WO2016140492A1 - Nouvelle structure adn-arn hybride de type tétraèdre régulier ou structure arn de type tétraèdre - Google Patents

Nouvelle structure adn-arn hybride de type tétraèdre régulier ou structure arn de type tétraèdre Download PDF

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WO2016140492A1
WO2016140492A1 PCT/KR2016/002048 KR2016002048W WO2016140492A1 WO 2016140492 A1 WO2016140492 A1 WO 2016140492A1 KR 2016002048 W KR2016002048 W KR 2016002048W WO 2016140492 A1 WO2016140492 A1 WO 2016140492A1
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rna
dna
sirna
present
tetrahedral
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이동기
강시내
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성균관대학교산학협력단
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    • AHUMAN NECESSITIES
    • A61MEDICAL OR VETERINARY SCIENCE; HYGIENE
    • A61KPREPARATIONS FOR MEDICAL, DENTAL OR TOILETRY PURPOSES
    • A61K47/00Medicinal preparations characterised by the non-active ingredients used, e.g. carriers or inert additives; Targeting or modifying agents chemically bound to the active ingredient
    • A61K47/06Organic compounds, e.g. natural or synthetic hydrocarbons, polyolefins, mineral oil, petrolatum or ozokerite
    • CCHEMISTRY; METALLURGY
    • C12BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12NMICROORGANISMS OR ENZYMES; COMPOSITIONS THEREOF; PROPAGATING, PRESERVING, OR MAINTAINING MICROORGANISMS; MUTATION OR GENETIC ENGINEERING; CULTURE MEDIA
    • C12N15/00Mutation or genetic engineering; DNA or RNA concerning genetic engineering, vectors, e.g. plasmids, or their isolation, preparation or purification; Use of hosts therefor
    • C12N15/09Recombinant DNA-technology
    • C12N15/10Processes for the isolation, preparation or purification of DNA or RNA
    • CCHEMISTRY; METALLURGY
    • C12BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12NMICROORGANISMS OR ENZYMES; COMPOSITIONS THEREOF; PROPAGATING, PRESERVING, OR MAINTAINING MICROORGANISMS; MUTATION OR GENETIC ENGINEERING; CULTURE MEDIA
    • C12N15/00Mutation or genetic engineering; DNA or RNA concerning genetic engineering, vectors, e.g. plasmids, or their isolation, preparation or purification; Use of hosts therefor
    • C12N15/09Recombinant DNA-technology
    • C12N15/11DNA or RNA fragments; Modified forms thereof; Non-coding nucleic acids having a biological activity
    • C12N15/113Non-coding nucleic acids modulating the expression of genes, e.g. antisense oligonucleotides; Antisense DNA or RNA; Triplex- forming oligonucleotides; Catalytic nucleic acids, e.g. ribozymes; Nucleic acids used in co-suppression or gene silencing

Definitions

  • the present invention relates to novel DNA-RNA hybrid tetrahedral constructs or RNA tetrahedral constructs that are capable of inhibiting expression of target genes or utilizing for drug delivery.
  • RNAi RNA interference
  • PTGS post-transcriptional process
  • siRNA small interfering RNA
  • RISC RNA induced silencing complex
  • RNAi units such as miRNA and siRNA have a problem of low intracellular delivery efficiency by themselves.
  • An example of attempts to solve this problem is a method using a positively charged polymer as a carrier. Since nucleic acids are basically negatively charged, they are positively charged polymers, which surround the nucleic acid molecules to create complexes that increase cell membrane permeation efficiency. Representative materials include lipofectamine and PEI. When these materials are treated together, the delivery efficiency is increased, but it is not preferable from the viewpoint of commercialization because it shows high cytotoxicity and requires an additional delivery process.
  • RNA since RNA is inherently low in stability to serum, it is likely to be degraded by RNA degrading enzymes before reaching the target cells. Therefore, even if the RNAi unit shows the result of RNA interference under in vitro conditions, it cannot be guaranteed that the results are reproduced in in vivo conditions, i.
  • the introduction of 2'-O-methyl modification has been reported to increase the stability of RNA degrading enzymes, but in this case there is a problem that the efficiency of RNA interference is lower than the RNAi unit without chemical modification.
