enzyme to the target base depends on dissociation of the primer from the template by several base pairs from the terminus (7880). These experiments show that there appears to be a correlation between Tm and repair efficiency as a function of neighboring environment.



View larger version (49K):
[in this window]
[in a new window]
 
Fig. 1. Time course of excision of aminopurine from a 17mer primer paired to a 30mer template. The 5' neighbor base to the aminopurine is varied as shown on the right. Reactions were initiated by addition of T4 polymerase to the primer/template at 20°C. The normalized intensity is that of fluorescence of unpaired aminopurine. Data taken from Bloom et al. (52).

 

    Sequence, modification and repair
 Top
 Historical perspective
 Sequence and repair
 Sequence, modification and...
 Sequence, thermodynamic...
 Conclusions
 References
 
Data from in vivo modification/repair can be obtained from natural DNA sequences or from a foreign sequence and gives a window on factors influencing both events. The general approach is to study a specific sequence such as a gene (e.g. lacI, PGK1, HPRT and p53) or a sequence in a vector in the cell. When DNA from these sources is reacted with a chemical, the spectrum of modification depends on both the specificity of a given reagent and the base composition of a given sequence. Consequently, repair can only take place at such modified sites and sequences. Some in vitro experiments on sequence specificity utilize a biologically relevent partial sequence from a genome. Sequences were also designed and synthesized to test the effects on repair of specific factors such as nearest neighbors, adduct type and position and thermodynamics.

Each approach has its limitations: particularly in vivo, it is generally not possible to study the effect of neighbor bases alone, but rather it is usually represented as a position effect which includes the influence of immediate sequence context. Chemical modification has also been found to depend not only on the chemical but also on sequence/position. Another important aspect of the in vivo studies is that a given adduct can be repaired by multiple pathways. For example, O6-alkylguanine can be repaired by at least two alternative pathways in E.coli: the Ada and Ogt methyltransferases and the NER pathway (17,81,82). The involvement of chromatin structure in vivo is also an important factor in repair, as shown by Li and Smerdon (45). Thus, interpretation of repair data obtained under different circumstances can be ambiguous and desired changes in the experimental design are not necessarily possible.

Extensive work on relating sequence dependence and mutation has been done by several groups using chemical modification of genomic DNA, followed by determination of the mutation spectra (see for example 6,7,9,11,12,16–18,83,84). These data were among the first used to substantiate the concept of `hot spots', i.e. for a given reagent, there was site specificity for DNA modification. There were also indications that selective repair may be a factor which affects persistence of the adduct at specific sites in DNA when different repair backgrounds were used. For example, in a 1986 paper, Burns et al. (12) reported the mutagenesis and selectivity of ethyl methanesulfonate in different repair backgounds in E.coli (Uvr+ versus UvrB strains). According to these authors, e6G lesions adjacent to A·T base pairs are better repaired than G·C pairs at either the 5'- or 3'-side.

Several groups in the mid 1990s examined the in vivo repair rates along a specifically modified DNA fragment in a more direct and sensitive way by using the ligation-mediated PCR technique (33,35,36,44). For example, Wei et al. (33) used BPDE modification in the HPRT gene of human fibroblasts. The repair rate differed markedly from site to site over a time period of 0–30 h, as measured by the percentage of adduct remaining (Figure 2Go). Tornaletti and Pfeifer (35) investigated the repair of cyclobutane pyrimidine dimers along the p53 gene in human cells irradiated with UV light. It was found that repair rates at different positions were also highly variable, ranging from 70–95% repaired to almost an absence of repair after 24 h. Interestingly, slow repair was observed at seven of eight positions which are frequently mutated in skin cancer (35). This is one of those few examples that clearly document a correlation between repair and the occurrence of mutation hot spots. These experiments show that quantitation of adduct, site and repair background can be used to study in vivo repair sequence specificity and that the data discussed above support the hypothesis that selectivity of repair of mutational events is an important factor in specificity of mutation.



View larger version (64K):
[in this window]
[in a new window]
 
Fig. 2. Rates of repair of BPDE adducts in nucleotides 197–238 of DNA from the HPRT gene of human fibroblasts. Ligation-mediated PCR generated bands were quantitated with a PhosphorImager. Intensities at time 0, representing the initial level of adducts, were taken as 100% (first bar of each set). The relative percentages of BPDE adducts remaining at each site after 10 (second bar), 20 (third bar) and 30 h (fourth bar) are shown. Data taken from Wei et al. (33).

