Pyrenylmethyldeoxyadenosine: a 3'-cap for universal DNA hybridization probes.

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 (DeltaT(m)) of duplexes increases by up to 29.1 degrees C. The modified residue lowers the base-pairing fidelity at the terminal and penultimate position of duplexes with a depression in DeltaDeltaT(m) 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.