  • DNA nanotechnology meanwhile, has evolved into the mainstream of nucleic acid research, pioneering Nadrian Seeman.
  • DNA is attracting attention as an excellent building block because it can easily design the desired structure based on complementary binding between bases and self-assembles only with appropriate buffer and temperature changes.
  • various structures of DNA nanostructures have been reported to exhibit interesting properties such as self-transmission and structural stability in cells.
  • the DNA tetrahedral structure is efficiently delivered within the cell without the aid of a carrier and remains structurally stable within the cell for at least 72 hours after delivery.
  • RNA synthesis technology enables the synthesis of RNA having a length of 50 bases or more.
  • RNA has a biological function that can be seen while preserving the physical properties of DNA nanostructures.
  • the present invention has been completed by synthesizing nanostructures comprising RNA.
  • the present invention provides a DNA-RNA hybrid tetrahedral structure or RNA tetrahedral structure comprising a small interfering RNA (siRNA) or miRNA (microRNA) sequence capable of inhibiting the target gene. .
  • siRNA small interfering RNA
  • miRNA miRNA
  • the DNA-RNA hybrid tetrahedral structure may comprise two or more sequences selected from the group consisting of the nucleotide sequences represented by SEQ ID NOs: 1-4.
  • the RNA tetrahedral structure may comprise two or more sequences selected from the group consisting of nucleotide sequences represented by SEQ ID NOs: 9-12.
  • the target gene may be an oncogene.
  • the present invention also provides a composition for inhibiting target gene expression comprising the tetrahedral construct, and a method for inhibiting target gene expression comprising treating the tetrahedral construct to cells.
  • the present invention provides a drug delivery composition comprising the tetrahedral structure in which a drug is loaded therein.
  • the present invention provides a target gene comprising two or more sequences selected from the group consisting of nucleotide sequences represented by SEQ ID NOs: 1 to 4, or two or more sequences selected from the group consisting of nucleotide sequences represented by SEQ ID NOs: 9 to 12. It provides a method for producing a DNA-RNA hybrid tetrahedral structure or RNA tetrahedral structure comprising the step of annealing with an inhibitory siRNA (small interfering RNA) or miRNA (microRNA) sequence.
  • siRNA small interfering RNA
  • miRNA miRNA
  • the present invention has the advantage of providing a functional RNA structure. That is, by introducing a unit such as siRNA, miRNA to produce a tetrahedral structure, it gives a biological function of RNA, such as RNAi and delivered to the cell through high efficiency through self-transfer and induces RNA interference mechanism to induce cell suicide of the target cell can do.
  • RNAi RNAi
  • the structure of the tetrahedron structure may be changed when a certain stimulus is applied to create a controllable structure in which materials in the pupil are released to the outside.
  • the positively charged polymer has a problem of showing cytotoxicity, but in the case of the DNA-RNA hybrid tetrahedron structure or RNA tetrahedral structure that does not require the carrier of the present invention, the nucleic acid as a component is a biopolymer. Inherently harmless to humans, cytotoxicity can be minimized.
  • RNA nanostructures that induce suicide of target cells using RNA interference can be commercialized as new drugs.
  • Figure 1 shows an example of the combined structure of the additional configuration to increase the potential for use as a therapeutic agent of the tetrahedral structure according to the present invention.
  • FIG. 2 is a view showing various designs of the tetrahedral structure according to the present invention.
  • Figure 3 shows the results confirming the formation of the RNA tetrahedron structure according to the present invention.
  • Figure 4 is a result of confirming the intracellular transfer of DNA and RNA tetrahedron, (a) and (b) is a graph showing the fluorescence intensity measured by flow cytometry, (c) shows an image observed with a fluorescence microscope Will: [TF]; Transfection with transfection reagent, transfection without [IB] transfection reagent.
  • Figure 5 shows a simplified schematic diagram of a DNA-RNA hybrid tetrahedron structure having Survivin as a target gene according to the present invention.
  • Figure 6 is a result of confirming the intracellular self-transmission of the DNA-RNA hybrid tetrahedral structure using Survivin as a target gene according to the present invention.
