Probing the stable G-quadruplex transition using quencher-free end-stacking ethynyl pyrene-adenosine

Area of Science:

• Biochemistry
• Molecular Biology
• Oligonucleotide Chemistry

Background:

• G-rich oligodeoxynucleotides can form G-quadruplex structures.
• Pyrene modifications can be used as fluorescent probes in nucleic acid studies.
• Understanding structural transitions in G-rich sequences is crucial for various biological processes.

Purpose of the Study:

• To investigate the pi-stacking behavior of pyrene-modified adenosines in G-rich oligodeoxynucleotides.
• To determine if pyrene modifications exhibit different stacking interactions in single-stranded versus G-quadruplex forms.
• To explore the utility of fluorescence spectroscopy for characterizing these structural changes.

Main Methods:

• Synthesis of G-rich oligodeoxynucleotides with pyrene-modified adenosines at dangling positions.
• Spectroscopic analysis using fluorescence spectroscopy to monitor changes in pyrene fluorescence.
• Comparison of fluorescence properties in single-stranded and G-quadruplex conformations.

Main Results:

• Pyrene-modified adenosines exhibit pi-stacking interactions specifically within the G-quadruplex structures.
• No significant pi-stacking of pyrene modifications was observed in the single-stranded oligodeoxynucleotides.
• A distinct shift in fluorescence emission maximum (lambda(max)) was observed upon G-quadruplex formation, correlating with pyrene stacking.

Conclusions:

• Pyrene modifications serve as effective probes for detecting G-quadruplex formation via pi-stacking.
• Fluorescence spectroscopy can reliably characterize the structural transitions and stacking interactions in G-rich sequences.
• This study provides insights into the structural dynamics of G-quadruplexes and their modified analogues.