The analysis of the recorded chromatograms at just one single wavelength may not always be enough to confirm the existence of a higher order structure. In these cases, recording the entire spectrum at each point of the chromatogram and applying appropriate chemometric resolution methods has shown to be a useful tool to resolve and quantify the contribution of all DNA structures to the analytical signal. In this work, the Multivariate Curve Resolution based on Alternating Least Squares (MCR-ALS) has been used to analyze the three-way data sets acquired along chromatographic runs.