  • Figure 7 shows a simplified schematic diagram of the DNA-RNA hybrid tetrahedron structure with the target gene Survivin and GFP according to the present invention.
  • Figure 8 shows the results of confirming the gene silencing induction effect of the DNA-RNA hybrid tetrahedral structure according to the present invention.
  • the present invention provides a DNA-RNA hybrid tetrahedron structure or RNA tetrahedral structure, or siRNA (small interfering RNA) capable of inhibiting a target gene, including two or more sequences selected from the group consisting of the nucleotide sequences represented by SEQ ID NOs: 9-12. Or a DNA-RNA hybrid tetrahedral structure or an RNA tetrahedral structure comprising a miRNA (microRNA) sequence.
  • miRNA miRNA
  • RNA nanostructures To prepare RNA nanostructures, the inventors first envisioned a framework that can exhibit interesting properties such as self-transfer.
  • the structure of the present invention is not limited to the tetrahedral skeleton, it can be applied to the production of boxes, nanotubes, etc. that can be opened and closed using a regular polyhedron, a hinge other than the tetrahedron.
  • RNAi unit was conceived to give biochemical functions to RNA nanostructures.
  • the sequence of an siRNA or miRNA can induce cell suicide by inhibiting the expression of various target genes such as, but not limited to, RNA interference mechanisms or other mechanisms.
  • the RNAi-derived siRNA base sequence was introduced into one side of the RNA tetrahedron to prepare a DNA-RNA hybrid tetrahedral structure by an annealing method, using survivin and GFP as target genes. Inhibition of expression of the target was confirmed (see Example 3).
  • the expression of several genes can be simultaneously controlled, thereby maximizing a therapeutic effect.
  • the siRNA capable of inhibiting the target gene may be siRNA such as survivin, GFP, and Luciferase, and may be Sox2, Oct4, etc., which target cancer stem cells.
  • the DNA-RNA hybrid tetrahedral constructs of the present invention can be designed to have six target genes, one to four, more than the number of sides of the tetrahedron. Examples of the design are shown in FIG. 2.
  • 2 (a) and 2 (b) show a simple three-dimensional structure of a nucleic acid tetrahedron having three target genes.
  • 2 (a) and 2 (b) are tetrahedrons in which siRNA sequences of Survivin, GFP, and Luciferase (blue, red, and green) are introduced, respectively, and genes capable of inhibiting target genes using cancer stem cells as target cells It is a tetrahedron with genes such as Sox2 and Oct4.
  • FIG. 2 (c) tetrahedral structures labeled with long-wave dyes such as Cy5 or Cy3 (red) may be used, and FIG. 2 (d) may be used to overcome limitations that may occur in structures or to improve titer. It shows a structure that introduces various moieties. For example, ligands that can target targeted cancer cells to induce targeted delivery, drugs to increase titer, and chemical modifications to increase serum stability can be introduced.
  • materials that may be introduced at the vertices of the tetrahedron may be peptides, targeting ligands, chemical modifications, biomarkers, fluorescent dyes, drugs, and the like.
  • the introduction of the materials can improve the delivery efficiency, enhance the endosome escape, improve the RNA interference efficiency, increase the resistance to serum, improve the targeted delivery, mechanism research, etc. Can be used.
  • FIG. 2 (e) shows an example of a functional nucleic acid tetrahedral structure that has been optimized, and targets one or more target genes, while compensating for the disadvantages of the structure and improving the efficiency of delivery and gene silencing. Proceed to manufacture.
  • Survivin is a representative oncogene used in siRNA research in association with the proliferation of cancer cells, and is a member of the inhibitor of apoptosis family (IAP), also called a baculoviral inhibitor of apoptosis repeat-containing 5 (BIRC5).
  • IAP apoptosis family
  • BIRC5 baculoviral inhibitor of apoptosis repeat-containing 5
  • Survivin proteins function to inhibit apoptosis (or programmed cell death), or cell suicide. Thus, if Survivin protein is not expressed, apoptosis increases and cancer cell growth decreases.
  • Survivin protein is also highly expressed in human cancer cells and fetal tissues, but is not found at all in differentiated cells. Therefore, targeting the Survivin gene is very useful in distinguishing between normal and modified cells to see if only cancer cells can be eliminated.
