Abstract
The equilibrium constant (K) of biochemical complex formation in aqueous buffers with high concentration (>20 wt %) of nonionic compounds can vary by orders of magnitude in comparison with the K in a pure buffer. The precise molecular mechanisms of these profound changes are not known. Herein, we show up to a 1000-fold decrease of the K value of DNA hybridization (at nM concentration) in standard molecular crowder systems such as PEG, dextrans, Ficoll, and glycerol. The effect responsible for the decrease of K is the complexation of positively charged ions from a buffer by nonionic polymers/small molecules. We determined the average equilibrium constant for the complexation of ions per monomer (∼0.49 M–1). We retrieve K’s original value for a pure buffer if we properly increase the ionic strength of the buffer crowded by the polymers, compensating for the loss of complexed ions.
Highlights
Value of DNA hybridization in standard molecular crowder systems such as PEG, dextrans, Ficoll, and glycerol
Biochemical reactions occur in the cytoplasm of living cells crowded by biomolecules
We prove that the general mechanism responsible for decreasing K is the complexation of positively charged ions from a buffer by nonionic polymers/small molecules
Summary
Value of DNA hybridization (at nM concentration) in standard molecular crowder systems such as PEG, dextrans, Ficoll, and glycerol.
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