A biomimetic colorimetric logic gate system based on multi-functional peptide-mediated gold nanoparticle assembly

Advances in the application of logic gates in nanozymes

Nanozymes are a class of nanomaterials with biocatalytic function and enzyme-like activity, whose advantages include high stability, low cost, and mass production. They can catalyze the substrates of natural enzymes based on specific nanostructures and serve as substitutes for natural enzymes. Their applied research involves a wide range of fields such as biomedicine, environmental governance, agriculture, and food. Molecular logic gates are a new cross-disciplinary discipline, which can simulate the function of silicon circuits on a molecular scale, perform single or multiple input logic operations, and generate logic outputs. A molecular logic gate is a binary operation that converts an input signal into an output signal according to the rules of Boolean logic, generating two signals, a high level, and a low level. The high and low levels represent the "true" and "false" values of the logic gates, and their outputs correspond to "l" and "0" of the molecular logic gates, respectively. The combination of nanozymes and logic gates is a novel and attractive research direction, and the cross-application of the two brings new opportunities and ideas for various fields, such as the construction of efficient biocomputers, intelligent drug delivery systems, and the precise diagnosis of diseases. This review describes the application of logic gates based on nanozymes, which is expected to provide a certain theoretical foundation for researchers' subsequent studies.

Recent progress in nanomaterial-based bioelectronic devices for biocomputing system

Bioelectronic devices have received the massive attention because of their huge potential to develop the core electronic components for biocomputing system. Up to now, numerous bioelectronic devices have been reported such as biomemory and biologic gate by employment of biomolecules including metalloproteins and nucleic acids. However, the intrinsic limitations of biomolecules such as instability and low signal production hinder the development of novel bioelectronic devices capable of performing various novel computing functions. As a way to overcome these limitations, nanomaterials have the great potential and wide applicability to grant and extend the electronic functions, and improve the inherent properties from biomolecules. Accordingly, lots of nanomaterials including the conductive metal, graphene, and transition metal dichalcogenide nanomaterials are being used to develop the remarkable functional bioelectronic devices like the multi-bit biomemory and resistive random-access biomemory. This review discusses the nanomaterial-based superb bioelectronic devices including the biomemory, biologic gates, and bioprocessors. In conclusion, this review will provide the interdisciplinary information about utilization of various novel nanomaterials applicable for biocomputing system.

Peptide-Based Sensing, Logic Computing, and Information Security on the Antimonene Platform

Peptides have higher information density than DNA and equivalent molecular recognition ability and durability. However, there are currently no reports on the comprehensive use of peptides' recognition ability and structural diversity for sensing, logic computing, information coding, and protection. Herein, we, for the first time, demonstrate peptide-based sensing, logic computing, and information security on the antimonene platform. The molecular recognition capability and structural diversity (amino acid sequence) of peptides (Pb²⁺-binding peptide DHHTQQHD as a model) adsorbed on the antimonene universal fluorescence quenching platform were comprehensively utilized to sense targets (Pb²⁺) and give a response (fluorescence turn-on) and then to encode, encrypt, and hide information. Fluorescently labeled peptides used as the recognition probe and the information carrier were quenched and hidden by the large-plane two-dimensional material antimonene and specifically bound by Pb²⁺ as the stego key, resulting in fluorescence recovery. The above interaction and signal change can be considered as a peptide-based sensing and steganographic process to further implement quantitative detection of Pb²⁺, complex logic operation, information coding, encrypting, and hiding using a peptide sequence and the binary conversion of its selectivity. This research provides a basic paradigm for the construction of a molecular sensing and informatization platform and will inspire the development of biopolymer-based molecular information technology (processing, communication, control, security).

Expanding nanoparticle multifunctionality: size-selected cargo release and multiple logic operations

Physically stimulated nanoparticles that deliver size-selected cargo and function as logic gates are reported. To achieve this goal the particle requires multiple components, and we recognized early on that the components, not just the released cargo, could be used to demonstrate logic operations (OR and AND logic). For stimuli, we chose two non-invasive types, red light and alternating magnetic fields (AMF), because they both have potential biological relevance. To realize cargo delivery with size selection and logic operations, we mechanized the surface of core@shell nanoparticles with a superparamagnetic core that generates localized heating when exposed to an AMF, and a mesoporous silica shell into which cargo molecules with different sizes were loaded. We demonstrate the core@shell nanoparticles can load the dual cargos with different sizes and subsequently release the smaller (∼0.5 nm) and bigger (∼2 nm) cargos in succession when stimulated by a red light followed by an AMF. Finally, we demonstrate that the multi-component nanoparticles could function as nanoparticle-based Boolean logic gates where AMF and red light served as the two inputs and the release of small cargo, and free cyclodextrin served as the outputs. The construction of two Boolean logic gates (OR, and AND) was realized.

