ACS Applied Materials & Interfaces
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2023
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IF 9.5
Chengtao Xu,Biao Ma,Xing Dong,Lanjie Lei,Qing Hao,Chao Zhao,Hong Liu
Due to its high coding density and longevity, DNA is a compelling data storage alternative. However, current DNA data storage systems rely on the de novo synthesis of enormous DNA molecules, resulting in low data editability, high synthesis costs, and restrictions on further applications. Here, we demonstrate the programmable assembly of reusable DNA blocks for versatile data storage using the ancient movable type printing principle. Digital data are first encoded into nucleotide sequences in DNA hairpins, which are then synthesized and immobilized on solid beads as modular DNA blocks. Using DNA polymerase-catalyzed primer exchange reaction, data can be continuously replicated from hairpins on DNA blocks and attached to a primer in tandem to produce new information. The assembly of DNA blocks is highly programmable, producing various data by reusing a finite number of DNA blocks and reducing synthesis costs (∼1718 versus 3000 to 30,000 US$ per megabyte using conventional methods). We demonstrate the flexible assembly of texts, images, and random numbers using DNA blocks and the integration with DNA logic circuits to manipulate data synthesis. This work suggests a flexible paradigm by recombining already synthesized DNA to build cost-effective and intelligent DNA data storage systems.
研究领域:
生物技术
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数据存储
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分子生物学
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纳米技术
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DOI
PubMed
高影响因子
JOURNAL OF ANALYTICAL ATOMIC SPECTROMETRY
·
2014
·Vol. 30
·期 4
·888-894
·
IF 3.396
Jing Hu,Xiandeng Hou,Peng Wu
Hydride generation atomic fluorescence spectrometry (HG-AFS) has been widely used for highly sensitive determination of more than 10 elements that are capable of hydride generation in geological, environmental and biological samples, but its bioanalytical potential has not been well-exploited yet. With CdS quantum dots (QDs) as both the signal labels for DNA sandwiching and analytes for HG-AFS (acid-released Cd2+ from QDs), here we proposed an ultrasensitive indirect method for HIV DNA analysis by HG-AFS. After a conventional sandwich-type hybridization reaction between capture DNA, target DNA and signal DNA labelled with CdS QD assembled silica microspheres, nitric acid was added to dissolve QDs and release Cd2+ from the QD-labels, which were then detected by HG-AFS. This efficient signal amplification strategy, coupled with the highly sensitive HG-AFS detection, gave rise to an impressive limit of detection of 0.8 aM and a wide dynamic concentration range (1 aM to 1 fM). This HG-AFS-based DNA biosensing platform holds great promise in future tumor marker detection and early cancerous diseases diagnosis.
研究领域:
生物分析化学
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分子生物学
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DOI
高影响因子
Science China-Technological Sciences
·
2022
·Vol. 65
·期 5
·1043-1051
·
IF 3.903
Yang Sen,Pan XiaoRui,Tang JianPu,Yao Chi,Yang DaYong
Supramolecular DNA hydrogels have been synthesized based on the assembly of DNA building-blocks such as branched DNA and long DNA chains. The structures and functions of sole-module DNA hydrogels remain limitations. New methodologies by integrating hybrid components are desired to expand the synthesis of DNA hydrogel. Herein, we synthesized a Ln 3+ -containing luminescent supramolecular hydrogel by employing the coordination and electrostatic interactions between lanthanide ions (Tb 3+ and Eu 3+ ) and linear single-stranded DNA (ssDNA). Through the coordination between ssDNA and Ln 3+ , a series of luminescent supramolecular hydrogels were synthesized, among which the Tb-G n /T n and Eu-T n hydrogels emitted the characteristic luminescence of Tb and Eu, respectively. The luminescent intensities of the hydrogels were adjusted by designing DNA sequences with programmable bases and chain lengths. Notably, the Tb/Eu co-doped luminescent supramolecular hydrogel displayed tunable luminescence from green to yellow by regulating the stoichiometric ratio of Tb/Eu. Moreover, the hydrogel had reversible luminescent stimulation responsiveness toward Ag + /L-Cys. We expected that the synthesis of Ln 3+ -containing luminescent supramolecular hydrogels enriched the strategies of the construction of DNA hydrogels, and promoted the development of stimuli-responsive supramolecular materials.
