ACS Nano
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2019
·
IF 13.903
Yi Du,Pai Peng,Tao Li
DNA logic nanodevices that in situ operate within living cells have attracted increasing interest and shown great promise for gene regulation and target recognition. A challenge remains how to control their activation inside specific cellular compartments. Toward this goal, here we report a lysosome-recognizing framework nucleic acid (FNA) nanodevice using an i-motif and an ATP-binding aptamer (ABA) incorporated into a DNA triangular prism (DTP) as the logic-controlling units. Once entering the lysosomal compartments, the FNA device responds to lysosomal pH and ATP via the folding of i-motif and ABA, which triggers a structural change of FNA and the release of a reporter structure for subcellular imaging. With endogenous proton and ATP as two inputs, an AND logic gate is built and in situ operated within living lysosomes by pH and ATP modulation with external drug stimuli. Given the abnormal levels of pH and ATP within some cancer cells or dysfunctional lysosomal cells, in this context our designed FNA logic device may find extended applications in controllable drug release and disease treatment.
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ANALYTICAL CHEMISTRY
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2018
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IF 6.042
Danya Lyu,Jing Li,Xiaowen Wang,Weiwei Guo,Erkang Wang
DNA-templated silver nanoclusters (DNA–Ag NCs) have shown great potential in various bioanalysis and bioimaging applications, owing to their facile synthesis and ultrasmall sizes and especially their programmable fluorescence emission depending on the sequences of DNA templates. However, the bioimaging applications of DNA–Ag NCs are severely limited by their poor stability in physiological environments and their poor cell permeability, resulting from the highly negatively charged DNA backbones. In this paper, cationic polyelectrolytes were used to modify fluorescent DNA–Ag NCs via electrostatic interactions between the positive polymer backbones and the negatively charged phosphate groups of the DNA strands. The fluorescence properties of a typical single-stranded-DNA (ssDNA)-templated Ag NC changed dramatically after incorporation with the cationic polyelectrolyte caused by conformational changes in the DNA, with a 3-fold fluorescence-emission enhancement of the Ag NCs observed after incorporation with a typical cationic polyelectrolyte, poly(diallyldimethylammonium chloride) (PDDA), whereas the fluorescence of double-stranded-DNA (dsDNA)-templated Ag NCs changed little after incorporation. Moreover, the modification with PDDA greatly prolonged the stability of both ssDNA- and dsDNA-stabilized Ag NCs against nuclease digestion and enhanced the cell uptake of the DNA–Ag NCs. Rapid cell imaging was demonstrated using NIH/3T3 cells as a model system.
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RSC Advances
·
2019
·Vol. 9
·期 6
·3407-3415
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IF 3.049
Xinglu Jiang,Chenggui Zhao,Xiaobo Fan,Wei Xu,Rui Zhang,Hongbo Xu,Guoqiu Wu
Cell-free DNA (cfDNA) in blood, which stems from the fetus of pregnant women and tumor in cancer patients, has gained attention in molecular diagnosis. However, cfDNA is less stable, and its amount in the serum is extremely low; these are critical barriers for the utilization of this resource. In this study, a DNA-modified polyacrylamide hydrogel (DNA-Gel) was prepared, and a specialized device was designed to simultaneously catch, purify, concentrate, and detect targeted cfDNA by electrophoresis. We demonstrated that 20–1000 bp ssDNA and dsDNA could be caught and released by the DNA-Gel-based device with high specificity and sensitivity. Upon increasing the number of cycles and electrophoresis time, higher DNA purity and density were achieved, and the separation of serum proteins, untargeted cfDNA, and other charged molecules was promoted. As low as 10 pg μL−1 of DNA could be detected using the DNA-Gel after four cycles of concentration. We also detected 1 fg μL−1 of DNA in the serum with 16 cycles of concentration, followed by 25 PCR cycles. We also designed a device to obtain DNA from the DNA-Gel. We found that the DNA loss rate was around 50%, and A260/A280 was close to 1.7. Thus, we have designed a cost-effective and highly economical device to purify DNA at low concentrations with high specificity and selectivity.
