Nanoscale Advances
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2019
·Vol. 2
·期 2
·717-723
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IF 0
Wenjun Li,Yubo Gao,Jiaona Zhang,Xiaofang Wang,Feng Yin,Zigang Li,Min Zhang
Although DNA recognition has been achieved using numerous biosensors with various sensing probes, the utilization of bio-interaction between DNA and biomolecules has seldom been reported in universal DNA detection. Peptides as natural molecules have the unique ability to bind to universal DNA and excellent selectivity for DNA after being functionalized with specific groups. In this work, we report a peptide based carbon nanotube (CNT) thin-film-transistor (TFT) biosensor, which can achieve sensitive sequence-independent DNA detection. In the presence of DNA, a significant increase of ΔIon could be observed within 5 minutes, which was considered to be due to the electrostatic adsorption between the DNA and peptide of opposite zeta potential. With the gradual increase of the concentration of DNA, the ΔIon signals agree with the Hill–Langmuir model (R2 = 0.98), indicating a negatively cooperative interaction between the peptide and DNA (the Hill coefficient n < 1). Compared with the former reported universal DNA bio-detector and NanoDrop (a spectrometer from Thermo Scientific™), this unique peptide based CNT-DNA sensor demonstrated a broader sensing range from nearly 1.6 × 10−4 to 5 μmol L−1 and a much lower detection limit of approximately 0.88 μg L−1. For the quantification of cDNA from T47D cancer cells, this unique peptide based CNT sensor could achieve efficient cDNA detection. To the best of our knowledge, this is the first report on the utilization of a peptide as a sensing element in the design of CNT based DNA biosensors, which enables highly efficient universal DNA detection.
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BIOSENSORS & BIOELECTRONICS
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2018
·
IF 8.173
Xing-Pei Liu,Jing-Shuai Chen,Chang-jie Mao,He-Lin Niu,Ji-Ming Song,Bao-Kang Jin
A novel enhanced photoelectrochemical DNA sensor, based on a TiO 2 /Au hybrid electrode structure , was developed to detect target DNA. The sensor was developed by successively modifying fluorine-tin oxide (FTO) electrodes with TiO 2 nanoparticles , gold (Au) nanoparticles, hairpin DNA (DNA1), and CdSe-COOH quantum dots (QDs), which acted as signal amplification factors . In the absence of target DNA, the incubated DNA1 hairpin and the CdSe-COOH QDs were in close contact with the TiO 2 /Au electrode surface , leading to an enhanced photocurrent intensity due to the sensitization effect. After incubation of the modified electrode with the target DNA, the hairpin DNA changed into a double helix structure, and the CdSe QDs moved away from the TiO 2 /Au electrode surface, leading to a decreased sensitization effect and photoelectrochemical signal intensity. This novel DNA sensor exhibited stable, sensitive and reproducible detection of DNA from 0.1 μM to 10 fM, with a lower detection limit of 3 fM. It provided good specificity, reproducibility, stability and is a promising strategy for the detection of a variety of other DNA targets, for early clinical diagnosis of various diseases.
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ANALYTICA CHIMICA ACTA
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2018
·
IF 5.123
Li Zou,Ruidi Shen,Liansheng Ling,Gongke Li
We developed a novel strategy for rapid colorimetric detection of specific DNA sequence based on gold nanoparticles assemblies induced by polymerase chain reaction (PCR) product. In the presence of target DNA , the two DNA-functionalized AuNP probes selectively hybridized with the prohibited nucleic acid segments of two primers owing to the zipping off of the hairpin structures during PCR process, resulted in the aggregation of AuNPs with a concomitant color change from red to blue-purple. It is a convenient and universal method for sensitive DNA detection with no need for any further post-treatment of the PCR products. Most importantly, our method showed a low limit of detection (LOD) of 4.3 fM with a wide range of target DNA from 16 fM to 1.6 nM. Owing to the versatility and low cost, the proposed strategy could be extremely useful for a wide range of applications, providing a promising tool for rapid disease diagnostics and gene sequencing.
