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Li X, Hu H, Wang H, Liu J, Jiang W, Zhou F, Zhang J. DNA nanotechnology-based strategies for minimising hybridisation-dependent off-target effects in oligonucleotide therapies. MATERIALS HORIZONS 2024. [PMID: 39692461 DOI: 10.1039/d4mh01158a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/19/2024]
Abstract
Targeted therapy has emerged as a transformative breakthrough in modern medicine. Oligonucleotide drugs, such as antisense oligonucleotides (ASOs) and small interfering RNAs (siRNAs), have made significant advancements in targeted therapy. Other oligonucleotide-based therapeutics like clustered regularly interspaced short palindromic repeat (CRISPR)/CRISPR-associated protein (Cas) systems are also leading a revolution in targeted gene therapy. However, hybridisation-dependent off-target effects, arising from imperfect base pairing, remain a significant and growing concern for the clinical translation of oligonucleotide-based therapeutics. These mismatches in base pairing can lead to unintended steric blocking or cleavage events in non-pathological genes, affecting the efficacy and safety of the oligonucleotide drugs. In this review, we examine recent developments in oligonucleotide-based targeted therapeutics, explore the factors influencing sequence-dependent targeting specificity, and discuss the current approaches employed to reduce the off-target side effects. The existing strategies, such as chemical modifications and oligonucleotide length optimisation, often require a trade-off between specificity and binding affinity. To further address the challenge of hybridisation-dependent off-target effects, we discuss DNA nanotechnology-based strategies that leverage the collaborative effects of nucleic acid assembly in the design of oligonucleotide-based therapies. In DNA nanotechnology, collaborative effects refer to the cooperative interactions between individual strands or nanostructures, where multiple bindings result in more stable and specific hybridisation behaviour. By requiring multiple complementary interactions to occur simultaneously, the likelihood of unintended partially complementary binding events in nucleic acid hybridisation should be reduced. And thus, with the aid of collaborative effects, DNA nanotechnology has great promise in achieving both high binding affinity and high specificity to minimise the hybridisation-dependent off-target effects of oligonucleotide-based therapeutics.
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Affiliation(s)
- Xiaoyu Li
- Laboratory of Advanced Theranostic Materials and Technology, Ningbo Institute of Materials Technology and Engineering, Chinese Academy of Sciences, Ningbo, China.
- Ningbo Cixi Institute of Biomedical Engineering, Ningbo, China
| | - Huanhuan Hu
- Laboratory of Advanced Theranostic Materials and Technology, Ningbo Institute of Materials Technology and Engineering, Chinese Academy of Sciences, Ningbo, China.
- Ningbo Cixi Institute of Biomedical Engineering, Ningbo, China
| | - Hailong Wang
- Laboratory of Advanced Theranostic Materials and Technology, Ningbo Institute of Materials Technology and Engineering, Chinese Academy of Sciences, Ningbo, China.
- Ningbo Cixi Institute of Biomedical Engineering, Ningbo, China
- School of Materials Science and Chemical Engineering, Ningbo University, Ningbo, China
| | - Jia Liu
- Laboratory of Advanced Theranostic Materials and Technology, Ningbo Institute of Materials Technology and Engineering, Chinese Academy of Sciences, Ningbo, China.
- Ningbo Cixi Institute of Biomedical Engineering, Ningbo, China
| | - Wenting Jiang
- Laboratory of Advanced Theranostic Materials and Technology, Ningbo Institute of Materials Technology and Engineering, Chinese Academy of Sciences, Ningbo, China.
- Ningbo Cixi Institute of Biomedical Engineering, Ningbo, China
- Cixi Biomedical Research Institute, Wenzhou Medical University, Zhejiang, China
| | - Feng Zhou
- Laboratory of Advanced Theranostic Materials and Technology, Ningbo Institute of Materials Technology and Engineering, Chinese Academy of Sciences, Ningbo, China.
- Ningbo Cixi Institute of Biomedical Engineering, Ningbo, China
| | - Jiantao Zhang
- Laboratory of Advanced Theranostic Materials and Technology, Ningbo Institute of Materials Technology and Engineering, Chinese Academy of Sciences, Ningbo, China.