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CHEMICAL PHYSICS LETTERS
·
2018
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IF 1.686
Qingqian Fan,Yueping Guan,Zhi Zhang,Guoli Xu,Yu Yang,Chen Guo
A new method was developed for preparing monodisperse Fe 3 O 4 @SiO 2 magnetic core-shell nanoparticles via three steps. The obtained nanoparticles exhibit high saturation magnetization, good surface topography and dispersion as characterized by FTIR, SEM and VSM. The experimental results of hydrochloric acid treatment show that the obtained nanoparticles have excellent acid resistance and stable and compact silicon coating. The magnetic core-shell nanoparticles were further tested for purification of plasmid DNA from E. coli DH5a cells. The result of purification leaded to better adsorption, elution and purity results in comparison with isolated commercial extraction kit.
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TALANTA
·
2019
·
IF 4.916
Yanli Zhang,Zhenyu Zhu,Xia Teng,Yanqiong Lai,Shaofu Pu,Pengfei Pang,Hongbin Wang,Chun Yang,Colin J. Barrow,Wenrong Yang
Microcystin-LR (MC-LR) is a potent hepatotoxin that is often associated with blooms of cyanobacteria. The analysis of trace MC-LR plays important role in environmental and health fields. Herein, we developed a low-cost and enzyme-free detection method of MC-LR by using hairpin DNA-templated copper nanoclusters (hpDNA-CuNCs) as fluorescent probe . The hpDNA-template was designed and fabricated by a MC-LR aptamer loop and a double strand stem, which can specifically recognize target MC-LR with strong affinity. The AT-rich and complementary double strand stem serves as a template for the formation of CuNCs. The formed fluorescent sensing probe of hpDNA-CuNCs exhibits maximum emission wavelength at 575 nm. Upon the addition of target MC-LR into the hpDNA-CuNCs, we observed fluorescence was quenched considerably due to the high affinity between MC-LR and hpDNA aptamer strand loop, which indicated a conformational change of hairpin probe from the stem-loop DNA structure to single-stranded DNA . Then, the change of fluorescence intensity can be used to monitor the concentration of MC-LR from 0.005 to 1200 μg L −1 with a detection limit of 0.003 ng L −1 . Compared with the previous reports, this method does not require complex DNA sequence design, fluorescence dye label and sophisticated experimental techniques. Moreover, the target MC-LR in real water samples has been detected.
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JOURNAL OF LUMINESCENCE
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2018
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IF 2.732
Ziyue Ni,Ting Ye,Yali Yu,Longlong Gao,Yifan Fei,Qiusha Li,Yufeng Zhou,Yong Shao,Lintao Zeng
DNA apurinic/apyrimidinic site (AP site) has received much attention due to its importance in disease evolution and development of selective genetic drugs. Fluorescence technique has been widely employed in identifying the AP sequence environment using fluorophores as the AP site-targeting probes. However, the sequence effect on the AP site binding of a ligand should be fully understood for illustrating the binding behavior. Triplex-forming oligonucleotide (TFO) can bind with its partner ds-DNA via specific hydrogen bonding interactions different from the canonical Watson-Crick pattern to form a triplex DNA structure . Due to its wide bioactivity, triplex has been recently investigated using small molecules as the structure identifiers and tuners. In this work, we spectroscopically characterized a novel fluorescent benz[ e ]indolium probe of BIFS and found that BIFS can selectively target the AP site and its fluorescence is significantly enhanced only when the TFO strand binds to the AP site-containing duplex DNA. The TFO binding restricts the non-radiative twist relaxation process of the excited state BIFS and results in the emissive BIFS. Because BIFS alone in aqueous solution is non-fluorescent, this selective lighting-up emission is advantageous for developing a practical sensor to target the triplex AP site with a weak fluorescence background. This selective recognition of the AP site by the lighting-up fluorescent probe would find wide applications including fluorescently evaluating the triplex-based small molecular binders.
