Characterization of the Nanostructure of Complexes Formed by Single- or Double-Stranded Oligonucleotides with a Cationic Surfactant

We report the use of dynamic light scattering (DLS), small-angle neutron scattering (SANS), and small-angle X-ray scattering (SAXS) to characterize the nanostructure of complexes formed by either single- or double-stranded oligonucleotides with a cationic surfactant (cetyltrimethylammonium bromide, CTAB) in aqueous solution (1 mM Li2SO4). For single-stranded oligonucleotides 5'-A(20)-3' and 5'-CCCCATTCTAG-CAGCCCGGG-3', both the appearance of two Bragg peaks (at 0.14 and 0.28 angstrom(-1)) in SAXS spectra with a spacing of 1:2 and form factor his to SANS spectra are consistent with the presence of multilamellar vesicles (with, on average, 6-9 layers with a periodicity of 45-48 angstrom). Some samples showed evidence of an additional Bragg peak (at 0 20 angstrom(-1)) associated with periodic packing (with a periodicity of 31 angstrom) of the oligonucleotides within the lamel ae of the nanostructure. The nucleotide composition of the single-stranded oligonucleotides was also found to impact the number and size of the complexes formed with CAB. In contrast to 5'-A(20)-3' and 5'-CCCCATTCTAGCAGCCCGGG-3', 5'-T-20-3' did not change the state of aggregation of CTAB (globular micelles) over a wide range of oligonucleotide:CTAB charge ratios. These results support the proposition that hydrophobic interactions, as well as electrostatics, play a central role in the formation of complexes between cationic amphiphiles and single-stranded oligonucleotides and thus give rise to nanostructures that depend on nucleotide composition. In contrast to the single-stranded oligonucleotides, for double-stranded oligonucleotides mixed with CTAB, three Bragg peaks (0.13, 0.23, and 0.25 angstrom(-1)) in SAXS spectra with a spacing ratio of 1:root 3:root 4 and characteristic changes in SANS spectra indicate formation of a hexagonal nanostructure. Also, the composition of the double-stranded oligonucleotides did not measurably impact the nanostructure of complexes formed with CTAB, suggesting that electrostatic interactions dominate the formation of these complexes. Overall, these results provide insights into the intermolecular interactions that occur between cationic amphiphiles and oligonucleotides and establish that single and double-stranded oligonucleotides form complexes with cationic surfactants that differ in nanostructure. The results also provide guidance for the design of oligonucleotide complexes with cationic amphiphiles.