Synthesis and triplex formation of oligonucleotides containing 8-thioxodeoxyadenosine

Area of Science:

• Biochemistry
• Molecular Biology
• Organic Chemistry

Background:

• DNA triplexes are important for gene targeting and regulation.
• Traditional DNA triplex formation often requires specific pH conditions (acidic) due to the protonation of cytosine bases.
• Developing methods for stable DNA triplex formation under neutral conditions is crucial for broader biological applications.

Purpose of the Study:

• To synthesize and evaluate novel triplex-forming oligonucleotides (TFOs) capable of stable formation under neutral pH.
• To investigate the hybridization efficiency of modified nucleosides in TFOs for enhanced DNA binding.

Main Methods:

• Synthesis of TFOs incorporating 8-thioxodeoxyadenosine (s(8)dA) residues.
• Evaluation of DNA triplex formation and stability using biophysical techniques.
• Comparison of hybridization ability of s(8)dA-containing TFOs with standard deoxycytidine (dC)-containing TFOs under neutral conditions.

Main Results:

• Successfully synthesized TFOs containing 8-thioxodeoxyadenosine (s(8)dA) residues.
• Demonstrated that s(8)dA can replace protonated deoxycytidines for third-strand binding in DNA triplexes under neutral conditions.
• Observed significantly stronger hybridization ability of TFOs with consecutive s(8)dA sequences compared to dC under neutral conditions.

Conclusions:

• 8-thioxodeoxyadenosine (s(8)dA) is a viable alternative to deoxycytidine for achieving effective DNA triplex formation at neutral pH.
• The enhanced hybridization ability of s(8)dA-containing TFOs opens new possibilities for DNA-based technologies requiring stable triplex structures under physiological conditions.