Rational design of guiding elements to control folding topology in i-motifs with multiple quadruplexes

Area of Science:

• Molecular Biology
• Biophysics
• Nanotechnology

Background:

• Nucleic acids are versatile macromolecules with tunable properties for various applications.
• Precise control over DNA folding is crucial for designing molecular devices like sensors and computing elements.
• Existing methods lack precise control over complex folding topologies, especially for multiple quadruplex structures.

Purpose of the Study:

• To develop a novel approach for precise folding of multiple DNA quadruplexes (i-motifs) within a single oligonucleotide.
• To demonstrate the ability to guide DNA folding towards specific, targeted topologies.
• To enable rational design of sophisticated DNA-based molecular devices.

Main Methods:

• Modification of DNA strands with kinetic control elements (hairpins and double-stranded stems).
• Utilizing elements that fold on a faster timescale to direct quadruplex formation.
• Characterization using thermodynamic techniques, Size Exclusion Chromatography (SEC), and Small-Angle X-ray Scattering (SAXS).
• Advanced SAXS analysis to compute electron density maps for shape and dimension insights.

Main Results:

• Successfully demonstrated precise folding of multiple i-motif structures within one DNA strand.
• Kinetic control elements effectively guided the DNA towards the targeted folding topology.
• Thermodynamic and scattering data confirmed the formation and stability of desired folded structures.
• SAXS provided direct visualization of the shape and dimensions of the folded DNA quadruplexes.

Conclusions:

• The developed method offers precise control over DNA conformational transitions.
• This approach facilitates the rational design and construction of complex DNA molecular devices.
• The findings open new avenues for advanced nanotechnology and molecular computing applications.