"Plug and Play" logic gate construction based on chemically triggered fluorescence switching of gold nanoparticles conjugated with Cy3-tagged aptamer

Gold nanoparticles (AuNPs) conjugated with Cy3-tagged aptamer which can specifically recognize chloramphenicol (CAP) (referred to as AuNPs-AptCAP) are described. CAP can trigger the configuration change of CAP binding aptamer, and thus switching the fluorescence of AuNPs-AptCAP through changing the efficiency of the fluorescence resonance energy transfer (FRET) system with Cy3 as donors and AuNPs as recipients. AuNPs-AptCAP exhibits a linear range of CAP concentrations from 26.0 to 277 μg L^-1 with a limit of detection of 8.1 μg L^-1 when Cy3 was excited at 530 nm and emission was measured at 570 nm. More importantly, AuNPs-AptCAP can be utilized as signal transducers for the build-up of a series of logic gates including YES, PASS 0, INH, NOT, PASS 1, and NAND. Utilizing the principle of a metal ion-mediated fluorescence switch together with a strong metal ion chelator, the fluorescence of AuNPs-AptCAP could be modulated by adding metal ions and EDTA sequentially. Therefore, a "Plug and Play" logic system based on AuNPs-AptCAP has been realized by simply adding other components to create new logic functions. This work highlights the advantages of simple synthesis and facile fluorescence switching properties, which will provide useful knowledge for the establishment of molecular logic systems. Graphical abstract.

Mitochondria-Targeting Polydopamine Nanocomposites as Chemophotothermal Therapeutics for Cancer

Mitochondria play a key role in a variety of physiological processes, and mitochondria-targeting drug delivery is helpful and effective in cancer therapy. Rhodamine123 (Rhod123) and Doxorubicin (Dox) are not new chemical molecules, and they both can inhibit the growth of cancerous cells. Here, we combine these two "old" chemicals with polydopamine nanoparticles (PDA NPs) to strengthen the antitumor effect with the aid of near-infrared irradiation. PDA NPs carry these two chemicals tightly by hydrogen bonds and π-π stacking besides chemical bonds. The better antitumor profile of PDA-Rhod-Dox comes from the mitochondria-targeting delivery, which decreases ATP in living cells, causing apoptosis of cancerous cells effectively and inhibiting the growth of tumors in mice. The synergistic effect of PDA, Rhod123, and Dox improves the treatment effect of conventional chemotherapy drugs.

Gold nanoparticle-based colorimetric method for the detection of prostate-specific antigen

Background

Prostate-specific antigen (PSA), a serine protease, is a biomarker for preoperative diagnosis and screening of prostate cancer and monitoring of its posttreatment.

Methods

In this work, we reported a colorimetric method for clinical detection of PSA using gold nanoparticles (AuNPs) as the reporters. The method is based on ascorbic acid (AA)-induced in situ formation of AuNPs and Cu²⁺-catalyzed oxidation of AA. Specifically, HAuCl₄ can be reduced into AuNPs by AA; Cu²⁺ ion can catalyze the oxidation of AA by O₂ to inhibit the formation of AuNPs. In the presence of the PSA-specific peptide (DAHSSKLQLAPP)-modified gold-coated magnetic microbeads (MMBs; denoted as DAHSSKLQLAPP-MMBs), complexation of Cu²⁺ by the MMBs through the DAH-Cu²⁺ interaction depressed the catalyzed oxidation of AA and thus allowed for the formation of red AuNPs. However, once the peptide immobilized on the MMB surface was cleaved by PSA, the DAHSSKLQ segment would be released. The resultant LAPP fragment remaining on the MMB surface could not sequestrate Cu²⁺ to depress its catalytic activity toward AA oxidation. Consequently, no or less AuNPs were generated.

Results

The linear range for PSA detection was found to be 0~0.8 ng/mL with a detection limit of 0.02 ng/mL. Because of the separation of cleavage step and measurement step, the interference of matrix components in biological samples was avoided.

Conclusion

The high extinction coefficient of AuNPs facilitates the colorimetric analysis of PSA in serum samples. This work is helpful for designing of other protease biosensors by matching specific peptide substrates.

A label-free visual platform for self-correcting logic gate construction and sensitive biosensing based on enzyme-mimetic coordination polymer nanoparticles

In molecular logic gates, the occurrence of erroneous procedures is a frequently encountered and critical problem in data transmission, and thus it is highly desirable to develop novel logic systems with self-correction abilities. Herein, based on the horseradish peroxidase (HRP)-like activity of the novel metal coordination polymer nanoparticles formed between Cu²⁺ and guanosine monophosphate (GMP), denoted as Cu-GMP CPNs, a label-free visual platform was constructed and successfully utilized for both self-correcting logic gate construction and sensitive biosensing. The HRP-mimicking ability of Cu-GMP CPNs was verified and utilized for the sensitive detection of both H₂O₂ and glucose. More importantly, a set of logic gates (AND, OR, NOR, INHIBIT, and XNOR) were fabricated, in which two intermediate outputs, i.e., color change and precipitate formation, were combined in an "AND" mode to produce the final output, and thus the as-proposed logic system exhibited the self-correction ability to automatically correct the erroneous intermediate outputs induced by interfering substances such as HRP. Moreover, in addition to the unique feature of self-correction, the as-proposed logic system also exhibited the advantages of simple operation, rapid response and easy detection of the visual outputs by the naked eye, thus expanding its practical applications to a variety of fields. Therefore, the label-free visual platform we have proposed here offers a promising strategy for logic gate fabrication and may pave the way for the development of novel molecular computing with self-correction abilities.

Surface charge tuneable fluorescent protein-based logic gates for smart delivery of nucleic acids

A versatile bio-logic system based on H₃₉GFP is operated in living cells with transfection of functional nucleic acids as the readout.

A plasmonic multi-logic gate platform based on sequence-specific binding of estrogen receptors and gold nanorods

A hybrid system made of gold nanorods (AuNRs) and double-stranded DNA (dsDNA) is used to build a versatile multi-logic gate platform, capable of performing six different logic operations. The sequence-specific binding of transcription factors to the DNA drives the optical response of the design.