Mixed deoxyribo- and ribo-oligonucleotides with catalytic activity

Area of Science:

• Biochemistry
• Molecular Biology
• RNA Catalysis

Background:

• Catalytic RNAs, known as ribozymes, can self-cleave to form specific RNA termini.
• Hammerhead ribozymes, characterized by a stem-loop structure, bring catalytic and substrate sequences together for this cleavage.
• Previous studies using ribonucleotide substitutions in hammerhead analogues altered their conformation, complicating mechanistic studies.

Purpose of the Study:

• To investigate the role of specific 2 eal;-OH groups in hammerhead ribozyme activity.
• To explore the impact of structural modifications on hammerhead ribozyme conformation and function.
• To determine if nucleic acid-type catalysis is exclusive to RNA.

Main Methods:

• Synthesis of mixed RNA-DNA hammerhead analogues by substituting deoxyribonucleotides for ribonucleotides.
• Utilizing a chemical synthesis strategy compatible with both RNA and DNA synthesis.
• Analyzing cleavage products of these analogues to assess catalytic activity and identify key residues.

Main Results:

• Confirmed the involvement of the 2 eal;-OH group adjacent to the cleavage site in the substrate.
• Demonstrated that certain 2 eal;-OH groups within the catalytic region significantly influence hammerhead ribozyme activity.
• Showed that structurally less-disrupted hammerhead analogues can be synthesized using mixed RNA-DNA polymers.

Conclusions:

• The 2 eal;-OH groups play crucial roles in hammerhead ribozyme catalysis and structure-activity relationships.
• Nucleic acid-type catalysis is not exclusively confined to RNA, as evidenced by the function of mixed RNA-DNA analogues.
• This research provides insights into the mechanism of hammerhead ribozymes and the broader potential of nucleic acid catalysis.