Biointerphases
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2019
·Vol. 14
·期 6
·
IF 2.009
Cheng Fang,Ma Xiaochun,Feng Qiancheng,Wang Hanqi,Yin Meng,He Wei
The reliability and stability of array slides are a big concern for array vendors and end users. Herein, we report on a new type of array slide with high reactivity toward DNA probes and low side reaction. A one-step surface reaction via the Michael addition involved in preparing array slides was developed and characterized by x-ray photoelectron spectroscopy, contact angle, and fluorescence labeling. The effects of array fabrication and storage conditions, i.e., spotting solution p H, high humidity, and long-term storage on the reactivity of the slides were examined. The fabricated DNA arrays could realize good hybridization efficiency (38.2% for slides with 0.88 pmol/cm 2 ), low limit of detection (4 × 10 −14 M), as well as high mismatch selectivity.
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Materials Today Bio
·
2024
·
IF 8.7
Yibiao Wang,Xiaomei Fu,Yang Zhu,Mingjing Lin,Renduan Cai,Yang Zhu,Tiantian Wu
Intratumor bacteria, which are involved with complex tumor development mechanisms, can compromise the therapeutic efficiencies of cancer chemotherapeutics. Therefore, the development of anti-tumor agents targeting intratumor bacteria is crucial in overcoming the drug inactivation induced by bacteria colonization. In this study, a double-bundle DNA tetrahedron-based nanocarrier is developed for intratumor bacteria-targeted berberine (Ber) delivery. The combination of aptamer modification and high drug loading efficacy endow the DNA nanocarrier TA@B with enhanced delivery performance in anti-tumor therapy without obvious systemic toxicity. The loaded natural isoquinoline alkaloid Ber exhibits enhanced antimicrobial, anticancer, and immune microenvironment regulation effects, ultimately leading to efficient inhibition of tumor proliferation. This intratumor bacteria-targeted DNA nanoplatform provides a promising strategy in intervening the bacteria-related microenvironment and facilitating tumor therapy.
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SPECTROCHIMICA ACTA PART A-MOLECULAR AND BIOMOLECULAR SPECTROSCOPY
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2012
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IF 2.098
Shucai Liang,Hui Yu,Jin Xiang,Wang Yang,Xiaohui Chen,Yanbin Liu,Chen Gao,Guoping Yan
A new naphthalimide modified polyethylenimine (PEI) nanoparticles (called NPEI-NPs) was synthesized and applied as fluorescent probe for rapid, selective and sensitive fluorometric detection of trace DNA. The synthesis involved the covalent modification of PEI with 4-butylamino-N-carboxymethyl-1,8-naphthalimide(BACMN) for getting amphiphilic polymer. Then the amphiphilic polymer was self-assembled in water to give the NPEI-NPs. NPEI-NPs was soluble in water and emitted fluorescence at 545 nm with exciting at 460 nm. The fluorescence spectra resulting from the interaction between NPEI-NPs and DNA indicated that the fluorescence of NPEI-NPs increased in the present of DNA. Therefore, a fluorescence enhancement method was developed for the determination of trace fish sperm DNA (fsDNA) and calf thymus DNA (ctDNA). Under the optimal conditions, the calibration curves were linear over the concentration ranges of 0.05–2.8 μg/mL for fsDNA and 0.08–3.0 μg/mL for ctDNA. The detection limits for fsDNA and ctDNA were 1.6 and 2.0 ng/mL, respectively. The proposed method has been employed to quantify DNA in synthetic samples with the satisfactory results.
