Single-Molecule Electrical Conductance in Z-form DNA:RNA

Abstract

Nucleic acids have emerged as new materials with promising applications in nanotechnology, molecular electronics, and biosensing, but their electronic properties, especially at the single-molecule level, are largely underexplored. The Z-form is an exotic left-handed helical oligonucleotide conformation that may be involved in critical biological processes such as the regulation of gene expression and epigenetic processes. In this work, the electrical conductance of individual Guanine Cytosine (GC)-rich DNA:RNA molecules is measured in physiological buffer and 2,2,2-Trifluoroethanol (TFE) solvent, corresponding to the natural (right-handed helix) A-form typical in DNA:RNA hybrids and the (left-handed) Z-form conformations, respectively. Single-molecule conductance measurements are performed using the Scanning Tunneling Microscopy (STM)-assisted break-junction method in the so-called "blinking" approach, recording the spontaneous formation of single-biomolecule junctions and performing statistical analysis of the signals. Circular Dichroism (CD) experiments and ab initio calculations are also done to rationalize the measured molecular conductivity with a simple structural and electronic model. These results show that the electrical conductivity of the Z-form is one order of magnitude lower than that of the more compact A-form. The longer molecular length and higher energy for the Highest Occupied Molecular Orbital (HOMO) of the Z-form account for the differences in single-molecule conductance observed experimentally.

Keywords: DFT; DNA:RNA; STM; Z‐form; biomolecular electronics; biophysics; circular dichroism; molecular electronics; nanoscience; single‐molecule conductance; solvent interactions.

Figure 1

A,B) Diagrams of the experimental setup showing the RNA:DNA hybrids in the A‐ and Z‐form, respectively, connected between two gold electrodes. C,D) Conductance histograms for the A‐ and Z‐form of RNA:DNA hybrids in blue and orange, respectively. The dark blue traces are a gaussian fitting of the peak to obtain the indicated statistical values for the center and broadness of the distributions, specifically the mean conductance (μ), deviation (σ), and full width at half maximum (FWHM). A total of 80 blinks were collected for each sample. Insets show typical blinks for each form. Experiments were performed using a 10 nA V⁻¹ amplifier and an applied bias voltage of 50 mV. The A‐ and Z‐form were induced using 100 mM buffer solution (pH 7.4) or 2,2,2‐Trifluoroethanol (TFE) solvent 60% in H ₂0 (v/v), respectively. E) Semi‐logarithmic histograms for the A‐ and Z‐form of RNA:DNA hybrids normalized to the total amount of accumulated current traces.

Figure 2

A) Circular dichroism spectra of A‐ and Z‐form RNA:DNA hybrids. The inset shows a zoom in of the CD spectra around 295 nm. B,C) Results from DFT calculation: Isosurfaces of the occupied molecular orbitals close to the HOMO for A‐ and Z‐form RNA:DNA hybrids, respectively. Isovalue = 2 × 10⁻² au.