Triplex formation by oligonucleotides containing novel deoxycytidine derivatives

Area of Science:

• Molecular Biology
• Biochemistry
• Chemical Biology

Background:

• Homopurine sequences in duplex DNA serve as recognition sites for triplex-forming oligodeoxyribopyrimidines.
• Understanding specific base-pair interactions is crucial for developing targeted nucleic acid technologies.

Purpose of the Study:

• To investigate the binding interactions of a synthetic oligodeoxyribopyrimidine containing a modified nucleoside (1) with duplex DNA targets.
• To characterize the selectivity and structural basis of triplex formation involving nucleoside 1.

Main Methods:

• UV melting analysis to assess triplex stability.
• Circular dichroism (CD) spectroscopy to evaluate structural changes upon triplex formation.
• Dimethylsulfate alkylation experiments to probe base accessibility within the triplex.

Main Results:

• Nucleoside 1 supports stable triplex formation at pH 7.0, forming a 1-Y-Z triad with target DNA.
• Selective interaction was observed with C-G base pairs, although other base pairs (A-T, T-A, G-C) were also recognized to varying extents.
• CD spectra indicated structural similarity between triplexes formed with 1-C-G and C(+)-G-C triads.
• Removal of the 6-amino group from nucleoside 1 abolished triplex formation.
• Dimethylsulfate alkylation experiments showed protection of the G residue in a 1-C-G triad, suggesting its involvement in binding.

Conclusions:

• The modified nucleoside 1 selectively binds to C-G base pairs in homopurine DNA sequences, forming stable triplex structures.
• The 6-amino-2-pyridinyl group of nucleoside 1 likely interacts with the major groove of the DNA duplex, forming hydrogen bonds with guanine (G) and cytosine (C).
• These findings provide insights into the design of novel nucleosides for specific DNA recognition and potential therapeutic applications.