Abasic sites, in DNA

Chaudry MA, Weinfeld M (1997) Reactivity of human apurinic/apyrimidinic endonuclease and Escherichia coli exonulcease III with bistranded abasic sites in DNA. J Biol Chem 272 15650-15655 Chaudry MA, Dedon PC, Wilson DM III, Demple B, Weinfeld M (1999) Removal by human apurinic/ apyrimidinic endonuclease 1 (Ape 1) and Escherichia coli exonuclease III of 3 -phosphoglyco-... 

Figure 23.7. Structure of an AP site (center) and structures produced by 5 AP endonuclease activity (left) or lyase activity (right). These are formed in double-strand DNA, but only one strand is represented in the figure. 5 AP-endonuclease activity results in the formation of a 5 -deoxyribose-phosphate end (5 -dRP), which must be subsequently processed by a dRPase (see text). Lyase activity results in the formation of 3 -unsaturated aldehydic a, P, 4-hydroxy-2-pentenal end, which must be subsequently acted upon by a 5 AP endonuclease. (Reproduced with permission from Boiteux, S., and Guillet, M. Abasic sites in DNA repair and biological consequences in Saccharomyces cerevisiae. DNA Repair 3,1-12, 2004.)...

Incubate integrase in INT cocktail with the oligonucleotide containing the enzymatically generated abasic site in DNA cocktail (as described in Subheading 3.5.) for 2 min at room temperature (see Note 4). 

Dong, M., Wang, C., Deen, W.M., and Dedon, P.C. (2003) Absence of 2 -deoxyoxanosine and presence of abasic sites in DNA exposed to nitric... 

Figure 35. Naturally occurring abasic sites in DNA I, II Unstable acetals in natural abasic sites. Ill Tetrahydrofuranyl derivatives after oligonucleotide synthesis.

The optical detection of abasic sites in DNA is difficult. Thus far, fluorescence probes have been attached to reactive groups that target abasic sites [315, 3l6], and a chemiluminescent reagent has been recently developed [317]. 2-Aminopur-ine, an isomer of adenine (see below) that is fluorescent, has been inserted into oligonucleotides across from and adjacent to abasic sites the fluorescence is sen-... 

Mazumder, A., Gerlt, J. A., Absalon, M. J., Stubbe, J., Cunningham, R. P., Withka, J., and Bolton, P. H. (1991). Stereochemical studies of the beta-elimination reactions at aldehydic abasic sites in DNA Endonuclease III from Escherichia coli, sodium hydroxide, and Lys-Trp-Lys. Biochemistry 30, 1119-1126. 

A few different methods of detection of an abasic site in DNA have been reported, the most common being the addition of a reagent that will occupy the space left by the missing nucleobase. The metallo-intercalator Rh(bpy)2(chrysi), where bpy is biphenyl and chrysi is chrysene-5,6-quinone diimide, is known to bind to DNA at mismatch sites where the duplex is disordered, but it will also bind at an abasic site, and has been shown to bind at abasic sites opposite both cytosine and guanine. The pteridine derivatives 6,7-dimethyllumazine and alloxazine both bind to adenine opposite to an abasic site, and both give a fluorescent signal in... 

Nucleosidic and nucleotidic phosphoramidite intermediates have also played an important role in biomedical investigations. For example, the mechanisms involved in the repair of abasic sites in DNA have... 

Constant, J. F Fkyerat, A. Demeunynck, M. Laval, J. O Connor, T. R. Lhomme, J. Design of molecules which specifically cleave abasic sites in DNA. Anti-Cancer Drug Des. 1990,5,59-62. 

Introduction of biotin markers at abasic aldehyde sites in DNA, resulting from oxidative damage (equation 59,... 

Gu J, Wang J, Rak J, Leszczynski L (2007). Findings on die electron-attachment-induced abasic site in a DNA double helix. Angew Chem Int Ed 46 3479—3481. 

When the complexes between the lactose operator and operator DNA [22] or that between the repair protein and abasic site-bearing DNA [23] are irradiated, the complexes are destroyed mainly due to the damage to the protein. When irradiated alone the lactose repressor or the repair protein Fpg lose their ability to bind DNA at a dose that is much lower than that necessary for destroying the complexes. The explanation lies in the reverse radioprotection provided to the protein by the DNA. RADACK calculations using the structural parameters for a free and a complexed repressor headpiece (Fig. 5) reveals the most probable sites of protein lesions. 

The presence of the probe in the abasic site is confirmed by hybridisation studies and by NMR. The authors have shown the existence of an apparent synergy with the anticancer agent BCNU. The incorporation of the hydroxyphenylben-zoxazole derivative (122) opposite an abasic site in a duplex is a reasonable mimic of a Watson-Crick base-pair.The analogue undergoes an excited state intramolecular proton transfer under photolysis conditions, which has been used to study tautomerisation within a DNA duplex. 

Abasic Sites and Mismatches. Abasic sites, in which the DNA s sugar-phosphate backbone is intact but the glycosidic bond to a base has been broken. 

Jakobsen U, Shelke SA, Vogel S, Sigurdsson ST (2010) Site-directed spin-labeling of nucleic acids by click chemistry detection of abasic sites in duplex DNA by EPR spectroscopy. J Am Chem Soc 132(30) 10424-10428. doi 10.1021/jal02797k... 

There are few mechanistic details on the formation and structures of the DNA oxidation products in the Cr + Red + O2 + DNA systems. Reduction of Cr(VI) with GSH or ascorbate induced simultaneous formation of comparable amounts of single-strand breaks and abasic sites in isolated DNA (376, 377, 381). Malondialdehyde was detected (by reaction with thiobarbituric acid) as an oxidation product of DNA or 2-deoxyribose in the Cr + Red + O2 systems (Red = GSH or ascorbate) (379). These features correspond to DNA oxidation by hydrogen abstraction at C4 atom of the deoxyribose moiety (405,406). More detailed studies of DNA oxidation mechanisms were performed using a model Cr(V) complex, [CrVO(ehba)2]- (Section III.C.4). 

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