Formation and structural determinants of multi-stranded guanine-rich DNA complexes

Area of Science:

• Biochemistry
• Molecular Biology
• Nucleic Acid Chemistry

Background:

• Guanine-rich sequences are known to form non-canonical DNA structures.
• Oligonucleotides can self-assemble into various complex architectures.
• Understanding these structures is crucial for fields like epigenetics and therapeutics.

Purpose of the Study:

• To investigate the structural diversity of d(T15,Gn) oligonucleotides.
• To elucidate the factors controlling the formation of distinct guanine-rich complexes.
• To characterize the differences between tetraplex and frayed wire structures.

Main Methods:

• Synthesis of oligonucleotides with varying lengths of contiguous guanine repeats (n=4-15).
• Structural analysis of formed complexes, including strand stoichiometry.
• Dimethyl sulfate (DMS) footprinting to assess guanine N7 accessibility.

Main Results:

• Two distinct structures, four-stranded tetraplexes and frayed wires, were identified.
• Oligonucleotides with fewer contiguous guanines (n=5-8) predominantly form tetraplexes.
• Oligonucleotides with more contiguous guanines (n>8) primarily form frayed wires.
• Frayed wires exhibit different strand stoichiometry and N7 guanine accessibility compared to tetraplexes.
• The number and arrangement of guanines are key determinants of complex stability.

Conclusions:

• The number of contiguous guanine residues dictates the formation of either tetraplex or frayed wire structures.
• These two guanine-rich assemblies are stabilized by distinct guanine-guanine interactions.
• Complex formation likely proceeds via parallel pathways with potentially shared intermediates.