 

    Sequence, thermodynamic stability and repair
 Top
 Historical perspective
 Sequence and repair
 Sequence, modification and...
 Sequence, thermodynamic...
 Conclusions
 References
 
These three variables have been linked in a few theoretical discussions (40,52,85,86). Most papers addressing these related issues generally do not include repair data but link sequence context and thermodynamics (see for example 87–89). Destabilization of a double-stranded structure by mismatched or modified bases has been measured by different groups using NMR and circular dichroism in addition to thermodynamics. For example, Gelfand et al. (87) studied an abasic site in defined oligomers with differing neighbor base sequences and concluded that an abasic site can significantly affect the thermodynamic features of 13mer duplexes. Either the base opposite or adjacent to the abasic site were found to have measurable effects. Similarly, Peyret et al. (89) systematically examined duplex stability with four single mismatches (A·A, C·C, G·G and T·T) and different neighbor groups in 9–12mers. The observed stability for the Watson–Crick pairs was in the order of 5'-neighbor base pairs: G·C >= C·G >= A·T >= T·A. The trend for relative stability of the 3'-neighbor base pairs is C·G >= G·C >= T·A >= A·T, which is assumed to reflect the influence of symmetry and not simply the number of hydrogen bonds. In a NMR study, Fagan et al. (86) studied the conformation of the 2-aminopurine·C mismatch in two different flanking sequences of 9mers and also found that the structure and stability of the mismatch is dependent on the neighbor bases, demonstrating the importance of local sequence context.

Another view on the effect of flanking bases on the conformation of nucleic acids is presented by Stivers (90), who used fluorescence spectroscopy to measure the stacking interactions of bases surrounding a 2-aminopurine residue opposite an abasic site in DNA. The basis for this design is that when NMR is used it is often difficult to detect transient structures or conformers in dynamic equilibrium. The results revealed that although the mismatch is less well stacked than in the control duplex, there is little difference in the stacking interactions of the 2-aminopurine·C pair regardless of whether purines or pyrimidine bases flank the site.

There are also studies that have addressed the possible correlation among types of mismatch, repair efficiency and thermodynamic parameters (85,89). In these papers they concluded that alterations in nucleic acid structure imposed by different mismatches are an important factor in influencing repair efficiency. In addition, Werntges et al. (85) measured Tm values of 12 possible mismatches, as compared with normal Watson–Crick pairs, and found that regardless of the strand orientation used for creating mismatches, e.g. A·C or C·A, these inverted mismatches did not appreciably alter the Tm values. These data suggest that the total nearest neighbor interactions are not significantly changed by base orientation.

In our laboratory, we undertook to investigate how repair is influenced by the immediate neighbor bases which also influence the thermal stability of the duplex substrates (37,51). The substrates used contained either {varepsilon}A or a synthetic abasic site (tetrahydrofuran) flanked by systematically changed base pairs. Repair by either alkylpurine-N-DNA glycosylase (APNG) for {varepsilon}A or E.coli endonuclease IV for the AP site was measured as well as the thermal stability of the same sets of oligomers. Both the repair enzymes used require a double-stranded substrate.

This experimental design enabled us to examine possible correlations between repair efficiency and thermodynamics as a function of neighbor base pairs. It was found earlier that {varepsilon}A in an oligomer duplex is a better substrate for APNG than 3-methyladenine (91), for which the enzyme was first described (92). Synthetic 15mer oligonucleotides with {varepsilon}A flanked by tandem 3' and 5' bases exhibited greatly varying repair efficiency: oligomers with C·G pairs flanking {varepsilon}A were 3- to 5-fold better repaired than when {varepsilon}A was flanked by A·T pairs (Figure 3AGo) (37). These results could be correlated with the thermal stability of the overall duplex, as shown in Figure 3BGo, since APNG protein only acts on a double-stranded substrate (37).



View larger version (21K):
[in this window]
[in a new window]
 
Fig. 3. (A) Cleavage of four 15mer oligomer duplexes containing {varepsilon}A as a function of time using 2.5 ng recombinant human APNG. The central 5 base sequences are shown on the right of the figure. The full sequence is given at the top. (B) Superimposed curves of two representative {varepsilon}A-containing 15mer oligomers. The extent of denaturation at 37°C (shown by the vertical line) is given in the figure for these two {varepsilon}A-containing 15mer oligomer duplexes. Calculated percent denaturation at 37°C for all four {varepsilon}A-containing oligomers is given in the figure. See table IGo in Hang et al. (37) for additional thermodynamic data and also the buffer conditions used. Data taken from Hang et al. (37).

 
The same type of experimental design was used to examine the repair of another type of lesion, a synthetic AP site (tedrahydrofuran), by E.coli endonuclease IV (93,94). In this case, in order to systematically evaluate the role of both base composition and position vis-à-vis triplet flanking sequences, 15mers were constructed as shown in Table IIGo (51). In Figure 4Go, the repair rate, regardless of position of flanking bases in the triplets, follows the number of G/C pairs, i.e. 3 C > 2 C + 1 A > 2 A + 1 C > 3 A. This order is paralleled by the thermal and thermodynamic stability of these oligomers (Table IIGo) (51). Again, the thermal stability of each of eight sequences was reflected in repair efficiency (Figure 5Go). Interestingly, there was also a significant difference in Tm, {Delta}G and repair rate when, for example, the relative positions of the bases to the AP site were changed from CCA to CAC to ACC (Figure 4Go, insert) (51). Such a position effect of neighbor bases was also found when using combinations of two A residues and one C (CAA, ACA and AAC). Further experiments are needed to fully understand the mechanism underlying these results. It could be argued that such short oligomers can be incompletely annealed at 37°C, the enzymatic reaction conditions. Thus, we also constructed 35mers on the same principle and found that there was a general correlation between the thermostability and cleavage efficiency of these 35mers except that the overall repair based on sequence showed lesser but distinct differences. Since the 35mers were shown to be more than 96% annealed at 37°C (51), the observed difference resulting from neighbor groups presumably reflects local stability and structure adjacent to the AP site. These data confirmed that the local thermal stability resulting from the nature of the neighbor base pairs is an important factor in determining repair efficiency when a double strand is required by the enzyme.


