30 results about "Nucleic acid secondary structure" patented technology

The invention provides compositions and methods for making closed nucleic acid structures in which one or both strands are continuous. The closed nucleic acid structures can be used as sequencing templates among other applications.

The invention provides a protein synthesis efficiency enhancing RNA element and particularly discloses a nucleic acid structure formed by coding sequences of optional promoters, yeast-derived IRES enhancers (such as ScGPR1, ScFLO8, ScNCE102, ScMSN1, KlFLO8, KlNCE102 and KlMSN1) and heterologous proteins. By application of the nucleic acid structure to a yeast in-vitro protein synthesis system, thesynthesized luciferase activity RLU (relative light unit) is extremely high.

The invention discloses a dual-functional probe and a preparation method and application in detection of a G-quadruplex structure thereof. The probe is simple to prepare, readily available, and stable in structure, and can be used for the specific detection of G-quadruplex nucleic acid secondary structure, and fast detection of the secondary structure of a DNA sample in a solution according to an ultraviolet and visible absorption spectrum, a fluorescence spectrophotometer, or direct visual inspection of naked eyes. The method for detecting the G-quadruplex nucleic acid secondary structure by the probe has the advantages of simple and convenient operation, excellent and fast selectivity, and visibility by naked eyes, and overcomes the defects of high cost and equipment requirement, relatively complex technical operation and the like of other detection methods.

The invention provides a nucleic acid nano structure as well as a preparation method and application thereof. The nucleic acid nano structure is a hexagonal DNA nano structure formed by assembling six triangular DNA paper folding structures constructed by a DNA paper folding technology, and particularly a hexagonal DNA nano structure formed by self-assembling in a mode of carrying out hybridization on scaffold chains and staple chains as well as capturing chains and then respectively carrying out hybridization on connection chains and scaffold chains of six triangular DNA paper folding structures. The nucleic acid nano structure is high in stability, two 80nm gold triangular prisms can be anchored, a prepared golden bow structure can generate a strong electromagnetic field, and single molecule Raman detection is implemented.

The invention discloses a nucleic acid structure of which the interchain exchange is achieved by a support DNA (deoxyribonucleic acid). The nucleic acid structure is a two-dimensional or three-dimensional nucleic acid structure with controllable size and shape, which is formed by achieving interchain exchange by the support DNA. The nucleic acid structure comprises a set of parallel double helices connected by interchain exchange and a single-chain DNA segment, wherein the double helices are formed by carrying out folding and interchain exchange by the support DNA, carrying out specific matching with a plurality of short-chain DNAs and carrying out annealing reaction; and the single-chain DNA is the part of the support DNA which does not form the double helices. The invention provides the multiple nucleic acid structures and synthesis methods thereof. The nucleic acid structure is a variant technique based on DNA paper folding. The invention aims to form the nucleic acid structure with controllable size, shape, complexity and modification by achieving interchain exchange by using the support DNA. The nucleic acid structure is completed by the support DNA/short-chain DNA self-assembly process, and has the advantages of higher yield and simple design; and the predicated two-dimensional and three-dimensional structures can be simultaneously synthesized.

The invention discloses a method for realizing over expression of the thermostable laccase gene through location transformation. Thermostable laccase produced from thermus thermophilus bacteria has great application potential in the industrial processes of pulp bleaching, textile decoloring, biomass hydrolysate detoxifying and the like, but the thermostable laccase gene has low expression level and can not become an enzyme source. In the invention, a carrier in a pHsh series is firstly applied to carrying out cloning, in-situ mutagenesis and induced expression on the laccase gene. By carryingout case analysis and multiple explorative site-directed mutagenesis on a special sequence of the thermostable laccase gene, the invention has the effects of reducing rare codons in the gene, lowering the GC base content and weakening formation of a nucleic acid secondary structure and the like, thereby enhancing the expression level of the gene in escherichia coli by 317 times compared with a natural gene.

The invention relates to a method for implementing targeted cleavage on arbitrary nucleic acid; a structural identification endonuclease is constructed and expressed for establishing the method. The method comprises the concrete steps: selecting a cleavage position of a target nucleic acid, and designing a nucleic acid probe complementary with target nucleic acid; adding into a reaction system, making the probe hybridized with a substrate, and forming a secondary structure which can be identified by the structural identification endonuclease; and adding the enzyme, and carrying out a cleavage reaction. The nucleic acid structure which can be identified includes a nucleic acid intrusive structure and the like; an endonuclease identification functional domain is composed of a peptide fragment which can identify a nucleic acid secondary-structure enzyme and can be selected from E.coliMuts and the like; the cleavage functional domain is selected from a cleavage function of an IIS type endonuclease; a connection fragment between the identification functional domain and the cleavage functional domain of the endonuclease is mainly composed of serine and glycine; and the method breaks through the limit of a sequence of a nucleic acid substrate, so that the method can realize effective targeted cleavage of nucleic acids with different sequences.

The present invention discloses a random nucleic acid editing composition and method. The composition for targeted cleavage of random nucleic acids comprises two main components: a component A: an oligonucleotide probe consists of two parts, one part is complementary to a target substrate, and the other part has a secondary structure of nucleic acids; and a component B: an endonuclease molecule: the endonuclease molecule can recognize the secondary structure of the nucleic acids of the oligonucleotide probe to bind with the probe, and can also cleave a DNA or RNA substrate. The secondary hairpin structure (stem-loop structure) on the oligonucleotide probe can be directly recognized by the endonuclease molecule to form a complex molecule. Probability that the complex molecule collides withthe target substrate is greater than probability that two independently diffused molecules of the probe and the enzyme simultaneously collide with the target substrate, thereby improving gene editingefficiency.

