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

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. HighlightsO_LIUltraviolet absorption spectroscopy can probe non-canonical DNA structures. C_LIO_LIAbsorbance at 295nm tends to increase as G-quadruplexes form. C_LIO_LIFour G-quartets are needed to form a quadruplex with less than 1mM potassium. C_LIO_LIFormation of DNA triplexes can also yield a small change in UV spectra. C_LIO_LIUV absorption is a cheap label-free method for studying DNA nanoswitches. C_LI