研究领域:
材料科学
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化学
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纳米技术
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生物物理
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DOI
高影响因子
JOURNAL OF CHROMATOGRAPHY B-ANALYTICAL TECHNOLOGIES IN THE BIOMEDICAL AND LIFE SCIENCES
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2017
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IF 2.603
Xiangyu Li,Lujuan Liu,Hongjuan Wang,Jian Chen,Beibei Zhu,Huan Chen,Hongwei Hou,Qingyuan Hu
A stable method, using isotope dilution liquid chromatography-tandem mass spectrometry (LC–MS/MS), to simultaneously determine six aldehyde-DNA adducts was developed and applied to the analysis of human salivary DNA samples. The detection limit of these six DNA adducts was in the range of 0.006–0.014 ng/mL and that of the quantification limit was 0.017–0.026 ng/mL. The intra-day and inter-day precision of all aldehyde-DNA adducts was <10%. The analysis was completed within 25 min. Additionally, a noninvasive technique was used to collect the DNA samples from human saliva. The new method was successfully applied for the analysis of salivary DNA of nonsmokers and smokers. Five aldehyde-DNA adducts were detected in both smoker and nonsmoker salivary DNA, while α-Acr-dG was not detected in all the samples. Among these detected DNA adducts, no significant differences were found between smoker and nonsmoker (p > 0.05). This may due to the individual detoxifying differences or environmental and endogenous exposure. Our study provides a rapid and selective method to simultaneously detect six aldehyde-DNA adducts and to assess potential DNA damage induced by aldehydes,
研究领域:
分析化学
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分子生物学
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毒理学
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DOI
高影响因子
SENSORS AND ACTUATORS B-CHEMICAL
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2020
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IF 7.1
Xiaoyan Zhang,Tingting Wu,Yuemeng Yang,Yongqiang Wen,Shutao Wang,Li-Ping Xu
Superwettable microchips exhibit excellent ability to anchor microdroplets and great potential in ultratrace sample detection. Herein, we present a superwettable electrochemical biosensor based on a dual-DNA walker strategy (dual-DW biosensor) for the attomolar detection of food-borne microorganisms ssDNA in microdroplets. In the presence of the target E. coli O157: H7 ssDNA, the blocked walking probe is activated as the first-step DNA walker. With the aid of the Nt.BsmAI nicking endonuclease, the partial sequence of the basal probe was released, thus achieving the first-step signal amplification. Then the hairpin probe 1(H1) was opened by the released basal probe and followed by the autonomous strand displacement of the ferrocene (Fc) labeled hairpin probe 2 (H2) and movement of the basal probe. Under optimized conditions, the dual-DNA walker strategy finally renders the dual-DW biosensor an ultrahigh sensitivity of 30 aM toward E. coli O157: H7 ssDNA and a broad detection linear range. The dual-DW biosensor also enables successful analysis of trace amount of E. coli O157: H7 ssDNA in real food samples. The superwettable electrochemical biosensor based on a dual-DNA walker strategy is expected to be a versatile tool for ultratrace DNA detection and be promising in food analysis.
研究领域:
生物化学
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分析化学
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食品科学
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分子生物学
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DOI
高影响因子
ANALYTICA CHIMICA ACTA
·
2024
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IF 5.7
Mengmeng Wu,Bing Yang,Lu Shi,Qiaorong Tang,Jing Wang,Wei Liu,Baoxin Li,Yan Jin
Background The human immunodeficiency virus (HIV) remains a major worldwide health problem. Nowadays, many methods have been developed for quantitative detecting human immunodeficiency virus DNA (HIV-DNA), such as fluorescence and colorimetry. However, these methods still have the disadvantages of being expensive and requiring professional technicians. Early diagnosis of pathogens is increasingly dependent on portable instruments and simple point-of-care testing (POCT). Therefore, it is meaningful and necessary to develop portable and cheap methods for detecting disease markers. Results In this work, a label-free chemiluminescence (CL) method was developed for detecting HIV-DNA via a handheld luminometer. To achieve label-free target detection, the CL catalyst, G-triplex-hemin DNAzyme (G3-hemin DNAzyme), was in-situ assembled in the presence of HIV-DNA. For improving sensitivity, HIV-DNA induced the cyclic strand displacement reaction (SDR), which can form three G3-hemin DNAzymes in one cycle. So, the chemiluminescence reaction between luminol and H 2 O 2 was highly effectively catalyzed, and the CL intensity was linearly related with the concentration of HIV-DNA in the range of 0.05–10 nM with a detection limit of 29.0 pM. Due to the high specificity of hairpin DNA, single-base mismatch can be discriminated, which ensured the specific detection of HIV-DNA. Significance In-situ formation of G3-hemin DNAzyme led to label-free and selective detection without complex synthesis and functionalization. Therefore, it offers a cheap, selective, sensitive and portable method for detecting disease-related genes, which is promising for POCT of clinical diagnosis in resource-limited settings.