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CHINESE JOURNAL OF ANALYTICAL CHEMISTRY
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2018
·
IF 0.824
Lian-Ming ZHANG,Dong-You ZHANG,Ying ZENG,Jian-Ping LI
A novel strategy based on DNA induced conformation change was developed by rendering the imprinting cavity with refined structure in order to further improve the selectivity of molecular imprinting membrane. The double-stranded DNA (dsDNA) were first self-assembled on the surface of the gold electrode, then cimaterol (CIM) molecule, taken as the representative target, would bind with the groove of dsDNA to form complex template, together with which the molecular imprinting polymers (MIPs) was prepared by electropolymerization in the monomer solution. After the elution of CIM, the obtained MIPs sensor had a remarkably high selectivity toward CIM. The combination process of CIM and DNA was studied by UV-Vis spectroscopy and was found to follow the groove combination model. The optimal conditions of the system were optimized by electrochemical method. The results showed that the sensor had the best recognition ability toward CIM when the elution time was 35 min by ethanol-acetic acid (8:1, V/V ) as an eluent and rebound time was 45 min. This sensor exhibited a linear detection range of 1.0 × 10 −13 −1.0 × 10 −10 M with a detection limit of 3.2 × 10 −14 M. The sensor was successfully applied for detection of CIM in pork samples.
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BIOSENSORS & BIOELECTRONICS
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2019
·
IF 9.518
Yaxing Zhang,Xiyue Cao,Ruixue Deng,Qingyun Liu,Jianfei Xia,Zonghua Wang
Enzyme-mediated cascade reaction is applied to amplify signal and decrease the background because enzyme can catalyze inactive substrates into active substrates to generate the signal. In this work, Au nanoparticles , as signal probe , are used to load DNA probe and ALP for dual signal amplification . Based on enzyme-mediated cascade reaction, a homogeneous biosensor is constructed for bioassay by employing thrombin as target molecule. When the target is present in the solution, ALP catalyzes the PPi into Pi and then reacts with molybdate in conjunction with Pi in the DNA backbone to produce redox precipitates on the surface of the reduced graphene oxide modified electrode with the help of magnetic separation. Compared with the conventional heterogeneous biosensor, the immobilization-free strategy, proposed in this homogeneous biosensor, improves the sensitivity because of its lower steric hindrance . As a result, this biosensor displayed a great sensitivity with a wide linear range from 1 fM to 10 nM and a detection limit of 0.26 fM, providing a promise and easy operating method for various proteins detection.
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SPECTROCHIMICA ACTA PART A-MOLECULAR AND BIOMOLECULAR SPECTROSCOPY
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2013
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IF 1.977
W. Wei,D.M. Zhang,L.H. Yin,Y.P. Pu,S.Q. Liu
A colorimetric method for detection of DNA damage was developed by using hemin-graphene nanosheets (H-GNs). H-GNs were skillfully synthesized by adsorping of hemin on graphene through π–π interactions. The as-prepared H-GNs possessed both the ability of graphene to differentiate the damage DNA from intact DNA and the catalytic action of hemin. The damaged DNA made H-GNs coagulated to different degrees from the intact DNA because there were different amount of negative charge exposed on their surface, which made a great impact on the solubility of H-GNs. As a result, the corresponding centrifugal supernatant of H-GNs solution showed different color in the presence of 3,3′,5,5′-tetramethylbenzidine (TMB) and H 2 O 2 , which could be discriminated by naked eyes or by ultraviolet (UV)–visible spectrometer. Based on this, the damaged effects of styrene oxide (SO), NaAsO 2 and UV radiation on DNA were studied. Results showed that SO exerted most serious damage effect on DNA although all of them damaged DNA seriously. The new method for detection of DNA damage showed good prospect in the evaluation of genotoxicity of new compounds, the maximum limit of pesticide residue, food additives, and so on, which is important in the fields of food science, pharmaceutical science and pesticide science.
