13 results about "Dna strand displacement" patented technology

The invention discloses construction and application of a biosensor for triggering controlled release based on adjacent induced DNA strand displacement, and belongs to the technical fields of electrochemical luminescence, biological analysis and nano science. According to the invention, by integrating adjacent induced DNA strand displacement and controlled release strategies, the ultra-sensitive self-closing dual-mode biosensor taking the Au-Ag nanocluster as a luminous body is developed, and the ultra-sensitive self-closing dual-mode biosensor is used for trace detection of neuron-specific enolase. Due to the synergistic characteristic between the double metals, the Au-Ag nanocluster has high electrochemical luminescence (ECL) efficiency. Meanwhile, the reduction of S2O8 < 2-> is catalyzed by cyclic conversion between Fe < 2 + > / Mn < 3 + > and Fe < 3 + > / Mn < 4 + >, and a large amount of SO4 <-> is generated for ECL emission. The specific binding between the target antigen and the antibody can drive DNA strand displacement to open a blocked hole, so that the electrochemical probe falls off and the probe is quenched to release, the self-closing of an electrochemical signal and an ECL signal is realized, the detection sensitivity and accuracy of the sensor are effectively improved, and the sensor is suitable for immunoassay of various biomarkers.

This invention discloses a method for implementing a novel biomolecular controller based on DNA strand substitution, comprising: modeling the enzymatic protein hydrolysis process using abstract chemical reactions; constructing a Brink controller BC based on a covalently modified cycle CMC; constructing a covalently modified cycle CMC-D with a direct positive self-regulating PAR structure; obtaining an improved Brink controller BC-DPAR using abstract CRNs; constructing a covalently modified cycle CMC-I with an indirect PAR structure; obtaining an improved Brink controller BC-IPAR using abstract CRNs; constructing an enzymatic protein hydrolysis model based on CRNs using a DNA strand substitution reaction; constructing controllers BC, BC-DPAR, and BC-IPAR respectively through the DNA strand substitution mechanism; and constructing different control schemes based on the differences between the controllers according to the enzymatic protein hydrolysis model. This invention utilizes the DNA strand substitution mechanism to realize control schemes for the enzymatic protein hydrolysis process under different controllers, which improves the output effect of hydrolysis products to a certain extent and can achieve the expected output level more quickly.

The application belongs to the technical field of biological computing, and discloses a ternary addition system and a computing method based on DNA strand displacement, which comprises an input unit, a computing unit and an output unit. The input unit adds the input information to the corresponding computing module. The computing unit comprises nine modules, each of which is provided with a competitive blocking circuit and a carry computing gate, and dynamically selects a result bit 1 or 2 and generates a carry signal. The output unit outputs the digital information of 0-2 according to the fluorescent signal of the result bit, extracts the next bit carry information generated by the carry computation, amplifies the signal and then adds it to the next bit computation. The application breaks through the limitation of the number of DNA computing bits through the cooperation of the ternary gate control architecture and the fuel chain amplification, can accurately calculate the ternary addition, can expand the number of bits calculated, can realize 10-bit addition operation, and can be integrated with the expansion of the multiplication logic, thereby providing a universal framework for the molecular arithmetic unit.

The application provides a method for building a 9-bit parity check molecular switch circuit, and the steps are as follows: based on DNA strand displacement technology, the structure and reaction mechanism of the molecular switch circuit are described; the reaction rate and leakage rate are set, and the input signal of the molecular switch circuit and the concentration ratio of the molecular switch at each stage are optimized; the fan-in molecular switch circuit and the fan-out molecular switch circuit are set according to the molecular switch circuit; the 3-bit parity check molecular switch circuit is built based on the fan-in molecular switch circuit and the fan-out molecular switch circuit by using the switch canvas routing strategy, the 9-bit parity check molecular switch circuit is built by using three 3-bit parity check molecular switch circuits with the same structure; and the correctness of the 9-bit parity check molecular switch circuit is verified by using a Simbiology simulation platform. In the construction of a large-scale complex logic circuit, the application has a simple and unified DNA chain structure, a fast reaction speed and good stability, and provides a new scheme for the construction of a modular DNA circuit.

