LNA effects on DNA binding and conformation: from single strand to duplex and triplex structures

Area of Science:

• Molecular Biology
• Biochemistry
• Drug Design

Background:

• The anti-gene strategy utilizes oligonucleotides (ONs) for sequence-specific DNA recognition to modulate gene expression.
• Efficient ONs require selective targeting and high affinity for DNA structures like duplexes and triplexes.

Purpose of the Study:

• To investigate the structural features of modified ONs that stabilize DNA duplex and triplex structures.
• To understand the role of locked nucleic acid (LNA) substitutions in ONs targeting c-MYC or FXN sequences.

Main Methods:

• Hybridization analysis
• Electrophoretic mobility shift assay (EMSA)
• Molecular dynamics (MD) simulations

Main Results:

• LNA-containing single-strand triplex-forming oligonucleotides (TFOs) are pre-organized for major groove binding.
• LNA content and placement at the 3'-end of TFOs influence triplex stability; Twisted Intercalating Nucleic Acid (TINA) enhances formation.
• A benzoquinoquinoxaline (BQQ) compound stabilizes LNA-containing triplexes.
• LNA substitution in the duplex pyrimidine strand favors triplex formation by altering DNA helix geometry.

Conclusions:

• Findings provide insights into designing potent anti-gene ONs by optimizing LNA modifications and incorporating intercalating agents.
• Strategic LNA substitution and TINA incorporation can enhance TFO binding affinity and triplex stability for gene regulation applications.