Using ultraviolet absorption spectroscopy to study nanoswitches based on non-canonical DNA structures

Blair McCarte; Owen T Yeung; Alexander J Speakman; Alistair Elfick; Katherine E Dunn

doi:10.1016/j.bbrep.2022.101293

Using ultraviolet absorption spectroscopy to study nanoswitches based on non-canonical DNA structures

Biochem Biophys Rep. 2022 Jun 4:31:101293. doi: 10.1016/j.bbrep.2022.101293. eCollection 2022 Sep.

Authors

Blair McCarte¹, Owen T Yeung¹, Alexander J Speakman¹, Alistair Elfick¹, Katherine E Dunn¹

Affiliation

¹ School of Engineering, Institute for Bioengineering, University of Edinburgh, The King's Buildings, Edinburgh, EH9 3DW, Scotland, UK.

Abstract

Non-canonical forms of DNA are attracting increasing interest for applications in nanotechnology. It is frequently convenient to characterize DNA molecules using a label-free approach such as ultraviolet absorption spectroscopy. In this paper we present the results of our investigation into the use of this technique to probe the folding of quadruplex and triplex nanoswitches. We confirmed that four G-quartets were necessary for folding at sub-mM concentrations of potassium and found that the wrong choice of sequence for the linker between G-tracts could dramatically disrupt folding, presumably due to the presence of kinetic traps in the folding landscape. In the case of the triplex nanoswitch we examined, we found that the UV spectrum showed a small change in absorbance when a triplex was formed. We anticipate that our results will be of interest to researchers seeking to design DNA nanoswitches based on quadruplexes and triplexes.

Keywords: DNA nanoswitches; DNA triplexes; G-quadruplexes; Non-canonical DNA structures; Ultraviolet absorption spectroscopy.