View this table:
[in this window]
[in a new window]
 
Table II. Thermal and thermodynamic stability of 15mer duplexes: effect of number of A·T and G·C pairs and their position relative to an AP site (x) (51)
 


View larger version (26K):
[in this window]
[in a new window]
 
Fig. 4. The cleavage efficiency of E.coli endonuclease IV with eight 15mer AP-containing oligomer duplexes. Twenty femtomoles of oligomer substrate were reacted with 0.75 ng of endonuclease IV at 37°C for various times. The central sequences are on the right. The entire sequence is 5'-TGCTNNNxNNNTGCT-3', where x indicates tetrahydrofuran. Data taken from Sági et al. (51). The insert shows the position effect on cleavage using three combinations of two C residues and one A in the flanking triplets 5' and 3' of the tetrahydrofuran residue using the same data as in the main figure.

 


View larger version (14K):
[in this window]
[in a new window]
 
Fig. 5. The relationship between cleavage efficiency of E.coli endonuclease IV and thermodynamic stability of the eight AP site-containing 15mer duplexes in Figure 4Go, as characterized by the transition free energy for duplex melting ({Delta}G°37). The cleavage efficiency is the average of three independent experiments, using 0.75 ng endonuclease IV at 37°C for 10 min. The {Delta}G°37 values are from Table IIGo. Data from Sági et al. (51).

 
On the basis of data from this and other laboratories we do not believe that there is necessarily a direct extrapolation from in vitro to in vivo repair, but we believe that the same general principles would hold true. In vivo there are a number of factors which can lead to single-stranded regions surrounding the lesion and thus resemble the in vitro situation. For example, DNA can have single-stranded regions as a result of mismatched bases, bulky adducts, thermal `breathing', replication forks and physiological unwinding processes. It is known that DNA continuously forms single strands which are likely to be in equilibrium with fully double-stranded DNA so that the mechanisms discussed above are likely to be valid, particularly for double strand-requring repair enzymes.


    Conclusions
 Top
 Historical perspective
 Sequence and repair
 Sequence, modification and...
 Sequence, thermodynamic...
 Conclusions
 References
 
Sequence context has now been generally accepted as one of the important factors influencing modification, replication and repair. Data on such dependence have been reported for virtually all repair pathways, including both in vivo and in vitro experiments. However, there appear to be few rules regarding sequence-dependence that can be deduced from this diverse body of work. The lack of consensus using different repair pathways, adducts and systems (in vivo vs in vitro) indicates this phenomenon is complex and multifactorial. So far our knowledge on mechanism is limited and scattered, as detailed in the examples cited. Ultimately, the validity and/or proof of any of the conclusions, based on in vitro experiments, must be tested in vivo. This is likely to be a long-term goal considering the much greater complexity of the variables in vivo.


    Notes
 
1 To whom reprint requests should be addressed. Back

In this short Commentary we regret that we cannot address all the important issues or review the entire field. We hope the readers will understand these constraints.


    Acknowledgments
 
This Commentary was conceived with the encouragement of Dr Tony Dipple who was a colleague of B.S. of long standing, dating back to his days at the Chester Beatty Research Institute. He is missed. This work was supported by grants CA 47723, CA 72079 and ES 07368 (to B.S.) from the National Institutes of Health and was administered under contract no. DE-AC03-76SF00098.


    References
 Top
 Historical perspective
 Sequence and repair
 Sequence, modification and...
 Sequence, thermodynamic...
 Conclusions
 References
 

