Oligonucleotides Containing Phenoxazine Artificial Nucleobases: Triplex-Forming Abilities and Fluorescence Properties

Area of Science:

• Molecular Biology
• Biochemistry
• Chemical Biology

Background:

• Phenoxazine, a cytosine analogue, enhances DNA duplex stability through guanine binding and π-π stacking.
• Its utility in improving duplex-forming abilities is well-established.
• The potential of phenoxazine and its analogue, 9-triaza-2-oxophenoxazine (9-TAP), in DNA triplex formation remains unexplored.

Purpose of the Study:

• To investigate the efficacy of phenoxazine and 9-TAP in forming DNA triplex structures.
• To determine the base-pairing behavior of these modified nucleobases within triplex DNA.
• To explore the potential of 9-TAP as a fluorescent probe in oligonucleotide nanotechnologies.

Main Methods:

• Synthesis and incorporation of phenoxazine and 9-TAP into triplex-forming oligonucleotides (TFOs).
• Assessment of binding affinities of modified TFOs with double-stranded DNA targets.
• Evaluation of base-pairing interactions within parallel triplex DNA motifs.

Main Results:

• Phenoxazine-containing TFOs exhibited reduced binding affinity, indicating it does not mimic protonated cytosine or thymine in triplexes.
• The 9-TAP analogue functioned effectively as a thymine analogue in parallel triplex DNA formation with AT base pairs.
• The fluorescence of the 9-TAP moiety was retained upon triplex formation (9-TAP:AT).

Conclusions:

• Phenoxazine is unsuitable for enhancing DNA triplex formation.
• 9-TAP acts as a functional thymine analogue in parallel triplex DNA.
• 9-TAP holds promise as a fluorescent imaging agent for triplex-based oligonucleotide nanotechnologies.