Oral 23rd International Society of Magnetic Resonance Conference 2023
Mapping the conformational flexibility of DNA G-quadruplexes - Influence of polymorphism and implications on biological functions (#38)
G-quadruplexes (G4s) are formed by guanosine (G-)rich nucleic acid sequences. The polymorphic nature of DNA G4s allows a given primary sequence to sample a wide range of structures. For instance, the human telomeric (GGGTTA)n repeat can form ~26 different structures! Such diversity affords G4s the ability to perform numerous functions in the biological context.
In addition to the structure-function paradigm in molecular biophysics, the past decade has unraveled the role of conformational flexibility toward biomolecular function. For instance, Watson-Crick base-pairs sample a lowly populated (~1%) Hoogsteen pairs in the duplex context, which provide additional functional relevance to the double helix than previously attributed. In the case of RNA, such sparsely populated states open avenues to their selective targeting with drugs. Remarkably, although implicated in many diseases, the characterization of conformational dynamics of DNA G4s has remained unexplored. In this talk, I shall summarise the efforts to map the same using structure survey, NMR chemical shifts, residual dipolar couplings (RDCs), and nuclear spin-relaxation measurements in conjunction with molecular dynamics simulations across all backbone topologies.
Summary of results:
1) NMR chemical shifts are excellent reporters of the tertiary structure of G4s.
2) We developed a machine-learning protocol for the semi-automated assignment of chemical shifts.
3) PDB structure survey unravels unique conformational preferences within G4 topologies, validated with NMR chemical shifts and RDCs.
4) Relaxation measurements directly correlate the glycosyl dihedral angle and the conformational fluctuations.
5) The conformational fluctuations observed in the terminal ends of the G4 suggest the ability to accommodate a duplex on the 5'-/3'-ends - which provides cues toward drug binding, intermolecular stacking, and enzyme activity.
The overall picture emerges where the G-tetrad provides the scaffold for the loop nucleotides to sample necessary conformations to aid in biomolecular transactions, such as protein binding.
