Intra-locked G-quadruplex structures formed by irregular DNA G-rich motifs

Area of Science:

• Structural Biology
• Biochemistry
• Genomics

Background:

• G-rich DNA sequences with G≥3 tracts form stable G-quadruplex (G4) structures.
• Human genome analysis indicates a high prevalence of G-rich sequences with shorter G-tracts (G≤2).
• Structural understanding of G4 formation from short G-tracts remains limited.

Purpose of the Study:

• To elucidate the folding principles and structural characteristics of G-quadruplexes formed from sequences with short G-tracts.
• To present the solution NMR structure of the AT26 sequence, which contains irregularly spaced G2 tracts and single guanines.

Main Methods:

• Solution Nuclear Magnetic Resonance (NMR) spectroscopy was employed to determine the three-dimensional structure.
• Bioinformatic analyses were used to identify the prevalence of G-rich sequences in the human genome.

Main Results:

• The AT26 sequence forms a stable four-layered G4 structure with two bi-layered blocks locked together.
• Novel structural features include two V-shaped loops: a 2-nt VS-loop and a 0-nt VR-loop.
• An intra-lock motif was identified, suggesting a basis for extending the G-tetrad core.

Conclusions:

• G-quadruplexes can form stable structures from sequences with irregularly spaced short G-tracts, including G2 tracts.
• The findings provide a foundation for understanding G4 folding from diverse G-tract compositions.
• This work contributes to understanding the structural diversity and stability of G-quadruplex topologies.