2.6- Diamino-4-hydroxy-5-formamidopyrimidine

Figure 22.5. Representatives of the major oxidative base damage. The 8-oxoguanine is also known as 8-hydroxyguanine due to isomerization. FaPy-G, 2,6-diamino-4-hydroxy-5-formamidopyrimidine FaPy-A, 2,6-diamino-5-formamidopyrimidine.

Fig. 8.3. An example of a gas chromatogram of the base-damage to DNA after exposure to hydroxyl radicals (generated radiolytically) - study of the trimethyl-silylated acidic hydrolysate of the modified DNA (modified from Dizdaroglu, 1988 with permission). Peaks I, phosphoric acid II, thymine III and Ilia, cytosine IV and IVa adenine V and Va guanine I uracil 2 5,6-dihydrothymine 3 5-hydroxy-5,6-dihydrothymine 4 5-hydroxyuracil 5 5-hydroxy-5,6-dihydrouracil 6 5-hydroxycytosine 7 cis-thymine glycol 8 /ra .s-thymine glycol 9 5,6-dihydroxyuracil 10 4,6-diamino-5-formamidopyr-imidine 11 8-hydroxyadenine 12 2,6-diamino-4-hydroxy-5-formamidopyrimidine 13...

Treatment of DNA with hydrogen peroxide or other free radical-generating systems (snch as xanthine/xanthine oxidase) can also result in the formation of an imidazole ring-opened derivative of guanine, designated 2,6-diamino-4-hydroxy-5-formamidopyrimidine (FaPy) (26). This lesion is prominent... 

Coste F., Ober M., Carell T., Boiteux S., Zelwer C., Castaing B., Structural basis for the recognition of the FapydG lesion (2,6-diamino-4-hydroxy-5-formamidopyrimidine) by the Fpg DNA glycosylase, J. Biol. Chem., 2004,279,44074-44083. 

Douki, T., Martini, R., Ravanat, J.L., Turesky, R.J., and Cadet, J. (1997) Measurement of 2,6-diamino-4-hydroxy-5-formamidopyrimidine and 8-oxo-7,8-dihydroguanine in isolated DNA exposed to y radiation in aqueous solution. Carcinogenesis, 18, 2385-2891. 

The AMBER software and AMBER force fields are widely used for the simulation of various systems of biological and material science importance. Some researchers develop proper additions and corrections to standard parameters for better description of specific systems. We refer to only two of many such examples. Perez et al. (2007) reparameterized the parm99 force field for nucleic acid simulations, improving the representation of the a/y conformational space, which seems to be poorly represented in very long DNA MD simulations with available AMBER force fields. Song et al. (2008) adjusted the AMBER force field to reproduce conformational properties of an oxidative DNA lesion, 2,6-diamino-4-hydroxy-5-formamidopyrimidine. 

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