  1. Benzer,S. (1961) On the topography of the genetic fine structure. Proc. Natl Acad. Sci. USA, 47, 403–416.[ISI]
  2. Koch,K.E. (1971) The influence of neighboring base-pairs upon base-pair substitution mutation rates. Proc. Natl Acad. Sci. USA, 68, 773–776.[Abstract]
  3. Fuchs,R.P., Schwartz,N. and Daune,M.P. (1981) Hot spots of frameshift mutations induced by the ultimate carcinogen N-acetoxy-N-2-acetylaminofluorene. Nature, 294, 657–659.[ISI][Medline]
  4. Sukumar,S., Notario,V., Martin-Zanca,D. and Barbacid,M. (1983) Induction of mammary carcinomas in rats by nitroso-methylurea involves malignant activation of H-ras1 locus by single point mutations. Nature, 306, 658–661.[ISI][Medline]
  5. Zarbl,H., Sukumar,S., Arthur,A.V., Martin-Zanca,D. and Barbacid,M. (1985) Direct mutagenesis of Ha-ras-1 oncogenes by N-nitroso-N-methylurea during initiation of mammary carcinogenesis in rats. Nature, 315, 382–385.[ISI][Medline]
  6. Koffel-Schwartz,N., Verdier,J.M., Bichara,M., Freund,A.M., Daune,M.P. and Fuchs,R.P. (1984) Carcinogen-induced mutation spectrum in wild-type, uvrA and umuC strains of Escherichia coli. Strain specificity and mutation-prone sequences. J. Mol. Biol., 177, 33–51.[ISI][Medline]
  7. Burns,P.A., Allen,F.L. and Glickman,B.W. (1986) DNA sequence analysis of mutagenicity and site specificity of ethyl methanesulfonate in Uvr+ and UvrB strains of Escherichia coli. Genetics, 113, 811–819.[Abstract/Free Full Text]
  8. Topal,M.D., Eadie,J.S. and Conrad,M. (1986) O6-methylguanine mutation and repair is nonuniform. Selection for DNA most interactive with O6-methylguanine. J. Biol. Chem., 261, 9879–9885.[Abstract/Free Full Text]
  9. Schaaper,R.M. and Dunn,R.L. (1987) Spectra of spontaneous mutations in Escherichia coli strains defective in mismatch correction: the nature of in vivo DNA replication errors. Proc. Natl Acad. Sci. USA, 84, 6220–6224.[Abstract]
  10. Mattes,W.B., Hartley,J.A. and Kohn,K.W. (1986) DNA sequence selectivity of guanine-N7 alkylation by nitrogen mustards. Nucleic Acids Res., 14, 2971–2987.[Abstract]
  11. Schaaper,R.M. and Dunn,R.L. (1987) Spectra of spontaneous mutations in Escherichia coli strains defective in mismatch correction: the nature of in vivo DNA replication errors. Proc. Natl Acad. Sci. USA, 84, 6220–6224.[Abstract]
  12. Burns,P.A., Gordon,A.J.E. and Glickman,B.W. (1987) Influence of neighbouring base sequence on N-methyl-N'-nitro-N-nitrosoguanidine mutagenesis in the lacI gene of Escherichia coli. J. Mol. Biol., 194, 385–390.[ISI][Medline]
  13. Dolan,M.E., Oplinger,M. and Pegg,A.E (1988). Sequence specificity of guanine alkylation and repair. Carcinogenesis, 9, 2139–2143.[Abstract]
  14. Burnouf,D., Koehl,P. and Fuchs,R.P. (1989) Single adduct mutagenesis: strong effect of the position of a single acetylaminofluorene adduct within a mutation hot spot. Proc. Natl Acad. Sci. USA, 86, 4147–4151.[Abstract]
  15. Richardson,F.C., Boucheron,J.A., Skopek,T.R. and Swenberg,J.A. (1989) Formation of O6-methyldeoxyguanosine at specific sites in a synthetic oligonucleotide designed to resemble a known mutagenic hotspot. J. Biol. Chem., 264, 838–841.[Abstract/Free Full Text]
  16. Schaaper,R.M. and Dunn,R.L. (1991) Spontaneous mutation in the Escherichia coli lacI gene. Genetics, 129, 317–326.[Abstract/Free Full Text]
  17. Bronstein,S.M., Cochrane,J.E., Craft,T.R., Swenberg,J.A. and Skopek,T.R. (1991) Toxicity, mutagenicity and mutational spectra of N-ethyl-N-nitrosourea in human cell lines with different DNA repair phenotypes. Cancer Res., 51, 5188–5197.[Abstract]
  18. Daubersies,P., Galiegue-Zouitina,S., Koffel-Schwartz,N., Fuchs,R.P.P., Loucheux-Lefebvre,M.-H. and Bailleul,B. (1992) Mutation spectra of the two guanine adducts of the carcinogen 4-nitroquinoline 1-oxide in Escherichia coli. Influence of neighboring base sequence on mutagenesis. Carcinogenesis, 13, 349–354.[Abstract]
  19. Cariello,N.F. and Skopek,T.R. (1993) Analysis of mutations occurring at the human hprt locus. J. Mol. Biol., 231, 41–57.[ISI][Medline]
