Question

1. Provide a chemical reason for why Na+ ions are associated with ds-DNA relative to single strands.

2. The addition of Na+ ions stabilized ds-DNA. Can you suggest other types of chemical species that might also stabilize ds-DNA? What types of chemical species would destabilize ds-DNA?

Answer 1

1. Na+ ions are inherently associated with ds-DNA as compared to single strands. Na+ ions with single stranded DNA tend to form a hairpin structure. Salt induces duplex formation in DNA , and Na+ does the same,shields from the phosphate charges on DNA by affecting activity of water.

2.Adding Na+ ions stabilizes ds-DNA since it helps in sheilding the negative phosphate charges on the ds-DNA. Na+ ions also have an impact on metling temperature of DNA, though there is not a linear relationship between the DNA melting temperature and Na+ ions.

Magnesium or Potassium (Mg2+ or K+) also at specific concentrations play a role in stabilizing DNA via helping it fold and neutralize negative charges on the DNA polyanion.

Many intercalating agents destabilize ds-DNA. Example monointercalating agents like acridine orange.bis-intercalating agents, DNA alkylating agents that tend to disrupt the helical structure.