Fluorescent <i>C</i>-Linked <i>C</i>⁸-Aryl-guanine Probe for Distinguishing <i>syn</i> from <i>anti</i> Structures in Duplex DNA

The synthesis and optical properties of the carbon (<i>C</i>)-linked <i>C</i>⁸-(2″-benzo­[<i>b</i>]­thienyl)-2′-deoxyguanosine (^BthdG), which acts as a fluorescent reporter of <i>syn</i> versus <i>anti</i> glycosidic conformations in duplex DNA, are described. In the <i>syn</i>-conformation, the probe stabilizes a G:G mismatch, emits at ∼385 nm (excitation ∼285 nm), and shows an induced circular dichroism (ICD) signal at ∼320 nm. Molecular dynamics (MD) simulations predict a wedge (W)-conformation for the mismatched duplex with the <i>C</i>⁸-benzo­[<i>b</i>]­thienyl moiety residing in the minor groove. In contrast, the probe destabilizes the duplex when base paired with its normal pyrimidine partner C. With flanking purine bases, a major groove B-type duplex is favored with ^BthdG present in the <i>anti</i>-conformation emitting at ∼413 nm (excitation ∼326 nm) and no ICD signal. However, with flanking pyrimidine bases, ^BthdG adopts the <i>syn</i>-conformation when base paired with C, and MD simulations predict a base-displaced stacked (S)-conformation, with the opposing C flipped out of the helix. The different duplex (B-, S-, and W-) conformers formed upon incorporation of ^BthdG are known to play a critical role in the biological activity of <i>N</i>-linked C8-dG adducts formed by arylamine carcinogens. Bulky environment-sensitive fluorescent <i>C</i>⁸-dG adducts that mimic the duplex structures formed by carcinogens may be useful in luminescence-based DNA polymerase assays