"high stringency" washes -NOT?

Peter Nilsson Peter.Nilsson at klinkemi.umu.se
Wed May 7 04:24:37 EST 1997


Hello Jim.

I can only add a biochemical explanation on the effect of ionic strength ([Na]) on the stability of the double helix: The negative charges on 
opposite strands in the backbone, the phosphate-groups, destabilize the helix by repulsing the the strands in the double helix from each other. 
This intrinsic instability is balanced by positivly charged ions (Na+) wich shields the negative charges on the backbone. With very high ionic 
strength one get not only shielding but also a ionic chemical bound between Na+ and P-. 
Also high ionic strength increases the hydrofobic interactions between the bases "inside" the helix, the base stacking, which also stabilize 
the interactions between the oppossite strands. Therefore, these two effects acting together gives a stabilization (higher Tm) with increased 
ionic strength. Decreasing the [Na] means higher stringency.

Regards, peter. 
-- 
Peter Nilsson, Molecular Biologist
Clinical Chemistry Department,
Umeå University Hospital,
S-901 85 Umeå,
Sweden.



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