- Ningbo Cixi Institute of Biomedical Engineering, Ningbo, China
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Liu J, Guo J, Li G, Zou L. Cascade signal amplification strategy for the electrochemical aptasensing of nucleic acid: Combination of dual-output toehold-mediated DNA strand displacement, DNA walker and Exo III. Anal Chim Acta 2024; 1297:342370. [PMID: 38438228 DOI: 10.1016/j.aca.2024.342370] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2023] [Revised: 01/27/2024] [Accepted: 02/10/2024] [Indexed: 03/06/2024]
Abstract
BACKGROUND Sensitive and selective analysis of low content nucleic acid sequences plays an important role in pathogen analysis, disease diagnosis and biomedicine. The electrochemical biosensor based on toehold-mediated strand displacement reaction (TMSD) is highly attractive in nucleic acid detection due to their improved sensitivity and rapid response. But the traditional TMSD carried out on the electrode always with low displacement efficiency and complicated electrode operation, resulting in compromised sensing performance. There is a great need to construct a novel TMSD based electrochemical detection strategy to overcome such challenges in nucleic acid detecting. RESULT Herein, a triple signal amplification electrochemical aptasensor was developed for ultrasensitive detection of CYFRA21-1 DNA. The dual-output toehold mediated strand displacement reaction (dTMSD) can convert one input to two strands output within one strand displacement cycle. So that it possesses a higher efficiency for improving the sensitivity in comparison with the single-output TMSD. And the fuel strand was configured with a tail to realize successive DNA circuits through self-propelling as a DNA walker. All the above processes were carried out on magnetic beads, which is conducive to achieving effective sample purification and minimizing the background signals. Besides, Exonuclease III was further amplified signal. As a result, through the cascade use of above three technologies, the proposed biosensing strategy realized sensitive detection of target DNA with a low detection limit of 0.35 fM (S/N = 3) and wide linear range (0.5 fM-500 pM). SIGNIFICANCE The proposed novel dTMSD combining multiple signal amplification strategies for electrochemical detection of CYFRA21-1 DNA with easy operation not only possesses excellent sensitivity and selectivity, but also has potential application value for monitoring DNA in serum. Meanwhile, the development of highly sensitive and specific CYFRA21-1 DNA detection methods is very important for the prevention and treatment of lung cancer.
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Affiliation(s)
- Jinzhi Liu
- College of Chemistry, Green Catalysis Center, Zhengzhou University, Zhengzhou, 450001, PR China
| | - Jiaxin Guo
- College of Chemistry, Green Catalysis Center, Zhengzhou University, Zhengzhou, 450001, PR China
| | - Gaiping Li
- College of Chemistry, Green Catalysis Center, Zhengzhou University, Zhengzhou, 450001, PR China
| | - Lina Zou
- College of Chemistry, Green Catalysis Center, Zhengzhou University, Zhengzhou, 450001, PR China.
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Li J, Zhang Y, Wang X, Zhang S, Tan Q, Hu B, Xu Q, Li H. Engineering Entropy-Driven Nanomachine-Mediated Morphological Evolution of Anisotropic Silver Triangular Nanoplates for Colorimetric and Photothermal Biosensing. Anal Chem 2023; 95:12032-12038. [PMID: 37542454 DOI: 10.1021/acs.analchem.3c01888] [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: 08/07/2023]
Abstract
A DNA/RNA biosensor capable of single nucleotide variation (SNV) resolution is highly desirable for drug design and disease diagnosis. To meet the point-of-care demand, rapid, cost-effective, and accurate SNV detection is of great significance but still suffers from a challenge. In this work, a unique nonenzymatic dual-modal (multicolorimetric and photothermal) visualization DNA biosensor is first proposed for SNV identification on the basis of an entropy-driven nanomachine with double output DNAs and coordination etching of anisotropic silver triangular nanoplates (Ag TNPs). When the target initiates the DNA nanomachine, the liberated multiple output DNAs can be utilized as a bridge to produce a superparamagnetic sandwich complex. The incoming poly-C DNA can coordinate and etch highly active Ag+ ions at the tips of Ag TNPs, causing a shift in the plasmon peak of Ag TNPs from 808 to 613 nm. The more target DNAs are introduced, the more output DNAs are released and thus the more Ag+ ions are etched. The noticeable color changes of anisotropic Ag TNPs can be differentiated by "naked eye" and accurate temperature reading. The programmable DNA nanotechnology and magnetic extraction grant the high specificity. Also, the SNV detection results can be self-verified by the two-signal readouts. Moreover, the dual-modal biosensor has the advantages of portability, cost-effectiveness, and simplicity. Particularly, the exclusive entropy-driven amplifier liberates double output DNAs to bridge more poly-C DNAs, enabling the dual-modal visualization DNA biosensor with improved sensitivity.
