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Kanarskaya MA, Pyshnyi DV, Lomzov AA. Diversity of Self-Assembled RNA Complexes: From Nanoarchitecture to Nanomachines. Molecules 2023; 29:10. [PMID: 38202593 PMCID: PMC10779776 DOI: 10.3390/molecules29010010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2023] [Revised: 12/11/2023] [Accepted: 12/13/2023] [Indexed: 01/12/2024] Open
Abstract
New tool development for various nucleic acid applications is an essential task in RNA nanotechnology. Here, we determined the ability of self-limited complex formation by a pair of oligoribonucleotides carrying two pairwise complementary blocks connected by a linker of different lengths in each chain. The complexes were analyzed using UV melting, gel shift assay analysis, and molecular dynamics (MD) simulations. We have demonstrated the spontaneous formation of various self-limited and concatemer complexes. The linear concatemer complex is formed by a pair of oligomers without a linker in at least one of them. Longer linkers resulted in the formation of circular complexes. The self-limited complexes formation was confirmed using the toehold strand displacement. The MD simulations indicate the reliability of the complexes' structure and demonstrate their dynamics, which increase with the rise of complex size. The linearization of 2D circular complexes into 1D structures and a reverse cyclization process were demonstrated using a toehold-mediated approach. The approach proposed here for the construction and directed modification of the molecularity and shape of complexes will be a valuable tool in RNA nanotechnology, especially for the rational design of therapeutic nucleic acids with high target specificity and the programmable response of the immune system of organisms.
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Affiliation(s)
| | | | - Alexander A. Lomzov
- Institute of Chemical Biology and Fundamental Medicine SB RAS, Novosibirsk 630090, Russia; (M.A.K.); (D.V.P.)
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Zamoskovtseva AA, Golyshev VM, Kizilova VA, Shevelev GY, Pyshnyi DV, Lomzov AA. Pairing nanoarchitectonics of oligodeoxyribonucleotides with complex diversity: concatemers and self-limited complexes. RSC Adv 2022; 12:6416-6431. [PMID: 35424594 PMCID: PMC8981972 DOI: 10.1039/d2ra00155a] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2022] [Accepted: 02/15/2022] [Indexed: 11/21/2022] Open
Abstract
The development of approaches to the design of two- and three-dimensional self-assembled DNA-based nanostructures with a controlled shape and size is an essential task for applied nanotechnology, therapy, biosensing, and bioimaging. We conducted a comprehensive study on the formation of various complexes from a pair of oligonucleotides with two transposed complementary blocks that can be linked through a nucleotide or non-nucleotide linker. A methodology is proposed to prove the formation of a self-limited complex and to determine its molecularity. It is based on the "opening" of a self-limited complex with an oligonucleotide that effectively binds to a duplex-forming block. The complexes assembled from a pair of oligonucleotides with different block length and different linker sizes and types were investigated by theoretical analysis, several experimental methods (a gel shift assay, atomic force microscopy, and ultraviolet melting analysis), and molecular dynamics simulations. The results showed a variety of complexes formed by only a pair of oligonucleotides. Self-limited associates, concatemer complexes, or mixtures thereof can arise if we change the length of a duplex and loop-forming blocks in oligonucleotides or via introduction of overhangs and chemical modifications. We postulated basic principles of rational design of native self-limited DNA complexes of desired structure, shape, and molecularity. Our foundation makes self-limited complexes useful tools for nanotechnology, biological studies, and therapeutics.
