Recognition of O6-benzyl-2′-deoxyguanosine by a perimidinone-derived synthetic nucleoside: A DNA interstrand stacking interaction

Ewa A. Kowal, Rahul R. Lad, Pradeep S. Pallan, Elizabeth Dhummakupt, Zdzislaw Wawrzak, Martin Egli, Shana J. Sturla*, Michael P. Stone

*Corresponding author for this work

    Research output: Contribution to journalArticlepeer-review

    14 Scopus citations


    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 O 6-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 The structure of the modified Dickerson-Drew dodecamer (DDD) in which guanine at position G4 has been replaced by O6-Bn-dG and cytosine C9 has been replaced with dPer to form the modified O6-Bn-dG:dPer (DDD-XY) duplex [5′-d(C 1G2C3X4A5A 6T7T8Y9G10C 11G12)-3′]2 (X =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(C1G 2C3G4A5A6T 7T8Y9G10C11G 12)-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.

    Original languageEnglish (US)
    Pages (from-to)7566-7576
    Number of pages11
    JournalNucleic acids research
    Issue number15
    StatePublished - Aug 2013

    ASJC Scopus subject areas

    • Genetics

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