pH-dependent structures of an i-motif DNA in solution

Area of Science:

• Biochemistry
• Structural Biology
• Biophysics

Background:

• The i-motif DNA structure is a four-stranded DNA secondary structure.
• It is known to form under acidic conditions and is implicated in various biological processes.
• Its application in DNA nanotechnology, particularly in nanomachines, necessitates a thorough understanding of its structural behavior.

Purpose of the Study:

• To elucidate the solution structure of i-motif DNA across a range of pH conditions.
• To provide atomic models for direct comparison of i-motif DNA conformations at different pH values.
• To investigate the structural dynamics and conformational flexibility of i-motif DNA.

Main Methods:

• Synchrotron small-angle X-ray scattering (SAXS) was employed to study i-motif DNA structure in solution.
• Atomic coordinates of i-motif DNA were generated, ranging from fully folded to unfolded models.
• Structural analysis was performed under various pH conditions, with a focus on mild acidic environments.

Main Results:

• i-motif DNA exhibits conformational flexibility across a wide pH range.
• Under mild acidic conditions, the solution structure resembles a partially unfolded i-motif model.
• The molecule transitions between folded i-motif structures and random coil conformations.

Conclusions:

• i-motif DNA is structurally dynamic and adopts multiple conformations depending on pH.
• The observed structural plasticity is vital for its function in DNA-based nanomachines.
• This research provides foundational structural evidence to advance the development of DNA-based molecular-actuator devices.