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Affiliation(s)
- Anastasia A Zamoskovtseva
- Institute of Chemical Biology and Fundamental Medicine, SB RAS 8 Lavrentiev Avenue Novosibirsk 630090 Russia
- Moscow Institute of Physics and Technology 9 Institutskiy per., Dolgoprudny 141701 Russia
| | - Victor M Golyshev
- Institute of Chemical Biology and Fundamental Medicine, SB RAS 8 Lavrentiev Avenue Novosibirsk 630090 Russia
| | - Valeria A Kizilova
- Institute of Chemical Biology and Fundamental Medicine, SB RAS 8 Lavrentiev Avenue Novosibirsk 630090 Russia
| | - Georgiy Yu Shevelev
- Institute of Chemical Biology and Fundamental Medicine, SB RAS 8 Lavrentiev Avenue Novosibirsk 630090 Russia
| | - Dmitrii V Pyshnyi
- Institute of Chemical Biology and Fundamental Medicine, SB RAS 8 Lavrentiev Avenue Novosibirsk 630090 Russia
| | - Alexander A Lomzov
- Institute of Chemical Biology and Fundamental Medicine, SB RAS 8 Lavrentiev Avenue Novosibirsk 630090 Russia
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Katrivas L, Kempinski B, Kuchuk K, Sivan U, Kotlyar A. Multiply Modified Repeating DNA Templates for Production of Novel DNA-Based Nanomaterial. Bioconjug Chem 2019; 30:2201-2208. [PMID: 31343869 DOI: 10.1021/acs.bioconjchem.9b00433] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Here, we report synthesis of long (thousands of base pairs), uniform double-stranded (ds) DNA comprising short (6-15 base pairs) tandem repeats. The synthesis method is based on self-assembly of short (6-15 bases) half-complementary 5'-end phosphorylated single-stranded oligonucleotides into long ds polymer molecules and covalent association of the oligonucleotide fragments in the polymer by DNA ligase to yield complete non-nicked ds DNA. The method is very flexible in regard to the sequence of the oligonucleotides and their length. Human telomeric DNA comprising thousands of base pairs as well as methylated, mismatched, and fluorescent dye-modified uniform dsDNA molecules can be synthesized. We have demonstrated by high resolution frequency-modulation atomic force microscopy that the structure of DNA containing mismatches is strongly different from that of the non-mismatched one. The DNA molecules comprising groups capable of anchoring metal particles and other redox active elements along the whole length of the nucleic acid polymer should find use as wires or transistors in future nanoelectronic applications.
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Affiliation(s)
- Liat Katrivas
- Department of Biochemistry and Molecular Biology, George S. Wise Faculty of Life Sciences and the Center of Nanoscience and Nanotechnology , Tel Aviv University , Ramat Aviv , Tel Aviv 69978 , Israel
| | - Benjamin Kempinski
- Department of Biochemistry and Molecular Biology, George S. Wise Faculty of Life Sciences and the Center of Nanoscience and Nanotechnology , Tel Aviv University , Ramat Aviv , Tel Aviv 69978 , Israel
| | - Kfir Kuchuk
- Department of Physics and the Russell Berrie Nanotechnology Institute , Technion - Israel Institute of Technology , Haifa , 3200003 , Israel
| | - Uri Sivan
- Department of Physics and the Russell Berrie Nanotechnology Institute , Technion - Israel Institute of Technology , Haifa , 3200003 , Israel
| | - Alexander Kotlyar
- Department of Biochemistry and Molecular Biology, George S. Wise Faculty of Life Sciences and the Center of Nanoscience and Nanotechnology , Tel Aviv University , Ramat Aviv , Tel Aviv 69978 , Israel
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Xu W, Tian J, Luo Y, Zhu L, Huang K. A rapid and visual turn-off sensor for detecting copper (II) ion based on DNAzyme coupled with HCR-based HRP concatemers. Sci Rep 2017; 7:43362. [PMID: 28266536 PMCID: PMC5339725 DOI: 10.1038/srep43362] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2016] [Accepted: 01/23/2017] [Indexed: 12/14/2022] Open
Abstract
To solve the requirement of on-site, rapid, and visual detection of copper (II) (Cu2+) in aqueous solution, a turn-off sensor for detecting copper (II) ion was developed based on Cu2+-dependent DNAzyme as the recognition element and hybridization chain reaction (HCR)-based horseradish peroxidase (HRP) concatemers as the signal amplifier and the signal report element. The detection unit, which was composed of the immobilized Cu2+-dependent DNAzyme coupled with HCR-based HRP concatemers via Waston-Crick base pairing, could catalyze hydrogen peroxide (H2O2) via TMB, generating obvious green color and turning yellow after sulfuric acid termination with optical absorption at 450 nm. Upon Cu2+ addition, the substrate strand of the Cu2+-dependent DNAzyme concatenated with the HCR-based HRP complex was irreversibly cleaved, efficiently causing dramatic reduction of the detection signal. Under optimal conditions, the detection signal decreased with the concentration of Cu2+ in 5 min, exhibiting a linear calibration from 0.05 to 3 μM with a detection limit of 8 nM. The sensor also displayed a high selectivity for Cu2+ given the specificity and anti-interference of the detection unit, and this system was applicable for monitoring Cu2+ in real water samples. Generally speaking, the proposed sensor exhibits good potential in environment surveys.
