Pyrenylmethyldeoxyadenosine: A 3′‐Cap for Universal DNA Hybridization Probes

Effect of a PAH on base pairing: A polycyclic aromatic hydrocarbon (PAH) covalently linked to the N6‐position of a dangling deoxyadenosine residue (see scheme) of an oligonucleotide increases target affinity, but decreases base‐pairing selectivity. Melting point increases of up to 28 °C (14 °C per residue) were observed, and 20 out of 24 mismatch‐containing duplexes are stabilized more strongly by the PAH substituent than their perfectly matched counterpart. magnified image A ligand that stabilizes a three‐dimensional structure can be expected to have a positive effect on the specificity with which this structure is formed. Here we report on a ligand covalently linked to an oligonucleotide that increases duplex stability, but decreases base‐pairing selectivity at the terminus. The ligand consists of a dangling 2′‐deoxyadenosine residue with a pyrenylmethyl substituent at the N6‐position, that is, a deoxynucleoside with a covalently linked polycyclic aromatic hydrocarbon (PAH). In the presence of the pyrene‐bearing nucleosides the UV melting point (ΔTm) of duplexes increases by up to 29.1 °C. The modified residue lowers the base‐pairing fidelity at the terminal and penultimate position of duplexes with a depression in ΔΔTm observable in 20 out of 24 sequence contexts tested. The effect can be rationalized based on a modeled three‐dimensional structure. The results are significant for the understanding of base‐pairing fidelity in DNA duplexes as modulated by the presence of a polycyclic aromatic hydrocarbon. The fidelity‐decreasing effect may be useful for universal hybridization probes that bind to a broader range of sequences than conventional oligonucleotides.