Unconventional Split Aptamers Cleaved at Functionally Essential Sites Preserve Biorecognition Capability

Abstract

Split aptamers (SPAs) are a pair of oligonucleotide fragments generated by cleaving a long parent aptamer. SPAs have many compelling advantages over the parent aptamer such as sandwich target binding, optimized concise structure, and low cost. However, only a limited number of SPAs have been developed so far, because the traditional theory restricts the splitting to the functionally dispensable site that many parent aptamers do not possesses. In this work, we challenge the traditional mechanism and hypothesize that SPAs can also be generated by splitting the parent aptamer at the functionally essential site while still preserving the biorecognition capability. To prove our hypothesis, we discoveried three SPAs with Broken initial small-molecule binding Pockets ( BP SPAs) and validate their binding capability both in wet lab and in silico. An allosteric binding mechanism of BP SPAs, in which a new binding pocket is formed upon the target binding, is revealed by all-atom microsecond-scale molecular dynamics simulations. Our findings will greatly promote discovery of new SPAs and their applications in molecular sensing in many fields.

Innovative Eco-Friendly Conductive Ink Based on Carbonized Lignin for the Production of Flexible and Stretchable Bio-Sensors

“…In conclusion, the results obtained prove the suitability of the developed carbonized lignin SPEs as a sustainable and efficient support for the development of sensors and biosensors. The demonstrated properties lend support to the possibility of employing the developed carbonized lignin electrodes with different biorecognition elements [47] or transduction systems [48].…”

Quantitative analysis of ecological suitability and stability of meandering rivers

“…Complex geomorphological features change water flow and sediment conditions, creating diverse microhabitats. As the natural river morphology changes, the river water environment changes in response, with changes in the diversity and abundance of river organisms and a certain responsive relationship [20,[24][25][26].…”

Strategies for Improving Small-Molecule Biosensors in Bacteria

“…Single-component bacterial biosensors using a similar mechanism have recently been constructed in the laboratory, using inducible dimerization of a transmembrane protein to build sensors that increase gene expression in response to caffeine [ 60 ] and bile salts [ 61 ]. Nucleic acids can also be used to build biosensors that rely on ligand-dependent dimerization, with various split aptamers [ 62 , 63 ], ribozymes [ 64 , 65 ], DNAzymes [ 66 ], and aptazymes [ 67 , 68 ] having been built to date. However, despite the relative abundance of existing aptamers, reliably splitting an aptamer or a catalytic nucleic acid element without abolishing its function remains a significant challenge [ 69 ].…”