Turning DNA Binding Motifs into a Material for Flow Cells

Abstract

Nanoscale assemblies of DNA strands are readily designed and can be generated in a wide range of shapes and sizes. Turning them into solids that bind biomolecules reversibly, so that they can act as active material in flow cells, is a challenge. Among the biomolecular ligands, cofactors are of particular interest because they are often the most expensive reagents of biochemical transformations, for which controlled release and recycling are desirable. We have recently described DNA triplex motifs that bind adenine‐containing cofactors, such as NAD, FAD and ATP, reversibly with low micromolar affinity. We sought ways to convert the soluble DNA motifs into a macroporous solid for cofactor binding. While assemblies of linear and branched DNA motifs produced hydrogels with undesirable properties, long DNA triplexes treated with protamine gave materials suitable for flow cells. Using exchangeable cells in a flow system, thermally controlled loading and discharge were demonstrated. Employing a flow cell loaded with ATP, bioluminescence was induced through thermal release of the cofactor. The results show that materials generated from functional DNA structures can be successfully employed in macroscopic devices.

Rational Design of Abasic Site-Containing DNA Triplexes To Bind Small Molecules with Low Nanomolar Dissociation Constants

“…It will benefit aptamer-based molecular devices, improving their diagnostic and therapeutic efficacy. Such design, along with other related studies, − is not only a test on our current understanding/knowledge of the basic principles that determine DNA structures but also, we hope, will stimulate exploration of rational designing functional DNA molecules in general and provide insights to improve the widely used SELEX method. , …”

Noncovalent Spin‐Labeling of DNA and RNA Triplexes

“…Reinforcing the gap with linkers can improve binding, and the binding capacity can be optimized by introducing several binding sites per triplex . Rationally designed triplex binding motifs can be turned into functional materials operating in macroscopic devices by precipitating them with protamines . Thus far, however, the binding properties of DNA and RNA triplexes have not been used for spin labeling.…”