Evaluation of single-stranded nucleic acids as carriers in the DNA-directed assembly of macromolecules

Current developments in nanosciences indicate that the self-assembly of mac romolecules, such as proteins or metallic nanoclusters, can be conveniently achieved by means of nucleic acid hybridization. Within this context, we h ere report on the evaluation of single-stranded nucleic acids to be utilize d as carrier backbones in DNA-directed self-assembly. A microplate solid-ph ase hybridization assay is described which allows rapid experimental determ ination of the hybridization efficiencies of various sequence stretches wit hin a given nucleic acid carrier strand. As demonstrated for two DNA fragme nts of different sequence, the binding efficiencies of several oligonucleot ides depend on the formation of specific secondary structure elements withi n the carrier molecule. A correlation of sequence-specific hybridization ca pability with modeled secondary structure is also obvious from experiments using the fluorescence gel-shift analysis. Electrophoretic studies on the e mployment of helper oligonucleotides in the formation of supramolecular con jugates of several oligonucleotide-tagged proteins indicate, that structura l constraints can be minimized by disruption of intramolecular secondary st ructures of the carrier molecule. To estimate the influences of the chemica l nature of the carrier, gel-shift experiments are carried out to compare a 170mer RNA molecule with its DNA analogue. Ternary aggregates, containing two protein components bound to the carrier, are formed with a greater effi ciency on the DNA instead of the RNA carrier backbone.