Single-molecule pH sensors have been developed by utilizing molecular imaging of pH-responsive shape transition of nanomechanical DNA origami devices with atomic force microscopy (AFM). Short DNA fragments that can form i-motifs were introduced to nanomechanical DNA origami devices with pliers-like shape (DNA Origami Pliers), which consist of two levers of 170-nm long and 20-nm wide connected at a Holliday-junction fulcrum. DNA Origami Pliers can be observed as in three distinct forms; cross, antiparallel and parallel forms, and cross form is the dominant species when no additional interaction is introduced to DNA Origami Pliers. Introduction of nine pairs of 12-mer sequence (5′-AACCCCAACCCC-3′), which dimerize into i-motif quadruplexes upon protonation of cytosine, drives transition of DNA Origami Pliers from open cross form into closed parallel form under acidic conditions. Such pH-dependent transition was clearly imaged on mica in molecular resolution by AFM, showing potential application of the system to single-molecular pH sensors.
Divalent DNA-AuNP (gold nanoparticle) conjugates comprising two DNA strands at diametrically opposed positions are prepared. Highly linear 1D and tetragonal lattice-like 2D AuNP arrays are constructed using the conjugates and DNA assemblies based on T- and double-crossover motifs and the Holliday junction.
A simple and conventional method to isolate gold nanoparticle (GNP)/oligo-DNA conjugates having defined number of oligo-DNAs by gel electrophoresis was developed using extension oligo-DNAs. Formation of self-organized assemblies of GNPs in two different sizes using the conjugates having one or two complementary oligo-DNAs was demonstrated. This method to prepare GNP/oligo-DNA conjugates with controlled number of DNA strands should be useful to build up functional nanoarrays of GNPs on DNA scaffolds.
Tetragonal lattice‐like 2D gold nanoparticle (AuNP) arrays are constructed by an assortment of Holliday junction‐forming divalent DNA–AuNP conjugates by Y. Ohya and co‐workers . The divalent DNA–AuNP conjugate with a single‐stranded DNA attached at diametrically opposed polar positions is prepared utilizing high replacement reactivity of the polar singularities of an AuNP coated with a self‐assembled monolayer consisting of a binary mixture of hydrophilic thiol compounds.
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