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Article
Chemistry, Multidisciplinary
Brandon Lu et al.
Summary: This study explores the possibility of self-assembling three-dimensional crystals using unconventional DNA tile motifs and showcases the highly complex symmetric structures that can be generated as a result. The results demonstrate the potential to generate unexpected material design pathways by modifying three-dimensional tiles.
Article
Engineering, Biomedical
Jae Chul Park et al.
Summary: A simple method for miRNA assay is presented, which is based on the one-pot self-assembly of Y-shaped DNAs with streptavidin via an miRNA-catalyzed TMSD cascade reaction. This method incorporates a single base-pair mismatch to facilitate RNA-triggered strand displacement while minimally disturbing nonspecific reactions. The detection limit is significantly reduced from the nanomolar level to the picomolar level.
ADVANCED HEALTHCARE MATERIALS
(2023)
Article
Biochemical Research Methods
Tao Song et al.
Summary: Deep learning has greatly improved and changed the process of de novo molecular design. The proposed DNMG model utilizes a deep generative adversarial network combined with transfer learning to consider the 3D spatial information and physicochemical properties of molecules, generating valid and novel drug-like ligands. The computational results demonstrate that the molecules generated by DNMG have better binding ability and physicochemical properties for target proteins.
Article
Biochemical Research Methods
Xue Li et al.
Summary: This study proposes a protein-protein interaction (PPI) prediction model called multi-scale architecture residual network for PPIs (MARPPI) that utilizes dual-channel and multi-feature methods. The model leverages Res2vec to obtain residue association information and uses various descriptors to capture amino acid composition and order information, physicochemical properties, and information entropy. MARPPI achieves high accuracy rates ranging from 91.80% to 99.01% on different datasets, outperforming other advanced methods. The results also demonstrate the model's ability to detect hidden interactions and predict cross-species interactions.
BRIEFINGS IN BIOINFORMATICS
(2023)
Article
Biochemistry & Molecular Biology
Donghun Lee et al.
Summary: Bacterial exonuclease III (ExoIII) is a multifunctional enzyme that has both apurinic/apyrimidinic (AP)-endonuclease and 3'->5' exonuclease activities. Through mutational analysis and single-molecule imaging, researchers have discovered the key amino acid residues that determine the functional selection between these two activities. Additionally, they found that stabilizing the melted state of the 3' terminal nucleobases is crucial for activating the exonuclease activity. Maintaining the DNA substrate as a B-form helix during the exonucleolytic cleavage process is also essential. This study provides insights into the mechanism of ExoIII's dual functionalities at the amino acid level.
NUCLEIC ACIDS RESEARCH
(2022)
Article
Chemistry, Multidisciplinary
Nuli Xie et al.
Summary: DNA logic circuits based on DNA molecular programming are used to implement specific algorithms using dynamic reaction networks. We have developed a compact yet efficient architecture using cooperative strand displacement reactions to construct a DNA full adder. By exploiting a parity-check algorithm, we were able to reduce the complexity of the circuit significantly compared to conventional designs and demonstrate the implementation of a 6-bit adder comparable in scale to an electronic chip.
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY
(2022)
Article
Biochemical Research Methods
Jianmin Wang et al.
Summary: This study constructs a dataset for protein-protein interaction (PPI) targeted drug-likeness and proposes a deep molecular generative framework to generate novel drug-like molecules based on the features of seed compounds. The results show that the generated molecules have better PPI-targeted drug-likeness and drug-likeness, and the model performs comparably to other state-of-the-art molecule generation models.
BRIEFINGS IN BIOINFORMATICS
(2022)
Article
Biochemistry & Molecular Biology
Tianci Xie et al.
Summary: A series of multiple logic circuits based on a single biomolecular platform have been constructed, capable of performing various nonarithmetic and arithmetic functions. The DNA-based encoder, as the output of the DNA circuit, enables the application of DNA circuits in non-binary biological environments. The designed nanodevices have a simple structure, low leakage, and low crosstalk, allowing for easy implementation of higher-level encoders and demultiplexers.
NUCLEIC ACIDS RESEARCH
(2022)
Article
Biotechnology & Applied Microbiology
Penghao Wang et al.
Summary: DNA storage is a natural storage medium with high storage density and long service life, and it can meet the storage requirements for massive data. This study proposes a DNA storage encoding scheme with hidden addressing, which improves the utilization of bases and ensures the correct rate of DNA storage.
FRONTIERS IN BIOENGINEERING AND BIOTECHNOLOGY
(2022)
Article
Biology
Ben Cao et al.