The invention provides a preparation method of a quinoxaline type fluorescent probe and application of the quinoxaline type fluorescent probe in detection of a G-quadruplex. The structural formula ofthe quinoxaline type fluorescent probe is as shown in the specification. In the formula, R1 adopts at least one of N-methylpiperazinyl, morpholinyl and diethylamino, R2 adopts F and methyl, and R3 adopts at least one of F, methyl, N-methylpiperazinyl and triazolyl. Compared with the prior art, the probe provided by the invention has the following advantages: (1) the probe is simple in preparation,easily available, stable in structure and convenient to store; (2) the probe provided by the invention can specifically detect a G-quadruplex structure to distinguish the G-quadruplex structure fromother secondary structures, the secondary structure of a nucleic acid sample can be identified by using a simple fluorescence spectrophotometer or even can be observed with naked eyes without any instrument, the process is fast, the operation is simple and convenient, the cost is low, and field inspection can be realized; and (3) the probe has no obvious influence on the secondary structure of thenucleic acid to be detected, and can accurately detect the original structure of the nucleic acid.

The invention relates to a nucleic acid structure detection method based on surface enhanced Raman spectroscopy. The nucleic acid structure detection method comprises: (1) preparing a silver nanoparticle sol modified and cleaned with iodine ions; and (2) adding a to-be-detected DNA sample to a centrifuge tube filled with the iodine ion modified silver nanoparticle, adding a buffer solution with the PH value of 3.0-5.0, adding an aluminum ion or titanium ion aggregating agent, and carrying out surface enhanced Raman spectroscopy detection. According to the present invention, the method effectively detect the secondary structure of nucleic acid, has the advantages of simpleness, rapidness and the like of SERS, and further has extremely high reproducibility and extremely high reliability; themethod overcomes the difficulty in the detection of the secondary structure of nucleic acid in the traditional SERS detection, has advantages of simple operation steps, rapidness, high sensitivity and good reproducibility, can obtain the signal with the extremely high signal-to-noise ratio, and achieves the high sensitivity detection on various nucleic acid secondary structures.

Nucleic acid hybridization under steady-state conditions is described by a kinetic model in which the intermediate state is assumed to be locally single stranded. An expression was derived that relates nucleic acid secondary structure to the rate of oligonucleotide-RNA hybridization. The model allows the calculation of a rate factor that is proportional to the rate constant for hybridization between complementary nucleic acids and is generally applicable to any RNA molecule with potential utility for rapid identification of sites for antisense attack of mRNA.

The invention discloses a double-stranded DNA (deoxyribonucleic acid)-based helicase activity determination method and application thereof. The method mainly realizes detection based on a nucleic acid secondary structure obtained by single-stranded hybridization of at least two DNAs. The tail end of at least one DNA single chain in the nucleic acid secondary structure is connected with a tail sequence, and the tail ends of any two different DNA single chains in the nucleic acid secondary structure are respectively connected with two substances or groups which are not interfered with each other and are specifically combined. Compared with other helicase detection methods, the detection method provided by the invention has a more accurate helicase activity quantitative effect, does not need tedious steps such as electrophoresis and membrane transfer, shortens the detection time by 3-4 hours, allows simultaneous detection of ATP consumption in the same solution system, and makes helicase activity evaluation more comprehensive.

The invention discloses a composition and a method for regulating any gene expression. The composition comprises an oligonucleotide probe and a protein molecule; the oligonucleotide probe is composed of two parts, one part of the oligonucleotide probe is provided with a nucleic acid secondary structure, the other part of the oligonucleotide probe is basically complementary to a target substrate, and basic groups at certain specific positions are not complementary to the target substrate; the protein molecule can recognize the nucleic acid secondary structure of the oligonucleotide probe, so that the protein molecule is bound with the probe, is guided by the probe and is bound with the target substrate to form a 'target substrate-protein molecule-probe' ternary complex; based on the fact that the basic groups on the certain specific positions of the oligonucleotide probe are not complementary with the target substrate, the protein molecule only has a binding reaction with the target substrate, and a cleavage reaction does not occur. The composition not only acts on a DNA target, but also acts on an RNA target; the composition not only can work in prokaryotic cells, but also can work in eukaryotic cells; and the composition not only can up-regulate gene expression, but also can down-regulate gene expression.

The invention discloses a polyaryl-substituted imidazole fluorescence probe. The structural formula of the polyaryl-substituted imidazole fluorescence probe is shown in the formula (I). The invention further discloses a preparation method of the polyaryl-substituted imidazole fluorescence probe and application of the polyaryl-substituted imidazole fluorescence probe in the specific detection of a G-quadruplex. The fluorescence probe is simple to prepare, stable in structure and can be applied to the specific detection of a wild c-MYC G-quadruplex nucleic acid secondary structure, the raw materials are easily available, the wild c-MYC G-quadruplex nucleic acid secondary structure in a solution can be rapidly detected by virtue of a fluorescence spectrometer, and the fluorescence probe has no fluorescent responsiveness to mutational c-MYC G-quadruplexes or other DNA secondary structures. The method for the specific detection of the wild c-MYC G-quadruplex nucleic acid secondary structure has the beneficial effects that the operation is simple and convenient, the sensitivity and the specificity are strong, and disadvantages of other detection methods that the cost is high, the equipment requirement is high, the technical operation is relatively complex, and the like can be overcome.