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Ma PQ, Huang FW, Xie YQ, Li HR, Li HD, Ye BC, Yin BC. Universal DNA-Based Sensing Toolbox for Programming Cell Functions. J Am Chem Soc 2023; 145:28224-28232. [PMID: 38108623 DOI: 10.1021/jacs.3c11232] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2023]
Abstract
By recombining natural cell signaling systems and further reprogramming cell functions, use of genetically engineered cells and bacteria as therapies is an innovative emerging concept. However, the inherent properties and structures of the natural signal sensing and response pathways constrain further development. We present a universal DNA-based sensing toolbox on the cell surface to endow new signal sensing abilities for cells, control cell states, and reprogram multiple cell functions. The sensing toolbox contains a triangular-prismatic-shaped DNA origami framework and a sensing core anchored inside the internal confined space to enhance the specificity and efficacy of the toolbox. As a proof of principle, the sensing toolbox uses the customizable sensing core with signal sensing switches and converters to recognize unconventional signal inputs, deliver functional components to cells, and then control cell responses, including specific tumor cell death, immune cell disinhibition and adhesion, and bacterial expression. This work expands the diversity of cell sensing signals and reprograms biological functions by constructing nanomechanical-natural hybrid cells, providing new strategies for engineering cells and bacteria in diagnosis and treatment applications.
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Affiliation(s)
- Pei-Qiang Ma
- Lab of Biosystem and Microanalysis, State Key Laboratory of Bioreactor Engineering, Shanghai Collaborative Innovation Center for Biomanufacturing Technology, East China University of Science and Technology, Shanghai 200237, China
| | - Fu-Wen Huang
- Lab of Biosystem and Microanalysis, State Key Laboratory of Bioreactor Engineering, Shanghai Collaborative Innovation Center for Biomanufacturing Technology, East China University of Science and Technology, Shanghai 200237, China
| | - Ya-Qi Xie
- Lab of Biosystem and Microanalysis, State Key Laboratory of Bioreactor Engineering, Shanghai Collaborative Innovation Center for Biomanufacturing Technology, East China University of Science and Technology, Shanghai 200237, China
| | - Hong-Rui Li
- Lab of Biosystem and Microanalysis, State Key Laboratory of Bioreactor Engineering, Shanghai Collaborative Innovation Center for Biomanufacturing Technology, East China University of Science and Technology, Shanghai 200237, China
| | - Hua-Dong Li
- Lab of Biosystem and Microanalysis, State Key Laboratory of Bioreactor Engineering, Shanghai Collaborative Innovation Center for Biomanufacturing Technology, East China University of Science and Technology, Shanghai 200237, China
| | - Bang-Ce Ye
- Lab of Biosystem and Microanalysis, State Key Laboratory of Bioreactor Engineering, Shanghai Collaborative Innovation Center for Biomanufacturing Technology, East China University of Science and Technology, Shanghai 200237, China
- Institute of Engineering Biology and Health, Collaborative Innovation Center of Yangtze River Delta Region Green Pharmaceuticals, College of Pharmaceutical Sciences, Zhejiang University of Technology, Hangzhou, Zhejiang 310014, China
| | - Bin-Cheng Yin
- Lab of Biosystem and Microanalysis, State Key Laboratory of Bioreactor Engineering, Shanghai Collaborative Innovation Center for Biomanufacturing Technology, East China University of Science and Technology, Shanghai 200237, China
- School of Chemistry and Chemical Engineering, Shihezi University, Shihezi, Xinjiang 832000, China
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2
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Ma L, Tao X, Wang W, Jiao J, Pu Y, Yang G, Liu L, Fang Y, Wu J, Sun W. Genome-wide identification of RNA recognition motif (RRM1) in Brassica rapa and functional analysis of RNA-binding protein (BrRBP) under low-temperature stress. BMC PLANT BIOLOGY 2023; 23:621. [PMID: 38057714 DOI: 10.1186/s12870-023-04639-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/09/2023] [Accepted: 11/29/2023] [Indexed: 12/08/2023]
Abstract