  20. Carothers,A.M., Urlaub,G., Mucha,J., Yuan,W., Chasin,L.A. and Grunberger,D. (1993) Mutational hot spot induced by N-hydroxy-aminofluorene in dihydrofolate reductase mutants of Chinese hamster ovary cells. Carcinogenesis, 14, 2181–2194.[Abstract]
  21. Singer,B. and Grunberger,D. (1983) Molecular Biology of Mutagens and Carcinogens. Plenum Press, New York, NY.
  22. Toorchen,D. and Topal,M.D. (1983) Mechanisms of chemical mutagenesis and carcinogenesis: effects on DNA replication of methylation at the O6-guanine position of dGTP. Carcinogenesis, 4, 1591–1597.[ISI][Medline]
  23. Petruska,J. and Goodman,M.F. (1985) Influence of neighboring bases on DNA polymerase insertion and proofreading fidelity. J. Biol. Chem., 260, 7533–7539.[Abstract/Free Full Text]
  24. Mendelman,L.V., Boosalis,M.S., Petruska,J. and Goodman,M.F. (1989) Nearest neighbor influences on DNA polymerase insertion fidelity. J. Biol. Chem., 264, 14415–14423.[Abstract/Free Full Text]
  25. Singer,B., Chavez,F., Goodman,M.F., Essigmann,J.M. and Dosanjh,M.K. (1989) Effect of 3' flanking neighbors on kinetics of pairing of dCTP or dTTP opposite O6-methylguanine in a defined primed oligonucleotide when Escherichia coli DNA polymerase I is used. Proc. Natl Acad. Sci. USA, 86, 8271–8274.[Abstract]
  26. Haseltine,W.A., Gordon,L.K., Lindan,C.P., Grafstrom,R.H., Shaper,N.L. and Grossman,L. (1980) Cleavage of pyrimidine dimers in specific DNA sequences by a pyrimidine dimer DNA-glycosylase of M. luteus. Nature, 285, 634–641.
  27. Jones,M., Wagner,R. and Radman,M. (1987) Repair of a mismatch is influenced by the base composition of the surrounding nucleotide sequence. Genetics, 115, 605–610.[Abstract/Free Full Text]
  28. Seeberg,E. and Fuchs,R.P.P. (1990) Acetylaminofluorene bound to different guanines of the sequence -GGCGCC- is excised with different efficiencies by the UvrABC excision nuclease in a pattern not correlated to the potency of mutation induction. Proc. Natl Acad. Sci. USA, 87, 191–194.[Abstract]
  29. Singer,B. and Essigmann,J.M. (1991) Site-specific mutagenesis: retrospective and prospective. Carcinogenesis, 12, 949–955.[ISI][Medline]
  30. Mu,D., Bertrand-Burggraf,E., Huang,J.-C., Fuchs,B.P.P. and Sancar,A. (1994) Human and E.coli excinucleases are affected differently by the sequence context of acetylaminofluorene–guanine adduct. Nucleic Acids Res., 22, 4869–4871.[Abstract]
  31. Delagoutte,E., Bertrand-Burggraf,E., Dunand,J. and Fuchs,R.P.P. (1997) Sequence-dependent modulation of nucleotide excision repair: the efficiency of the incision reaction is inversely correlated with the stability of the pre-incision UvrB-DNA complex. J. Mol. Biol., 266, 703–710.[ISI][Medline]
  32. Mekhovich,O., Tang,M.-S. and Romano,L.J. (1998) Rate of incision of N-acetyl-2-aminofluorene and N-2-aminofluorene adducts by UvrABC nuclease is adduct- and sequence-specific: comparison of the rates of UvrABC nuclease incision and protein-DNA complex formation. Biochemistry, 37, 571–579.[ISI][Medline]
  33. Wei,D., Maher,V.M. and McCormick,J.J. (1995) Site-specific rates of excision repair of benzo[a]pyrene diol epoxide adducts in the hypoxanthine phosphoribosyltransferase gene of human fibroblasts: correlation with mutation spectra. Proc. Natl Acad. Sci. USA, 92, 2204–2208.[Abstract]
  34. Svoboda,D.L., Smith,C.A., Taylor,J.-S.A. and Sancar,A. (1993) Effect of sequence, adduct type and opposing lesions on the binding and repair of ultraviolet photodamage by DNA photolyase and (A)BC excinuclease J. Biol. Chem., 268, 10694–10700.[Abstract/Free Full Text]
  35. Tornaletti,S. and Pfeifer,G.P. (1994) Slow repair of pyrimidine dimers at p53 mutation hotspots in skin cancer. Science, 263, 1436–1438.[ISI][Medline]
  36. Gao,S., Drouin,R. and Holmquist,G.P. (1994) DNA repair rates mapped along the human PGK1 gene at nucleotide resolution. Science, 263, 1438–1440.[ISI][Medline]
  37. Hang,B., Sagi,J. and Singer,B. (1998) Correlation between sequence-dependent glycosylase repair and the thermal stability of oligonucleotide duplexes containing 1,N6-ethenoadenine. J. Biol. Chem., 273, 33406–33413.[Abstract/Free Full Text]