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JOURNAL OF LUMINESCENCE
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2012
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IF 2.102
Shujuan Xu,Yong Shao,Fei Wu,Guiying Liu,Lingling Liu,Jian Peng,Yanwei Sun
Many efforts have been made for sequence-specific recognition of DNA by small molecules. In this study, abasic site (AP site) in a DNA duplex was found to be targeted by myricetin (Myr), one of the natural 3-hydroxyflavonols. Steady-state and transient-state fluorescence, FRET , and DNA melting experiments confirmed that the AP site binding of Myr favors an emission from its tautomer that is derived from excited-state intramolecular proton transfer (ESIPT) reaction between the 3-OH and 4-carbonyl moieties. The selective recognition of Myr is less dependent on the flanking bases of the AP site, although the ESIPT emission is more lighting up for the DNAs with cytosine and thymine opposite the AP site. Because Myr alone in aqueous solution is non-fluorescent, this selective lighting-up emission is advantageous for developing a practical sensor to target the DNA AP site with a weak fluorescence background. This selective recognition of the AP site by the lighting-up fluorescence response would find wide applications including efficiently evaluating DNA damage/repair and screening antitumor/antioxidation drugs.
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Small
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2014
·Vol. 10
·期 8
·1500-1503
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IF 7.514
Xiang Ran,Fang Pu,Jinsong Ren,Xiaogang Qu
Graphical Upconversion applied in logic gate : The Upconversion nanoparticles (UCNPs) give multi emissions when excited by midrange IR radiation. A ternary logic system is designed which combines the unique characters of UCNPs with the ensemble of DNA. By regulating the emission of UCNPs, this logic system involvs more than two states, and the density of information can be increased.
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JOURNAL OF MASS SPECTROMETRY
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2014
·Vol. 49
·期 1
·103-107
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IF 2.709
Ning Xu,Konstantin Chingin,Huanwen Chen
The fundamental aspects of charging in electrospray ionization (ESI) are hotly debated. In the present study, ESI charging of DNA oligonucleotides was explored in both positive (ESI+) and negative (ESI−) polarity using mass spectrometry detection. Single-stranded 12-mer CCCCAATTCCCC in buffer solution (aqueous NH 4 Ac, 100 mM) produced similar charge state distribution (CSD) in either ESI+ or ESI−. Similarity of CSD in ESI+ and ESI− was also observed for the double-stranded 12-mer CGCGAATTCGCG. By adding typical low-vapor reagents (e.g. m-nitro benzyl alcohol, m-NBA; sulfolane) into the same buffer solution (<0.5% w/v), both CCCCAATTCCCC and CGCGAATTCGCG revealed strong supercharging (SC) effect in ESI−, while very little or no SC effect was observed in ESI+. With either sulfolane or m-NBA, the CGCGAATTCGCG duplex dissociated into single strands in ESI−. No SC was observed in both ESI+ and ESI− for thermally denatured CGCGAATTCGCG duplex in NH 4 Ac buffer without the reagents. These findings are difficult to reconcile with the earlier model, which attributes SC in aqueous buffer solution to the conformational changes of analytes. Our observations suggest that the ionic strength of ESI droplets strongly affects the CSD of biopolymers such as DNA oligonucleotides and that SC effect is related to the depletion of ionic strength during the ESI process. Copyright © 2014 John Wiley & Sons, Ltd.
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BIOSENSORS & BIOELECTRONICS
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2017
·
IF 7.78
Li Zhang,Xiaofen Xiao,Yuzhi Xu,Danping Chen,Jun Chen,Yingjun Ma,Zong Dai,Xiaoyong Zou
A simple electrochemical strategy is reported for continuous monitoring of dynamic DNA methylation process over time. An electrochemical sensor was prepared by co-assembling of DNA probe and 6-mercapto-1-hexanol onto a gold electrode. The top of the DNA probe was labeled with 6-ferrocenylhexanethiol modified gold nanoparticle . The charge density between the C•G base pair was verified to be slightly reduced by DNA methylation, and could be further decelerated by ~ 25% upon co-locating a Br group onto methylated cytosine (mC). Therefore, in the presence of NaIO 4 /LiBr, the progressively methylated DNA on the sensor showed a clearly decreasing current over methylation time. The dynamic DNA methylation process was indicated continuously from the current decrease ratio, with a limit of detection of 0.0372 µM. The strategy is convenient, cost-effective, and enable continuous profiling methylation process without distortion. Besides, the strategy was successfully applied for the studies on inhibitor screening and flanking sequence preference of DNA methyltransferase 3a. The results show that the activity of DNA methyltransferase 3a can be mildly inhibited by epigallocatechin gallate , and varies towards different flanking sequence with an order of 5′-CCGG-3′ < 5′-CGCG-3′ < 5′-CGCA-3′.