BACKGROUND The RNA recognition motif (RRM) is primarily engaged in the processing of mRNA and rRNA following gene transcription as well as the regulation of RNA transport; it is critical in preserving RNA stability. RESULTS In this study, we identified 102 members of the RRM1 gene family in Brassica rapa, which were dispersed across 10 chromosomes with the ninth chromosome being the most extensively distributed. The RRM1 gene family members of Brassica rapa and Arabidopsis thaliana were grouped into 14 subclades (I-XIV) using phylogenetic analysis. Moreover, the results of transcriptome analysis and RT-qPCR indicated that the expression of Brapa05T000840 was upregulated in the cultivars 'Longyou 7' and 'Longyou 99' following exposure to cold stress at a temperature of 4 °C for 24 h. The levels of expression in the leaves and growth cones of the 'Longyou 7' variety were found to be significantly higher than those observed in the 'Longyou 99' variety under conditions of low temperature and NaCl stress. It illustrates the involvement of the RRM1 gene in the physiological response to both low temperature and salt stress. In addition, it was observed that the survival rate of transgenic BrRBP (Brapa05T000840) Arabidopsis thaliana plants was notably higher compared to that of wild-type plants when subjected to varying durations of low temperature treatment. Furthermore, the expression of the BrRBP gene in transgenic plants exhibited an upward trend as the duration of low temperature treatment increased, reaching its peak at 24 h. The in-vivo enzymatic activity of reactive oxygen species-scavenging enzymes were found to be significantly elevated in comparison to wild-type plants, suggesting that the BrRBP gene may enhance the cold tolerance of Arabidopsis thaliana. CONCLUSIONS This study offers a significant foundation for comprehending the regulation mechanism of the RRM1 gene family in winter Brassica rapa subjected to cold stress, as well as for finding key genes associated with cold resistance.
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Affiliation(s)
- Li Ma
- State Key Laboratory of Aridland Crop Science, Gansu Agricultural University, Lanzhou, 730070, China
| | - Xiaolei Tao
- State Key Laboratory of Aridland Crop Science, Gansu Agricultural University, Lanzhou, 730070, China
- College of Agronomy, Gansu Agricultural University, Lanzhou, 730070, China
| | - Wangtian Wang
- State Key Laboratory of Aridland Crop Science, Gansu Agricultural University, Lanzhou, 730070, China
| | - Jintang Jiao
- State Key Laboratory of Aridland Crop Science, Gansu Agricultural University, Lanzhou, 730070, China
- College of Agronomy, Gansu Agricultural University, Lanzhou, 730070, China
| | - Yuanyuan Pu
- State Key Laboratory of Aridland Crop Science, Gansu Agricultural University, Lanzhou, 730070, China
- College of Agronomy, Gansu Agricultural University, Lanzhou, 730070, China
| | - Gang Yang
- State Key Laboratory of Aridland Crop Science, Gansu Agricultural University, Lanzhou, 730070, China
- College of Agronomy, Gansu Agricultural University, Lanzhou, 730070, China
| | - Lijun Liu
- State Key Laboratory of Aridland Crop Science, Gansu Agricultural University, Lanzhou, 730070, China
| | - Yan Fang
- State Key Laboratory of Aridland Crop Science, Gansu Agricultural University, Lanzhou, 730070, China
| | - Junyan Wu
- State Key Laboratory of Aridland Crop Science, Gansu Agricultural University, Lanzhou, 730070, China.
- College of Agronomy, Gansu Agricultural University, Lanzhou, 730070, China.
| | - Wancang Sun
- State Key Laboratory of Aridland Crop Science, Gansu Agricultural University, Lanzhou, 730070, China.
- College of Agronomy, Gansu Agricultural University, Lanzhou, 730070, China.
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Malecka K, Ferapontova EE. Femtomolar Detection of Thrombin in Serum and Cerebrospinal Fluid via Direct Electrocatalysis of Oxygen Reduction by the Covalent G4-Hemin-Aptamer Complex. ACS APPLIED MATERIALS & INTERFACES 2021; 13:37979-37988. [PMID: 33878266 DOI: 10.1021/acsami.1c03784] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
Thrombin, a serine protease playing a central role in the coagulation cascade reactions and a potent neurotoxin produced by injured brain endothelial cells, is a recognized cardiac biomarker and a critical biomarker for Alzheimer's disease development. Both in vivo and in vitro, its low physiological concentrations and nonspecific binding of other components of physiological fluids complicate electroanalysis of thrombin. Here, femtomolar levels of thrombin in serum and an artificial cerebrospinal fluid (CSF) were detected by the indicator-free electrochemical methodology exploiting the O2 reduction reaction directly, with no electron transfer mediators, electrocatalyzed by the covalent G4-hemin DNAzyme complex naturally self-assembling upon thrombin binding to the hemin-modified 29-mer DNA aptamer sequence tethered to gold via an alkanethiol linker. Coadsorbed PEG inhibited nonspecific protein binding and allowed the sought signal resolution. The proposed assay exploiting the "oxidase" activity of G4-hemin DNAzyme does not require any coreactants necessary for the traditional peroxidase activity-based assays with this DNAzyme, such as H2O2 and redox mediators, or solution deaeration and allows fast, overall 30 min analysis of thrombin in aerated buffer, CSF, and 1% human serum solutions. This pioneer approach exploiting the oxidase activity G4-hemin DNAzyme is simple, sensitive, and selective and represents a new tool for ultrasensitive electrocatalytic assays based on simple and efficient O2-dependent DNAzyme labels.
