Oligonucleotide Binding to Non-B-DNA in MYC

Area of Science:

• Molecular Biology
• Genetics
• Oncology

Background:

• The MYC oncogene is frequently deregulated in cancers, notably Burkitt's lymphoma (BL) due to translocations.
• Specific translocation sites in sporadic BL occur near MYC promoters P1 and P2, involving non-B-DNA forming sequences.
• These sequences can form structures like intramolecular triplexes (H-DNA) or G-quadruplexes.

Purpose of the Study:

• To investigate triplex formation at a specific non-B-DNA forming site in the MYC promoter region.
• To explore the potential therapeutic implications of targeting non-B-DNA structures.
• To determine the influence of non-B-DNA formation on anti-gene oligonucleotide (ON) strand invasion.

Main Methods:

• Electrophoretic mobility shift assay (EMSA) using a triplex-forming oligonucleotide (TFO) and MYC dsDNA target.
• BQQ-OP based triplex-specific cleavage assay to detect H-DNA formation in supercoiled plasmids.
• In vitro assays to assess the effect of non-B-DNA formation on anti-gene ON strand invasion.

Main Results:

• An antiparallel purine-motif triplex was detected at the MYC sequence using EMSA.
• H-DNA formation was confirmed in the MYC promoter region using the BQQ-OP assay.
• Non-B-DNA formation was shown to facilitate the strand invasion of anti-gene oligonucleotides in vitro.

Conclusions:

• Non-B-DNA structures, including H-DNA, can form in the vicinity of the MYC gene.
• The formation of these structures enhances the binding of anti-gene oligonucleotides.
• Targeting these non-B-DNA structures represents a promising strategy for developing novel anti-cancer therapies.