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Affiliation(s)
- Wentao Xu
- Beijing Advanced Innovation Center for Food Nutrition and Human Health, College of Food Science & Nutritional Engineering, China Agricultural University, Beijing 100083, China
- Beijing Laboratory for Food Quality and Safety, College of Food Science and Nutritional Engineering, China Agricultural University, Beijing 100083, China
| | - Jingjing Tian
- Beijing Laboratory for Food Quality and Safety, College of Food Science and Nutritional Engineering, China Agricultural University, Beijing 100083, China
| | - Yunbo Luo
- Beijing Advanced Innovation Center for Food Nutrition and Human Health, College of Food Science & Nutritional Engineering, China Agricultural University, Beijing 100083, China
| | - Longjiao Zhu
- Beijing Laboratory for Food Quality and Safety, College of Food Science and Nutritional Engineering, China Agricultural University, Beijing 100083, China
| | - Kunlun Huang
- Beijing Advanced Innovation Center for Food Nutrition and Human Health, College of Food Science & Nutritional Engineering, China Agricultural University, Beijing 100083, China
- Beijing Laboratory for Food Quality and Safety, College of Food Science and Nutritional Engineering, China Agricultural University, Beijing 100083, China
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Xu W, Tian J, Shao X, Zhu L, Huang K, Luo Y. A rapid and visual aptasensor for Lipopolysaccharides detection based on the bulb-like triplex turn-on switch coupled with HCR-HRP nanostructures. Biosens Bioelectron 2016; 89:795-801. [PMID: 27816585 DOI: 10.1016/j.bios.2016.10.012] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2016] [Revised: 09/24/2016] [Accepted: 10/04/2016] [Indexed: 10/20/2022]
Abstract
For previously reported aptasensor, the sensitivity and selectivity of aptamers to targets were often suppressed due to the reporter label of single-stranded molecular beacon or hindrance of the duplex DNA strand displacement. To solve the affinity declining of aptamers showed in traditional way and realize on-site rapid detection of Lipopolysaccharides (LPS), we developed an ingenious structure-switching aptasensor based on the bulb-like triplex turn-on switch (BTTS) as the effective molecular recognition and signal transduction element and streptavidin-horseradish peroxidase modified hybridization chain reaction (HCR-HRP) nanocomposites as the signal amplifier and signal report element. In the presence of LPS, the bulb-like LPS-aptamer (BLA) and LPS formed the LPS/aptamer complex, while the BTTS disassembled and liberated the dissociative bridge probes (BP) to achieve molecular recognition and signal transduction. Immobilized BP, captured by immobilized capture probes (CP), triggered hybridization chain reactions (HCR) to amplify the switching signal, and the HCR products were then modified with streptavidin-horseradish peroxidase (SA-HRP) to form HCR-HRP nanostructures to output colorimetric signals. In less than four hours, the proposed biosensor showed a detection limit of 50pg/mL of LPS quantitatively with the portable spectrophotometer and the observation limit of 20ng/mL semi-quantitatively with the naked eye, opening up new opportunities for LPS detection in future clinical diagnosis, food security and environment monitoring.