  38. Hang,B., Chenna,A., Sagi,J. and Singer,B. (1998) Differential cleavage of oligonucleotides containing the benzene-derived adduct 1,N6-benzetheno-dA, by the major human AP endonuclease HAP1 and Escherichia coli exonuclease III and endonuclease IV. Carcinogenesis, 19, 1339–1343.[Abstract]
  39. Georgiadis,P., Smith,C.A. and Swann,P.F. (1991) Nitrosamine-induced cancer: selective repair and conformational differences between O6-methylguanine residues in different positions in and around codon 12 of rat H-ras. Cancer Res., 51, 5843–5850.[Abstract]
  40. Foley,C.K., Pedersen,L.G., Darden,T.A., Glickman,B.W. and Anderson,M.W. (1991) Theoretical and experimental measures of DNA helix stability and their relation to sequence specific repair of O6-ethylguanine lesions. Mutat. Res., 255, 89–93.[ISI][Medline]
  41. Graves,R., Laval,J. and Pegg,A.E. (1992) Sequence specificity of DNA repair by Escherichia coli Fpg protein. Carcinogenesis, 13, 1455–1459.[Abstract]
  42. Fried,M.G., Kanugula,S., Bromberg,J.L. and Pegg,A.E. (1996) DNA binding mechanism of O6-alkylguanine-DNA alkyltransferase: stoichio- metry and effects of DNA base composition and secondary structure on complex stability. Biochemistry, 35, 15295–15301.[ISI][Medline]
  43. Bender,K., Federwisch,M., Loggen,U., Nehls,P. and Rajewsky,M.F. (1996) Binding and repair of O6-ethylguanine in double-stranded oligodeoxynucleotides by recombinant human O6-alkylguanine-DNA alkyltransferase do not exhibit significant dependence on sequence context. Nucleic Acids Res., 24, 2087–2094.[Abstract/Free Full Text]
  44. Ye,N., Holmquist,G.P. and O'Connor,T.R. (1998) Heterogeneous repair of N-methylpurines at the nucleotide level in normal human cells. J. Mol. Biol., 284, 269–285.[ISI][Medline]
  45. Li,S. and Smerdon,M.J. (1999) Base excision repair of N-methylpurines in a yeast minichromosome. J. Biol. Chem., 274, 12201–12204.[Abstract/Free Full Text]
  46. Delaney,J.C. and Essigmann,J.M. (1999) Context-dependent mutagenesis by DNA lesions. Chem. Biol., 6, 743–753.[ISI][Medline]
  47. Ullah,S., Gallinari,P., Xu,Y.-Z., Goodman,M.F., Bloom,L.B., Jiricny,J. and Day,R.S. (1996) Base analog and neighboring base effects on substrate specificity of recombinant human G:T mismatch-specific thymine DNA-glycosylase. Biochemistry, 35, 12926–12932.[ISI][Medline]
  48. Saparbaev,M. and Laval,J. (1999) In Singer,B. and Bartsch,H. (eds) Enzymology of the Repair of Etheno Adducts in Mammalian Cells and in Escherichia coli, IARC Scientific Publications no. 150. IARC, Lyon, pp. 249–261.
  49. Delort,A.M., Duplaa,A.M., Molko,D., Teoule,R., Leblanc,J.P. and Laval,J. (1985) Excision of uracil residues in DNA: mechanism of action of Escherichia coli and Micrococcus luteus uracil-DNA glycosylases. Nucleic Acids Res., 13, 319–335.[Abstract]
  50. Eftedal,I., Volden,G. and Krokan,H.E. (1994) Excision of uracil from double-stranded DNA by uracil-DNA glycosylase is sequence specific. Ann. N. Y. Acad. Sci., 726, 312–316.[ISI][Medline]
  51. Sági,J., Hang,B. and Singer,B. (1999) Sequence-dependent repair of synthetic AP sites in 15-mer and 35-mer oligonucleotides: role of thermodynamic stability imposed by neighbor bases. Chem. Res. Toxicol., 12, 917–923.[ISI][Medline]
  52. Bloom,L.B., Otto,M.R., Eritja,R., Reha-Krantz,L.J., Goodman,M.F. and Beechem,J.M. (1994) Pre-steady-state kinetic analysis of sequence-dependent nucleotide excision by the 3'-exonuclease activity of bacteriophage T4 DNA polymerase. Biochemistry, 33, 7576–7586.[ISI][Medline]
  53. Modrich,P. (1994) Mismatch repair, genetic stability and cancer. Science, 266, 1959–1960.[ISI][Medline]
  54. Friedberg,E., Walker,G.C. and Seide,W. (1995) DNA Repair and Mutagenesis. ASM Press, Washington, DC.
  55. Seeberg,E., Eide,L. and Bjoras,M. (1995) The base excision repair pathway. Trends Biochem. Sci., 20, 391–397.[ISI][Medline]
  56. Sancar,A. (1996) DNA excision repair. Annu. Rev. Biochem., 65, 43–81.[ISI][Medline]
  57. Modrich,P. and Lahue,R. (1996) Mismatch repair in replication fidelity, genetic recombination and cancer biology. Annu. Rev. Biochem., 65, 101–133.[ISI][Medline]