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Affiliation(s)
- Kamila Malecka
- Interdisciplinary Nanoscience Center (iNANO), Science and Technology, Aarhus University, Gustav Wieds Vej 1590-14, Aarhus C DK-8000, Denmark
- Institute of Animal Reproduction and Food Research, Polish Academy of Sciences, Tuwima 10, Olsztyn 10-748, Poland
| | - Elena E Ferapontova
- Interdisciplinary Nanoscience Center (iNANO), Science and Technology, Aarhus University, Gustav Wieds Vej 1590-14, Aarhus C DK-8000, Denmark
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4
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Citartan M. Aptamers as the powerhouse of dot blot assays. Talanta 2021; 232:122436. [PMID: 34074421 DOI: 10.1016/j.talanta.2021.122436] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2021] [Revised: 04/13/2021] [Accepted: 04/15/2021] [Indexed: 12/21/2022]
Abstract
Dot blot assays have always been associated with antibodies as the main molecular recognition element, which are widely employed in a myriad of diagnostic applications. With the rising of aptamers as the equivalent molecular recognition elements of antibodies, dot blot assays are also one of the diagnostic avenues that should be scrutinized for their amenability with aptamers as the potential surrogates of antibodies. In this review, the stepwise procedures of an aptamer-based dot blot assays are underscored before reviewing the existing aptamer-based dot blot assays developed so far. Most of the applications center on monitoring the progress of SELEX and as the validatory assays to assess the potency of aptamer candidates. For the purpose of diagnostics, the current effort is still languid and as such possible suggestions to galvanize the move to spur the aptamer-based dot blot assays to a point-of-care arena are discussed.
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Affiliation(s)
- Marimuthu Citartan
- Advanced Medical & Dental Institute (AMDI), Universiti Sains Malaysia, Bertam, 13200, Kepala Batas, Penang, Malaysia.
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Burkin KM, Bodulev OL, Gribas AV, Sakharov IY. One-step label-free chemiluminescent assay for determination of exonuclease III activity towards hairpin oligonucleotides. Enzyme Microb Technol 2019; 131:109419. [PMID: 31615661 DOI: 10.1016/j.enzmictec.2019.109419] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2019] [Revised: 08/27/2019] [Accepted: 08/29/2019] [Indexed: 02/06/2023]
Abstract
Fast label-free chemiluminescent assay for determination of exonuclease III (ExoIII) activity measured towards hairpin oligonucleotide substrates was developed. The designed substrates consisted of EAD2 aptamer to hemin which was associated with DNA sequence complementary to 5'-terminus fragment of EAD2. In the presence of ExoIII the associated sequence of the hairpin stem was digested, producing EAD2 aptamer which reacted with hemin with the formation of peroxidase-mimicking DNAzyme (PMDNAzyme). The catalytic activity of the produced PMDNAzyme was measured towards luminol/H2O2. Under the optimized conditions the limit of detection and sensitivity of the one-step chemiluminescent assay of ExoIII were 7.3 nM and 1.7 × 108 M-1, respectively. The coefficient of variation (CV) was lower than 6%.
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Affiliation(s)
- Konstantin M Burkin
- Department of Chemistry, Lomonosov Moscow State University, Leninskie gory, bldg.1, Moscow 119991, Russia
| | - Oleg L Bodulev
- Department of Chemistry, Lomonosov Moscow State University, Leninskie gory, bldg.1, Moscow 119991, Russia
| | - Anastasia V Gribas
- Department of Chemistry, Lomonosov Moscow State University, Leninskie gory, bldg.1, Moscow 119991, Russia
| | - Ivan Yu Sakharov
- Department of Chemistry, Lomonosov Moscow State University, Leninskie gory, bldg.1, Moscow 119991, Russia.
