查找使用阿拉丁产品的科研文献

Mismatch-guided DNA competitive converter enables expanded detection window for discriminating single nucleotide polymorphisms

Yunshan Zhang,Tuo Huang,Fang Yang,Qianglong Tan,Sisi Bu,Siyu Yu,Jing Ye,Tian Hang,Xianzhong Feng,Diming Zhang

The subtle free energy differences resulting from single nucleotide mutations pose a challenge for the specificity of nearly all DNA hybridization probes in identifying single nucleotide polymorphisms (SNPs). The narrow detection window between mutant target (MT) and wild-type target (WT) concentrations that produce the same level of detection signals limits the widespread application of current SNP detection technologies. In this paper, we introduce an efficient method for converting single-base information using a rationally designed ratio-signal DNA competitive converter (RDCC). This converter significantly expands the detection window for single-base mutations in nucleic acid sequences by enabling a user-defined conversion of quantitative relationships between detection signals and target concentrations. Both computer simulations and experimental validations have confirmed the effectiveness of RDCC in converting single-base information and expanding the detection window. By balancing both MT and WT signals, RDCC excels in identifying heterozygous samples with low mutation abundances. Additionally, RDCC has been proven to be harmoniously compatible with commonly used nucleic acid amplification techniques, such as PCR. Furthermore, we have demonstrated the practical application value of RDCC through genotyping tests on genomic samples from soybean leaves. Therefore, this study not only develops a powerful tool for SNP detection but also provides a paradigm for the design of specific nucleic acid probes.

Renal Clearable Luminescent WSe2 for Radioprotection of Nontargeted Tissues during Radiotherapy

Haixia Liu,Junying Wang,Yaqi Jing,Jiang Yang,Xueting Bai,Xiaoyu Mu,Fujuan Xu,Xuhui Xue,Lingfang Liu,Yuan-Ming Sun,Qiang Liu,Haitao Dai,Changlong Liu,Xiao-Dong Zhang

High-energy ionizing radiation is widely used in medical diagnosis and cancer radiation therapy. However, high-energy radiation can also impose significant damages in healthy tissues during medical treatments via direct DNA damages and indirect damages from production of reactive oxygen species (ROS). Therefore, it is urgent to develop highly effective radioprotectants with low toxicities that can meet the increasing needs for alleviating the adverse effects from cancer radiation therapy and nuclear emergency. In this work, strongly catalytic ultrasmall (sub-5 nm) cysteine-protected WSe 2 dots are employed to protect healthy tissues against radiation via diminishing radiation-induced free radicals. The WSe 2 dots with high surface activities can recover radiation-induced DNA damages and eliminate the excessive ROS generated from radiation. In vivo experiments confirm that the survival rate of mice treated with WSe 2 dots is significantly elevated with radiation damages postponed under exposure to high-dose ionizing radiation. Furthermore, the free radicals in major organs and hematological system can be appreciably omitted, suggesting their unique role as free radical scavengers. These WSe 2 dots in ultrasmall size show rapid renal clearance of ≈74% injection dose via urine excretion in 24 h and do not cause any apparent toxicity in vivo for up to 30 d.

Novel thin-film composite nanofiltration membranes fabricated via the incorporation of ssDNA for highly efficient desalination

B.-Q. Huang,H. Ding,Z.-L. Xu,Y.-J. Tang

In this work, the biomacromolecule, single-stranded deoxyribonucleic acid (ssDNA) was innovatively incorporated into the polyamide layer to tailor the permeate flux and antifouling performance of the nanofiltration (NF) membranes. With active amines groups, the ssDNA was as the aqueous phase monomers along with piperazine (PIP), and reacted with trimesoyl chloride on polyethersulfone substrate to fabricate thin-film composite (TFC) NF membranes. The NF membrane prepared under optimal ratio of ssDNA/PIP had a pure water permeability of 75.8 L m −2 h −1 (improved 58% compared to PIP NF membrane) and Na 2 SO 4 rejection of 98.0% at 6.0 bar. The rejections for different inorganic salts were the order: Na 2 SO 4 (98.0%) > MgSO 4 (89.2%) > MgCl 2 (72.8%) > NaCl (23.0%). Furthermore, the TFC NF membranes showed good antifouling performance in long-term running with 300 ppm bovine serum albumin and humic acid solution. © 2018 Wiley Periodicals, Inc. J. Appl. Polym. Sci. 2018 , 135 , 47102.