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TRANSITION METAL CHEMISTRY
·
2018
·Vol. 43
·期 3
·259-271
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IF 1.261
Liu Ya-Xian,Mo Hui-Wen,Lv Zhen-Yu,Shen Fang,Zhang Chun-Lian,Qi Yong-Yu,Mao Zong-Wan,Le Xue-Yi
A copper complex [Cu(HPBM)( l -Phe)(H 2 O)]·ClO 4 (1) (HPBM = 5-methyl-2-(2′-pyridyl)benzimidazole, l -Phe = l -phenylalanine anion) was synthesized and characterized by elemental analysis, IR, ESI–MS, HR–ESI–MS, ESR spectroscopy, and by X-ray single-crystal analysis. The binding constant of the complex with calf thymus DNA (CT-DNA) was determined as 7.38 (± 0.57) × 10 4 M −1 . Further studies indicated that the complex interacts with CT-DNA through minor groove binding. The in vitro cytotoxic activities of both the free proligand and the complex against Eca-109, HeLa and A549 cancer cells and normal LO2 cells were evaluated by the MTT method. The IC 50 values range from 5.7 ± 0.1 to 8.3 ± 0.6 µM. Free HPBM displays no cytotoxic activity against the selected cancer cells, with IC 50 values more than 100 µM. Double staining analysis showed that the complex can induce apoptosis in Eca-109 cells. Comet assays demonstrated that the complex can damage DNA and cause apoptosis. The complex also induces an increase in intracellular reactive oxygen species and a reduction in mitochondrial membrane potential. The complex can also increase the intracellular Ca 2+ level and induce release of cytochrome c . The cell cycle arrest was investigated by flow cytometry. The results demonstrate that the complex induces apoptosis in Eca-109 cells through DNA-binding and ROS-mediated mitochondrial dysfunctional pathways.
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ADVANCED FUNCTIONAL MATERIALS
·
2018
·Vol. 28
·期 14
·1707152
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IF 13.325
Zhi Li,Ganglin Wang,Yi Shen,Nannan Guo,Nan Ma
Circulating tumor cell (CTC) enumeration and analysis has emerged as an important platform for cancer diagnosis and prognosis. A great challenge, however, is to efficiently capture low abundant CTCs with high purity from blood samples in a rapid and high-throughput manner for accurate and sensitive CTC detection. Herein, a new class of DNA-templated magnetic nanoparticle-quantum dot (QD)-aptamer copolymers (MQAPs) is developed for rapid magnetic isolation of CTCs from human blood with high capture efficiency and purity approaching 80%. The phenotype of CTCs is simultaneously profiled with QD photoluminescence (PL) at single cell level. These MQAPs are constructed through hybridization chain reaction to achieve amplified magnetic response, extraordinary binding selectivity for target cells over background cells, and ultra bright ensemble QD PL for single cell detection. MQAPs are free from nonspecific binding that would otherwise compromise the capture purity of target cells. As a result, facile isolation and enumeration of rare CTCs in blood samples could be achieved in 20 min with high sensitivity and accuracy.
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COLLOIDS AND SURFACES A-PHYSICOCHEMICAL AND ENGINEERING ASPECTS
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2018
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IF 2.829
Boyi Niu,Yixian Zhou,Ting Wen,Guilan Quan,Vikramjeet Singh,Xin Pan,Chuanbin Wu
Packaging enough genetic materials is necessary for gene delivery, but functional modification of the carriers may affect their gene loading capacity. In this study, RGD peptide-modified mesoporous silica nanoparticles were synthesized to investigate the influences of functionalization on their DNA adsorption and desorption behaviors. Effects of the functionalization degree of the nanocarriers and the adsorption conditions including DNA concentration, pH, ionic strength and temperature were studied. The DNA adsorption of the nanocarriers were enhanced by reducing pH or adding moderate amounts of ionic salt. Compared with nonfunctional nanoparticles, nanoparticles with low degree of functionalization possessed decreased DNA adsorption capacity but increased adsorption stability. High degree of functionalization resulted in both poor adsorption capacity and stability. Systematic studies showed that the adsorption processes were spontaneous and endothermic, and could be well described by pseudo-second-order kinetic model , Langmuir and Freundlich models. In summary, the DNA loading capacity of mesoporous silica nanoparticles can be improved by proper functionalization and optimized adsorption conditions.
