H-DNA formation

The formation of three-stranded nucleic acid complexes was first demonstrated over five decades ago [56] but the possible biological role of an extended triplex was expanded by the discovery of the H-DNA structure in natural DNA samples [57-59]. H-DNA is an intermolecular triplex that is generally of the pyrimidine-purine x pyrimidine type ( dot -Watson-Crick pairing and cross Hoogsteen base paring) and can be formed at mirror repeat sequences in supercoiled plasmids [59]. 

Kasai, H., Crain, P.F., Kuchino, Y., Nishimura, S., Oot-suyama, A. and Tanooka, H. (1986). Formation of 8-hydroxyguanine moiety in cellular DNA by agents producing oxygen radicals and evidence for its repair. Carcint nesis 7, 1849-1858. 

Devasagayam, T.P.A., Steenken, S., Obendorf, M.S.W., Schultz, W.A. and Sies, H. (1991). Formation of 8-hydroxy(deoxy)guanosine and generation of strand breaks at guanine residues in DNA by singlet oxygen. Biochemistry 30, 6283-6289. 

Potaman, V. N., Ussery, D. W. and Sinden, R. R. Formation of a combined H-DNA/open TATA box structure in the promoter sequence of the human Na,K-ATPase alpha2 gene. J. Biol. Chem. 271 13441-13447,1996. 

FA and FA-DNA adducts in various tissues were isolated in various tissues of male rats 24h after a single intraperitoneal injection of [ H]FA. Formation and distribution of DNA adducts after chronic administration of FA in the diet were also studied. FA-derived radioactivity was widely distributed throughout the animal after a single dose, and excreta contained the greatest amounts of radioactivity at all dose levels. 

Gansewendt, B., Foest, U., Xu, D., Hallier, E., Bolt, H.M. Peter. H. (1991) Formation of DNA adducts in F-344 rats after oral administration or inhalation of [ C]methyl bromide. Food chem. Toxicol., 29, 557-563... 

Htun, H Dahlberg, J.E. (1989) Tbpology and formation of triple-stranded H-DNA Science 243, 1571—1576. 

Figure 5-34 (A) Two conformations of a segment of the yeast phenylalanine tRNA gene. The segment shown codes for the 3 end of the tRNA molecule shown in Fig. 5-30, including the T /C loop. (B) Formation of H-DNA (Fig. 5-24) proposed for a sequence in plasmid pGG32. The major element of the structure is the triplex, which is formed from the Watson-Crick duplex ( ) associated with the homopyrimidine loop through Hoogsteen base pairing (o, +). One of the two possible "isomeric" forms is shown. See Mirkin et al.378...

In the previous chapter we discussed DNA-binding proteins that regulate transcription in prokaryotes. The principles that govern recognition between proteins in eukaryotes show some similarities and some differences. In both cases specific recognition is dominated by interactions that take place in the major groove of the DNA. The specific interactions usually involve H bond formation... 

Yermilov V, Rubio J, Ohshima H (1995) Formation of 8-nitroguanine in DNA treated with peroxyni-trite in vitro and its rapid removal from DNA by depurination. FEBS Lett 376 207-210 Yermilov V, Yoshie Y, Rubio J, Oshima H (1996) Effects of carbon dioxide/bicarbonate on induction of DNA single-strand breaks and formation of 8-nitroguanine, 8-oxoguanine and base-propenal mediated by peroxynitrite. FEBS Lett 399 67-70... 

Distel L, Distel B, Schussler H (2002) Formation of DNA double-strand breaks and DNA-protein crosslinks by irradiation of DNA in the presence of a protein. Radiat Phys Chem 65 141-129 Dizdaroglu M (1986) Chemical characterization of ionizing radiation-induced damage to DNA. Bio Techniques 4 536-546... 

V. Yermilov, J. Rubio and H. Oshima, Formation of 8-nitroguanine in DNA treated with peroxinitrite in vitro and its rapid removal from DNA by depurination, FEBS Lett., 376 (1995) 207-210. 

DNA is prone to structural polymorphism its sttucture can differ markedly from the classical donble hehx. For example, under snperhehcal stress, circnlar closed DNA can adopt an unnsnal structure, denoted H-DNA, in which homopurine-homopyrimidine tracts unwind and ntUize the pyrimidine-rich strand to form an intramolecnlar triplex with another homopnrine homopyrimidine tract the remaining purine single strand is left unpaired. The formation of H-DNA reqnires the presence of metal ions such as Mg + or... 

H-DNA a DNA sequence consisting of a polypurine segment hydrogen bonded to a polypyrimidine strand that forms a triple helix involves the formation of nonconven-tional base pairing... 

Murata-Kamiya, N., Kamiya, H., Iwamoto, N., and Kasai, H. (1995) Formation of a mutagen, glyoxal, from DNA treated with oxygen free radicals. Carcinogenesis, 16, 2251—... 

If aqueous solutions of eis- or traws-DDP are allowed to equilibrate, the kinetics of the reactions of these equated species with DNA can be measured Atlow r j the reaction is pseudo-first-order with respect to platinum concentration. For eis-DDP, the half-life of the reaction of the diaquo species with 10"4 M DNA at 25 C, pH 5-6 is 0,8 min and the monoaquo species, and t2 ans-[Pt(NH3)2(H20)Cl]J have half-lives of 6 h and 2 h respectively The forms [Pt(NH3)2Cl(OH)] and [Pt(NH3)2(OH)2] do not react with DNA and ais-[Pt(NH372 (H2O) (OH) ]" reacts with the same kinetics as the diaquo form (20). However, if freshly dissolved solutions of platinum compounds are added to the DNA, formation of the monoaquo species is the rate limiting step (22). Figure 2 shows the reactions of fresh solutions of the three compounds with DNA at 37 C Under these conditions the half-lives of the reactions were 3.9, 2.5 and 0.65 h for ais-DDP, trons-DDP and [Pt(dien)Cl]Cl respectively (19). 

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