Zinc is the second most abundant trace element essential for all living organisms. In human body, 30-40% of the total zinc ion (Zn(2+)) is localized in the nucleus. Intranuclear free Zn(2+) sparks caused by reactive oxygen species have been observed in eukaryotic cells, but question if these free Zn(2+) outrages could have affected annealing of complementary single-stranded (ss) DNA, a crucial step in DNA synthesis, repair and recombination, has never been raised. Here the author reports that Zn(2+) blocks annealing of complementary ssDNA in a sequence-selective manner under near-physiological conditions as demonstrated in vitro using a low-temperature EDTA-free agarose gel electrophoresis (LTEAGE) procedure. Specifically, it is shown that Zn(2+) does not block annealing of repetitive DNA sequences lacking CG/GC sites that are the major components of junk DNA. It is also demonstrated that Zn(2+) blocks end-joining of double-stranded (ds) DNA fragments with 3' overhangs mimicking double-strand breaks, and prevents renaturation of long stretches (>1 kb) of denatured dsDNA, in which Zn(2+)-tolerant intronic DNA provides annealing protection on otherwise Zn(2+)-sensitive coding DNA. These findings raise a challenging hypothesis that Zn(2+)-ssDNA interaction might be among natural forces driving eukaryotic genomes to maintain the Zn(2+)-tolerant repetitive DNA for adapting to the Zn(2+)-rich nucleus.