A SERS probe for adenyl residues available for intermolecular interactions. Part II—Reactive adenyl sites in highly diluted DNA

Abstract

Surface‐enhanced Raman spectroscopy (SERS) with an (Ag)_n⁺ substrate detects picomoles of adenyl residues (Ayl) in a mildly salted aqueous medium (10⁻² M NaCl). Chloride binding to Ayl enhances the Ayl affinity for silver. The SER spectral profile provides information on Ayl orientation. If silver plasmons are closely related, Ayl SERS intensities depend on the extent of the adsorption. This allows us to compare Ayl availability in poly(dA), d(CCA AAA ACC) and d(GCC GAC CCG), in the corresponding double strands or in the self‐complementary d(CGA TCG) oligomer. Single‐strand self‐association constrains Ayl reactivity but less than duplex arrangements. Ayl reactivity is notably amplified in A tracts. In highly diluted poly(dA)–poly(dT) mixtures Ayl adsorption is available along flexible bulges. In the d(GCC GAC CCG).d(CGG GC GGC) duplex, where a thymidine is missing, Ayl is not more accessible than in the canonical duplex. Mg²⁺–nucleic acid complexation has a dual activity on the nucleic bases. At specific Mg²⁺ to nucleotide ratios, C6N/N7 Ayl sides are hidden in Mg²⁺ cross‐bridged structures involving homologous or complementary strands. Alternatively, below these ratios a 1 : 1 Mg²⁺–phosphate interaction enhances Ayl but also thymyl and cytosyl interactions with the electron‐depleted sites. Exploring salt effects and concentration dependences on nucleic base reactivity is crucial to predict elementary conditions for topological recognition in ‘living’ DNA, especially when temporarily unpaired or coiled in hairpins. Copyright © 2001 John Wiley & Sons, Ltd.