Fluorescent C-Linked C super(8)-Aryl-guanine Probe for Distinguishing syn from anti Structures in Duplex DNA

• Published in: Chemical research in toxicology 2012-06, Vol.25 (6), p.1271-1282-1271-1282
• Main Authors: Manderville, Richard A, Omumi, Alireza, Schlitt), Katherine MRankin (nee, Wilson, Katie A, Millen, Andrea L, Wetmore, Stacey D
• Format: Article
• Language: English
• ISSN: 0893-228X; 1520-5010
• DOI: 10.1021/tx300152q

The synthesis and optical properties of the carbon (C)-linked C super(8)-(2 double prime -benzo[b]thienyl)-2' -deoxyguanosine ( super(Bth)dG), which acts as a fluorescent reporter of syn versus anti glycosidic conformations in duplex DNA, are described. In the syn-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 C super(8)-benzo[b]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 super(Bth)dG present in the anti-conformation emitting at 413 nm (excitation 326 nm) and no ICD signal. However, with flanking pyrimidine bases, super(Bth)dG adopts the syn-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 super(Bth)dG are known to play a critical role in the biological activity of N-linked C8-dG adducts formed by arylamine carcinogens. Bulky environment-sensitive fluorescent C super(8)-dG adducts that mimic the duplex structures formed by carcinogens may be useful in luminescence-based DNA polymerase assays.