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FOOD AND CHEMICAL TOXICOLOGY
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2017
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IF 3.778
Jing Yin,Feilong Zhu,Weiyu Hao,Qi Xu,Jin Chang,Huili Wang,Baoyuan Guo
Acylamino acid chiral fungicides (AACFs) are low-toxicity pesticides and considered as non-carcinogenic chemicals to laboratory animals. Though AACFs have potential toxicological effects on mammals by non-genotoxic mechanisms, the toxicoepigenomics of AACFs has not been documented. In this article, we explored toxiciepigenetics of metalaxyl , benalaxyl and furalaxyl through epigenetics research on lambda DNA under different concentration exposure. The toxicoepigenomic difference of stereoisomers was examined also. Our results showed that AACFs would affect methyltransferase activity resulting in modulating DNA methylation levels and pattern. The LOAEL of R-metalaxyl and S-metalaxyl were 30 mM and 0.3 mM, respectively. The LOAEL of (R, S)-benalaxyl and (R, S)-furalaxyl were 0.3 Mm and 30 mM, respectively. A significant dose-response effect between (R, S)-benalaxyl and global methylation level was observed. Global methylation level was more susceptible to S-enantiomer compared to R-enantiomer, which indicated enantiomers of AACFs have the enantioselectivity in toxiciepigenetics. Moreover, the dependence of the methylation inhibition on the chiral center of metalaxyl may suggest a considerable specificity of the compound of AACFs for DNA methyltransferases . The inhibition effect between R-enantiomer and S-enantiomer of AACFs on DNA methylation levels generated in this study is important for low-toxicity pesticides toxicoepigenomics evaluation.
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BIOCONJUGATE CHEMISTRY
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2016
·
IF 4.5
Jianbo Li,Dawei Jiang,Baoliang Bao,Yulin He,Lei Liu,Xuemei Wang
Self-assembled DNA nanostructures, as a new type of nanocarriers, have shown great potential in molecular imaging probes. DNA bipyramid nanostructures (DBNs), as a classic kind of DNA nanostructure, can be precisely constructed through the unparalleled base-pairing precision of oligonucleotide strands. DBNs were prepared by self-assembly of six oligonucleotides with equal molar amounts in a single annealing step, and purified by high performance liquid chromatography (HPLC). DBNs were stable in 10% FBS as well as 80% mouse serum for at least 8 h. To prepare 99mTc-labeled DBNs, N-hydroxysuccinimidyl S-acetylmercaptoacetyl triglycinate (Sacetyl-MAG3-NHS ester) tagged single-stranded DNA (ssDNA) was first radiolabeled with Tc-99m, and DBNs with an overhang were assembled and then hybridized with 99mTc-ssDNA to prepare 99mTc-labeled DNA bipyramid nanostructures (99mTc-MAG3-DBNs). DBNs were radiolabeled, with the radiochemical purity being over 90%. The plasma half-life of 99mTc-MAG3-DBNs in normal KM mice was about 6 min. The biodistribution and SPECT/CT imaging were conducted with 99mTc-MAG3-DBNs in KM mice, and both showed that 99mTc-MAG3-DBNs mainly concentrated in the intestine, liver, and kidneys, and there was also prominent uptake in the gallbladder and bladder. We successfully obtained a new class of SPECT molecular probes based on this DNA polyhedron structure.
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