Triplex Addressability as a Basis for Functional DNA Nanostructures

Abstract

Here, we present the formation of a fully addressable DNA nanostructure that shows the potential to be exploited as, for example, an information storage device based on pH-driven triplex strand formation or nanoscale circuits based on electron transfer. The nanostructure is composed of two adjacent hexagonal unit cells (analogous to naphthalene) in which each of the eleven edges has a unique double-stranded DNA sequence, constructed using novel three-way oligonucleotides. This allows each ten base-pair side, just 3.4 nm in length, to be assigned a specific address according to its sequence. Such constructs are therefore an ideal precursor to a nonrepetitive two-dimensional grid on which the "addresses" are located at a precise and known position. Triplex recognition of these addresses could function as a simple yet efficient means of information storage and retrieval. Future applications that may be envisaged include nanoscale circuits as well as subnanometer precision in nanoparticle templating. Characterization of these precursor nanostructures and their reversible targeting by triplex strand formation is shown here using gel electrophoresis, atomic force microscopy, and fluorescence resonance energy transfer (FRET) measurements. The durability of the system to repeated cycling of pH switching is also confirmed by the FRET studies.

Sensitive detection of transcription factors using an Ag+-stabilized self-assembly triplex DNA molecular switch

“…[16][17][18][19][20] Among those designs, the sequence-specific recognition of double-stranded DNA is realized by constructing a triplex DNA. 19 Another typical example is continuous assays for DNA translocation using fluorescent triplex DNA dissociation.…”

Targeting duplex DNA with chimeric α,β-triplex-forming oligonucleotides

“…Minor shift of the duplex bands in lanes 2 and 8 in Figure 4 presumably has the same origin.

Figure 6.Native gel electrophoresis of triplexes c3–h5 (1) c1–h5 (2) and a3–h3 (3), annealed with a 1.5-fold excess of the third strand and the duplex hairpin h3 (4) at 30, 40 and 50°C.

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Secondary binding sites for heavily modified triplex forming oligonucleotides

“…However, longer TFOs may show significant interaction with secondary sites at these concentrations. Other applications of triplexes, for instance, in detection/diagnostics or nanostructure formation (41), may well involve conditions of low pH, as they are not limited by physiological constraints. These applications with heavily modified TFOs might be affected by annealing to secondary binding sites.…”