What's the difference btw native and denatured DNA??

[ahkian82]

Does the conformation of both native and denatured DNA show any difference? I'm looking for double-stranded DNA which is in helix form in solution. Recently, i'd bought a calf-thymus DNA from Invitrogen. In the product description, it's said that "...the DNA is prepared from highly pure, phenol-chloroform extracted DNA, and DNAse-free, RNase-free, distilled, deionized water. Once dissolved, the DNA solution is sheared to an average size of <2000bp and the concentration is adjusted to 10mg/ml..." Does the shearing process destroy the helixity of the DNA?

Upon diluting the DNA, some undissolved material was observed (the solution was not clear due to this little suspension).. Does this a sign of DNA degradation? If i remove the undissolved material via centrifugation, do you think the DNA still ok for use? (According to one of my friend, the DNA solution should be clear in the concentration that i prepared. The solution was in 4e(-4) M in Tris / DMSO (9:1) solution. Tris buffer contains 5mM Tris, 50mM NaCl in pH 7.2)

Any idea to help?? Thanks..

[enigma]

I think, the shearing process doesn't detroy hilical DNA however it maybe cut the DNA in the short fragments.

[moleculardude]

Hello Ahkian

Keep your DNA don't throw it out! Have you loaded/run your DNA on an agarose gel to view it?

That way you can see the quality of your DNA.

Also you can do a UV spec on your DNA to check if there is any proteins (maybe that is your dirty problem!?) or contaminants.

Check the 260/280 ratio to check this

[ahkian82]

haha, i like your cartoon - the crazy-looked scientist ... ^_^

Hi, moleculardude.. Regarding my problem, i did check the A260/A280 ratio. It's in the range of 1.8 to 1.92 (usually). So, I already exclude the possibility of protein contamination.. All the glasswares are acid-washed, then washed extensively with deionized water.. So...that's what i can do..Any other suggestions??
About running gel, it is a good suggestion.. but i dun have it in the lab.. So, I'm only rely on the UV absorption technique to characterise the DNA..

By the way, is the denatured DNA still in double helix form?? Any idea bout the term "duplex"? Can denatured DNA or double-stranded DNA form hairpin loop structure?? Hahah.. too many questions.. don't run away please .... :>

cheers..

[phluxified]

Hey Ahkian,
Denatured DNA is single stranded, it is when your H-bonds dissociate between the nucleic acid base pairs.
Duplex means double stranded DNA.
Denatured DNA can form hair pins if the strand is long enough and if the buffer is it is in and temperature it's at are both permissible. Double stranded DNA can not form hairpin structures. The internal bonds are already saturated with their complementary bases.
I hope this helps, although the response is a bit late.
Kind Regards,
Chadi