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Many DNA isolation protocols use a Proteinase K digestion to remove proteins. This is often performed at 50 °C. Why is this?

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Proteinase K activity is greatly increased by addition of denaturing agents like SDS or urea (Hilz et al., 2008), indicating that the denaturation of the substrates helps Proteinase K to degrade them.

Increasing the temperature to 50°C will also unfold some proteins already, making it easier for the Proteinase K to degrade them. The proteinase K seems to be a pretty stable enzyme, and can still work at this temperature.

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In your linked wiki article: "An elevation of the reaction temperature from 37 °C to 50 - 60 °C may increase the activity (of Proteinase K) several times." The enzyme works faster at 50°C.

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some proteins are deactivated at that temperature... they are all different, aren't they? –  shigeta May 19 '12 at 2:07
    
@shigeta yup, they are all different. –  JoeHobbit May 19 '12 at 14:24
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