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Affiliation(s)
- Wentao Xu
- Beijing Advanced Innovation Center for Food Nutrition and Human Health, College of Food Science & Nutritional Engineering, China Agricultural University, Beijing 100083, China; Beijing Laboratory for Food Quality and Safety, College of Food Science and Nutritional Engineering, China Agricultural University, Beijing 100083, China
| | - Jingjing Tian
- Beijing Laboratory for Food Quality and Safety, College of Food Science and Nutritional Engineering, China Agricultural University, Beijing 100083, China
| | - Xiangli Shao
- Beijing Advanced Innovation Center for Food Nutrition and Human Health, College of Food Science & Nutritional Engineering, China Agricultural University, Beijing 100083, China
| | - Longjiao Zhu
- Beijing Laboratory for Food Quality and Safety, College of Food Science and Nutritional Engineering, China Agricultural University, Beijing 100083, China
| | - Kunlun Huang
- Beijing Advanced Innovation Center for Food Nutrition and Human Health, College of Food Science & Nutritional Engineering, China Agricultural University, Beijing 100083, China; Beijing Laboratory for Food Quality and Safety, College of Food Science and Nutritional Engineering, China Agricultural University, Beijing 100083, China
| | - Yunbo Luo
- Beijing Advanced Innovation Center for Food Nutrition and Human Health, College of Food Science & Nutritional Engineering, China Agricultural University, Beijing 100083, China.
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Xu M, Gao Z, Wei Q, Chen G, Tang D. Hemin/G-quadruplex-based DNAzyme concatamers for in situ amplified impedimetric sensing of copper(II) ion coupling with DNAzyme-catalyzed precipitation strategy. Biosens Bioelectron 2015; 74:1-7. [DOI: 10.1016/j.bios.2015.05.056] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2015] [Revised: 05/11/2015] [Accepted: 05/26/2015] [Indexed: 12/29/2022]
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Hou L, Wu X, Chen G, Yang H, Lu M, Tang D. HCR-stimulated formation of DNAzyme concatamers on gold nanoparticle for ultrasensitive impedimetric immunoassay. Biosens Bioelectron 2015; 68:487-493. [DOI: 10.1016/j.bios.2015.01.043] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2014] [Revised: 01/13/2015] [Accepted: 01/19/2015] [Indexed: 12/16/2022]
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Sun L, Akerman B. Characterization of self-assembled DNA concatemers from synthetic oligonucleotides. Comput Struct Biotechnol J 2014; 11:66-72. [PMID: 25379145 PMCID: PMC4212282 DOI: 10.1016/j.csbj.2014.08.011] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022] Open
Abstract
Studies of DNA-ligand interaction on a single molecule level provide opportunities to understand individual behavior of molecules. Construction of DNA molecules with repetitive copies of the same segments of sequences linked in series could be helpful for enhancing the interaction possibility for sequence-specific binding ligand to DNA. Here we report on the use of synthetic oligonucleotides to self-assembly into duplex DNA concatemeric molecules. Two strands of synthetic oligonucleotides used here were designed with 50-mer in length and the sequences are semi-complimentary so to hybridize spontaneously into concatemers of double stranded DNA. In order to optimize the length of the concatemers the oligonucleotides were incubated at different oligomer concentrations, ionic strengths and temperatures for different durations. Increasing the salt concentration to 200 mM NaCl was found to be the major optimizing factor because at this enhanced ionic strength the concatemers formed most quickly and the other parameters had no detectable effect. The size and shape of formed DNA concatemers were studied by gel electrophoresis in agarose, polyacrylamide gels and by AFM. Our results show that linear DNA constructs up to several hundred base pairs were formed and could be separated from a substantial fraction of non-linear constructs.
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Affiliation(s)
- Lu Sun
- Department of Chemical and Biological Engineering, Chalmers University of Technology, S41296 Goteborg, Sweden
| | - Björn Akerman
- Department of Chemical and Biological Engineering, Chalmers University of Technology, S41296 Goteborg, Sweden
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Tang J, Hou L, Tang D, Zhang B, Zhou J, Chen G. Hemin/G-quadruplex-based DNAzyme concatamers as electrocatalysts and biolabels for amplified electrochemical immunosensing of IgG1. Chem Commun (Camb) 2012; 48:8180-2. [DOI: 10.1039/c2cc33390b] [Citation(s) in RCA: 68] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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