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Analytical Methods
·
2024
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IF 2.7
Chu Cheng,Qingzhou Cheng,Wei Zhou,Yulong Chen,Wenbin Liu,Zhiling Zhang,Jingsi Ye,Pengfeng Xiao
Eliminating errors in next-generation sequencing has proven to be challenging. Here we present a novel strategy for DNA sequencing, called correctable two-color fluorogenic DNA decoding sequencing, which can significantly improve sequencing accuracy and throughput by employing a dual-nucleotide addition combined with fluorogenic sequencing-by-synthesis (SBS) chemistry. This sequencing method involves introducing a mixture of natural nucleotide X, labeled unblocked nucleotide X′, 3′ blocked nucleotide Y*, and labeled 3′ blocked nucleotide Y* into each reaction cycle. By cyclically interrogating a template twice with different nucleotide combinations, two sets of base-encoding are sequentially obtained, enabling accurate deduction of base sequence. We demonstrate the remarkable efficacy of this approach in detecting and correcting sequencing errors, achieving a theoretical error rate of 0.0005%, which is twice as accurate as Sanger sequencing. Furthermore, we show the capability to detect known mutation sites using information from only a single sequencing run. The correctable two-color fluorogenic DNA decoding sequencing approach should enable accurate identification of extremely rare genomic variations in diverse applications in biology and medicine.
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BIOSENSORS & BIOELECTRONICS
·
2016
·
IF 7.476
Haimeng Pei,Yiqun Zheng,Rongmei Kong,Lian Xia,Fengli Qu
We describe a highly sensitive nanoparticle–based fluorescence resonance energy transfer (FRET) probe developed without using molecular fluorophores as donors and acceptors. The success of this work relies on the strategy that DNA scission was designed to occur to the probe when target presented, which enabled the fluorescence signal “turn-on” of graphene quantum dots (GQDs) and thus quantitative analysis . In particular, amino-modified SiO 2 NPs were initially coated by GQDs to form highly emitting SiO 2 /GQDs, followed by conjunction with DNA functionalized gold nanoparticles (Au NPs–DNA) to form SiO 2 /GQDs–DNA–Au NPs composite. Owing to the FRET interactions between the GQDs and Au NPs, the fluorescence of GQDs was effectively quenched by Au NPs. When bleomycin (BLM), a model analyte , was mixed with the probe, the fluorescence signal of GQDs would be restored due to the removal of Au NPs from the SiO 2 /GQDs surface by DNA scission treatment with BLM in the presence of Fe (II). The current FRET probe shows a good linear relationship between the fluorescence intensity and the concentration of BLM in the range from 0.5 nM to 1 μM with a detection limit of 0.2 nM. The probe also shows satisfactory results for the analysis of clinical serum samples. This method provides versatility to the application of GQDs in FRET biosensing and could be potentially extended to other similar systems by replacing the linker between the GQDs and Au NPs.
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Epigenomics
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2017
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IF 4.541
Hanze Wang,Huican Ke,Yansong Zheng,Junzhong Lai,Qianping Luo,Qi Chen
Aim: Our purpose is to improve the conventional procedures for bisulfite conversion used to detect 5-methylcytosine in DNA. Methods: Impacts of different bisulfite salts, bisulfite conversion temperature, antioxidants and denaturants on DNA conversion and degradation were assessed by methylation-sensitive melt curve analysis. The modified method was tested on different genes and the conversion efficiency was analyzed by bisulfite sequencing. Results: We developed a modified bisulfite conversion method that completes this process within 2 h. We demonstrate that high temperature denaturation is the major cause for DNA degradation, and the addition of ethylene glycol dimethyl ether is an effective way to accelerate the bisulfite conversion. The conversion efficiency is comparable to many other commercial kits. Conclusion: Our modified bisulfite conversion method is simple, cost efficient and less time consuming and is compatible with different genes and samples, thus has a great potential for the future research and clinical applications.