Summary: A new DNA storage coding method based on the frequency matrix game graph (FMG) is proposed in this study, which solves the problems of low efficiency and high complexity in current coding methods. The proposed method optimizes the coding results by observing visible characteristics. It has a positive impact on the development of carbon-based storage coding.
COMPUTERS IN BIOLOGY AND MEDICINE
(2022)
Article
Engineering, Environmental
Shuo Qi et al.
Summary: In this study, a split aptamer remodeling strategy was developed to realize high-sensitivity, specific, and high signal-to-background ratio determination of 17 beta-estradiol in food samples using a DNA walker. The proposed strategy exhibited excellent linearity, low limit of detection, and good precision for the detection of 17 beta-estradiol. Furthermore, the DNA walker-based biosensor achieved sensitive analysis of 17 beta-estradiol in complex food matrix. This split aptamer-based strategy expands the principles of DNA walker design and provides a universal signal amplification platform for trace analysis.
JOURNAL OF HAZARDOUS MATERIALS
(2022)
Article
Chemistry, Physical
Lijun Sun et al.
Summary: This study proposes a new DNA triplex design approach (TripDesign) based on interaction forces. The experimental results show that the sequences produced by TripDesign have high stability and reversibility, which can promote the application of DNA triplexes in nanotechnology.
JOURNAL OF PHYSICAL CHEMISTRY B
(2022)
Article
Biophysics
Jingwen Ge et al.
Summary: Timely and accurate detection of viral RNA fragments is crucial for preventing disease spread and early treatment. Researchers have designed a colorimetric DNA walker for detecting viral RNA, such as SARS-CoV-2, with high specificity and a low detection limit.
BIOSENSORS & BIOELECTRONICS
(2022)
Article
Computer Science, Artificial Intelligence
Xiewei Xiong et al.
Summary: The development of artificial DNA circuits for neural network-like computations presents challenges in scaling up to recognize a large number of patterns. Xiong, Zhu and colleagues demonstrate a convolutional neural network algorithm using a synthetic DNA-based regulatory circuit and reduce computation time through a freeze-thaw approach. This advancement paves the way for more powerful biomolecular classifiers.
NATURE MACHINE INTELLIGENCE
(2022)
Article
Chemistry, Analytical
Xiaoyong Lu et al.
Summary: A fluorescent biosensor based on enzyme-involved catalytic hairpin assembly (CHA) was developed to detect both APE1 and miRNA-21, improving the accuracy of early-phase cancer diagnosis. The biosensor achieved a low limit of detection (LOD) and exhibited good selectivity and stability for the two biomarkers. Additionally, it acted as an AND logic gate.
Article
Chemistry, Multidisciplinary
Chengye Zou et al.
Summary: This article presents a nonlinear neural network framework based on DNA toehold mediated strand displacement reaction, which has similar architecture to error back propagation neural network and possesses learning and robustness. The investigation highlights the potential of analog DNA displacement reaction circuits in artificial intelligence.
Article
Chemistry, Multidisciplinary
Jae Young Lee et al.
Summary: The computational method presented in this study allows for rapid analysis of structured DNA assemblies at near-atomic resolution, accurately predicting their shape, dynamic properties, and mechanical rigidities. The method achieves high computational efficiency and molecular-level accuracy through a multiscale analysis framework, making it a valuable tool for iterative design-analysis-revision processes in DNA nanotechnology.
Article
Chemistry, Analytical
Jinhua Shang et al.
Summary: The versatile cascaded DNA amplification circuit enables accurate evaluation of intracellular PNK activity, providing an important method for monitoring kinase activity.
ANALYTICAL CHEMISTRY
(2021)
Article
Biophysics
Zhen Zhao et al.
Summary: A self-propelled DNA machine for enzyme-free and ultrasensitive electrochemical detection of nucleic acid was developed using a new strategy of fuel strand-powered target recycling and successive proximity-based inter-strand displacement. The system showed tunable detection performance and achieved a low detection limit of 0.1 fM, making it a powerful tool for amplified detection of nucleic acid with potential applications in bioanalysis, disease diagnosis, and biomedicine.
BIOSENSORS & BIOELECTRONICS
(2021)
Article
Multidisciplinary Sciences
Tung-Chang Liu et al.
Summary: APE1 is an important exonuclease for processing matched/mismatched terminus during DNA repair. By determining the structures of APE1 with various dsDNA substrates, the authors found that both exonucleolytic and endonucleolytic cleavage can be understood through an induced space-filling model. The binding of dsDNA induces the RM bridge, defining a long and narrow product pocket for substrate selection machinery.
NATURE COMMUNICATIONS
(2021)
Article
Chemistry, Multidisciplinary
Na Li et al.
