DNA/Polymeric Micelle Self‐Assembly Mimicking Chromatin Compaction

Abstract

Through self-assembly, a large variety of nanomaterials have been fabricated, which are useful in many applied and research fields. However, broader development of nanoscience and nanotechnology requires more complex nanostructures whose fabrication requires precise control of morphology, structural parameters, and distributions of components within the nanomaterials, which remains a great challenge for nanotechnology. Nature is masterful at building nanostructures with great complexity by precisely controlling multi-stage self-assembly processes. One example is the self-assembly of genomic DNA and histone octamers into chromatin in eukaryotic cells. Histone octamers are discshaped nanostructures with positively-charged binding sites specifically distributed on the edge of the disc. In the first stage, a DNA chain organizes histone octamers into a beadson-a-string structure (10 nm chromatin fiber); the bead is a nucleosome composed of one DNA segment wrapping around the edge of one histone octamer, and between neighboring beads is a short DNA linker. In the second stage, histone octamers that are preorganized on the 10 nm chromatin fiber, self-assemble further in a zigzag manner into the 30 nm chromatin fiber with a two-start helical structure. Histone octamers do not self-assemble into the 30 nm fiber until they are preorganized by the first stage of self-assembly; the first stage self-assembly initiates the second stage self-assembly. Inspired by such efficient self-assembly processes from nature, a number of DNA/sphere systems were studied; artificial nanospheres were used in the place of histone octamers. Computer simulation of the interaction between a polyelectrolyte with long DNA-like semi-flexible chains and the spheres with a uniform oppositely-charged surface reveals that the beads-on-a-string structure, similar to the 10 nm chromatin fiber, is the thermodynamic favored structure. However, experimentally, other kinetically trapped structures were inevitably produced in the reported systems because the DNA/sphere interactions were relatively strong. Herein, we prepared thermodynamically optimal structures of a DNA/artificial particle complex by controlling the interaction between DNA and the particles. We selected the block-copolymer micelles with an inert shell and a positively charged core to interact with DNA (Figure 1A); the interaction strength between DNA and the core can be continuously adjusted by the pH value of the medium. It was found that under certain conditions the strings (that are similar to the 10 nm chromatin fibers in both morphology and structure) formed exclusively. Under such conditions, only the thermodynamically favored beads-on-a-string structure can persist, while any kinetically trapped structures cannot. When monodisperse DNA was used, the strings formed were monodisperse, and the earlier-formed long strings evolved to shorter, but also monodisperse, strings; the different strings formed and evolved in a similar manner. Then, in a second stage, the micelles preorganized in the beads-on-a-string structure self-assembled along the strings into core–shell structured solenoidal nanofibers. The preorganization induced and guided the second stage of self-assembly. When monodisperse DNAs are used, the resulting nanostructures are monodisperse. This self-assembly process can be used for synthesis of monodisperse one-dimensional nanostructures with controlled dimensions and various compositions. Poly(ethylene glycol)113-b-poly(4-vinylpyridine)58 (PEG113b-P4VP58, subscripts represent the average degrees of polymerization;Mw/Mn= 1.20) micelles were prepared in a water/ methanol (4:1, v/v) mixture (see Supporting Information, Text S1). The micelles were monodisperse in size with an average hydrodynamic radius hRhi of 16.0 nm, a polydispersity index (PDI) of 0.05, and an average molecular weight of 1.74 10 gmol , based on light scattering (LS) measurements. In the TEM images, the micelles are monodisperse with a size of 17.5 1.5 nm (Figure 1B). The micelles shown have PEG as the shell and P4VP as the core. An aqueous solution of monodisperse linear doublestrandedDNA 5427 bp long (L5427) at 25 8Cwas added to the micelles in the water/methanol mixture to give a DNA/ micelle mass ratio of 1:20. The solution had a pH value of 6.6 in the presence of carbon dioxide (see Experimental Section), which provided the proper strength for the electrostatic interaction between DNA and the micelles (Supporting Information, Text S2). After 0.5 hours incubation, strings with a beads-on-a-string structure formed exclusively (Figure 1C). These strings have a linear structure without any branches, indicating that each string is composed of a single L5427 DNA chain, as detailed below. For each string, the beads were very similar in shape and size to the micelles. Between neighboring beads was a linker, which appears to be a short DNA segment. Additionally, the strings were shown to [*] K. Zhang, Prof. M. Jiang, Prof. D. Chen The State Key Laboratory of Molecular Engineering of Polymers and Department of Macromolecular Science, Fudan University Handan Road 220, Shanghai 200433 (P.R. China) E-mail: chendy@fudan.edu.cn