Three pyrene-modified nucleotides: synthesis and effects in secondary nucleic acid structures

Area of Science:

• Biochemistry
• Organic Chemistry
• Molecular Biology

Background:

• Nucleoside modifications are crucial for developing novel nucleic acid functionalities.
• Pyrene's fluorescent properties make it a valuable probe for studying nucleic acid structures and interactions.

Purpose of the Study:

• To synthesize pyrene-modified nucleosides using click chemistry.
• To investigate the impact of pyrene's position and linker type on oligonucleotide secondary structures.
• To evaluate the potential of these modified oligonucleotides as recognition probes.

Main Methods:

• Copper(I)-catalyzed alkyne-azide cycloaddition (CuAAC) reaction for nucleoside synthesis.
• Incorporation of modified nucleosides into oligonucleotides.
• Thermal stability assays (melting temperature).
• Fluorescence spectroscopy (intensity and excimer formation).

Main Results:

• Different pyrene modifications (5'-thymidine, 2'-deoxyuridine with triazolemethylene or rigid triazole linkers) were successfully synthesized.
• Pyrene's position and linker significantly affected oligonucleotide duplex stability and fluorescence.
• Pyrene at the 5'-position and 2'-position with a rigid linker tended to intercalate, while the 2'-position with a triazolemethylene linker favored minor groove binding.
• All modifications stabilized bulged duplexes and three-way junctions.
• Fluorescence changes, including excimer formation, indicated hybridization events.

Conclusions:

• The position and linker of pyrene modifications critically influence oligonucleotide structure and stability.
• Pyrene-modified oligonucleotides can serve as sensitive probes for detecting hybridization and specific nucleic acid structures.
• This work provides a foundation for designing novel nucleic acid-based sensors and functional materials.