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Issue 7, 2011
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Influence of nano-viscosity and depletion interactions on cleavage of DNA by enzymes in glycerol and poly(ethylene glycol) solutions: qualitative analysis

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Abstract

Biochemical reactions in living systems take place in an environment crowded by various macromolecules and ligands. Therefore experimental data obtained in buffer do not reflect in vivo conditions. We have used glycerol, poly(ethylene glycol) (PEG) 6000 and PEG 8 M solutions to investigate the influence of the crowded environment on cleavage of plasmid DNA by restriction enzyme HindIII. PEG 6000 solution can effectively slow down the cleavage process. However, neither PEG 8 M solution of the same viscosity as PEG 6000 solution nor glycerol solution of the same concentration as PEG 6000 solution slows the cleavage of DNA appreciably. The viscosity experienced by the biomolecules (here called nano-viscosity) and aggregation induced by the depletion interactions between DNA molecules in polymer solution (PEG 6000) are two factors responsible for slow cleavage of DNA. We have ruled out the change of pH and denaturation of HindIII as possible sources for the effect.

Graphical abstract: Influence of nano-viscosity and depletion interactions on cleavage of DNA by enzymes in glycerol and poly(ethylene glycol) solutions: qualitative analysis

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Publication details

The article was received on 31 Aug 2010, accepted on 08 Nov 2010 and first published on 15 Dec 2010


Article type: Paper
DOI: 10.1039/C0SM00899K
Citation: Soft Matter, 2011,7, 3092-3099
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    Influence of nano-viscosity and depletion interactions on cleavage of DNA by enzymes in glycerol and poly(ethylene glycol) solutions: qualitative analysis

    S. Hou, N. Ziebacz, T. Kalwarczyk, T. S. Kaminski, S. A. Wieczorek and R. Holyst, Soft Matter, 2011, 7, 3092
    DOI: 10.1039/C0SM00899K

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