magnesium in pcr - what does it do?

[brett]

>hi,....
>
>title says it all really.....i know dntps, dna and proteins all bind mg but 
>what is it that mg actually does in the mix?......make dna more accesible to 
>polymerase or what?.......and whats the relationship between mg and dntp 
>concentrations?
>
>thanks
>
>vid
>k9mhc at rfhsm.ac.uk

Divalent cations, and in particular Mg++, affect the duplex structure by
interfacing with the nucleic acid and H2O (remember nucleic acids are
polyanions). To answer your question, Mg++ is used to stabilize dsDNA,
and raising the Tm (compared to Tm w/o cations....if it's even in
solution!). Therefore, [Mg++] is an important parameter in controlling
specificity of your reaction (low Mg++ --> more stringent base pairing
requirements). In addition, your annealing temperature also is important.
Well, I hope this answers your
question, its what I remember from my Nucleics course from 2 years ago.
If there are any ommisions, please don't flame me....educate me (I've had
some fiesty responses lately). &^}



Brett Lindenbach
    
Program in Immunology                              
Washington University - St Louis                  
brett at borcim.wustl.edu                             

"I own my own pet virus. I get to pet and name her." - Cobain