An artificial intelligence process of immunoassay for multiple biomarkers based on logic gates

We present a universal platform to synchronously analyze the possible existing state of two protein biomarkers. This platform is based on the integration of three logic gates: NAND, OR and NOT. These logic gates were constructed by the principle of immune recognition and fluorescence quenching between fluorescein labelled antibodies/antigens and antibody-conjugated graphene oxide (GO). An artificial intelligence (AI) protein analysis process was designed by us and accordingly a small program was written in JAVA. This protein analysis process with its JAVA code may be applied to give logic judgments on the possible existing state of two protein components. We expect that our fundamental research on multiple biomarker analysis can provide potential application in AI-assisted medical diagnosis with the interface for remote medical treatment.

Reversible reconfiguration of high-order DNA nanostructures by employing G-quartet toeholds as adhesive units

G-quadruplex structures are becoming useful alternative interaction modules for the assembly of DNA nanomaterials because of their unique inducibility by cations. In this study, we demonstrated a new strategy for the assembly of polymeric DNA nanoarchitectures in the presence of cations, such as K⁺ and Na⁺, by employing G-quartet toeholds at the edges of discrete mini-square DNA building blocks as adhesive units. In comparison with the Watson-Crick base-paired duplex linkers, G-quadruplex arrays embedded in the self-assembled DNA system exhibit higher thermal stability. The morphology of these doughnut-shaped or spherical-shaped DNA nanostructures is highly regulated by the orientation of the folded G-quadruplexes either in parallel or antiparallel orientation in response to different cations. Furthermore, this G-quadruplex-mediated assembly strategy is able to manipulate the cycling of DNA assemblies between discrete and polymeric states by means of introducing cations and chelating agents sequentially. This property enables the reversible manipulation of the DNA-based nanosystems for at least 4 cycles. The G-quadruplex array embedded in this self-assembled DNA system can become a scaffold for functional molecules, as a number of organic molecules and proteins exhibit specific binding to these G-quadruplex structures. Besides, embedded G-quadruplexes are also considered as functional components of nanoscale electronic materials due to their electron transport through the stacked orientation of the G-quartet. Therefore, this work is an important step towards obtaining reversible, responsive G-quadruplex-induced DNA-based nanomaterials with versatile functionalities which will be highly useful in further electronic, biomedical and drug-delivery applications.

Repressor logic modules assembled by rolling circle amplification platform to construct a set of logic gates

Small molecule metabolites and their allosterically regulated repressors play an important role in many gene expression and metabolic disorder processes. These natural sensors, though valuable as good logic switches, have rarely been employed without transcription machinery in cells. Here, two pairs of repressors, which function in opposite ways, were cloned, purified and used to control DNA replication in rolling circle amplification (RCA) in vitro. By using metabolites and repressors as inputs, RCA signals as outputs, four basic logic modules were constructed successfully. To achieve various logic computations based on these basic modules, we designed series and parallel strategies of circular templates, which can further assemble these repressor modules in an RCA platform to realize twelve two-input Boolean logic gates and a three-input logic gate. The RCA-output and RCA-assembled platform was proved to be easy and flexible for complex logic processes and might have application potential in molecular computing and synthetic biology.

Aptamer-Based K(+) Sensor: Process of Aptamer Transforming into G-Quadruplex

G-rich aptamers have been widely applied to develop various sensors for detecting proteins, small molecules, and cations, which is based on the target-induced conformational transfer from single strand to G-quadruplex. However, the transforming process is unclear. Here, with PW17 as an aptamer example, the forming process of G-quadruplex induced by K(+) is investigated by circular dichroism spectroscopy, electrospray ionization mass spectroscopy, and native gel electrophoresis. The results demonstrate that PW17 undergoes a conformational transforming process from loose and unstable to compact and stable G-quadruplex, which is strictly K(+) concentration-dependent. The process contains three stages: (1) K(+) (<0.5 mM) could induce PW17 forming a loose and unstable G-quadruplex; (2) the compact and stable K(+)-stabilized G-quadruplex is almost formed when K(+) is equal to or larger than 7 mM; and (3) when K(+) ranges from 0.5 mM to 7 mM, the transformation of K(+)-stabilized PW17 from loose and unstable to compact and stable occurs. Interestingly, dimeric G-quadruplex through 5'-5' stacking is involved in the forming process until completely formed at 40 mM K(+). Moreover, the total process is thermodynamically controlled. With PW17 as a sensing probe and PPIX as a fluorescent probe for detection of K(+), three linear fluorescent ranges are observed, which corresponds to the three forming stages of G-quadruplex. Clarifying the forming process provides a representative example to deeply understand and further design aptamer-based biosensers and logic devices.

Nuclease-containing media for resettable operation of DNA logic gates

We designed and tested a system that allows DNA logic gates to respond multiple times to the addition of oligonucleotide inputs. After producing an output signal, the system spontaneously resets to the background state. This system does not require any operator action to achieve reset of a DNA logic gate, and may become useful for construction of reusable DNA-based computational devices.

Biomacromolecular logic gate, encoder/decoder and keypad lock based on DNA damage with electrochemiluminescence and electrochemical signals as outputs

Biomacromolecular logic devices including a keypad lock were developed based on the damage of natural DNA in Ru(bpy)₃²⁺ solution.

Construction of DNA logic gates utilizing a H+/Ag+ induced i-motif structure

A simple technology to construct diverse DNA logic gates (OR and INHIBIT) has been designed utilizing a H(+) and/or Ag(+) induced i-motif structure. The logic gates are easily controlled and also show a real time response towards inputs. The research provides a new insight for designing DNA logic gates using an i-motif DNA structure.

Single-molecule electronics: from chemical design to functional devices

The use of single molecules in electronics represents the next limit of miniaturisation of electronic devices, which would enable to continue the trend of aggressive downscaling of silicon-based electronic devices.