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

Robby Fritzsch, Paul M. Donaldson, Gregory M. Greetham, Michael Towrie, Anthony W. Parker, Matthew J. Baker, Neil T. Hunt

Research output: Contribution to journalArticle

6 Citations (Scopus)
20 Downloads (Pure)

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.
Original languageEnglish
Pages (from-to)2732-2740
Number of pages9
JournalAnalytical Chemistry
Volume90
Issue number4
Early online date23 Jan 2018
DOIs
Publication statusPublished - 20 Feb 2018

Keywords

  • infrared spectroscopy
  • 2D-IR
  • DNA
  • proteins
  • two-dimensional infrared

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