Self-assembly of ssDNA-amphiphiles into micelles, nanotapes and nanotubes

Abstract

The field of DNA nanotechnology utilizes DNA as a construction material to create functional supramolecular and multi-dimensional structures like two-dimensional periodic lattices and three-dimensional polyhedrons with order on the nanometer scale for many nanotechnology applications including molecular templating, nanosensors, and drug delivery. Single-stranded DNA (ssDNA) is often used to create these nanostructures as the DNA bases provide an intrinsic molecular code that can be exploited to allow for the programmed assembly of structures based upon Watson-Crick base-pairing. However, engineering these complex structures from biopolymers alone requires careful design to ensure that the intrinsic forces responsible for organizing the materials can produce the desired structures. Additional control over supramolecular assembly can be achieved by chemically modifying the ssDNA with hydrophobic moieties to create amphiphilic molecules, which adds the hydrophobic interaction to the list of contributing forces that drive the self-assembly process. We first explored the self-assembly behavior of a set of ssDNA aptamer-amphiphiles composed of the same hydrophobic tail and hydrophilic ssDNA aptamer headgroup but with different spacer molecules linking these groups together. Through the use of cryo-transmission electron microscopy (cryo-TEM), small angle x-ray scattering (SAXS), and circular dichroism (CD) we show that the aptamer-amphiphiles can assemble into a variety of structures depending on the spacer used. We demonstrated, for the first time, the creation of self-assembled aptamer-amphiphile nanotape structures and show that the choice of the spacer used in the design of aptamer-amphiphiles can influence their supramolecular self-assembly as well as the secondary structure of the aptamer headgroup. We next explored the role of the ssDNA headgroup on the amphiphile self-assembly behavior by designing amphiphiles with headgroups of multiple lengths and nucleotides sequences. Amphiphiles of each headgroup length that contained hydrophobic spacers were found to assemble into twisted nanotapes, helical nanotapes and nanotubes as the nanotapes grew in width. In few instances, guanine-rich headgroups were capable of forming nanotape and nanotube structures in the absence of the hydrophobic spacer. Together, these studies demonstrate the ability of ssDNA-amphiphiles to form complex nanostructures that may be useful in a variety of DNA nanotechnology applications.