研究领域:
生物医学
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分子诊断
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临床检验
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DOI
PubMed
高影响因子
MICROCHIMICA ACTA
·
2024
·Vol. 191
·期 11
·1-11
·
IF 5.3
Wei Yuxin,Fu Yang,Li Chuanhai,Chen Siyu,Xie Linzhi,Chen Mei
A electrochemical biosensor was designed utilizing a CRISPR Cas9n-driven DNA walker combined with gold-nanosphere-like covalent organic frameworks (COFs-AuNPs) to detect breast cancer markers (PIK3CA E545K ctDNA). The DNA walker probe is activated only in the presence of circulating tumor deoxyribonucleic acid (ctDNA), binding to a support probe to form a double strand that is then specifically cleaved by the Cas9n/sgRNA complex. This cleavage produces numerous DNA fragments for signal amplification. The COF-AuNPs as electrode materials facilitate electronic transfer and provide additional active sites for the immobilization of nucleic acid probes. This setup achieves a detection limit of 1.76 aM, demonstrating high sensitivity. Additionally, Cas9n improves the specificity of the sensor, accurately distinguishing a pair of base-mismatched sequences, and reducing the occurrence of false positives. Overall, the sensor exhibits excellent selectivity, reproducibility, and potential for early diagnosis of breast cancer. Graphical Abstract
研究领域:
生物技术
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癌症生物学
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纳米技术
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电化学
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分子诊断
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产品关联
DOI
PubMed
高影响因子
CHEMICAL ENGINEERING JOURNAL
·
2024
·
IF 13.3
Dezhi Feng,Chengtao Xu,Biao Ma,Chao Zhao,Hong Liu
Chemically synthesized DNA has been considered a promising medium for data storage. Among various methods, electrochemical synthesis is simple and easy to miniaturize, attracting much attention. However, conventional DNA synthesis uses phosphoramidite chemistry involving multi-step liquid-phase reactions and complicated liquid manipulation, restricting scalability and practical application. Here, we report the quasi-solid-state electrochemical DNA synthesis based on gels. All reagents required for different synthesis steps are contained in separate gels without mixing or dilution. Instead of complicated liquid manipulation, DNA synthesis on the electrode requires only relative motion between the electrode and gels. Similarly, blank gels with only acetonitrile are reused to clean the electrode surface without washing with plenty of liquid. We demonstrate our method is scalable using an electrode array for parallel DNA synthesis.
研究领域:
数据存储
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电化学
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分子生物学
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生物技术
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DOI
高影响因子
CHEMICAL RESEARCH IN TOXICOLOGY
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2020
·
IF 3.184
Yuhe Kan,Lu Chen,Dao Lin,Xinya Bu,Mengwu Mo,Liang Yan,Zhenjun Yang,Longfei Yuan,Li Wu,Yujian He
DNA damage can occur naturally or through environmental factors, leading to mutations in DNA replication and genomic instability in cells. Normally, natural d-nucleotides were selected by DNA polymerases. The template l-thymidine (l-T) has been shown to be bypassed by several types of DNA polymerases. However, DNA replication fidelity of nucleotide incorporation opposite l-thymidine in vivo remains unknown. Here, we constructed plasmids containing a restriction enzyme (PstI) recognition site in which the l-T lesion was site-specifically located within the PstI recognition sequence (CTGCAG). Further, we assessed the efficiencies of nucleotide incorporation opposite the l-T site and l-T lesion bypass replication in vitro and in vivo. We found that recombinants containing the l-T lesion site inhibited DNA replication. In addition, A was incorporated opposite the l-T lesion by routine PCR assay, whereas preference for nucleotide incorporation opposite the l-T site was A (13%), T (22%), C (46%), and G (19%), and no nucleotide insertion and deletions were detected in E. coli cells. In particular, a novel restriction enzyme-mediated method for detection of the mutagenic properties of DNA lesion was established, which allows us to readily detect restriction–digestion of the l-T-bearing plasmids. The study provided significant insight into how mirror-image nucleosides perturb the fidelity of DNA replication in vivo and whether they elicit mutagenic effects, which may help to understand both how DNA damage interferes with the flow of genetic information during DNA replication and development of diseases caused by gene mutation.
