Assembly and melting of DNA nanotubes from single-sequence tiles

Abstract

DNA melting and renaturation studies are an extremely valuable tool to study the kineticsand thermodynamics of duplex dissociation and reassociation reactions. These areimportant not only in a biological or biotechnological context, but also for DNAnanotechnology which aims at the construction of molecular materials by DNAself-assembly. We here study experimentally the formation and melting of a DNA nanotubestructure, which is composed of many copies of an oligonucleotide containing severalpalindromic sequences. This is done using temperature-controlled UV absorptionmeasurements correlated with atomic force microscopy, fluorescence microscopy andtransmission electron microscopy techniques. In the melting studies, important factors suchas DNA strand concentration, hierarchy of assembly and annealing protocol areinvestigated. Assembly and melting of the nanotubes are shown to proceed via differentpathways. Whereas assembly occurs in several hierarchical steps related to the formation oftiles, lattices and tubes, melting of DNA nanotubes appears to occur in a single step. Thisis proposed to relate to fundamental differences between closed, three-dimensional tube-likestructures and open, two-dimensional lattices. DNA melting studies can lead to abetter understanding of the many factors that affect the assembly process whichwill be essential for the assembly of increasingly complex DNA nanostructures.