Molecular Recognition Drives Oligonucleotide Binding to Nucleolipid Self-Assemblies

Plasmonic Chirality Imprinting on Nucleobase-Displaying Supramolecular Nanohelices by Metal-Nucleobase Recognition

Supramolecular self-assembly is an important process that enables the conception of complex structures mimicking biological motifs. Herein, we constructed helical fibrils through chiral self-assembly of nucleobase-peptide conjugates (NPCs), where achiral nucleobases are helically displayed on the surface of fibrils, comparable to polymerized nucleic acids. Selective binding between DNA and the NPC fibrils was observed with fluorescence polarization. Taking advantage of metal-nucleobase recognition, we highlight the possibility of deposition/assembly of plasmonic nanoparticles onto the fibrillar constructs. In this approach, the supramolecular chirality of NPCs can be adaptively imparted to metallic nanoparticles, covering them to generate structures with plasmonic chirality that exhibit significantly improved colloidal stability. The self-assembly of rationally designed NPCs into nanohelices is a promising way to engineer complex, optically diverse nucleobase-derived nanomaterials.

Investigation of Supramolecular Nanofibers Formed from Multicomponent Nucleotide-Appended Bolaamphiphiles and Heteropolymeric DNA as a Template

A novel DNA-templated multicomponent self-assembly of well-defined, molecular-level-controlled nanostructures in aqueous solution is demonstrated by using a thermal cycling procedure. The strategy uses four building blocks comprising 1,18-nucleotide-appended bolaamphiphiles (3'-phosphorylated adenosine, thymidine, guanosine, or cytidine connected to each end of an oligomethylene chain) and a heteropolymeric 58-mer containing a palindromic sequence as the template DNA. Atomic force microscopic observations, circular dichroism, and temperature-dependent absorption spectra revealed that the multicomponent self-assembly of the four nucleotide bolaamphiphiles and template DNA formed right-handed helical nanofibers with complementary base pairs during thermal cycling. Nanofibers were not formed if one of the four nucleotide bolaamphiphiles was missing, suggesting that construction of the helical nanofiber resulted from self-assembly of all four bolaamphiphiles to form matched base pairs sorted according to the sequence of the template DNA.

Construction of helical J-aggregates self-assembled from a thymidylic acid appended anthracene dye and DNA as a template

The thymidylic acid appended anthracene dye 2,6-bis[5-(3'-thymidylic acid)pentyloxy]anthracene (1) was synthesized, and the self-assembly of 1 and the binary self-assembly of 1 with a complementary single-stranded 20-meric oligodeoxyadenylic acid (dA(20)) were performed in 0.1 x TE buffer solution (i.e., 1.0 x 10(-3) M Tris-HCl, 1.0 x 10(-4) M ethylenediaminetriacetic acid (EDTA)). The characteristic J-band, small Stokes shift (6 nm), Cotton effect, and helical nanofibers 5.1 nm in diameter are observed in UV/Vis, fluorescence, and circular dichroism (CD) spectroscopies and atomic force microscopy (AFM) measurements for the binary self-assembly of 1 and dA(20) in aqueous solution. These observations revealed that the helical J-aggregates, in which the short-axis transition dipoles of the anthracene moieties are aligned in a head-to-tail fashion, are formed from the binary self-assembly of 1 and dA(20). The UV/Vis absorption and CD band of the anthracene L(a) region were found to be strongly dependent on temperature and showed cooperative changes for the binary self-assembly of 1 and dA(20). The self-assembly of the single-component 1 produced right- and left-handed helical nanofibers with diameters ranging from 4.0 to 10 nm. In contrast, for the binary self-assembly, the UV/Vis and fluorescence spectra showed no J-band and the Stokes shift was at approximately 107 nm for the single-component 1 in aqueous solution. In addition, the binary self-assembly of 1 and noncomplementary single-stranded 20-meric oligothymidylic acid (dT(20)) showed a small J-band and the J-band disappeared at 50 degrees C upon heating. On the basis of these observations, we concluded that thymine-adenine base-pair formation induced supramolecular helical J-aggregates in the binary self-assembly of 1 and dA(20) in aqueous solutions.