Duplex Stabilization of DNA: Oligonucleotides containing 7-substituted 7-deazaadenines

The oligonucleotide building blocks 4b–d derived from 7-bromo-, 7-chloro-, and 7-methyl-substituted 7-deaza-2′-deoxyadenosines 3b–d were prepared. They were employed in the solid-phase synthesis of the oligonucleotides 7–25 . The dA residues of the homomer d(A₁₂), the alternating d[(A-T)₆], and the palindromic d(G-T-A-G-A-A-T-T-C-T-A-C) were replaced by 3b–d as well as by the parent 7-deaza-2′-deoxyadenosine ( 3a ). The melting profiles and CD spectra of oligonucleotide duplexes, showing this major groove modification, were measured, and the T_m values as well as the thermodynamic data were determined. It was found that small substituents such as Br, Cl, or Me introduced in the 7-position of a 7-deazaadenine residue increase the duplex stability compared to oligonucleotides containing adenine.