A molecular device: A DNA molecular lock driven by the nicking enzymes

Zhang, Xiaokang; Zhang, Qiang; Liu, Yuan; Wang, Bin; Zhou, Shihua

doi:10.1016/j.csbj.2020.08.004

Cited by 26 publications

(19 citation statements)

References 56 publications

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“…This result again demonstrates the superiority of the constrained coding scheme based on the EORS algorithm and its rationality in practical application. In addition, in other applications of DNA, such as long-time tracking [31] and neural network optimization [32], [33], DNA coding optimization [34,35], DNA molecular lock [36] and DNA image encryption [37], some excellent solutions have also emerged, providing new ideas for coding schemes in future work.…”

Section: Plos Onementioning

confidence: 99%

Combinatorial constraint coding based on the EORS algorithm in DNA storage

Xiaoru

2021

PLoS ONE

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The development of information technology has produced massive amounts of data, which has brought severe challenges to information storage. Traditional electronic storage media cannot keep up with the ever-increasing demand for data storage, but in its place DNA has emerged as a feasible storage medium with high density, large storage capacity and strong durability. In DNA data storage, many different approaches can be used to encode data into codewords. DNA coding is a key step in DNA storage and can directly affect storage performance and data integrity. However, since errors are prone to occur in DNA synthesis and sequencing, and non-specific hybridization is prone to occur in the solution, how to effectively encode DNA has become an urgent problem to be solved. In this article, we propose a DNA storage coding method based on the equilibrium optimization random search (EORS) algorithm, which meets the Hamming distance, GC content and no-runlength constraints and can reduce the error rate in storage. Simulation experiments have shown that the size of the DNA storage code set constructed by the EORS algorithm that meets the combination constraints has increased by an average of 11% compared with previous work. The increase in the code set means that shorter DNA chains can be used to store more data.

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Section: Plos Onementioning

confidence: 99%

Combinatorial constraint coding based on the EORS algorithm in DNA storage

Xiaoru

2021

PLoS ONE

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“…To demonstrate the selectivity of the proposed strategy, the interfering proteins such as UDG, T4 DNA Ligase and Nb. BtsI, in the same concentration as ALP [ 13 , 14 , 36 ], were evaluated using the present method. As illustrated in Figure 4 , the interfering proteins all arouse strong fluorescence responses except ALP, indicating the prominent specificity of the proposed approach.…”

Section: Resultsmentioning

confidence: 99%

An Exonuclease I-Aided Turn-Off Fluorescent Strategy for Alkaline Phosphatase Assay Based on Terminal Protection and Copper Nanoparticles

et al. 2021

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As an important DNA 3′-phosphatase, alkaline phosphatase can repair damaged DNA caused by replication and recombination. It is essential to measure the level of alkaline phosphatase to indicate some potential diseases, such as cancer, related to alkaline phosphatase. Here, we designed a simple and fast method to detect alkaline phosphatase quantitively. When alkaline phosphatase is present, the resulting poly T-DNA with a 3′-hydroxyl end was cleaved by exonuclease I, prohibiting the formation of fluorescent copper nanoparticles. However, the fluorescent copper nanoparticles can be monitored with the absence of alkaline phosphatase. Hence, we can detect alkaline phosphatase with this turn-off strategy. The proposed method is able to quantify the concentration of alkaline phosphatase with the LOD of 0.0098 U/L. Furthermore, we utilized this method to measure the effects of inhibitor Na3VO4 on alkaline phosphatase. In addition, it was successfully applied to quantify the level of alkaline phosphatase in human serum. The proposed strategy is sensitive, selective, cost effective, and timesaving, having a great potential to detect alkaline phosphatase quantitatively in clinical diagnosis.

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“…We will also continue to explore DNA storage and hope to come up with an original way of encoding for the payload and non-payload that will reduce redundancy and ensure accurate information recovery. In addition, the constructed coding sets can also be applied to other fields, including DNA image encryption ( Zhou et al, 2020 ), DNA-binding proteins ( Zhao et al, 2012 ), DNA computing ( Li et al, 2020 ), and information security ( Zhang et al, 2020 ).…”

Section: Discussionmentioning

confidence: 99%

CLGBO: An Algorithm for Constructing Highly Robust Coding Sets for DNA Storage

Zheng

Wang

2021

Front. Genet.

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In the era of big data, new storage media are urgently needed because the storage capacity for global data cannot meet the exponential growth of information. Deoxyribonucleic acid (DNA) storage, where primer and address sequences play a crucial role, is one of the most promising storage media because of its high density, large capacity and durability. In this study, we describe an enhanced gradient-based optimizer that includes the Cauchy and Levy mutation strategy (CLGBO) to construct DNA coding sets, which are used as primer and address libraries. Our experimental results show that the lower bounds of DNA storage coding sets obtained using the CLGBO algorithm are increased by 4.3–13.5% compared with previous work. The non-adjacent subsequence constraint was introduced to reduce the error rate in the storage process. This helps to resolve the problem that arises when consecutive repetitive subsequences in the sequence cause errors in DNA storage. We made use of the CLGBO algorithm and the non-adjacent subsequence constraint to construct larger and more highly robust coding sets.

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A molecular device: A DNA molecular lock driven by the nicking enzymes

Cited by 26 publications

References 56 publications

Combinatorial constraint coding based on the EORS algorithm in DNA storage

Combinatorial constraint coding based on the EORS algorithm in DNA storage

An Exonuclease I-Aided Turn-Off Fluorescent Strategy for Alkaline Phosphatase Assay Based on Terminal Protection and Copper Nanoparticles

CLGBO: An Algorithm for Constructing Highly Robust Coding Sets for DNA Storage

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