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Affiliation(s)
- Jing Li
- School of Chemistry and Chemical Engineering, Yancheng Institute of Technology, Yancheng 224051, P. R. China
| | - Yansong Zhang
- School of Chemistry and Chemical Engineering, Yancheng Institute of Technology, Yancheng 224051, P. R. China
| | - Xin Wang
- School of Chemistry and Chemical Engineering, Yancheng Institute of Technology, Yancheng 224051, P. R. China
| | - Shenlong Zhang
- School of Chemistry and Chemical Engineering, Yancheng Institute of Technology, Yancheng 224051, P. R. China
| | - Qingqing Tan
- School of Chemistry and Chemical Engineering, Yancheng Institute of Technology, Yancheng 224051, P. R. China
| | - Bingtao Hu
- School of Chemistry and Chemical Engineering, Yancheng Institute of Technology, Yancheng 224051, P. R. China
| | - Qin Xu
- College of Chemistry and Chemical Engineering, Yangzhou University, Yangzhou 225002, P. R. China
| | - Hongbo Li
- School of Chemistry and Chemical Engineering, Yancheng Institute of Technology, Yancheng 224051, P. R. China
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Zhang X, Liu X, Yao Y, Liu Y, Zeng C, Zhang Q. Programmable Molecular Signal Transmission Architecture and Reactant Regeneration Strategy Driven by EXO λ for DNA Circuits. ACS Synth Biol 2023; 12:2107-2117. [PMID: 37405388 DOI: 10.1021/acssynbio.3c00168] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/06/2023]
Abstract
The characteristics of DNA hybridization enable molecular computing through strand displacement reactions, facilitating the construction of complex DNA circuits, which is an important way to realize information interaction and processing at a molecular level. However, signal attenuation in the cascade and shunt process hinders the reliability of the calculation results and further expansion of the DNA circuit scale. Here, we demonstrate a novel programmable exonuclease-assisted signal transmission architecture, where DNA strand with toehold employed to inhibit the hydrolysis process of EXO λ is applied in DNA circuits. We construct a series circuit with variable resistance and a parallel circuit with constant current source, ensuring excellent orthogonal properties between input and output sequences while maintaining low leakage (<5%) during the reaction. Additionally, a simple and flexible exonuclease-driven reactant regeneration (EDRR) strategy is proposed and applied to construct parallel circuits with constant voltage sources that could amplify the output signal without extra DNA fuel strands or energy. Furthermore, we demonstrate the effectiveness of the EDRR strategy in reducing signal attenuation during cascade and shunt processes by constructing a four-node DNA circuit. These findings offer a new approach to enhance the reliability of molecular computing systems and expand the scale of DNA circuits in the future.
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Affiliation(s)
- Xun Zhang
- School of Computer Science and Technology, Dalian University of Technology, Dalian 116024, China
| | - Xin Liu
- School of Computer Science and Technology, Dalian University of Technology, Dalian 116024, China
| | - Yao Yao
- School of Computer Science and Technology, Dalian University of Technology, Dalian 116024, China
| | - Yuan Liu
- School of Computer Science and Technology, Dalian University of Technology, Dalian 116024, China
| | - Chenyi Zeng
- Key Laboratory of Advanced Design and Intelligent Computing, Dalian University, Dalian 116622, China
| | - Qiang Zhang
- School of Computer Science and Technology, Dalian University of Technology, Dalian 116024, China
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Hao H, Li Y, Yang B, Lou S, Guo Z, Lu W. Simulation-Guided Rational Design of DNA Probe for Accurate Discrimination of Single-Nucleotide Variants Based on "Hill-Type" Cooperativity. Anal Chem 2023; 95:2893-2900. [PMID: 36695821 DOI: 10.1021/acs.analchem.2c04446] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
The accurate discrimination of single-nucleotide variants is of great interest for disease diagnosis and clinical treatments. In this work, a unique DNA probe with "Hill-type" cooperativity was first developed based on toehold-mediated strand displacement processes. Under simulation, this probe owns great thermodynamics advantage for specificity due to two mismatch bubbles formed in the presence of single-nucleotide variants. Besides, the strategies of ΔG' = 0 and more competitive strands are also beneficial to discriminate single-nucleotide variants. The feasibility of this probe was successfully demonstrated in consistent with simulation results. Due to "Hill-type" cooperativity, the probe allows a steeper dynamic range compared with previous probes. With simulation-guided rational design, the resulting probe can accurately discriminate single-nucleotide variants including nucleotide insertions, mutation, and deletions, which are arbitrarily distributed in target sequence. Two specificity parameters were calculated to quantitatively evaluate its good discrimination ability. Hence, "Hill-type" cooperativity can serve as a novel strategy in DNA probe's design for accurate discrimination of single-nucleotide variants.
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Affiliation(s)
- Huimin Hao
- Key Laboratory of Environmentally Friendly Chemistry and Applications of Ministry of Education, College of Chemistry, Xiangtan University, Xiangtan410005, P. R. China
| | - Ye Li
- Key Laboratory of Environmentally Friendly Chemistry and Applications of Ministry of Education, College of Chemistry, Xiangtan University, Xiangtan410005, P. R. China
| | - Bin Yang
- Key Laboratory of Environmentally Friendly Chemistry and Applications of Ministry of Education, College of Chemistry, Xiangtan University, Xiangtan410005, P. R. China
| | - Shuyan Lou
- Key Laboratory of Environmentally Friendly Chemistry and Applications of Ministry of Education, College of Chemistry, Xiangtan University, Xiangtan410005, P. R. China
| | - Zihua Guo
- Key Laboratory of Environmentally Friendly Chemistry and Applications of Ministry of Education, College of Chemistry, Xiangtan University, Xiangtan410005, P. R. China
| | - Weiyi Lu
- Key Laboratory of Environmentally Friendly Chemistry and Applications of Ministry of Education, College of Chemistry, Xiangtan University, Xiangtan410005, P. R. China
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