Local Environment Affects the Activity of Enzymes on a 3D Molecular Scaffold

Abstract

The ability to coordinate and confine enzymes presents an opportunity to affect their performance and to create chemically active materials. Recent studies show that polymers and biopolymers can be used to scaffold enzymes, and that can lead to the modulated biocatalytic efficiency. Here, we investigated the role of microenvironments on enzyme activity using a well-defined molecular scaffold. An enzyme, glucose oxidase (GOx), was positioned at different locations of a three-dimensional (3D) octahedral DNA scaffold (OS), allowing the enzyme’s polyanionic environments to be altered. Using electrical sensing, based on a bipolar junction transistor, we measured directly and in real-time the enzyme’s proton generation at these different microenvironments. We found a 200% enhancement of immobilized enzyme over free GOx and about a 30% increase in catalytic rates when the enzyme was moved on the same molecular scaffold to a microenvironment with a higher local concentration of polyanions, which suggests a role of local pH on the enzymatic activity.

Cascaded Enzyme Reactions over a Three-Dimensional, Wireframe DNA Origami Scaffold

“…DNA nanotechnology offers an immense capability for fabrication complexity in designed scaffolds, 9 , 24 , 25 but due to the contribution of different effects it is difficult to distill the leading causes of activity changes of enzymatic cascades scaffolded on such systems. Specifically, DNA scaffold effects can induce changes in local proton concentration, consequently affecting local pH, 18 , 26 , 27 as well as potential substrate channeling either by direct proximity 12 , 27 − 30 or intermediate exchange through a scaffold hydration layer. 5 , 15 , 16 , 27 , 31 These topics have been a source of discussion in recent years, particularly regarding the contributing factors behind increased colocalized enzyme activity on DNA scaffolds, 5 , 27 , 32 − 36 such as impacts on substrate diffusion.…”

Rationally Programming Nanomaterials with DNA for Biomedical Applications

“…[ 111 ] The recent detailed studies revealed that DNA origami can affect local pH environments of enzyme which affect its activity. [ 146 ]…”

Bioinspired Self‐Assembling Materials for Modulating Enzyme Functions

“…Gang and co‐workers employed a 3D DNA origami scaffold of octahedral shape to place a glucose oxidase (GOx), which was prescribed to either externally at one of the vertices or internally, along one of the duplex bundles ( Figure A). [ 28 ] The two positions had different densities of the negative charges, as defined by the amount of DNA spatially surrounding the enzyme. They demonstrated that the GOx conjugated on vertices had 30% higher catalytic activity than that on the duplex bundle, which had less local polyanions and more acidity.…”

“…The oxidation efficiency of glucose was affected by the density of negative charge at different positions of the scaffold. [ 28 ] Reproduced with permission. [ 28 ] Copyright 2020, American Chemical Society.…”

“…[ 28 ] Reproduced with permission. [ 28 ] Copyright 2020, American Chemical Society. B) Reversible regulation of enzyme cascade reaction by a DNA machine.…”