DNA denaturing

[eudovcic]

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I started studying Biology using EK recently and came across some confusing (mis)information. Anyway it essentially says "when heated or immersed in high concentration salt solution" DNA will denature.

Now I know that "high salt concentration" will decrease strand repulsion by shielding the negative charge of the phosphates thereby making denaturing more difficult, not less.

My confusion came later when I was reading about Southern Blotting, it states "the gel is made alkaline to denature the DNA fragments."

I don't know why, but I thought salt and alkaline were referencing the same thing?

My friend tried to explain it like this: a salt solution is essentially Na+Cl- where the Na+ can associate with the O- from the phosphate and shield the negative charge whereas an alkaline solution contains more OH- (basic) thus it will disrupt the H bonds holding the ds together.

If for example, NaOH is used to make the solution alkaline, wouldn't the Na+ in solution help decrease charge repulsion? Conversely, why would the Cl- in a salt solution not disrupt the H-bonds in a similar way to OH- for the alkaline solution?

The only thing that comes to mind for me is that the Cl- is a weak conjugate base of a strong acid (HCl) whereas OH- is a strong conjugate base of a weak acid (H2O).

This probably will not be tested directly on the mcat but I would like to be able to understand this without having to spend time trying to look up information or trying to piece together exactly how it works.

What I know to be true is that alkaline solutions are basic and have higher OH- concentrations than H+ and LOW salt concentration, not HIGH, denature DNA.

Can anyone simplify the difference between a salt solution and alkaline? I tried google but came up with nothing.

 

[FeinMS]

It's one of the many typos in EK. I asked the same question weeks ago.
Low salt will favor denaturation.

Salt solution is not necessarily an alkaline solution. Alkaline solution means the solution is basic. Salt can even come in neutral or acidic salt. You're right about both statements at the end.

 

[monkeyvokes]

I started studying Biology using EK recently and came across some confusing (mis)information. Anyway it essentially says "when heated or immersed in high concentration salt solution" DNA will denature.

Now I know that "high salt concentration" will decrease strand repulsion by shielding the negative charge of the phosphates thereby making denaturing more difficult, not less.

It seems if a salt concentration is too high then the base pairing can also be disrupted. But, cations (like Mg2+) in nonexcessive amounts are good to stabilize the negative backbone.

My confusion came later when I was reading about Southern Blotting, it states "the gel is made alkaline to denature the DNA fragments."

Hey, we're both learning. Check out what i found:

At pH greater than 11.3 (alkaline conditions) all hydrogen bonds are eliminated and DNA is completely denatured (in single stranded form).

Acid conditions also denature DNA but... there is damage to phosphodiester linkages. Phosphodiester bonds are resistant to alkaline pH so use of alkaline pH is method of choice for deliberately denaturing DNA in the laboratory.
(source: http://bioweb.wku.edu/courses/biol220CAR/78DNAdenaturation/)

I don't know why, but I thought salt and alkaline were referencing the same thing?

.. why?

My friend tried to explain it like this: a salt solution is essentially Na+Cl- where the Na+ can associate with the O- from the phosphate and shield the negative charge whereas an alkaline solution contains more OH- (basic) thus it will disrupt the H bonds holding the ds together.

If for example, NaOH is used to make the solution alkaline, wouldn't the Na+ in solution help decrease charge repulsion? Conversely, why would the Cl- in a salt solution not disrupt the H-bonds in a similar way to OH- for the alkaline solution?

When increasing alkalinity, ignore spectator ions. Just imagine the addition of -OH.

Also, "salt" is a general term and does not mean to imply NaCl here.

The only thing that comes to mind for me is that the Cl- is a weak conjugate base of a strong acid (HCl) whereas OH- is a strong conjugate base of a weak acid (H2O).

This probably will not be tested directly on the mcat but I would like to be able to understand this without having to spend time trying to look up information or trying to piece together exactly how it works.

What I know to be true is that alkaline solutions are basic and have higher OH- concentrations than H+ and LOW salt concentration, not HIGH, denature DNA.

Can anyone simplify the difference between a salt solution and alkaline? I tried google but came up with nothing.

hope that helps!