Zn2+ Blocks Annealing of Complementary Single-Stranded DNA in a Sequence-Selective Manner

Abstract

Zinc is the second most abundant trace element essential for all living organisms. In human body, 30–40% of the total zinc ion (Zn2+) is localized in the nucleus. Intranuclear free Zn2+ sparks caused by reactive oxygen species have been observed in eukaryotic cells, but question if these free Zn2+ 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 Zn2+ 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 Zn2+ 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 Zn2+ 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 Zn2+-tolerant intronic DNA provides annealing protection on otherwise Zn2+-sensitive coding DNA. These findings raise a challenging hypothesis that Zn2+-ssDNA interaction might be among natural forces driving eukaryotic genomes to maintain the Zn2+-tolerant repetitive DNA for adapting to the Zn2+-rich nucleus.

Molecular Characterization and Functional Analysis of PR-1-Like Proteins Identified from the Wheat Head Blight FungusFusarium graminearum

“…This contrast resembles that observed in certain plant genes (e.g., the wheat TaPr-1-rk genes that all contain A+T-rich introns) (Lu et al 2017). This commonality supports the hypothesis that "junk" DNA such as intronic sequences may benefit DNA replication or repair because it protects the annealing of singlestranded DNA (Lu 2014).…”

A Biodegradable Gel Electrolyte for Use in High-Performance Flexible Supercapacitors

“…On the basis of the above-mentioned features, agarose-based hydrogels have been widely used in fields ranging from food production and biological research to various gel-based device systems such as ion current diodes, memristors, photovoltaic devices, and polyelectrolyte diodes. − To the best of our knowledge, however, practical applications of agarose gels as an electrolyte material in supercapacitor configurations have not been reported. Moreover, securing mechanical flexibility and environmental benignity of electrolytes while retaining their electrochemical performance continue to be a challenging issue.…”

The Effect of Common Cations on DNA Degradation

“…This may be one of the processes that accounts for nickel's carcinogenic properties, as well as why it has been found to interfere with DNA repair and facilitate oxidative stress (16). A similar affinity for guanine was reported for the aforementioned zinc (10), and Duguid et al indicate other transition metals may also act in a similar manner. Such effects would need to be investigated further to be confirmed.…”

“…In lower concentrations, magnesium ions complexed with DNA can increase the T m , and thus the stability of the polymer; however, in high concentrations, magnesium salts will lower the T m and facilitate the denaturation and degradation of the molecule. Effects of calcium, copper, and zinc have also been analyzed; calcium was shown to have a similar effect as magnesium in increasing DNA stability, while zinc inhibited the annealing, or rejoining, of single-stranded DNA molecules into doublestranded DNA, especially in sections with many repeats of guanine and cytosine (8,9,10). Clearly, different cations can have unique and interesting effects on DNA, which can be utilized in processes involving denaturation -magnesium is already used in PCR, for example, as a cofactor for Taq polymerase to stabilize the DNA strand to which the polymerase adheres (11).…”