  58. Wood,R.D. (1996) DNA repair in eukaryotes. Annu. Rev. Biochem., 65, 135–167.[ISI][Medline]
  59. Singer,B. and Hang,B. (1997) What structural features determine repair enzyme specificity and mechanism in chemically modified DNA? Chem. Res. Toxicol., 10, 713–732.[ISI][Medline]
  60. Singer,B. and Bartsch,H. (1986) The Role of Cyclic Nucleic Acid Adducts in Carcinogenesis and Mutagenesis, IARC Scientific Publications no. 70. IARC, Lyon.
  61. Marnett,L.J. and Burcham,P.C. (1993) Endogenous DNA adducts: potential and paradox. Chem. Res. Toxicol., 6, 771–785.[ISI][Medline]
  62. Singer,B. and Bartsch,H. (1999) Enzymology of the Repair of Etheno Adducts in Mammalian Cells and in Escherichia coli, IARC Scientific Publications no. 150. IARC, Lyon.
  63. Koffel-Schwartz,N., Verdier,J.M., Bichara,M., Freund,A.M., Daune,M.P. and Fuchs,R.P. (1984) Carcinogen-induced mutation spectrum in wild-type, uvrA and umuC strains of Escherichia coli. Strain specificity and mutation-prone sequences. J. Mol. Biol., 177, 33–51.[ISI][Medline]
  64. Radman,M. and Wagner,R. (1986) Mismatch repair in Escherichia coli. Annu. Rev. Genet., 20, 523–538.[ISI][Medline]
  65. Neddermann,P. and Jiricny,J. (1993) The purification of a mismatch-specific thymine-DNA glycosylase from HeLa cells. J. Biol. Chem., 268, 21218–21224.[Abstract/Free Full Text]
  66. Neddermann,P., Gallinari,P., Lettieri,T., Schmid,D., Truong,O., Hsuan,J.J., Wiebauer,K. and Jiricny,J. (1996) Cloning and expression of human G/T mismatch-specific thymine-DNA glycosylase. J. Biol. Chem., 271, 12767–12774.[Abstract/Free Full Text]
  67. Neddermann,P. and Jiricny,J. (1994) Efficient removal of uracil from G.U mispairs by the mismatch-specific thymine DNA glycosylase from HeLa cells. Proc. Natl Acad. Sci. USA, 91, 1642–1646.[Abstract]
  68. Hang,B., Medina,M., Fraenkel-Conrat,H. and Singer,B. (1998) A 55-kDa protein isolated from human cells shows DNA glycosylase activity toward 3,N4-ethenocytosine and the G/T mismatch. Proc. Natl Acad. Sci. USA, 95, 13561–13566.[Abstract/Free Full Text]
  69. Saparbaev,M. and Laval,J. (1998) 3,N4-ethenocytosine, a highly mutagenic adduct, is a primary substrate for Escherichia coli double-stranded uracil-DNA glycosylase and human mismatch-specific thymine-DNA glycosylase. Proc. Natl Acad. Sci. USA, 95, 8508–8513.[Abstract/Free Full Text]
  70. Dosanjh,M.K., Galeros,G., Goodman,M.F. and Singer,B. (1991) Kinetics of extension of O6-methylguanine paired with cytosine or thymine in defined oligonucleotide sequences. Biochemistry, 30, 11595–11599.[ISI][Medline]
  71. Bloom,L.B., Otto,M.R., Beechem,J.M. and Goodman,M.F. (1993) Influence of 5'-nearest neighbors on the insertion kinetics of the fluorescent nucleotide analog 2-aminopurine by Klenow fragment. Biochemistry, 32, 11247–11258.[ISI][Medline]
  72. Goodman,M.F., Cai,H., Bloom,L.B. and Eritja,R. (1994) Nucleotide insertion and primer extension at abasic template sites in different sequence contexts. Ann. N. Y. Acad. Sci., 726, 132–142.[Abstract]
  73. Belguise-Valladier,P. and Fuchs,R.P. (1995) N-2-aminofluorene and N-2 acetylaminofluorene adducts: the local sequence context of an adduct and its chemical structure determine its replication properties. J. Mol. Biol., 249, 903–913.[ISI][Medline]
  74. Moriya,M., Spiegel,S., Fernandes,A., Amin,S., Liu,T., Geacintov,N. and Grollman,A.P. (1996) Fidelity of translesional synthesis past benzo[a]pyrene diol epoxide-2'-deoxyguanosine DNA adducts: marked effects of host cell, sequence context and chirality. Biochemistry, 35, 16646–16651.[ISI][Medline]
  75. Rao,S., Chenna,A., Slupska,M. and Singer,B. (1996) Replication of O4-methylthymine-containing oligonucleotides: effect of 3' and 5' flanking bases on formation and extension of O4-methylthymine.guanine basepairs. Mutat. Res., 356, 179–185.[ISI][Medline]
  76. Hashim,M.F. and Marnett,L.J. (1996) Sequence-dependent induction of base pair substitutions and frameshifts by propanodeoxyguanosine during in vitro DNA replication. J. Biol. Chem., 271, 9160–9165.[Abstract/Free Full Text]