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6
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Xing Y, Liu X, Pu Q, Wu M, Zhao JX. Biocompatible G-Quadruplex/Hemin for Enhancing Antibacterial Activity of H2O2. ACS APPLIED BIO MATERIALS 2018; 1:1019-1027. [DOI: 10.1021/acsabm.8b00211] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Affiliation(s)
- Yuqian Xing
- Department of Chemistry, University of North Dakota, Grand Forks, North Dakota 58202, United States
| | - Xiao Liu
- Department of Chemistry, University of North Dakota, Grand Forks, North Dakota 58202, United States
| | - Qinqin Pu
- Department of Biomedical Sciences, School of Medicine and Health Sciences, University of North Dakota, Grand Forks, North Dakota 58202, United States
| | - Min Wu
- Department of Biomedical Sciences, School of Medicine and Health Sciences, University of North Dakota, Grand Forks, North Dakota 58202, United States
| | - Julia Xiaojun Zhao
- Department of Chemistry, University of North Dakota, Grand Forks, North Dakota 58202, United States
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7
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Bodulev OL, Sakharov IY. Chemiluminescent Determination of MicroRNA-141 Using Target-Dependent Activation of the Peroxidase-Mimicking DNAzyme. ANAL LETT 2018. [DOI: 10.1080/00032719.2018.1498506] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
Affiliation(s)
- Oleg L. Bodulev
- Department of Chemistry, Lomonosov Moscow State University, Moscow, Russia
| | - Ivan Yu Sakharov
- Department of Chemistry, Lomonosov Moscow State University, Moscow, Russia
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Kosman J, Żukowski K, Juskowiak B. Comparison of Characteristics and DNAzyme Activity of G4⁻Hemin Conjugates Obtained via Two Hemin Attachment Methods. Molecules 2018; 23:molecules23061400. [PMID: 29890720 PMCID: PMC6100319 DOI: 10.3390/molecules23061400] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2018] [Revised: 05/30/2018] [Accepted: 06/07/2018] [Indexed: 11/16/2022] Open
Abstract
Two conjugation methods using different linkers were applied for the investigation of the spectral characteristics and activity of G-quadruplex (G4)–hemin conjugates. For this purpose, two G-quadruplex-forming DNA sequences were selected, and then conjugated to a hemin molecule via either amine coupling or a click reaction. The products obtained via these two methods differed in their chemistry and the length of the linker between the DNA and hemin molecules. Spectral characteristics revealed that both methods produced conjugates that were more thermally stable than G4/hemin complexes. Despite similar spectral characteristics, the conjugates obtained via these two methods differed in their DNAzyme activity. G4–hemin conjugates obtained through amine coupling exhibited higher activity than conjugates obtained through a click reaction. This was potentially due to the length and chemistry of the linker, which was 30 atoms long following the click reaction, but only six atoms long following amine coupling. A longer connector favors higher flexibility, and hence, reduces the binding of hemin with G4. The aromatic groups present in the linker obtained through the click reaction can also disturb the G4–hemin interaction. However, the conjugation of G4 DNA to hemin via the click reaction was connected to a higher yield, and did not require any sophisticated synthesis equipment.
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Affiliation(s)
- Joanna Kosman
- Laboratory of Bioanalytical Chemistry, Faculty of Chemistry, Adam Mickiewicz University, Umultowska 89b, 61-614 Poznań, Poland.
| | - Krzysztof Żukowski
- Laboratory of Bioanalytical Chemistry, Faculty of Chemistry, Adam Mickiewicz University, Umultowska 89b, 61-614 Poznań, Poland.
| | - Bernard Juskowiak
- Laboratory of Bioanalytical Chemistry, Faculty of Chemistry, Adam Mickiewicz University, Umultowska 89b, 61-614 Poznań, Poland.