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FOOD CHEMISTRY
·
2018
·
IF 4.946
Nana Sun,Yuan Ding,Zhexuan Tao,Hongjie You,Xiude Hua,Minghua Wang
An upconversion fluorescence DNA probe which consists of aptamer-conjugated magnet nanoparticles (apt-MNPs) and complementary DNA-conjugated upconversion nanoparticles (cDNA-UCNPs) was developed to detect acetamiprid. Acetamiprid can specifically conjugate with the apt-MNPs to dissociate the cDNA-UCNPs from the apt-MNPs and resulted in reduced fluorescence intensity through an external magnet. The change of fluorescence intensity (△I) is positively related to the concentration of acetamiprid, which can be applied for the quantification of acetamiprid. Under optimal conditions, a linear detection range and detection limit are 0.89–114.18 μg/L and 0.65 μg/L, respectively. The probe was successfully used to detect acetamiprid in spiked paddy water, soil, pear, apple, wheat and cucumber. Average recoveries are 78.2%–103.5% with intra-day relative standard deviations (RSDs) of 2.6%–10.9% and inter-day RSDs of 4.3%–10.2%. The amounts of acetamiprid in the authentic paddy water and pear samples detected by the DNA probe are significantly correlated with that detected by high-performance liquid chromatography (HPLC).
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TALANTA
·
2019
·
IF 4.916
Wei He,Xiangying Sun,Bin Liu,Jiangshan Shen
In this paper, deoxyribonucleic acid (DNA) with different lengths were used to control the distance between carbon dots (CDs) and silver nanoparticles (AgNPs) in self-assembled multilayers (SAMs). Surface-enhanced fluorescence and fluorescence resonance energy transfer (SEF-FRET) could be achieved based on changing DNA strands. The fluorescence intensity of CDs SAMs with 6-base DNA strands could be enhanced up to ca. 5.6 times by AgNPs. As-fabricated CDs SAMs with excellent luminescent properties, superior stability have been employed for the development of a label-free fluorescence sensing platform for DNA detection. Since DNA would hybridize with the complemented one which was attached on the surface of SAMs, resulting in a close distance between CDs and AgNPs, FRET could thus occur between AgNPs and CDs, resulting in quenching the fluorescence of CDs SAMs. This sensitive sensing platform could show excellent analytical performance for detecting DNA with a linear response ranging from 93.07 pM to 5.433 nM and a detection limit of 16.36 pM, which could be further employed to probe human blood samples. This could prove a promising method for the detection of DNA.
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TALANTA
·
2018
·
IF 4.244
Zi-Han Chen,Xin-Yue Han,Ling-Xue Deng,Zi-Yang Lin,Fang-Ya Mu,Shengqiang Zhang,Guoyue Shi,Min Zhang
Tb 3+ -doped carbon dots (Tb 3+ @CDs) were prepared in a facile hydrothermal method by using ammonium citrate as carbon source and Tb 3+ as dopant. A 15-bp GT-rich single-strand DNA (ssDNA) was introduced to sensitize Tb 3+ via the antenna effect for generating two fluorescence signals (CDs and Tb 3+ ), forming a conjugate of Tb 3+ @CDs/ssDNA. The ratiometric fluorescence of Tb 3+ @CDs/ssDNA could be reversibly regulated by Ag + and Cys, in which the fluorescence peak at 546 nm of Tb 3+ could be switched to “On” or “Off” as the signal indicator while the fluorescence peak at 444 nm of CDs remained constant as the build-in reference. The proposed Ag + /Cys-mediated reversible fluorescence changes in Tb 3+ @CDs/ssDNA was also proven for the design of a self-calibrating ratiometric fluorescence logic system. By integrated with the specific reaction between H 2 O 2 and Cys, Tb 3+ @CDs/ssDNA was applied for ratiometric fluorescence detection of H 2 O 2 . More importantly, the sensing strategy could be further successfully extended to the monitoring of H 2 O 2 -produced oxidase-related reactions, such as GOx-biocatalyzed oxidation of glucose (the limit of detection: 0.06 μM) and was well applied in rat serum compared to commercial kits. This work unveiled a novel ratiometric fluorescent design, which is cost-effective, simple to prepare and easy-to-use without chemical modification or fluorescence labeling .
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