  77. Litinski,V., Chenna,A., Sagi,J. and Singer,B. (1997) Sequence context is an important determinant in the mutagenic potential of 1,N6-ethenodeoxyadenosine ({varepsilon}A): formation of {varepsilon}A base pairs and elongation in defined templates. Carcinogenesis, 18, 1609–1615.[Abstract]
  78. Freemont,P.S., Friedman,J.M., Beese,L.S., Sanderson,M.R. and Steitz,T.A. (1988) Cocrystal structure of an editing complex of Klenow fragment with DNA. Proc. Natl Acad. Sci. USA, 85, 8924–8928.[Abstract]
  79. Cowart,M., Gibson,K.J., Allen,D.J. and Benkovic,S.J. (1989) DNA substrate structural requirements for the exonuclease and polymerase activities of procaryotic and phage DNA polymerases. Biochemistry, 28, 1975–1983.[ISI][Medline]
  80. Beese,L.S., Derbyshire,V. and Steitz,T.A. (1993) Structure of DNA polymerase I Klenow fragment bound to duplex DNA. Science, 260, 352–355.[ISI][Medline]
  81. Samson,L., Thomale,J. and Rajewsky,M.F. (1988) Alternative pathways for the in vivo repair of O6-alkylguanine and O4-alkylthymine in Escherichia coli: the adaptive response and nucleotide excision repair. EMBO J., 7, 2261–2267.[Abstract]
  82. Voigt,J.M., Van Houten,B., Sancar,A. and Topal,M.D. (1989) Repair of O6-methylguanine by ABC excinuclease of Escherichia coli in vitro. J. Biol. Chem., 264, 5172–5176.[Abstract/Free Full Text]
  83. Daubersies,P., Galiegue-Zouitina,S., Koffel-Schwartz,N., Fuchs,R.P.P., Loucheux-Lefebvre,M.-H. and Bailleul,B. (1992) Mutation spectra of the two guanine adducts of the carcinogen 4-nitroquinoline 1-oxide in Escherichia coli. Influence of neighboring base sequence on mutagenesis. Carcinogenesis, 13, 349–354.[Abstract]
  84. Kamiya,H., Murata-Kamiya,N., Koizume,S., Inoue,H., Nishimura,S. and Ohtsuka,E. (1995) 8-Hydroxyguanine (7,8-dihydro-8-oxoguanine) in hot spots of the c-Ha-ras gene: effects of sequence contexts on mutation spectra. Carcinogenesis, 16, 883–889.[Abstract]
  85. Werntges,H., Steger,G., Riesner,D. and Fritz,H.-J. (1986) Mismatches in DNA double strands: thermodynamic parameters and their correlation to repair efficiencies. Nucleic Acids Res., 14, 3773–3790.[Abstract]
  86. Fagan,P.A., Fàbrega,C., Eritja,R., Goodman,M.F. and Wemmer,D.E. (1996) NMR study of the conformation of the 2-aminopurine:cytosine mismatch in DNA. Biochemistry, 35, 4026–4033.[ISI][Medline]
  87. Gelfand,C.A., Plum,G.E., Grollman,A.P., Johnson,F. and Breslauer,K.J. (1998) Thermodynamic consequences of an abasic lesion in duplex DNA are strongly dependent on base sequence. Biochemistry, 37, 7321–7327.[ISI][Medline]
  88. Allawi,H.T. and SantaLucia,J.Jr (1998) Nearest-neighbor thermodynamics of internal A.C mismatches in DNA: sequence dependence and pH effects. Biochemistry, 37, 9435–9444.[ISI][Medline]
  89. Peyret,N., Seneviratne,P.A., Allawi,H.T. and SantaLucia,J.Jr (1999) Nearest-neighbor thermodynamics and NMR of DNA sequences with internal A.A, C.C, G.G and T.T mismatches. Biochemistry, 38, 3468–3477.[ISI][Medline]
  90. Stivers,J.T. (1998) 2-Aminopurine fluorescence studies of base stacking interactions at abasic sites in DNA: metal-ion and base sequence effects. Nucleic Acids Res., 26, 3837–3844.[Abstract/Free Full Text]
  91. Dosanjh,M.K., Roy,R., Mitra,S. and Singer,B. (1994) 1,N6-ethenoadenine is preferred over 3-methyladenine as substrate by a cloned human N-methylpurine-DNA glycosylase (3-methyladenine-DNA glycosylase). Biochemistry, 33, 1624–1628.[ISI][Medline]
  92. Lindahl,T. (1982) DNA repair enzymes. Annu. Rev. Biochem., 51, 61–87.[ISI][Medline]
  93. Takeshita,M., Chang,C.N., Johnson,F., Will,S. and Grollman,A.P. (1987) Oligodeoxynucleotides containing synthetic abasic sites. Model substrates for DNA polymerases and apurinic/apyrimidinic endonucleases. J. Biol. Chem., 262, 10171–10179.[Abstract/Free Full Text]
  94. Wilson,D.M., Takeshita,M., Grollman,A.P. and Demple,B. (1995) Incision activity of human apurinic endonuclease (Ape) at abasic site analogs in DNA. J. Biol. Chem., 270, 16002–16007.[Abstract/Free Full Text]
Received November 1, 1999; accepted December 10, 1999.