研究领域:
分子生物学
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遗传学
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微生物学
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DOI
PubMed
高影响因子
POLYMER
·
2022
·
IF 4.432
Cheng Deng,Hai Yang,Simin Liu,Zhiyong Zhao
Nanomaterials self-assembled by DNA amphiphiles have great potential application in catalysis, bioimaging and biomedicine. Here, we constructed two kinds of DNA-dendrimer amphiphiles including the G-quadruplex-dendrimer hybrid (G20-Den) and single-stranded DNA-dendrimer hybrid (D20-Den) as a control. Both of them self-assembled into nanofibers with a length of several micrometers in MES buffer, and the diameter of G20-Den nanofibers was smaller than that of D20-Den nanofibers due to the compact stacking of G-quadruplex formed in G20-Den hybrids. At the same time, the catalytic properties of G20-Den nanofiber/hemin, as horseradish peroxidase-mimicking DNAzymes, were investigated. Our results showed that G20-Den nanofiber/hemin, as well as the single-stranded G20/hemin system, exhibited higher catalytic peroxidation activity than D20-Den nanofiber/hemin. Furthermore, through simple ultrafiltration, the recycle of these nanofibers can be simply achieved. This research has provided a new solution for the construction of functional DNA nanomaterials.
研究领域:
生物化学
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纳米医学
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材料科学
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DOI
高影响因子
RSC Advances
·
2023
·Vol. 13
·期 38
·26324-26329
·
IF 3.9
Shuhua Cao,Anlin Wang,Kaoxue Li,Zhiteng Lin,Hongwei Yang,Xiaolei Zhang,Jianmei Qiu,Xishi Tai
A novel tetranuclear Cu(II) complex (TNC) was successfully synthesized and characterized by X-ray single crystal diffraction. The interaction of the complex with calf thymus DNA (CT-DNA) has been studied by UV-vis absorption titration, fluorescence technology and molecular docking. The results indicated that TNC could bind to the DNA through an intercalative mode. The agarose gel electrophoresis experiment showed that TNC could cleave supercoiled plasmid DNA into linear DNA. The anticancer activity of TNC was tested on four cancer cell lines: MCF7, A549, 4T1 and HepG2. The results indicated that TNC shown significant activity against all of above cell lines.
研究领域:
生物化学
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分子生物学
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药理学
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DOI
PubMed
高影响因子
ACS Applied Materials & Interfaces
·
2015
·
IF 6.723
Sai Bi,Bao Xiu,Jiayan Ye,Ying Dong
Here we report a target-catalyzed DNA four-way junction (DNA-4WJ) on the basis of toehold-mediated DNA strand displacement reaction (TM-SDR), which is readily applied in enzyme-free amplified chemiluminescence resonance energy transfer (CRET) imaging of microRNA. In this system, the introduction of target microRNA-let-7a (miR-let-7a) activates a cascade of assembly steps with four DNA hairpins, followed by a disassembly step in which the target microRNA is displaced and released from DNA-4WJ to catalyze the self-assembly of additional branched junctions. As a result, G-quadruplex subunit sequences and fluorophore fluorescein amidite (FAM) are encoded in DNA-4WJ in a close proximity, stimulating a CRET process in the presence of hemin/K+ to form horseradish peroxidase (HRP)-mimicking DNAzyme that catalyzes the generation of luminol/H2O2 chemiluminescence (CL), which further transfers to FAM. The background signal is easily reduced using magnetic graphene oxide (MGO) to remove unreacted species through magnetic separation, which makes a great contribution to improve the detection sensitivity and achieves a detection limit as low as 6.9 fM microRNA-let-7a (miR-let-7a). In addition, four-input concatenated logic circuits with an automatic reset function have been successfully constructed relying on the architecture of the proposed DNA-4WJ. More importantly, DNA nanohydrogels are self-assembled using DNA-4WJs as building units after centrifugation, which are driven by liquid crystallization and dense packaging of building units. Moreover, the DNA nanohydrogels are readily functionalized by incorporating with aptamers, bioimaging agents, and drug loading sites, which thus are served as efficient nanocarriers for targeted drug delivery and cancer therapy with high loading capacity and excellent biocompatibility.
研究领域:
生物化学
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分子生物学
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纳米医学
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分析化学
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DOI
PubMed
高影响因子
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