Preservation of cfRNA in cytological supernatants for cfDNA & cfRNA double detection in non-small cell lung cancer patients

Yidan Ma,Yifei Wang,Lei He,Jun Du,Lin Li,Zhixin Bie,Yuanming Li,Xiaomao Xu,Wei Zhou,Xiaonan Wu,Li Yang,Jing Di,Chenyang Li,Xiaoguang Li,Dongge Liu,Zheng Wang

Backgroud Supernatants from various cytological samples, including body cavity effusion, sputum, bronchoalveolar lavage fluid (BALF), and needle aspiration, have been validated for detecting genetic alterations using cell-free DNA (cfDNA) in patients with non-small cell lung cancer (NSCLC). However, the sensitivity of fusion variations detection remains challenging. The protection of cell-free RNA (cfRNA) is critical for resolving the issue. Methods A protective solution (PS) was applied for preserving cfRNA in cytological supernatant (CS), and the quality of protected cfRNA was assessed by cycle threshold (CT) values from reverse transcription quantitative polymerase chain reaction (RT-qPCR). Furthermore, we collected an additional set of malignant cytological and matched tumor samples from 84 NSCLC patients, cfDNA & cfRNA extraction and double detection for driver gene mutations was validated using the multi-gene mutations detection by RT-qPCR. Results Under the optimal protection system, 91.0% (101/111) of cfRNA were protected effectively. Among the 84 NSCLC patient samples, seven cytological samples failed the tests. In comparison with tumor samples, the overall sensitivity and specificity of detecting driver genes of supernatant cfDNA and cfRNA were 93.8% (74/77) and 100% (77/77), respectively. Notably, when focusing exclusively on patients with fusion gene changes, both sensitivity and specificity reached 100% (11/11) for EML4-ALK, ROS1, RET fusions, and MET ex14 skipping. Conclusion These findings suggest that cfDNA & cfRNA extraction and double detection strategy recommended in this study improve the accuracy of driver genes mutations test, especially for RNA-based assay.

Selection, identification, and characterization of aptamers for pro-gastrin-releasing peptide (31–98), a tumor marker for small cell lung cancer

Hui-Fang Cui,Ya-Jun Li,Jia Wang,Xiao-Jia Li,Qiong-Lin Wang,Yan-Feng Bai

Pro-gastrin-releasing peptide (31–98) (ProGRP31–98) is a highly reliable, sensitive, and specific tumor marker for small cell lung cancer (SCLC). DNA aptamers for ProGRP31–98 were selected in this study from an 89-mer DNA library with a random region of 48 nucleotides (nt) flanked with two primer hybridization sites, by using the systematic evolution of ligands by the exponential enrichment (SELEX) method. The DNA sequences binding to ProGRP31–98 immobilized magnetic beads were selected by running 12 SELEX cycles and 3 negative selection cycles. The selected DNA sequences were separated by cell based DNA cloning, and then sequence analyzed. The DNA sequences obtained were screened and investigated for binding specificity to ProGRP31–98 by using electrochemiluminescence (ECL) measurement with [Ru(bpy)2dppz]2+, a molecular light-switch, as the ECL probe. One DNA sequence (89 nt) and its random region (48 nt) were identified as specific aptamers for ProGRP31–98. Based on the secondary structures of the obtained DNA aptamers, two other truncated DNA aptamers, 40 nt and 15 nt long, respectively, were identified. The obtained aptamers have strong affinities to ProGRP31–98, with a Kd value of 16 nM, and can detect ProGRP31–98 with a detection limit of 17 nM using the label-free ECL measurement.

