Communication: Polarization-angle-scanning two-dimensional infrared spectroscopy of antiparallel β-sheet polypeptide: Additional dimensions in two-dimensional optical spectroscopy

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 the polarization dependences of 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.

Structure analysis of substrate catalyst complexes in mixtures with ultrafast two-dimensional infrared spectroscopy

The understanding of reaction mechanisms requires structure elucidation of short-lived intermediates, even in the presence of other, similar structures. Here we show that polarization dependent two-dimensional infrared spectroscopy is a powerful method to determine the structure of molecules that participate in fast equilibria, in a regime where standard techniques such as nuclear magnetic resonance spectroscopy are beyond their limits. Using catalyst-substrate complexes in a Lewis acid catalyzed enantioselective Diels-Alder reaction as an example we present two methods that allow the resolution of molecular structure in mixtures even when the spectroscopic signals partially overlap. The structures of N-crotonyloxazolidin-2-one, a reactant carrying the Evans auxiliary, and its complex with the Lewis acid SnCl(4) were determined in a mixture as used under the typical reaction conditions. In addition to the chelate that mainly forms, three additional substrate-catalyst complexes were detected and could be tentatively assigned. Observation of minor complex conformers suggests a rationale for the observed diastereoselectivity of the reaction using SnCl(4) as compared to other Lewis acids. Knowledge about additional species may lead to a better understanding of the different selectivities for various Lewis acids and allow reaction optimization.