Rapid screening of DNA-ligand complexes via 2D-IR spectroscopy and ANOVA-PCA

Fritzsch, Robby and Donaldson, Paul M. and Greetham, Gregory M. and Towrie, Michael and Parker, Anthony W. and Baker, Matthew J. and Hunt, Neil T. (2018) Rapid screening of DNA-ligand complexes via 2D-IR spectroscopy and ANOVA-PCA. Analytical Chemistry, 90 (4). pp. 2732-2740. ISSN 0003-2700

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    Abstract

    Two-dimensional infrared spectroscopy is well-established as a specialized, high-end technique for measuring structural and solvation dynamics of biological molecules. Recent technological developments now make it possible to acquire time-resolved 2D-IR spectra within seconds and this opens up the possibility of screening-type applications comparing large datasets spanning multiple samples. However, such applications bring new challenges associated with finding accurate, efficient methodologies to analyze the large datasets in a timely, informative manner. Here, we demonstrate such an application by screening 1728 2D-IR spectra of 12 double-stranded DNA oligonucleotides obtained in the presence and absence of minor groove binding therapeutic molecule Hoechst 33258. By applying analysis of variance combined with principal component analysis (ANOVA-PCA) we demonstrate the ability to efficiently retrieve the base composition of a DNA sequence and discriminate ligand-DNA complexes from unbound sequences. We further show accurate differentiation of the induced fit and rigid-body binding modes that is key to identifying optimal binding interactions of Hoechst 33258, while ANOVA-PCA results across the full sequence range correlate directly with thermodynamic measurements of ligand-binding strength that require significantly longer data acquisition times.