Harnessing DNA for nanothermometry

Abstract

Temperature measurement at the nanoscale has brought insight to a wide array of research interests in modern chemistry, physics, and biology. These measurements have been enabled by the advent of nanothermometers, which relay nanoscale temperature information through the analysis of their intrinsic photophysical behavior. In the past decade, several nanothermometers have been developed including dyes, nanodiamonds, fluorescent proteins, nucleotides, and nanoparticles. However, temperature measurement using intact DNA has not yet been achieved. Here, we present a method to study the temperature sensitivity of the DNA molecule within a physiologic temperature range when complexed with fluorescent dye. We theoretically and experimentally report the temperature sensitivity of the DNA-Hoechst 33342 complex in different sizes of double-stranded oligonucleotides and plasmids, showing its potential use as a nanothermometer. These findings allow for extending the thermal study of DNA to several research fields including DNA nanotechnology, optical tweezers, and DNA nanoparticles.

Keywords: DNA; Hoechst; anisotropy; nanothermometers; temperature; thermal information.

Figure 1.

(a) Schematic illustration of DNA-based ABNT synthesis. (b-f) show the experimental temperature sensitivity of different 0.1 mg/ml (b-e) and 0.01 mg/ml* (f) DNA-based ABNTs (100:1 DNA:HOECHST ratio in grams). Error bars represent the standard error of the mean value. (*) The concentration of 16 kbps DNA-based ABNTs was selected to be 0.01 mg/ml because for DNA fragments longer than 11 kbps, the temperature sensitivity is compromised above concentrations of 0.03 – 0.09 mg/ml (see discussion of viscosity below).

Figure 2.

(a) Theoretical and experimental sensitivity as a function of number of base pairs for oligonucleotide-Hoechst ABNTs (fluorescence lifetime of 2.2 ns). Green arrow shows the deviation from expected temperature sensitivity for long DNA molecules.

Figure 3.

Theoretical DNA-Hoechst ABNT sensitivity evaluated at 37 °C from the Barkley-Zimm model (torsion, rotation, bending motions) with the experimental data.

Figure 4.

Temperature sensitivity of the 4 kbps pGEMTe-RagC circular plasmid (a) versus the same linear plasmid (b) after Ndel enzyme treatment (plasmid concentration 0.1 mg/mL, Hoechst concentration 0.001 mg/mL). Error bars represent the standard error of the mean value. Gel electrophoresis (c) showing the circular uncut plasmid (middle row - two bands) and linear conformation (right row - one band).