The invention provides a microfluidic chip and method based on DNA strand displacement neurons and electronic equipment, the chip comprises a data acquisition module, a microfluidic module and at least one DNA strand displacement module, the microfluidic module is respectively connected with the data acquisition module and the DNA strand displacement module, and the data acquisition module is connected with the DNA strand displacement module; the data acquisition module is used for acquiring a DNA single strand to be replaced and at least one replacement neuron; the replacement neuron is used for carrying out primary replacement on the DNA single strand to be replaced; the micro-fluidic module is used for driving a DNA single strand to be replaced and a replacement neuron to move from the data acquisition module to the DNA strand replacement module; the DNA strand replacement module is used for determining a target DNA single strand after the DNA single strand to be replaced is replaced on the basis of the DNA single strand to be replaced and each replacement neuron; the target DNA single strand is used for identifying the DNA single strand to be replaced. According to the invention, miniaturization and automation of replacement operation are realized in an integrated chip, DNA molecular signals are detected in time, and the detection precision of DNA molecules is improved.

Multiplexed fluorescent imaging methods are essential for resolving cellular transcriptional state with high resolution spatial information, but multiplexity is mostly limited to low numbers because of spectral overlap between the fluorophores that can be used. Although sequential fluidic exchange of DNA imagers expands its multiplexity, it requires time-consuming workflows and complex instrumentation. To eliminate such problems, here the toehold-FISH method as well as pre-programmed DNA probes is introduced, which is a novel imaging method that uses rapid and orthogonal DNA strand displacement reactions to enable highly multiplexed RNA imaging without buffer exchange steps and necessary accessories. In toehold-FISH, signal switching from one RNA target to the next is achieved by strand displacement reactions with sequentially added non- fluorescent DNA displacer strands, which take less than 30 seconds to complete signal switching in fixed cells. Because of vast sequence design space of DNA probes, unlimited multiplexity can be achieved.

This invention relates to a novel image encryption method based on DNA strand displacement reaction rules, belonging to the field of information processing and encryption technology. The method involves constructing a cross-hybrid coupled mapping lattice chaotic system; generating a key using the original image, and then assigning the key to the chaotic system as an initial value; iterating the chaotic system to generate a chaotic sequence, and using the chaotic sequence to generate DNA strand displacement reaction rules; generating an S-box using a bijective function; scrambling the original image using the S-box; and performing DNA encryption on the scrambled image using the DNA strand displacement reaction rules to obtain a ciphertext image. This encryption algorithm effectively improves the information security of the ciphertext image and is resistant to brute force cracking and various statistical attacks.

The application discloses a kind of based on DNA chain replacement's delayed enzymatic reaction ultra-sensitive Brink control implementation method, comprising: with single molecule and bimolecular chemical reaction to describe enzymatic reaction process, introduce time delay factor, obtain the enzymatic reaction process model with time delay;Brink controller based on CRN is constructed;The static mapping expression between the output of the Brink controller and the system output under steady-state condition is obtained, and then the analytical condition for ensuring the performance of the controller is obtained;The construction of Brink controller is realized using DNA strand displacement reaction;Through DNA strand displacement mechanism, and based on delay material and compensation mechanism, obtain time delay representation, apply the time delay representation to the DNA implementation of enzymatic reaction process model;At the same time, in combination with the constructed Brink controller, the control of rewritten enzymatic reaction process model is realized.The application does not involve subtraction operation in structure, reduces the number of abstract chemical reactions required for implementation, greatly simplifies the complexity of DNA implementation.

The invention discloses a method for accelerating DNA strand displacement reaction by using n-butyl alcohol, and belongs to the technical field of nucleic acid reaction. The method comprises the following steps: providing a water-phase DNA solution containing an input chain and double-chain compound; under proper conditions, the aqueous-phase DNA solution is in full contact with n-butyl alcohol, so that an input chain and a bottom chain of the double-chain compound are subjected to complementary pairing, a top chain is released, and the DNA chain replacement reaction is completed. Instantaneous phase separation and dehydration concentration of a water phase / an organic phase are carried out on a system by utilizing n-butyl alcohol, and the effective concentration and the molecular collision frequency of DNA molecules are instantaneously improved, so that the reaction rate of DNA strand displacement is remarkably accelerated. The method can provide a new strategy for DNA calculation and acceleration of a nucleic acid molecule logic circuit.

