A deoxyribozyme with a novel guanine quartet-helix pseudoknot structure

Area of Science:

• Molecular Biology
• Biochemistry
• Structural Biology

Background:

• Deoxyribozymes are catalytic DNA molecules with diverse functions.
• Guanine quadruplexes are non-canonical DNA structures with significant biological roles.
• Understanding complex nucleic acid structures is crucial for molecular biology.

Purpose of the Study:

• To characterize a novel deoxyribozyme with a unique structural motif.
• To investigate the interplay between guanine quadruplexes and helical regions in a deoxyribozyme.
• To report the first instance of a pseudoknot structure involving a guanine quadruplex.

Main Methods:

• In vitro selection and sequence mutation were employed to identify and validate the active deoxyribozyme structure.
• Methylation interference assays were used to pinpoint critical guanine residues.
• Circular dichroism spectroscopy analyzed the formation and stability of the guanine quadruplex.

Main Results:

• A self-phosphorylating deoxyribozyme was identified, possessing a unique structure comprising a two-tiered guanine quadruplex linked to a Watson-Crick duplex.
• The active structure includes two helical regions, with one GG element of the quadruplex integrated into a hairpin loop within a helix.
• Antiparallel quadruplex formation was demonstrated to be dependent on the integrity of this helix.

Conclusions:

• This study reports the first pseudoknot nucleic acid structure incorporating a guanine quadruplex.
• The findings demonstrate that guanine quadruplexes can be integral components of complex structural arrangements.
• This expands the known structural diversity of guanine quadruplexes and suggests their potential involvement in more intricate biological systems.