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JOURNAL OF FLUORESCENCE
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2017
·Vol. 27
·期 5
·1815-1828
·
IF 1.461
Xia Kaixin,Zhang Guowen,Li Song,Gong Deming
Vanillin (VAN) and ethyl vanillin (EVA) are widely used food additives as flavor enhancers, but may have a potential security risk. In this study, the properties of binding of VAN or EVA with calf thymus DNA (ctDNA) were characterized by multi-spectroscopic methods, multivariate curve resolution-alternating least-squares (MCR–ALS) algorithm and molecular simulation. The concentration profiles for the components (VAN or EVA, ctDNA and VAN–ctDNA or EVA–ctDNA complex) by the MCR–ALS analysis showed that VAN or EVA interacted with ctDNA and formed VAN–ctDNA or EVA–ctDNA complex. The groove binding of VAN or EVA to ctDNA was supported by the results from viscosity measurements, melting studies, denaturation experiments, and competitive binding investigations. Analysis of the Fourier transform infrared spectra corroborated the prediction by molecular docking that VAN and EVA preferentially bound to thymine bases region of ctDNA. The circular dichroism and DNA cleavage assays indicated that both VAN and EVA induced conformational change (from B − like DNA structure toward to A − like form), but didn’t lead to a significant damage on DNA. The fluorescence quenching of Hoechst 33,258–ctDNA complex by VAN or EVA was a static quenching, and hydrogen bonding and van der Waals forces were main forces. This study has provided insights into the mechanism of interaction between VAN or EVA with ctDNA, and may also help better understand their potential toxicity with regard to food safety.
VAN or EVA binds to A–T rich regions of ctDNA in the minor groove.
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ACS Applied Materials & Interfaces
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2017
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IF 7.504
Ni Hui,Xiaotian Sun,Shuyan Niu,Xiliang Luo
Biofouling arising from nonspecific adsorption is a substantial outstanding challenge in diagnostics and disease monitoring, and antifouling sensing interfaces capable of reducing the nonspecific adsorption of proteins from biological complex samples are highly desirable. We present herein the preparation of novel composite nanofibers through the grafting of polyethylene glycol (PEG) polymer onto polyaniline (PANI) nanofibers and their application in the development of antifouling electrochemical biosensors. The PEGylated PANI (PANI/PEG) nanofibers possessed large surface area and remained conductive and at the same time demonstrated excellent antifouling performances in single protein solutions as well as complex human serum samples. Sensitive and low fouling electrochemical biosensors for the breast cancer susceptibility gene (BRCA1) can be easily fabricated through the attachment of DNA probes to the PANI/PEG nanofibers. The biosensor showed a very high sensitivity to target BRCA1 with a linear range from 0.01 pM to 1 nM and was also efficient enough to detect DNA mismatches with satisfactory selectivity. Moreover, the DNA biosensor based on the PEGylated PANI nanofibers supported the quantification of BRCA1 in complex human serum, indicating great potential of this novel biomaterial for application in biosensors and bioelectronics.
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BIOSENSORS & BIOELECTRONICS
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2016
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IF 7.476
Yanchen Liu,Xiangqing Wang,Hui Wu
Mercury is a bioaccumulative and highly toxic heavy metal . Thus, the removal and detection of Hg 2+ from the environment is a major challenge. This paper reports a novel bio-nanomaterial for the simultaneous determination and removal of Hg 2+ with the use of rGO-Fe 3 O 4 functionalized with Hg 2+ -specific thymine oligonucleotide (T-DNA). T-DNA interacts with Hg 2+ and changes from having a random coil into a hairpin structure, thereby increasing the fluorescence of SYBR Green I. Such fluorescence turn-on process allows the detection of Hg 2+ in the concentration range of 1–20 ng/mL, with a detection limit of 0.82 ng/mL. Removal is achieved by exploiting the T-Hg 2+ -T base pairs and the large surface area of graphene; these bio-nanocomposites exhibit excellent removal efficiency (over 80%) and rapid separation from the aqueous solution. Moreover, bio-nanomaterials can be regenerated after a simple treatment. The proposed method also demonstrates the evident practicability of the simultaneous detection and removal of Hg 2+ in lake water samples.
