Ion Complexation Explains Orders of Magnitude Changes in the Equilibrium Constant of Biochemical Reactions in Buffers Crowded by Nonionic Compounds

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.

Effective screening of Coulomb repulsions in water accelerates reactions of like-charged compounds by orders of magnitude

“…We chose DNA hybridization because it is a well-known ion-sensitive process that occurs between two negatively charged reactants at neutral pH (Fig. 5 a) 14 . This example also introduces broader generality since the product of CoA with CoA-M reaction is formed via covalent bonds, whereas DNA duplex assembles via non-covalent interactions.…”

A Careful Insight into DDI-Type Receptor Layers on the Way to Improvement of Click-Biology-Based Immunosensors

“…To overcome the mutual repulsion of DNA strands, buffers with high ionic strength are typically required. These provide screening of the negative charge by the cations present in solution [ 30 ]. However, this approach imposes limitations with respect to the composition of immobilization and hybridization media.…”

Physicochemical Perspective of Biological Heterogeneity

“…For example, when it comes to modeling chemical reactions, not only reagents interact with each other. The effect of the solventinherent surroundings of the moleculesis an essential part of theories on chemical reaction rates. , More recent research shows that buffer ingredients, or even container material, can influence the model as well. − Neglecting particular terms of the models should be preceded with detailed investigations based on experiments in well-controlled conditions . This extensive control over the experimental environment is accessible in chemical laboratories.…”

“…One strategy is to use artificial crowders like polymers. However, their contribution to the studied reaction can go beyond steric restrictions, as adding polymers to the buffer can significantly change ionic strength and affect biomolecule conformation . Thus, isolating the influence of only one factor seems to be an exceptionally difficult task.…”