Abstract
The 2′-deoxynucleoside containing the synthetic base 1-[(2R,4S,5R)-4-hydroxy-5-(hydroxymethyl)-tetrahydrofuran-2-yl)-1H-perimidin-2(3H)-one] (dPer) recognizes in DNA the O6-benzyl-2′-deoxyguanosine nucleoside (O6-Bn-dG), formed by exposure to N-benzylmethylnitrosamine. Herein, we show how dPer distinguishes between O6-Bn-dG and dG in DNA. The structure of the modified Dickerson–Drew dodecamer (DDD) in which guanine at position G4 has been replaced by O6-Bn-dG and cytosine C9 has been replaced with dPer to form the modified O6-Bn-dG:dPer (DDD-XY) duplex [5′-d(C1G2C3X4A5A6T7T8Y9G10C11G12)-3′]2 (X = O6-Bn-dG, Y = dPer) reveals that dPer intercalates into the duplex and adopts the syn conformation about the glycosyl bond. This provides a binding pocket that allows the benzyl group of O6-Bn-dG to intercalate between Per and thymine of the 3′-neighbor A:T base pair. Nuclear magnetic resonance data suggest that a similar intercalative recognition mechanism applies in this sequence in solution. However, in solution, the benzyl ring of O6-Bn-dG undergoes rotation on the nuclear magnetic resonance time scale. In contrast, the structure of the modified DDD in which cytosine at position C9 is replaced with dPer to form the dG:dPer (DDD-GY) [5′-d(C1G2C3G4A5A6T7T8Y9G10C11G12)-3′]2 duplex (Y = dPer) reveals that dPer adopts the anti conformation about the glycosyl bond and forms a less stable wobble pairing interaction with guanine.
Highlights
The alkylation of deoxyguanosine in DNA at the O6 position, exemplified by exposure to N-benzylmethylnitrosamine and the formation of O6-benzyl-20-deoxyguanosine nucleoside (O6-Bn-dG), is cytotoxic [1] and mutagenic [2,3]
The unfolding of the Drew dodecamer (DDD), DDD-XY and DDD-GY duplexes was examined by temperature-dependent UV spectroscopy
The simultaneous insertion of Per and the benzyl group of O6-Bn-dG unwinds the duplex at the recognition site (Figure 1 and Supplementary Figure S1), as suggested by the weak sequential NOE connectivity crosspeak observed between C3 H10 and X4 H8
Summary
The alkylation of deoxyguanosine in DNA at the O6 position, exemplified by exposure to N-benzylmethylnitrosamine and the formation of O6-benzyl-20-deoxyguanosine nucleoside (O6-Bn-dG), is cytotoxic [1] and mutagenic [2,3]. The O6-Bn-dG lesion is representative of bulky DNA adducts involved in the initiation of gene mutations [4,5]. It predominantly causes G!A transitions [6,7] and is observed in human cells [8]. The 20-deoxynucleoside containing the synthetic base 1-[(2R,4S,5R)-4-hydroxy-5-(hydroxymethyl)tetrahydrofuran-2-yl)-1H-perimidin-2(3H)-one] (dPer; Chart 1) recognizes the O6-Bn-dG in DNA [23]. Developing an understanding of the structural basis for O6-Bn-dG recognition is critical to further developing nucleosides such as dPer to recognize these mutagenic lesions
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