The Polarization Dependence of 2D IR Cross-Peaks Distinguishes Parallel-Stranded and Antiparallel-Stranded DNA G-quadruplexes

Guanine-rich nucleic acid sequences have a tendency to form four-stranded non-canonical motifs known as G-quadruplexes. These motifs may adopt a wide range of structures characterized by size, strand orientation, guanine base conformation, and fold topology. Using three K+-bound model systems, we show that vibrational coupling between guanine C6=O and ring modes varies between parallel-stranded and antiparallel-stranded G-quadruplexes, and that such structures can be distinguished by comparison of polarization dependent cross-peaks in their two-dimensional infrared (2D IR) spectra. Combined with previously defined vibrational frequency trends, this analysis reveals key features of a 30-nucleotide unimolecular variant of the Bcl-2 proximal promoter that are consistent with its reported structure. This study shows that 2D IR spectroscopy is a convenient method for analyzing G-quadruplex structures that can be applied to complex sequences where traditional high-resolution methods are limited by solubility and disorder.

Infrared Hide-and-Seek: Vibrational Excitons Conceal Surfactants at the Air/Water Interface

<p>Surface-sensitive vibrational spectroscopy is a common tool for measuring molecular organization and intermolecular interactions at interfaces. Peak intensity ratios are typically used to extract molecular information from one-dimensional spectra but vibrational coupling between surfactant molecules can manifest as signal depletion in one-dimensional spectra. Through a combination of experiment and theory, we demonstrate the emergence of vibrational excitons in infrared reflection-absorption spectra of soluble and insoluble surfactants at the air/water interface. Vibrational coupling yields a signicant decrease in peak intensities corresponding to C-F vibrational modes of perfluorooctanoic acid molecules. Vibrational excitons also form between arachidic acid surfactants within a compressed monolayer, manifesting as signal reduction of C-H stretching modes. The aqueous phase ionic composition impacts surfactant intermolecular distances, thereby modulating vibrational coupling strength between surfactants. Our results serve as a cautionary tale against employing alkyl and fluoroalkyl vibrational peak intensities in analyses that are ubiquitous in interface science.</p>