Summary: The COVID-19 pandemic has had a significant impact on human health and the global economy. A self-resetting molecular probe has been developed using DNA nanotechnology to detect SARS-CoV-2 RNA repeatedly, with consistent signal amplitudes and fingerprint signals suitable for high confidential identifications of single-nucleotide variants. The probe also shows the ability to detect multiple human-infectious RNA viruses, enhancing screening capabilities for COVID-19 and other infectious diseases.
Article
Chemistry, Multidisciplinary
Liping Zhu et al.
Summary: A label-free and immobilization-free electrochemiluminescence resonance energy transfer system based on graphitic carbon nitride nanosheets and Ru(phen)(3)(2+) is developed. This system allows for the regulation of ECL-RET through logical DNA hybridization reactions, opening up possibilities for constructing complex logic gates and circuits.
Article
Multidisciplinary Sciences
Saskia Groeer et al.
Summary: By combining DNA strand displacement (DSD) reaction networks with structural nanotechnology, highly controllable self-reconfiguring hierarchical system states can be achieved with various regulatory functions such as negative feedback, signal amplification, and signal thresholding.
Article
Biochemistry & Molecular Biology
Shaoxia Xu et al.
Summary: This paper proposes a DNA matrix operation method based on the mechanism of DNAzyme binding to auxiliary strands for cleaving the substrate. By connecting two auxiliary strands, matrix multiplication operation is realized, providing a new method for matrix operations and offering ideas for more complex computing systems.
Article
Chemistry, Multidisciplinary
Wonjin Lee et al.
Summary: In this paper, a programmable DNA-based microfluidic processing unit (MPU) chip is introduced for performing DNA calculations, offering basic AND and OR operations as well as combinational AND and OR operations. A few examples of Boolean logic operations, such as a 2-to-1 multiplexer and XOR operation, are demonstrated using a simple DNA-based MPU. Through logic combination, this DNA-based Boolean logic MPU is expected to facilitate the development of complex functional circuits.
Article
Chemistry, Multidisciplinary
Dallas N. Taylor et al.
Summary: DNA catalysts play a crucial role in molecular information processing, and recently developed DNA catalysts with allosteric control have shown great potential. The cooperative catalyst, which utilizes two signal species to drive output production, demonstrates near-complete output generation with input and activator concentrations that are only 0.1 times the gate concentration. This simple and modular design makes the cooperative DNA catalyst an exciting addition to general-purpose computation and dynamics in strand-displacement motifs.
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY
(2021)
Article
Multidisciplinary Sciences
Jungmin Yoo et al.
Summary: The study reveals that during base excision repair, Exonuclease III creates a gap and transient ssDNA loop through an AP site anchor-based mechanism. The size of the gap is determined by the rigidity of the ssDNA loop and the duplex stability of the DNA.
Article
Chemistry, Multidisciplinary
Jiafeng Pan et al.
Summary: Two fragments of the COVID-19 genome were used to construct an AND logic gate for detection based on exonuclease III and DNAzyme. The sensitivity of the assay can reach fM levels, and satisfactory recovery values were obtained in real sample analysis.
CHEMICAL COMMUNICATIONS
(2021)
Article
Chemistry, Analytical
Danhua Zhou et al.
Article
Multidisciplinary Sciences
Guillaume Gines et al.
Article
Chemistry, Multidisciplinary
Jinyi Dong et al.
ANGEWANDTE CHEMIE-INTERNATIONAL EDITION
(2020)
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Yijun Guo et al.
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Shuang Liu et al.
ANALYTICAL CHEMISTRY
(2020)
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Chemistry, Analytical
Yangjie Zhou et al.
ANALYTICAL CHEMISTRY
(2020)
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Chemistry, Multidisciplinary
Shengnan Fu et al.
Article
Nanoscience & Nanotechnology
Tianqi Song et al.
NATURE NANOTECHNOLOGY
(2019)
Article
Biophysics
Xinyi Huang et al.
BIOSENSORS & BIOELECTRONICS
(2019)
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Chunyang Zhou et al.
Article
Multidisciplinary Sciences
Haomiao Su et al.
NATURE COMMUNICATIONS
(2019)
Article
Multidisciplinary Sciences
Yinan Zhang et al.
NATURE COMMUNICATIONS
(2019)
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Omer Lustgarten et al.
ANGEWANDTE CHEMIE-INTERNATIONAL EDITION
(2019)
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Chemistry, Multidisciplinary
Lana Zou et al.
CHEMICAL COMMUNICATIONS
(2019)
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Zongwen Wang et al.
NUCLEIC ACIDS RESEARCH
(2018)
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Kevin M. Cherry et al.
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Daoqing Fan et al.
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Lulu Qian et al.
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Xiaolei Zuo et al.
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY
(2010)
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B Yurke et al.
