The Transition from Unfolded to Folded G‑Quadruplex DNA Analyzed and Interpreted by Two-Dimensional Infrared Spectroscopy

A class of DNA folds/structures
known collectively as
G-quadruplexes
(G4) commonly forms in guanine-rich areas of genomes. G4-DNA is thought
to have a functional role in the regulation of gene transcription
and telomerase-mediated telomere maintenance and, therefore, is a
target for drugs. The details of the molecular interactions that cause
stacking of the guanine-tetrads are not well-understood, which limits
a rational approach to the drugability of G4 sequences. To explore
these interactions, we employed electron-vibration-vibration two-dimensional
infrared (EVV 2DIR) spectroscopy to measure extended vibrational coupling
spectra for a parallel-stranded G4-DNA formed by the Myc2345 nucleotide
sequence. We also tracked the structural changes associated with G4-folding
as a function of K+-ion concentration. To classify the
structural elements that the folding process generates in terms of
vibrational coupling characteristics, we used quantum-chemical calculations
utilizing density functional theory to predict the coupling spectra
associated with given structures, which are compared against the experimental
data. Overall, 102 coupling peaks are experimentally identified and
followed during the folding process. Several phenomena are noted and
associated with formation of the folded form. This includes frequency
shifting, changes in cross-peak intensity, and the appearance of new
coupling peaks. We used these observations to propose a folding sequence
for this particular type of G4 under our experimental conditions.
Overall, the combination of experimental 2DIR data and DFT calculations
suggests that guanine-quartets may already be present before the addition
of K+-ions, but that these quartets are unstacked until
K+-ions are added, at which point the full G4 structure
is formed.