  • the tetrahedral structure of the present invention may be added to the additional configuration to increase the potential as a therapeutic agent, for example, aptamer or targeting ligand can be delivered specifically to the specific cell.
  • the RNA aptamer may be extended to form a structure, or a ligand that specifically binds to cancer cells such as folic acid may be attached to the vertex of the polyhedron as shown in FIG. 1.
  • an endosome-escape enhancer to the structure of the present invention it is possible to efficiently deliver the structure in the cell.
  • the therapeutic effect can be maximized by incorporating low molecular weight drugs such as anticancer drugs into the cavity of the tetrahedral structure or intercalating between the double strands of nucleic acid.
  • low molecular weight drugs such as anticancer drugs
  • the present invention can provide a target gene expression inhibition or drug delivery use of the tetrahedral structure.
  • the annealing uses a TEM as a buffer, denaturing at a high temperature by using a thermocycler, and then lowering the temperature to induce self-assembly into a designed design through complementary bonding of bases.
  • a TEM as a buffer
  • thermocycler denaturing at a high temperature by using a thermocycler
  • lowering the temperature to induce self-assembly into a designed design through complementary bonding of bases.
  • the strands of Table 1 are each composed of 55 bases, and three pairs of edges forming one vertex of the tetrahedron are composed of 17 bases.
  • SEQ ID NOs: 1 to 4 are described in Russell P. Goodman et al. The single-step synthesis of a DNA tetrahedron (2004, Chem. Commun.).
  • the two bases present between the edges act as a kind of hinge that provides fluidity to the structure, and are two pairs in total because they exist between the edges.
  • the fluorescent substance Cy3 was attached to the 3 'end of SEQ ID NO: 4 through chemical modification so that the transmission efficiency could be confirmed by a fluorescence microscope.
  • Survivin is selected as a target gene for confirming RNAi effect, and in order to hybridize siRNA (siSurvivin) that targets it to tetrahedron, using the SEQ ID NOs 1 and 2 in Table 1, a new sequence with antisense and sense, respectively. Envisioned.
  • the part that becomes the egde in the sequence is 17 bases
  • the universal siRNA siSurvivin
  • SEQ ID NO: 5 and 6 of Table 2 the problem of 19 bases and the 5 'end of the antisense strand ago2
  • AS antisense strand
  • S sense strand
  • RNA strands as shown in Table 3 were synthesized based on the sequence of the DNA tetrahedron of Table 1 to anneal the RNA tetrahedral nanostructures.
  • RNA strand of Table 3 tetrahedral structures were formed according to the experimental method proposed by R. P. Goodman (R. P. Goodman, Chem. Commun., 2004, 1372-1373). More specifically, the method was used to induce annealing by mixing in 1X TEM buffer so that the strand final concentration of 100 ⁇ M was diluted to 1/10, respectively, and placed at 5 ° C. for 5 minutes at 54 ° C., 30 minutes at 95 ° C. and 5 minutes at 4 ° C. If not stored at -20 °C.
  • RNA tetrahedral structure (Oligonucleotide) was formed.
  • electrophoresis was performed for 30 minutes at 150 V using a 6% polyacrylamide gel, and after EtBr staining for about 5 minutes to check the UV image, to determine the formation of tetrahedral nucleic acid structure Confirmed.
  • the band of the RNA tetrahedral structure on the right side (Lane 3) appeared in a higher position than the single-stranded band (Lane 1), the same pattern as the DNA tetrahedron on the left side.
  • RNA tetrahedral structure of the present invention was successfully produced.
  • RNA-Td 10 nM RNA tetrahedron
  • DNA-Td DNA tetrahedron
  • NC3000 Nucleocounter
  • DNA-RNA hybrid tetrahedron substituted with RNAi units of SEQ ID Nos. 2 and 3 using only one side of the tetrahedron with the DNA sequence of Table 1 as a basic skeleton was synthesized by PAGE analysis. It was confirmed.
  • the side of each color corresponds to a sequence of the same color of each strand, and the same index means complementary to each other (anti-parallel).
  • the starting point of the arrow means the 5 'end and the arrow-shaped end means the 3' end.
