Conformation of a dodecane DNA hairpin linker. Multiple gauche bonds cover the bases

Alkane linkers derived from α,ω-alkane diols have been employed for the preparation of DNA mini-hairpins, which are suitable for studies of the spectroscopy and photochemistry of short base pair domains. The solution structure of a DNA hairpin having a n-dodecane linker and six AT base pairs has been determined using (1)H NMR data with restrained molecular dynamics. The chemical shifts of the 12 diastereotopic pairs of linker protons show a distribution of values depending on their locations within the shielding region of the ring-currents of the adjacent base pair. Chemical shifts calculated from the mean NMR solution structure show the same overall distribution, but with larger absolute values for the upfield shifts. The C12 linker lies approximately parallel to the adjacent base pair and adopts a highly curved structure having an average of 4-5 gauche C-C bonds, in contrast to a modeled B-DNA structure which has a more fully extended alkane chain. This curved structure results in an average P-P distance of 15.4 Å, substantially shorter than the 17.7 Å average distance for B-DNA. This structure appears to maximize the hydrophobic interactions between the linker and the adjacent base pair. Partial NMR assignments for the C12 linker in a second hairpin having a different base-pair sequence indicates that it adopts a similar curved geometry having multiple gauche bonds. The hairpin base pair domain adopts a B-DNA geometry in which the AT base pair adjacent to the linker displays Watson-Crick base pairing, in spite of the relatively short P-P distance. The terminal bases-pair shows evidence of extensive end-fraying. The four interior base pairs display a normal B-DNA geometry, thus providing good models for base pair domains embedded in longer duplexes.