High-Sensitive Assay of Nucleic Acid Using Tetrahedral DNA Probes and DNA Concatamers with a Surface-Enhanced Raman Scattering/Surface Plasmon Resonance Dual-Mode Biosensor Based on a Silver Nanorod-Covered Silver Nanohole Array

Chunyuan Song,Xinyu Jiang,Yanjun Yang,Jingjing Zhang,Steven Larson,Yiping Zhao,Lianhui Wang

A novel surface-enhanced Raman scattering/surface plasmon resonance (SERS/SPR) dual-mode biosensor prepared on a silver nanorod-covered silver nanohole (Ag NR-NH) array by surface modification of tetrahedral DNA probes is proposed for highly sensitive detecting nucleic acids by a special signal amplification strategy of DNA supersandwich. The Ag NR-NH with a large area and uniformly arrayed nanostructure possesses excellent anisotropic extraordinary optical transmission and strong localized surface plasmon resonance, which lead to sensitive SPR response to the change of a local refractive index and strong localized electric fields for excellent SERS activity. To obtain high sensitivity and specificity, smart tetrahedral DNA probes are immobilized onto the Ag NR-NH array and the DNA supersandwich sensing strategy, including the signal amplification of DNA concatamers, is used. About 10 times signal enhancement for SPR and 4 times for SERS are achieved by this sensing strategy. In the detection of the target DNA in the human serum, the two sensing modes have complementary performances, i.e., the limit of detection for the SPR array is high (0.51 pM), while for SERS, it is low (0.77 fM), but the specificity for SPR is much higher than that of SERS. This improves the robustness of the DNA sensors, and subsequent recovery tests also confirm good reliability of the biosensor. The proposed SERS/SPR dual-mode biosensor has a great potential for high performance and reliable detection of trace disease-related nucleic acid biomarkers in the serum and is a powerful sensing platform for early-stage disease diagnosis.

DNAzyme-based cascade signal amplification strategy for highly sensitive detection of lead ions in the environment

Jiamin Xu,Mingbin Liu,Weihua Zhao,Suqin Wang,Minfang Gui,Hongbo Li,Ruqin Yu

Lead ions are one of many common environmental pollutants, that can cause posing a serious threat to people’s health, thus, their efficient and sensitive detection is important. We propose a cascade signal amplification sensor using a DNAzyme-based strand displacement amplification (SDA) and hybridization chain reaction (HCR) for the high-sensitivity detection of Pb 2+ . In the demonstrated sensor system, the target metal ion can activate DNAzyme to cause a strand displacement reaction. Under the synergistic action of polymerase and nickase, large numbers of DNA strands are generated that can initiate HCR. The subsequent HCR can restore the fluorescence intensity of the FAM quenched for the fluorescence resonance energy transfer effect, which exhibits a strong fluorescence signal. The DNAzyme-based sensor allowed the detection of Pb 2+ down to 16.8 pM and resulted in a good dynamic line relationship ranging from 50 pM to 500 nM, and the biosensor also showed good selectivity . Furthermore, we confirmed that the proposed sensor can still detect lead ions in complex environments such as lake water, milk, and serum. We believe these findings will provide new ideas for the detection of toxic elements ions in the environment and food.

Structural basis of copper-efflux-regulator-dependent transcription activation

Wei Shi,Baoyue Zhang,Yanan Jiang,Chang Liu,Wei Zhou,Ming Chen,Yang Yang,Yangbo Hu,Bin Liu

The copper efflux regulator (CueR), a representative member of mercury resistance regulator (MerR) family metalloregulators, controls expression of copper homeostasis-regulating genes in bacteria. The mechanism of transcription activation by CueR and other MerR family regulators is bending the spacer domain of promoter DNA. Here, we report the cryo-EM structures of the intact CueR-dependent transcription activation complexes. The structures show that CueR dimer bends the 19-bp promoter spacer to realign the −35 and −10 elements for recognition by σ 70 -RNA polymerase holoenzyme and reveal a previously unreported interaction between the DNA-binding domain (DBD) from one CueR subunit and the σ 70 nonconserved region (σNCR). Functional studies have shown that the CueR-σNCR interaction plays an auxiliary role in CueR-dependent transcription, assisting the activation mechanism of bending promoter DNA by CueR dimer. Because DBDs are highly conserved in sequence and structure, this transcription-activating mechanism could be generally used by MerR family regulators.