  • nt sequences of 17 nt were replaced with the sequences of AS and SS of siSurvivin from the 5 'ends of strand2 and strand3, respectively.
  • AS and SS sequences of AS and SS of siSurvivin from the 5 'ends of strand2 and strand3, respectively.
  • 2nt overhang was allowed from the 5 'end.
  • the 5 'end of the AS is designed to be a structure that is open (so that RNA interference can be made intact).
  • this tetrahedron was made of a construct that targets the Survivin gene.
  • the structure was fluoresced by attaching Cy3 to Strand4 among four nucleic acid strands constituting the tetrahedron structure. After annealing, 50 nM of Td-siSurvivin was treated with HeLa cells without a separate transfection reagent. After 4 hours, Cy3 fluorescence images were obtained through a fluorescence microscope. As can be seen in Figure 6, the DNA-RNA hybrid tetrahedral structure showed no fluorescence compared to the control (no treatment, the same media of the same volume only) without any treatment (no Cy3 fluorescence). Therefore, the self-transmission characteristics of the structure were confirmed through this.
  • SEQ ID NOs 1 to 4 of Table 1 above are used.
  • the new sequence was conceived by antisense and sense, respectively.
  • Universal siGFP is as shown in SEQ ID NOs: 13 and 14 in Table 4 below.
  • RNAi units of SEQ ID NOs: 7 and 8 instead of SEQ ID NOs: 2 and 3, and the SEQ ID NOs of Table 4 below instead of SEQ ID NOs: 1 and 4.
  • DNA-RNA hybrid tetrahedra were synthesized by replacing with RNAi units of 15 and 16.
  • this construct is a multi-targeting functional tetrahedral construct that simultaneously inhibits expression of Survivin and GFP proteins.
  • HeLa cells were used as target cells, and the external environment was maintained at 37 ° C. and 5% CO 2 , and DMEM containing 10% FBS, 1% penicillin, and stretomycin was used as a culture medium. HeLa cells were first seeded on 24-well plates overnight. Passage was performed about once every 3 days to allow for confluency.
  • the functional DNA-RNA hybrid tetrahedral construct which targets the Survivin gene as a target gene, was annealed before the experiment. Seeded cells in DMEM media containing 10% serum were washed with opti-mem, a serum-free media, and opti-mem was used as media during incubation.
  • L2K Lipofectamine 2000
  • siSurvivin and Td-siSurvivin were well mixed with L2K and then treated with HeLa cells. Final concentrations were 50 nM each. After incubation for about 4 hours, real-time qPCR was used to determine the mRNA levels of survivin genes.
  • Td-siSurvivn was found to induce gene silencing with an efficiency similar to siSurvivin.
  • Td-DNA DNA tetrahedral structure without the RNAi unit
  • the gene expression was not inhibited in the same manner as when no treatment was performed (0nM).
  • DNA-RNA hybrid tetrahedron treatment Td-DNA / siRNA
  • knockdown was almost the same level as siRNA (siSurvivin).
  • the DNA-RNA hybrid tetrahedral structure according to the present invention shows excellent gene silencing induction effect.
  • the present invention can provide functional RNA constructs.
  • siRNA and miRNA units to produce tetrahedral structures, it is possible to induce cell suicide of target cells by giving RNA functionalities such as RNAi and delivering them with high efficiency through self-transfer and inducing RNA interference mechanism.
  • RNA functionalities such as RNAi
  • RNAi RNA functionalities
  • RNAi RNAi
  • RNAi RNAi
  • RNA interference mechanism RNA interference mechanism
  • the structure of the tetrahedron structure is changed, thereby making a controllable structure in which materials in the pupil are released to the outside.
  • DNA-RNA hybrid tetrahedral constructs or RNA tetrahedral constructs that do not require the carrier of the present invention can be minimized because cytotoxicity as a constituent nucleic acid is essentially harmless to the human body as a biopolymer. Therefore, the technology of the present invention can provide a cornerstone of the development of new nucleic acid drugs as a source technology in the pharmaceutical technology industry. For example, it may be commercialized as a new drug by preparing RNA nanostructures that cause suicide of target cells using RNA interference.

