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

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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 (https://doi.org/10.1021/acs.analchem.7b04727)

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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.

ORCID iDs

Fritzsch, Robby ORCID logoORCID: https://orcid.org/0000-0003-0198-1691, Donaldson, Paul M., Greetham, Gregory M., Towrie, Michael, Parker, Anthony W., Baker, Matthew J. ORCID logoORCID: https://orcid.org/0000-0003-2362-8581 and Hunt, Neil T. ORCID logoORCID: https://orcid.org/0000-0001-7400-5152;
CORE (COnnecting REpositories)