DNA duplexes and triplex-forming oligodeoxynucleotides incorporating modified nucleosides forming stable and...

Area of Science:

• Synthetic biology
• Nucleic acid chemistry
• Biochemistry

Background:

• Previous work established DNA triplexes with G-PPI·C3 unnatural base triads.
• PPI is an indole-fused cytosine derivative, and C3 is an abasic site in triplex-forming oligonucleotides (TFOs).

Purpose of the Study:

• To develop a new unnatural base triad A-ψ·C(R1) for DNA triplex formation.
• To investigate selective recognition between modified bases and TFOs.
• To achieve selective triplex formation with various DNA duplexes.

Main Methods:

• Synthesis of 2'-deoxypseudouridine (ψ) and 5-substituted deoxycytidine (C(R1)) bases.
• Examination of electron-withdrawing substituents for R1, identifying 5-bromocytosine (C(Br)).
• Development of a new PPI derivative, PPI(Me).
• UV-melting and gel mobility shift assays to study triplex formation.

Main Results:

• Identified 5-bromocytosine (C(Br)) for selective recognition of ψ.
• Developed PPI(Me) for selective triplex formation with various DNA duplexes (T-A, C-G, A-ψ, G-PPI(Me)) and TFOs (T, C, C(Br), C3).
• Demonstrated selective triplex formation using biophysical assays.

Conclusions:

• Successfully developed novel unnatural base triads for DNA triplex formation.
• Achieved selective base pairing and enhanced stability in DNA triplexes.
• These findings advance the design of synthetic nucleic acid structures.