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Unconventional Split Aptamers Cleaved at Functionally Essential Sites Preserve Biorecognition Capability.
Ruoyu Wang1, Qiansen Zhang2, Yi Zhang3
1Research Centre of Environmental and Health Sensing Technology, School of Environment , Tsinghua University , Beijing , 100084 , China.
Analytical Chemistry
|October 19, 2019
Summary
Split aptamers (SPAs) can be generated from essential sites, challenging traditional methods. These novel aptamers, discovered through wet lab and in silico validation, offer new possibilities for molecular sensing applications.
Area of Science:
- Biochemistry
- Molecular Biology
- Computational Chemistry
Background:
- Split aptamers (SPAs) offer advantages like sandwich binding and lower cost compared to parent aptamers.
- Traditional SPA development is limited by the requirement to split aptamers at non-essential sites.
- Many parent aptamers lack functionally dispensable sites, hindering SPA discovery.
Purpose of the Study:
- To challenge the traditional hypothesis that aptamers can only be split at dispensable sites.
- To explore the generation of SPAs by cleaving parent aptamers at functionally essential sites.
- To validate the biorecognition capability of newly discovered SPAs.
Main Methods:
- Discovery and validation of three SPAs with broken initial small-molecule binding pockets (BP SPAs).
- Experimental validation (wet lab) of BP SPA binding capabilities.
- In silico validation using all-atom microsecond-scale molecular dynamics (MD) simulations.
Main Results:
- Successfully generated and validated three novel BP SPAs.
- Revealed an allosteric binding mechanism for BP SPAs, where binding pockets form upon target interaction.
- Demonstrated the efficacy of MD simulations in predicting aptamer-ligand binding.
Conclusions:
- SPAs can be generated from functionally essential sites, expanding SPA development possibilities.
- BP SPAs exhibit an allosteric binding mechanism, forming new pockets upon target binding.
- MD simulations are crucial for predicting aptamer binding and advancing functional nucleic acid applications.
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