Does Raman spectroscopy recognize different G-quadruplex arrangements?

In this work, we demonstrate the underused potential of Raman spectroscopy in detecting formation of DNA G-quadruplex (G4) and differentiating between various G4-folding topologies. As model structures, we used a 22-mer human telomere fragment AG3(TTAG3)3 (denoted here as wt) and its two variants with adenine abasic lesions at the position 19 (ap19) or at the positions 7, 13, and 19 (ap7-13-19), the structures of which were previously characterized. These oligonucleotides adopt three basic G4-folds: a basket-type form for wt in Na+, a (3+1) hybrid form for ap19 in K+, and a parallel G4 for ap7-13-19 in K+, the last one furthermore stabilized at increased temperatures. We show that although wt and ap7-13-19 in Na+ adopt predominately antiparallel G4-folds, these oligonucleotides in K+ display several Raman features of parallel G4 folds. Interestingly, ap19 has a Raman spectrum with some features of parallel G4 folds in both Na+ and K+ solutions. Raman signals indicative of parallel G4 are most obvious with ap7-13-19 in K+. The population of ap7-13-19 guanosines (unlike of wt and ap19 in K+) in the C2'-endo/anti geometry gradually increases with increasing temperature, reaching its maximum at ~50°C, where an all-parallel topology is observed. In summary, Raman spectroscopy has been proven to distinguish between different conformational properties of G4-DNA structures, with reliability comparable with circular dichroism spectra, and with the potential to provide additional structural information.