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Topic: denature DNA  (Read 32382 times)

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briteyellowness

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denature DNA
« on: August 11, 2005, 08:01:07 PM »
if i want to denature doublestranded DNA, would I use an acidic or basic solution?  i know you can also denature it with heat, but can an acidic or basic solution work too?

Offline Donaldson Tan

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Re:denature DNA
« Reply #1 on: August 11, 2005, 09:19:52 PM »
denature DNA reversibly by treatment with 0.5M NaOH.
"Say you're in a [chemical] plant and there's a snake on the floor. What are you going to do? Call a consultant? Get a meeting together to talk about which color is the snake? Employees should do one thing: walk over there and you step on the friggin� snake." - Jean-Pierre Garnier, CEO of Glaxosmithkline, June 2006

briteyellowness

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Re:denature DNA
« Reply #2 on: August 11, 2005, 09:23:28 PM »
thanks, but why is it only in basic solution?  why won't an acidic solution work?

savoy7

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Re:denature DNA
« Reply #3 on: August 12, 2005, 12:05:57 AM »
Both acidic and basic conditions will denature DNA (pH <3 or >10).  I have only used a basic solution like the one mentioned above.

Offline Donaldson Tan

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Re:denature DNA
« Reply #4 on: August 12, 2005, 12:56:34 AM »
savoy: does the phosphodiester bond in DNA undergo acid/alkali hydrolysis?
"Say you're in a [chemical] plant and there's a snake on the floor. What are you going to do? Call a consultant? Get a meeting together to talk about which color is the snake? Employees should do one thing: walk over there and you step on the friggin� snake." - Jean-Pierre Garnier, CEO of Glaxosmithkline, June 2006

Offline Yggdrasil

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Re:denature DNA
« Reply #5 on: August 12, 2005, 03:45:16 AM »
I wouldn't use acid to denature DNA for most applications as acids tend to destroy (hydrolyze) DNA.   Sodium hydroxide, as geodome mentioned, is a good way to denature DNA because the hydroxide ions will interfere with the hydrogen bonding between base pairs.

savoy7

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Re:denature DNA
« Reply #6 on: August 15, 2005, 11:04:15 AM »
In reply to geodomes statements:

Denaturing DNA usually means splitting the H-bonds of the DNA.  NaOH is the preferred way - in fact the only way I have ever done it.  Having a pH<3 will also disrupt the bonding, but like Yggdrasil stated - it usually destroys the DNA.  Early papers from the 60's were looking at how do denature and renature DNA (pH and temperature).  If I remember correctly it was Doty, Marmur and someone like sauerkraut(it's not sauerkraut but thats the way I remember).  I only stated the low pH because biteyellowness asked if it could be done.

 

paperclip

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Re:denature DNA
« Reply #7 on: August 17, 2005, 04:43:53 AM »
We know that when H2SO4 is used to DENATURE DNA it creates alkenes out of it by a mechanism of hydrolysis ie -H20 creates a C=C bond.

However, alcohol are also known to be DEHYDRATING AGENTS. Does it have the same mechanism of -H20 creates a C=C bond? Probably not. But I'd like to see how that can be obtained that we can PRECIPITATE DNA OUT OF SOLUTION BY simply ADDING ALCOHOL IN THE RIGHT WAY.

KEEP ME POSTED! :-\

paperclip

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Re:denature DNA
« Reply #8 on: August 17, 2005, 05:08:29 AM »
Alcohol as dehydrating agent

The oxygen in alcohol is so strongly affiniated with the hydrogen in water that no other molecule can bind to it.

Nooooo . not even ribose n phosphate n lipopolysaccharides n .. n... n... n .

SO our aw (water activity) goes down ==> water become 'sluggish'/deactivated doesn't want to partake in any more 'water polo' games such as hydrogen bonding.. n.... n... n.... ?n.... So DNA has to somehow find its way 'out of solution'.

We can also observe this 'salting out' phenomenon by adding heavy metallic salts (not sure if we can do the same with NaCl & heavy sugars like sucrose n... n... n....). But anyway, this must also imply that heavy metals have even more so higher affinity for hydrogen in water than DNA or... or.... or....


Is it correct that alcohol (because of the OH) doesn't at all behave as a dehydrating agent but rather a stronger water ligand. It only looks like its dehydrating cause nothing seems to want to get close to water once alcohol comes into the picture?

Check me on this one pls.

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