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ANALYTICAL CHEMISTRY
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2012
·
IF 5.856
Mo Wang,Zhenning Xu,Lijian Chen,Huanshun Yin,Shiyun Ai
In this paper, we developed a novel electrochemical method to quantify DNA methyltransferase (MTase) and analyze DNA MTase activity. After the double DNA helix structure was assembled on the surface of gold nanoparticle modified glassy carbon electrode, it was first methylated by M. SssI MTase and then digested by restriction endonuclease HpaII, which could not recognize the methylated CpG site. Successively, anti-5-methylcytosine antibody was specifically conjugated on the CpG methylation site and horseradish peroxidase labeled goat antimouse IgG (HRP-IgG) was conjugated on anti-5-methylcytosine antibody. In the detection buffer solution containing H2O2 and hydroquinone, HRP-IgG can catalyze hydroquinone oxidation by H2O2 to generate benzoquinone, resulting in a highly electrochemical reduction signal. Consequently, the activity of M. SssI MTase was assayed, and DNA methylation was detected using the signal change with and without methylation. Furthermore, the inhibition investigation demonstrated that, in the presence of 160 μM S-adenosyl-l-methionine as methyl donor, 5-aza-2′-deoxycytidine, procaine, epicatechin, and caffeic acid could inhibit the M. SssI MTase activity with the IC50 values of 45.77, 410.3, 129.03, and 124.2 μM, respectively. Therefore, this study may provide a sensitive platform for screening DNA MTase inhibitors.
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JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY
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2014
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IF 3.107
Guowen Zhang,Langhong Wang,Xiaoyue Zhou,Yu Li,Deming Gong
The binding characteristics of sodium saccharin (SSA), an artificial sweetener, with calf thymus DNA (ctDNA) were investigated by multispectroscopic techniques, chemometrics, and molecular simulation. A combined fluorescence and UV–vis spectroscopic data matrix was resolved by the multivariate curve resolution–alternating least-squares (MCR–ALS) chemometrics algorithm. The MCR–ALS analysis extracted simultaneously the concentration profiles and spectra for the three components (SSA, ctDNA, and SSA–ctDNA complex) to quantitatively monitor the SSA–ctDNA interaction, which is difficult to perform by conventional spectroscopic approach. The binding mode of SSA to ctDNA was principally through groove binding as revealed by ctDNA melting temperature studies, viscosity measurements, and iodide and salt quenching effects. Analysis of the Fourier transform infrared and circular dichroism spectra as well as molecular docking indicated that SSA preferentially bound to the guanine base of ctDNA and led to a transformation from B-like DNA structure to A-like conformation. Moreover, gel electrophoresis results suggested that SSA did not induce any significant cleavage in plasmid DNA.
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BIOSENSORS & BIOELECTRONICS
·
2014
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IF 6.451
Zhao Zhang,Liqiang Luo,Guifang Chen,Yaping Ding,Dongmei Deng,Chunhai Fan
A novel simple protocol of synthesizing tryptamine-functionalized reduced graphene oxide (TRA–rGO) was proposed to fabricate label-free electrochemical impedance DNA biosensor. TRA was anchored to rGO with its indole ring via π-stacking interaction. The morphology, conductivity and interaction of TRA–rGO were characterized by atomic force microscopy , high resolution transmission electron microscopy , cyclic voltammetry , electrochemical impedance spectroscopy (EIS) as well as Raman and fluorescence spectroscopy. The amino-substituted oligonucleotide probe was conjugated to TRA by cross-linker glutaraldehyde for preparing an electrochemical biosensing platform. The DNA hybridization reaction of oligonucleotide probe with target DNA was monitored by EIS. Under optimum conditions, the proposed biosensor exhibited high sensitivity and low detection limit for detecting complementary oligonucleotide. The target oligonucleotide could be quantified in a wide range of 1.0×10 −12 –1.0×10 −7 M with low detection limit of 5.2×10 −13 M ( S/N =3).
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