Zn2+ blocks annealing of complementary single-stranded DNA in a sequence-selective manner

Area of Science:

• Molecular Biology
• Genomics
• Biochemistry

Background:

• Zinc is an essential trace element, with a significant portion localized within the cell nucleus.
• Intranuclear free zinc ion (Zn2+) fluctuations are known, but their impact on DNA processes remains largely unexplored.
• DNA annealing is critical for DNA synthesis, repair, and recombination.

Purpose of the Study:

• To investigate the effect of Zn2+ on the annealing of complementary single-stranded DNA (ssDNA).
• To determine if Zn2+ influences DNA end-joining and dsDNA renaturation.
• To explore the potential role of Zn2+-DNA interactions in genome evolution.

Main Methods:

• In vitro experiments using low-temperature EDTA-free agarose gel electrophoresis (LTEAGE).
• Testing the effect of Zn2+ on the annealing of various DNA sequences, including repetitive and coding DNA.
• Assessing Zn2+ impact on the end-joining of double-stranded DNA (dsDNA) fragments with 3' overhangs.

Main Results:

• Zn2+ was found to block ssDNA annealing in a sequence-selective manner under near-physiological conditions.
• Annealing of repetitive DNA sequences lacking CG/GC sites was not inhibited by Zn2+.
• Zn2+ inhibited the end-joining of dsDNA fragments and the renaturation of long denatured dsDNA stretches, with intronic DNA showing protection.

Conclusions:

• Zn2+ can interfere with crucial DNA processes like annealing and end-joining.
• Sequence-selective DNA annealing inhibition by Zn2+ may favor the maintenance of Zn2+-tolerant repetitive DNA in eukaryotic genomes.
• Zn2+-ssDNA interactions could be a driving force for genome adaptation in Zn2+-rich nuclear environments.