Research Projects

G-quadruplexes (G4s) are polymorphic systems formed by guanosine rich nucleic acid sequences. Unlike proteins where reliable primary sequence to tertiary structure prediction exists, G4s lack such an approach as their structure depends upon numerous factors. For instance, subtle changes in the primary sequence could result in altered topology, as seen in the case of telomeric G4 DNA. In cases where the sequence remains the same, changes in buffer conditions (e.g., sodium to potassium) alter the fold of G4s. As G4s are implicated in many biological functions and contexts, approaches that can reliably and rapidly predict their conformations from the primary sequence are required. To achieve this, the factors that drive G4 folding need to be charted, akin to the protein folding problem tackled for the past 50 years. Recently, our group has established NMR chemical shifts and machine learning-based methodology for characterising the topology of G4s. In this proposal, we shall strive to further the frontiers of the sequence-structure paradigm and also extend it to the sequence-dynamics paradigm. In this project, we aim to determine the significant factors that alter the structure and conformational dynamics of G4s. In particular, we will begin the proposal by investigating the role of hydrogen (H-)bonds and sugar puckering on the stability and flexibility of G4s. Following this, we aim to understand how subtle changes in the terminal and loop nucleotide sequences influence the conformational plasticity of G4s. In addition to characterising them at thermal equilibrium, we will monitor the real-time refolding of a model G4 system to obtain an atomistic understanding of the factors that drive folding. To this end, we shall apply high-resolution solution-state NMR spectroscopy, circular dichroism and classical molecular dynamics simulations.