Biomimic Construction Of Biomolecular Logic System And Biosensing Platform

Bio-molecular logic gates are the basic units of biological computer,which perform Boolean logic operations depending on biological reactions at a molecular level.During computing procedures,bio-molecular logic gates excute a series of actions,including sensing input,processing the input information,and making decisions to output the final signals.In this way,it can greatly enhance our ability to understand complex biological events,including gene expression regulation,enzymatic activity regulation,and signal transduction networks.In addition,rational design and engineering of biomolecular logic gates hold great significance in biosensor investigation,which benefit the development of logical detection,intelligent diagnosis,and artificial intelligence.From the view of computer processing,the organism itself is a bio-computer,especially the human brain as a natural computer of smart enforcement acti ons.Moreover,the natural existed biological responses and biological activities are also regulated and controlled in programmatic procedures.Herein,it is highly intriguing to mimic the natural biological events for the design and engineering of bio-logic gate system.In this paper,we introduced the backgrounds of bio-molecular logic gate/computer and the current researches of biosensor.Then,taking usage of natural biomolecule-involved switching reactions/responses,regulatory networks,and bio-mineralization phenomena,we artificially constructed a series of bio-logic gate systems and bio-sensing platforms,which are described as the following:(1)Firstly,a novel Au(I)-Co A coordination polymer-based fluorescent assay method was developed.According to the proposed method,we constructed a biomimetic logic system for cascading enzymatic interactions in tricarboxylic acid cycle(TCA)cycle.In the TCA cycle-derived logic system,AND-AND-AND-cascaded gate could be realized to carry out the chemical information processing.This biomimetic logic system is rigorously operated step by step in one pot,and is outputted as a label-free fluorescent signal with visualized readout,which is significant for developing high-density biocomputer.(2)Secondly,a biomimetic peptide-based bio-logic system was constructed by utilizing multi-functional peptide probes and the peptide-mediated nanoparticle assembly system.Taking advantage of Zn2+ ion and chymotrypsin as the model inputs,we constructed a peptide logic system computed by the multi-functional peptide probes and outputted by readable colour change of gold nanoparticles(Au NPs).In this logic system,representative binary basic logic gates(AND,OR,INHIBIT,NAND,IMPLICATION)have been achieved through delicately coding the peptide sequence.Additionally,we demonstrated that the three-input combinational logic gate(INHIBIT-OR)could also be successfully integrated,and further applied as a multi-tasking biosensor for colorimetric det ection of dual targets.This nanoparticles-based peptide logic system presents a valid strategy to illustrate peptide information processing and provides a practical platform for executing peptide computing or peptide-related multiplexing sensing,implying that the controllable nanomaterials assembly is a promising and potent methodology for the advance of bio-mimic bio-logic computation.(3)Thirdly,we further built up a versatile and modularized peptide-based logic system based on the selective chemoenzymatic ligation by Sortase A.This peptide logic system was facilely interfaced with both nanoparticles assembly and cell state regulation,allowing the fluorescent visualization of logic output using QDs and the logically-mediated apoptosis of He La cells.Based on its unique module design strategy,we implemented not only several basic binary logic gates,but also a preliminary multi-input logic gates,and even complex computing circuits,such as peptide half-adder and multi-inputted molecular keypad lock,which significantly improve the circuit complexity and functionality compared to existing peptide logic systems.Moreover,the Sortase A-processed logic system was successfully applied at cell level,achieving logic regulation of cell apoptosis.The propos ed logic system presents a scalable platform capable of realizing more complex computing tasks and functional logic devices via further integrating(1)diverse functional and structural peptide motifs,(2)other variants of Sortase A with different substrate specificity,and(3)other emerging chemoenzymatic peptide ligation toolkits,such as intein-mediated peptide ligation and Spy Tag-Spy Catcher system.This sortase-processed peptide bio-computing system has great potentials in cell reprogramming,tissue e ngineering,and disease diagnosis and treatment.(4)Fourthly,we developed a fluorescent biosensing system based on this unique DNA-mediated supercharged green protein(Sc GFP)/graphene oxide(GO)interaction.Based on this system,a label-free and homogenous assay for uracil-DNA glycosylase(UDG)activity and its inhibition was established.The high quenching ratio of Sc GFP/GO and the specific recognition of UDG on DNA lesion give this UDG assay method good sensitivity and selectivity.Meanwhile,compared to other UDG assays requiring radioactive or dye labeling,our method demonstrates several practical advantages,including label-free,facile,cost-effective,and mix-and-read operation.Our method presents a potential platform for high throughput screeni ng assay of base excision repair(BER)-targeted anti-cancer drug candidates in pharmaceutical development.Furthermore,this system is versatile and can be expanded to monitor other DNA-related enzymes in vitro.(5)Finally,peptide-coated gold nanoclusters(Au NCs)were synthesized through a biomimetic mineralization method,and the interactions between Sc GFP and Au NCs were also investigated.Based on Au NCs/Sc GFP nano-compound,a fluorescent bio-sensing platform was developed for sensitive and selective bi oassay of protein post-translation modification enzyme activity(Sirt1 and PP1)and the inhibition.The sensing method has the following advantages:(a).simple and easy operation,and quick readout through fluorescence colour changes;(b).stable performa nce and applicable to high throughput screening;(c).eco-friendly and mild reaction,without addition of toxic reagents;(d).economy and time saving,without expensive equipment and avoiding complex modification and detection procedures.To be a proof of concept,this work greatly enrich and extend the field of application of fluorescent protein,and further revealed that the interactions of functional proteins with nanomaterials might be a promising toolkit to develop new bio-sensing mechanisms.