Single-stranded adenine-rich DNA and RNA retain structural characteristics of their respective double-stranded conformations and show directional differences in stacking pattern.

The structural preorganization of isosequential ssDNA and ssRNA hexamers d/r(GAAAAC)(1) [J. Am. Chem. Soc. 2003, 125, 9948] have been investigated by NMR and molecular dynamics simulations. Analysis of the nuclear Overhauser effect spectrometry (NOESY) footprints in the aqueous solution has shown that there is a substantial population of ordered right-handed helical structure in both hexameric single-stranded DNA and RNA, which are reminiscent of their respective right-handed helical duplex form, despite the fact these single-stranded molecules are devoid of any intermolecular hydrogen bonds. The NMR-constrained molecular dynamics (1.5 ns) derived geometries of the adenine-adenine overlaps at each dinucleotide step of the hexameric ssDNA (1a) and ssRNA (1b) show that the relatively electron-rich imidazole stacks above the electron-deficient pyrimidine in 5' to 3' direction in ssDNA (1a) while, in contradistinction, the pyrimidine stacks above the imidazole in the 5' to 3' direction in ssRNA (1b). This also means that the pi-frame of the 5'-pyrimidine can interact with the relatively positively charged imino and amino protons in the 3' direction in ssRNA and in the 5' direction in ssDNA, thereby stabilizing the twist and slide observed in the stacked oligonucleotides. The differently preferred stacking geometries in ssDNA and ssRNA have direct physicochemical implications for self-assembly and pK(a) modulation by the nearest-neighbor interactions, as well as for the dangling-end stabilization effects and imino-proton reactivity.