Inverted strand polarity yields thermodynamically stable G-quadruplexes and prevents duplex formation within extended...

Area of Science:

• Biochemistry
• Molecular Biology
• Structural Biology

Background:

• DNA G-quadruplexes (G4) are crucial for genome stability but challenging to study due to their transient nature and tendency to form duplexes.
• G-rich DNA typically favors duplex formation over G4 structures, hindering structural and functional investigations.

Purpose of the Study:

• To develop a method for stabilizing DNA G-quadruplexes (G4) for structural and functional studies.
• To investigate the impact of internal polarity inversions on G4 formation and stability.

Main Methods:

• Incorporation of native nucleotides with inverted 3'-O-DMT-5'-O-phosphoramidites to create 3'-3' and 5'-5' linkages within G-rich sequences.
• Utilized circular dichroism, 1H nuclear magnetic resonance spectroscopy, and native gel electrophoresis to analyze G4 structures.
• Assessed G4 stability in the presence of complementary DNA and evaluated binding to Heterochromatin Protein 1α (HP1α).

Main Results:

• Demonstrated that polarity-inverted DNA sequences form stable parallel G-quadruplexes with defined loop structures.
• Confirmed G4 stability even when complementary C-rich DNA is present.
• Showcased binding of these inverted G4s to the Heterochromatin Protein 1α (HP1α) hinge region.

Conclusions:

• Internal polarity inversions in DNA are a valuable tool for controlling G4 topology and stability.
• This strategy facilitates the study of G4s and their interactions with proteins, overcoming limitations of canonical DNA structures.
• Polarity-inverted G4s can be used to probe protein-G4 interactions, such as with HP1α.