Nucleic acid-binding molecules with high affinity and base sequence specificity: intercalating agents covalently...

Area of Science:

• Chemical Biology
• Molecular Biology
• Biochemistry

Background:

• Oligonucleotides are key molecules in molecular biology, but their binding specificity can be enhanced.
• Intercalating agents are known to interact with DNA, potentially modifying its properties.

Purpose of the Study:

• To synthesize and characterize novel oligodeoxyribonucleotides covalently linked to an intercalating agent.
• To investigate the sequence-specific binding interactions and thermodynamic stability of these hybrid molecules.

Main Methods:

• Synthesis of oligothymidylates covalently attached to an acridine dye via a polymethylene linker.
• Absorption and fluorescence spectroscopy to study complex formation with complementary sequences (poly(rA)).
• Thermodynamic analysis to quantify binding affinity and cooperative interactions.

Main Results:

• The synthesized hybrid molecules [(Tp)n(CH2)mAcr] specifically bind to complementary sequences, forming n A X T base pairs.
• The acridine moiety intercalates between base pairs, significantly stabilizing the complex.
• Binding stability is dependent on linker length (m), with m=5 showing greater stability than m=3.

Conclusions:

• Covalent attachment of an intercalating agent to oligonucleotides enhances binding affinity and specificity.
• Linker length is a critical factor in modulating the stability of these DNA-drug complexes.
• These findings pave the way for designing molecules with tailored recognition of specific nucleic acid sequences.