Quinolone-DNA interaction: sequence-dependent binding to single-stranded DNA reflects the interaction within the...

Area of Science:

• Molecular Biology
• Medicinal Chemistry
• Biochemistry

Background:

• Quinolones are a class of antibiotics that target bacterial DNA gyrase.
• Understanding the precise interaction between quinolones and DNA is crucial for developing more potent antibacterial agents.

Purpose of the Study:

• To investigate the correlation between quinolone binding modes and their antibacterial potency.
• To elucidate the role of metal ions in quinolone-DNA interactions.
• To compare quinolone binding specificities in the context of DNA cleavage by DNA gyrase.

Main Methods:

• Plasmid DNA unwinding assays to assess pBR322 interaction.
• Surface plasmon resonance (SPR) to measure binding affinities to DNA oligonucleotides.
• Comparative analysis of quinolone-mediated DNA cleavage by DNA gyrase.

Main Results:

• Two distinct patterns of quinolone-mediated DNA cleavage by DNA gyrase were observed, dependent on quinolone potency.
• Quinolone binding to plasmid DNA showed no correlation with potency.
• Quinolones exhibited sequence-dependent, higher-affinity binding to single-stranded DNA (ssDNA) compared to double-stranded DNA (dsDNA), in an Mg(2+)-dependent manner.
• Magnesium ions (Mg2+) promoted tighter, more specific binding to ssDNA than other divalent metal ions (Mn2+, Cd2+).

Conclusions:

• Single-stranded DNA binding by quinolones correlates with their in vitro potency.
• The sequence-dependent binding to ssDNA, particularly in the presence of Mg2+, likely reflects the in vivo mechanism of quinolone action within the DNA gyrase-DNA complex.
• These findings provide insights into quinolone-DNA interactions, potentially guiding the design of novel antibiotics.