Programming DNA‐Based Systems through Effective Molarity Enforced by Biomolecular Confinement

Abstract

The fundamental concept of effective molarity is observed in av ariety of biological processes, such as protein compartmentalization within organelles, membrane localization and signaling paths. To controlm olecular encountering and promotee ffective interactions, nature places biomolecules in specific sites inside the cell in order to generate a high, localized concentration different from the bulk concentration. Inspired by this mechanism, scientists have artificially recreated in the lab the same strategy to actuate and control artificial DNA-based functional systems. Here, it is discussed how harnessing effective molarity has led to the development of an umber of proximity-induced strategies, with applications ranging from DNA-templated organic chemistry and catalysis, to biosensing and protein-supported DNA assembly.

Controlling Dynamic DNA Reactions at the Surface of Single-Walled Carbon Nanotube Electrodes to Design Hybridization Platforms with a Specific Amperometric Readout

“…The possibility to perform toehold-free strand exchange reactions that leverage a basic poly­(A) sequence as the invader strand is particularly appealing for the development of sequence-independent electrochemical platforms enabling detection of non-nucleic-acid analytes. Many molecular systems have been recently developed in which generation or release of an arbitrary nucleic acid sequence can be controlled upstream by a specific protein, including antibodies, transcription factors, and other functional proteins. ,− An electrochemical platform designed to respond to an arbitrary protein-controlled poly­(A)-based input by simple disassembly of poly­(T)-melamine structures would require no efforts in sequence design, and it could be applied to any molecular system engineered to provide a poly­(A) strand as a molecular output. Furthermore, more complex architectures based on the same strategy could be designed in which toehold-mediated and toehold-free reactions are performed in an orthogonal way, facilitating the design of molecular interfaces for multiplex analyses.…”

“…DNA Hybridization Studies. Solutions of different concentrations (30,50,70, 100, 300, and 500 nM) of Atto-MB2-modified poly(A) DNA strands were prepared in TAE buffer, of which 50 μL were deposited on SWCNT-SPEs previously functionalized with amine-modified poly(T) probes and left incubating for 2 h. Next, the electrode surface was washed with TAE buffer and amperometric measurements were carried out in reading buffer. Control experiments for the evaluation of nonspecific amperometric signal due to DNA physisorption were conducted using a 100 nM solution of noncomplementary Atto-MB2-modified poly(T) strands.…”

Mechanistic Aspects for the Modulation of Enzyme Reactions on the DNA Scaffold

“…As speculated for the confined cellular environments, a confined 3D DNA space could provide a favorable environment for enzyme cascade reactions [ 106 ]. The typical enzyme pair GOx/HRP was also investigated in the 3D DNA nanostructures.…”

Protein-Controlled Actuation of Dynamic Nucleic Acid Networks Using Synthetic DNA Translators

“…One clever strategy makes use of proteins as substrates that promote molecular interactions in a confined volume and induce the hybridization between complementary DNA strands through the increase of their local concentration. [11][12][13][14][15][16] This strategy is however limited by the availability of specific affinity ligands that must be conjugated to the interacting DNA strands and by the need of multiple binding sites on the target protein. Alternatively, protein-responsive sensing technologies and DNAbased architectures have been engineered capitalizing on the natural DNA binding activity of transcription factors.…”