Eps2Fold: a rapid method to characterize G-quadruplex DNA structures using single absorbance spectra.

Abstract

G-rich oligonucleotides can fold into non-canonical secondary structures called G-quadruplexes (G4s), consisting of stacked G-tetrads, i.e. planar arrays of four guanines connected by eight hydrogen bonds and coordinating cations such as K+ and Na+. G4s are remarkably polymorphic structures, which enables them to participate in various biological processes and find applications in nanotechnology. The development of simple and rapid assays to better understand how and when G4s form remains very important. Here, we present Eps2Fold (Epsilon-to-Fold), a method for detection and characterization of G4 conformations by simply measuring a single UV-absorbance spectrum. Eps2Fold is conceptually similar to isothermal differential spectra or thermal differential spectra but is generated by the subtraction of an experimentally recorded UV absorbance spectrum of the G4 in its folded state and a calculated UV absorbance spectrum that mimics the G4 in its unfolded state. Through comprehensive biophysical and principal component analysis (PCA) analysis of thirty G4-forming oligonucleotides, we demonstrate that Eps2Fold provides spectral signatures with unexpectedly high structural resolution remarkably similar to that obtained with circular dichroism spectra. Both techniques allow precise topology assignment based on the number and composition of stacked syn or anti guanines glycosidic bond angle stacks. The spectral differences between conformers are subtle and best analyzed using multivariate statistical approaches such as PCA rather than visual inspection alone. We provide an open-source GUI program to facilitate such analysis. Users simply upload the UV absorbance spectrum of the G4 on the web application (https://github.com/EricLarG4/Eps2Fold); structural analysis will run automatically. Eps2Fold represents a rapid and inexpensive structural approach enabling precise characterization of G4 structures from a single UV absorbance spectrum.