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Abstract

La présente invention concerne une nouvelle structure ADN-ARN hybride de type tétraèdre régulier ou une structure ARN de type tétraèdre qui peut être utilisée pour inhiber l'expression d'un gène cible ou administrer un médicament et, plus spécifiquement, une structure ADN-ARN hybride de type tétraèdre régulier ou une structure ARN de type tétraèdre contenant des séquences de petits ARN interférents (ARNsi) ou de microARN (miARN) d'un gène cible. Un ARNsi ou miARN est introduit dans une nanostructure ARN fonctionnelle selon l'invention, la structure étant administrée dans une cellule par auto-administration à un rendement élevé, et pouvant donner naissance à mécanisme d'interférence ARN pour induire l'apoptose d'une cellule cible. De plus, l'invention concerne une structure contrôlable dans laquelle un médicament est libéré à l'extérieur par support dudit médicament dans ses pores. Une nanostructure ARN menant à l'apoptose d'une cellule cible peut également être préparée à l'aide de l'interférence d'ARN obtenue avec la technologie selon l'invention à titre de technologie originale, ladite nanostructure ARN devant être commercialisée à titre de nouveau médicament.
PCT/KR2016/002048 2015-03-02 2016-03-02 Nouvelle structure adn-arn hybride de type tétraèdre régulier ou structure arn de type tétraèdre WO2016140492A1 (fr)

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KR1020160024040A KR101804039B1 (ko) 2015-03-02 2016-02-29 신규 dna-rna 하이브리드 정사면체 구조물 또는 rna 정사면체 구조물

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CN107727705A (zh) * 2017-09-28 2018-02-23 东南大学 一种酶反应检测纳米孔电学传感器
CN108721634A (zh) * 2018-05-30 2018-11-02 郑州大学 一种双靶点dna纳米治疗体系的构建方法及应用
CN111298129A (zh) * 2019-08-28 2020-06-19 中国人民解放军陆军军医大学第二附属医院 二甲双胍介导核酸纳米材料自组装方法及采用该方法制备的纳米制剂和应用
CN111803511A (zh) * 2020-06-12 2020-10-23 南京邮电大学 Dna四面体核酸框架型胃癌诊疗一体化试剂及其制备方法和应用
CN115121803A (zh) * 2021-03-11 2022-09-30 上海交通大学医学院附属仁济医院 一种基于dna框架结构的多聚纳米团簇的合成方法
WO2023043239A1 (fr) * 2021-09-15 2023-03-23 올릭스 주식회사 Arn double brin présentant un effet d'induction d'une réponse immunitaire innée, et utilisation associée

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Cited By (10)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
CN107727705A (zh) * 2017-09-28 2018-02-23 东南大学 一种酶反应检测纳米孔电学传感器
CN107727705B (zh) * 2017-09-28 2019-12-10 东南大学 一种酶反应检测纳米孔电学传感器
CN108721634A (zh) * 2018-05-30 2018-11-02 郑州大学 一种双靶点dna纳米治疗体系的构建方法及应用
CN108721634B (zh) * 2018-05-30 2021-06-04 郑州大学 一种双靶点dna纳米治疗体系的构建方法及应用
CN111298129A (zh) * 2019-08-28 2020-06-19 中国人民解放军陆军军医大学第二附属医院 二甲双胍介导核酸纳米材料自组装方法及采用该方法制备的纳米制剂和应用
CN111803511A (zh) * 2020-06-12 2020-10-23 南京邮电大学 Dna四面体核酸框架型胃癌诊疗一体化试剂及其制备方法和应用
CN111803511B (zh) * 2020-06-12 2022-11-08 南京邮电大学 Dna四面体核酸框架型胃癌诊疗一体化试剂及其制备方法和应用
CN115121803A (zh) * 2021-03-11 2022-09-30 上海交通大学医学院附属仁济医院 一种基于dna框架结构的多聚纳米团簇的合成方法
CN115121803B (zh) * 2021-03-11 2024-04-30 上海交通大学医学院附属仁济医院 一种基于dna框架结构的多聚纳米团簇的合成方法
WO2023043239A1 (fr) * 2021-09-15 2023-03-23 올릭스 주식회사 Arn double brin présentant un effet d'induction d'une réponse immunitaire innée, et utilisation associée

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