Apurinic site

The base substitutions are primarily transversions at G C base pairs and the available evidence suggests that these mutations are induced by apurinic sites which are generated as secondary consequences of the initial alkylation event. The significance of these results in the context of carcinogenesis is briefly considered. 

BPDE reacts at several different sites on DNA to generate several kinds of lesions at the N2 (43-45) and N7 (46,47) positions of guanine, apurinic sites (48,49), and strand breaks (50). Which of these lesions are responsible for the transversion mutations at G C sites Evidence derived from a number of experiments suggests the hypothesis that apurinic sites generated by BPDE reactions with DNA are responsible for the transversion mutations ... 

The work of Loeb and Kunkel and their colleagues (70-72) has clearly established that apurinic sites in DNA are mutagenic they specifically cause transversion mutations, due to a strong preference for the incorporation of adenine residues during bypass of apurinic sites in template DNA. Thus, A T to T A and G C to T A transversions are the major mutagenic outcome generated by depurination of DNA. 

DNA has only a limited stability in the temperature and pH conditions of an organism. Spontaneous changes in the DNA structure may occur and cleavage of purine bases is assigned an important role. The apurinic sites resulting from depurination may give rise to mutations if not repaired. 

The production of apurinic and apyrimidinic sites can both be caused by alkylating agents. When, for example, the N7 of guanine is alkylated, this causes the bond from base to sugar to become labile and so the base can be lost completely. Thus, apurinic sites are formed. Insertion of an incorrect base at this site can then cause a mutation. Loss of purines and pyrimidines can also occur spontaneously. 

PAH cation radicals contains relatively large amounts of apurinic sites as well as some stable adducts. Enzymes, many of which move along the polymeric strand in a particular direction, process DNA. Thus the enzymes will see damaged parts of DNA (depurinated or stretched and unwound) and provoke tumorigenic replications. Of course, particular DNA sequences are more prone to mutation than others. These hot spots vary in different organisms. PAH cation radicals can serve as a useful tool in studying this particular problem. 

Weinfeld M, Liuzzi M, Paterson MC (1990) Response of phage T4 polynucleotide kinase toward dinucleotides containing apurinic sites design of a 32P-postlabeling assay for apurinic sites in DNA. Biochemistry 29 1737-1743... 

Ogasawara, T., Sawasaki, T., Morishita, R., Ozawa, A., Madin, K., and Endo, Y. (1999) A new class of enzyme acting on damaged ribosomes ribosomal RNA apurinic site specific lyase found in wheat germ. EMBO J. 18, 6522-6531. 

Poly(ADP-ribose) polymerase (PADPRP) hypothesis. - In this theory DNA is the initial target of the mustard agent. Alkylated DNA purines undergo spontaneous and enzymatic depurination, leading to the production of apurinic sites which are cleaved by apurinic endonucleases to yield DNA breaks. Accumulation of DNA breaks leads to activation of the chromosomal enzyme PADPRP, which utilizes nicotinamide adenine dinucleotide (NAD ) as a substrate to ADP-ribosylate and a variety of nuclear... 

Lindahl T, Andersson A. Rate of chain breakage of apurinic sites in double-stranded DNA. Biochemistry 1972 11 3618-3623. 

Figure 27.48. Structure of DNA-Repair Euzyme. A complex between the DNA-repair enzyme AlkA and an analog of an apurinic site. Note that the damaged base is flipped out of the DNA double helix into the active site of the enzyme for excision. 

Lindahl, T., and Andersson, A (1972). Rate of chain breakage at apurinic sites in double-stranded deoxyribonucleic acid. Biochemistry 11(19) 3618-3623. 

Kingma, P. S. and Osheroff, N. (1997) Apurinic sites are position-specific topoisomerase II poisons. J. Biol. Chem. 272, 1148-1155. 

Castaing B., Boiteux S., Zelwer C., DNA containing a chemically reduced apurinic site is a high affinity ligand for the E. co//formamidopyrimidine-DNA glycosylase. Nucleic Acids Res., 1992,20,389-394. 

Hom, T. and Urdea, M. S. 1988. Solid supported hydrolysis of apurinic sites in synthetic oligonucleotides for rapid and efficient purification on reverse-phase cartridges. Nucleic Acids Res., 16 11559-11571. 

The role of depurinating adducts and apurinic sites in the PAH-induced cancer process is controversial and has yet to be fully elucidated. There are lines of evidence that both support and refute this theory. In support of this theory, the levels of depurinating adducts of B[a]P correlated with mutations in the H-ras oncogene in DNA isolated from mouse skin papillomas initiated by this compound (Chakravarti et al. 1995). It is well known that the initiation of skin tumors in mice is associated with the formation of mutations in the H-ras gene [reviewed by Ross and Nesnow (1999)]. DB[a,/]P treatment of mouse skin forms papillomas which contain the H-ras codon 61 (CAA to CTA) mutation. These same mutations were induced in early preneoplastic skin within one day after DB[a,/]P treatment and appear to be related to DB[a,/]P-Ade-depurinating adducts. Studies have shown that apurinic... 

Chakravarti, D., Pelhng, J. C., Cavaheri, E. L., and Rogan, E. G. (1995). Relating aromatic hydrocarbon-induced DNA adducts and c-H-ras mutations in mouse skin papillomas The role of apurinic sites. Proc Natl Acad Sci USA 92, 10422-10426. 

Melendez-Colon, V. J., Luch, A., Seidel, A., and Baird, W. M. (1999a). Cancer initiation by polycyclic aromatic hydrocarbons results from formation of stable DNA adducts rather than apurinic sites. 

Figure 5.28 Apurinic site lyase mechanism. The probable products of sodium borotritide labelling are also shown.

Papirmeister and his colleagues showed that these alkylated purines (guanine and adenine are purines, cytosine and thymine are pyrimidines) are rapidly removed from DNA a depurination process that may occur spontaneously or as a result of activation of endonucleases. Interestingly, it was shown that alkylation of the N3 site of adenine had the greatest sensitizing effects on endonucleases derived from extracts of bacterial and mammalian cells (Papirmeister et al., 1970 Lindahl, 1979). For further details of endonuclease activation, the reader should refer to the original papers. Depurination leads to apurinic sites appearing in DNA and these are attacked by apurinic endonucleases. These specific endonucleases lead to breaks in the DNA chain a critical step in the pathway proposed. Papirmeister summed up the process as ... 

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