The application discloses a parameter-unknown chaotic system adaptive synchronization control method based on DNA strand displacement, and comprises the following steps: a chemical reaction module of a nonlinear differential equation with square terms and product terms is obtained by describing emergent reactions, trigger reactions and degradation reaction processes through double-molecule chemical reactions; a Yang chaotic system is constructed by using a DNA strand displacement reaction; an adaptive controller capable of realizing synchronization and an adaptive law expression for unknown parameter estimation are obtained; and the effectiveness of the adaptive controller is verified according to the Lyapunov stability principle. Through the DNA strand displacement mechanism, an internal synchronization mode without the participation of an external chaotic system, i.e. the synchronization between subsystems in a chaotic system, is realized; and under random reactions or other disturbances, the synchronization between the subsystems and the estimation of the unknown parameters by the adaptive law are verified. The method has robustness to parameter deviation, and through triggering a series of DNA reactions, different one-to-one and one-to-many combinations between the subsystems are synchronized.

Nucleic acid strand displacement systems and methods for detecting presence or absence of cleavage of an endonuclease cleavage site. In an example, nucleic acid strand displacement systems comprise a nucleic acid molecule comprising: a toehold region; an endonuclease recognition cleavage site; and a toehold blocker region configured to couple to the toehold region, wherein the toehold blocker region is further configured to release from the toehold region when a cleavage occurs at the endonuclease recognition cleavage site. In an example, the system comprises a signal nucleic acid molecule configured to couple to a signal complementary region of the nucleic acid molecule. In an example, the signal nucleic acid molecule further comprises a fluorophore tag configured to generate detectable signal. In an example, the nucleic acid molecule further comprises a quencher tag configured to quench the detectable signal when the nucleic acid molecule is coupled to the signal nucleic acid molecule.

The invention belongs to the technical field of biological computing, and discloses a general graph problem solving method and system based on DNA strand displacement, and the method comprises the steps: S1, carrying out graph structure modeling, and carrying out graph representation module based on DNA strand displacement; s2, constructing a detection module, and realizing parallel biochemical identification of constraint conditions by using a detection gate D (u) containing a fluorescence label; and S3, carrying out parallel detection on candidate solutions, supporting a unified solution framework of problems such as a minimum control set and a maximum independent set, and realizing rapid screening of the solutions through candidate solution enumeration and a fluorescence signal criterion. The method and the system provided by the invention adopt a modular cascade structure, realize direct solution of a complex problem on the premise of not depending on electronic calculation conversion, compress a solution space in combination with a graph feature value preprocessing technology, have the technical advantages of high neighborhood recognition accuracy, strong leakage reaction inhibition, strong experimental process universality and the like, and have a wide application prospect. And the application efficiency and stability of DNA calculation in the field of combinatorial optimization are remarkably improved.

Multiplexed fluorescent imaging methods are essential for resolving cellular transcriptional state with high resolution spatial information, but multiplexity is mostly limited to low numbers because of spectral overlap between the fluorophores that can be used. Although sequential fluidic exchange of DNA imagers expands its multiplexity, it requires time-consuming workflows and complex instrumentation. To eliminate such problems, here the toehold-FISH method as well as pre-programmed DNA probes is introduced, which is a novel imaging method that uses rapid and orthogonal DNA strand displacement reactions to enable highly multiplexed RNA imaging without buffer exchange steps and necessary accessories. In toehold-FISH, signal switching from one RNA target to the next is achieved by strand displacement reactions with sequentially added non- fluorescent DNA displacer strands, which take less than 30 seconds to complete signal switching in fixed cells. Because of vast sequence design space of DNA probes, unlimited multiplexity can be achieved.