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9
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Gribas AV, Sakharov IY. Homogeneous Chemiluminescent Determination of Mercury(II) Using a Peroxidase-Mimicking DNAzyme Assay. ANAL LETT 2018. [DOI: 10.1080/00032719.2017.1378229] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Affiliation(s)
| | - Ivan Yu. Sakharov
- Department of Chemistry, Lomonosov Moscow State University, Moscow, Russia
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10
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Fapyane D, Kékedy-Nagy L, Sakharov IY, Ferapontova EE. Electrochemistry and electrocatalysis of covalent hemin-G4 complexes on gold. J Electroanal Chem (Lausanne) 2018. [DOI: 10.1016/j.jelechem.2017.11.053] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
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11
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Bodulev OL, Gribas AV, Sakharov IY. Microplate chemiluminescent assay for HBV DNA detection using 3-(10'-phenothiazinyl)propionic acid/N-morpholinopyridine pair as enhancer of HRP-catalyzed chemiluminescence. Anal Biochem 2017; 543:33-36. [PMID: 29203136 DOI: 10.1016/j.ab.2017.11.026] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2017] [Revised: 11/29/2017] [Accepted: 11/30/2017] [Indexed: 01/15/2023]
Abstract
A sensitive sandwich assay for hepatitis B virus (HBV) DNA detection based on use of commercial CL-ELISA microplates was developed. To reveal the target the covalent conjugate of reporter oligonucleotide and horseradish peroxidase (HRP) was synthesized. An employment of enhanced chemiluminescence reaction, where 3-(10'-phenothiazinyl)propionic acid/N-morpholinopyridine pair was used as enhancer of HRP-catalyzed chemiluminescence, permitted to measure the enzyme activity of the conjugate with high sensitivity. Under the favorable conditions the limit of detection and a linear range of the assay were 3 pM and 0.07-2.0 nM, respectively. The coefficient of variation (CV) for determination of HBV DNA concentrations within the working range was lower than 4%. The obtained results demonstrated that the developed assay had high sensitivity and precision.
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Affiliation(s)
- Oleg L Bodulev
- Department of Chemistry, Lomonosov Moscow State University, Leninskie gory, Moscow 119991, Russia
| | - Anastasia V Gribas
- Department of Chemistry, Lomonosov Moscow State University, Leninskie gory, Moscow 119991, Russia
| | - Ivan Yu Sakharov
- Department of Chemistry, Lomonosov Moscow State University, Leninskie gory, Moscow 119991, Russia.
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12
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Gribas AV, Zatsepin TS, Korolev SP, Gottikh MB, Sakharov IY. Suicide inactivation of covalent peroxidase-mimicking DNAzyme with hydrogen peroxide and its protection by a reductant substrate. Talanta 2016; 155:212-5. [DOI: 10.1016/j.talanta.2016.04.033] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2016] [Revised: 04/12/2016] [Accepted: 04/16/2016] [Indexed: 12/29/2022]
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13
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Gribas AV, Korolev SP, Zatsepin TS, Gottikh MB, Sakharov IY. Structure–activity relationship study for design of highly active covalent peroxidase-mimicking DNAzyme. RSC Adv 2015. [DOI: 10.1039/c5ra03167b] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023] Open
Abstract
We synthesized a series of conjugates of hemin and its aptamer EAD2, named covalent peroxidase-mimicking DNAzymes (PMDNAzymes), varying the length, rigidity and 5′-/3′-position of the linker between the oligonucleotide and hemin.
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Affiliation(s)
| | - Sergey P. Korolev
- Department of Chemistry
- Lomonosov Moscow State University
- Moscow 119991
- Russia
- Belozersky Institute of Physical and Chemical Biology
| | - Timofey S. Zatsepin
- Department of Chemistry
- Lomonosov Moscow State University
- Moscow 119991
- Russia
- Belozersky Institute of Physical and Chemical Biology
| | - Marina B. Gottikh
- Belozersky Institute of Physical and Chemical Biology
- Lomonosov Moscow State University
- Moscow 119991
- Russia
| | - Ivan Yu. Sakharov
- Department of Chemistry
- Lomonosov Moscow State University
- Moscow 119991
- Russia
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14
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Gribas AV, Zhao S, Sakharov IY. Homogeneous chemiluminescent DNA assay based on allosteric activation of peroxidase-mimicking DNAzyme. RSC Adv 2015. [DOI: 10.1039/c5ra17222e] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023] Open
Abstract
We developed a homogeneous chemiluminescent DNA assay based on allosteric activation of peroxidase-mimicking DNAzyme.
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Affiliation(s)
| | - Shulin Zhao
- Key Laboratory for the Chemistry and Molecular Engineering of Medicinal Resources (Ministry of Education)
- Guangxi Normal University
- Guilin 541004
- China
| | - Ivan Yu. Sakharov
- Department of Chemistry
- Lomonosov Moscow State University
- Moscow 119991
- Russia
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