Target recycling amplification for label-free and sensitive colorimetric detection of adenosine triphosphate based on un-modified aptamers and DNAzymes

Xue Gong,Jinfu Li,Wenjiao Zhou,Yun Xiang,Ruo Yuan,Yaqin Chai

Based on target recycling amplification, the development of a new label-free, simple and sensitive colorimetric detection method for ATP by using un-modified aptamers and DNAzymes is described. The association of the model target molecules (ATP) with the corresponding aptamers of the dsDNA probes leads to the release of the G-quadruplex sequences. The ATP-bound aptamers can be further degraded by Exonuclease III to release ATP, which can again bind the aptamers of the dsDNA probes to initiate the target recycling amplification process. Due to this target recycling amplification, the amount of the released G-quadruplex sequences is significantly enhanced. Subsequently, these G-quadruplex sequences bind hemin to form numerous peroxidase mimicking DNAzymes, which cause substantially intensified color change of the probe solution for highly sensitive colorimetric detection of ATP down to the sub-nanomolar (0.33   nM) level. Our method is highly selective toward ATP against other control molecules and can be performed in one single homogeneous solution, which makes our sensing approach hold great potential for sensitive colorimetric detection of other small molecules and proteins.

Electrochemical aptasensor for ampicillin detection based on the protective effect of aptamer-antibiotic conjugate towards DpnII and Exo III digestion

Tingting Wang,Huanshun Yin,Yuting Zhang,Linkui Wang,Yue Du,Yuping Zhuge,Shiyun Ai

A simple and sensitive electrochemical method was developed for ampicillin detection based on the protective effect of aptamer-antibiotic conjugate towards endonuclease DpnII activity. Without ampicillin, DNA aptamer firstly hybridizes with the capture probe to form double strand DNA (dsDNA) structure. Then, dsDNA is cleaved by DpnII restriction endonuclease to form two dsDNA fragments. In which, one fragment is released from electrode surface and the other fragment is kept on electrode surface. Then, the dsDNA fragment kept on electrode surface is further digested by Exo III, which leads to the release of the dsDNA fragment from electrode surface. Thus, the electrochemical signal increases due to the decrease of the interface electron transfer resistance causing by the release of dsDNA from electrode surface. However, the formation of dsDNA is blocked when forming aptamer-ampicillin conjugate, which makes the obstruction of the digestion of DpnII and Exo III towards capture probe. Thus, a weak electrochemical signal is achieved due to the increase of the interface electron transfer resistance causing by the dsDNA on the electrode surface. Based on the relationship between ampicillin concentration and the decrease of the electrochemical signal, antibiotic is detected with low detection limit of 32 pM under optimal conditions, which is lower than the mandated maximum residue limit of European Union (9.93 nM). The developed method also presents good detection selectivity . Moreover, the applicability is confirmed by detecting antibiotic in milk and water samples with satisfactory results.

DNA damage protection and 5-lipoxygenase inhibiting activity of areca (Areca catechu L.) inflorescence extracts

W Chen,C Zhang,Y Huang,F Cheng,S Zhao,Y Shen,J Liu

Recognition of DNA abasic site nanocavity by fluorophore-switched probe: Suitable for all sequence environments

Ying Wang,Yuehua Hu,Tao Wu,Lihua Zhang,Hua Liu,Xiaoshun Zhou,Yong Shao

Removal of a damaged base in DNA produces an abasic site (AP site) nanocavity. If left un-repaired in vivo by the specific enzyme, this nanocavity will result in nucleotide mutation in the following DNA replication. Therefore, selective recognition of AP site nanocavity by small molecules is important for identification of such DNA damage and development of genetic drugs. In this work, we investigate the fluorescence behavior of isoquinoline alkaloids including palmatine (PAL), berberine (BER), epiberberine (EPI), jatrorrhizine (JAT), coptisine (COP), coralyne (COR), worenine (WOR), berberrubine (BEU), sanguinarine (SAN), chelerythrine (CHE), and nitidine (NIT) upon binding with the AP nanocavity. PAL is screened out as the most efficient fluorophore-switched probe to recognize the AP nanocavity over the fully matched DNA. Its fluorescence enhancement occurs for all of the AP nanocavity sequence environments, which has not been achieved by the previously used probes. The bridged π conjugation effect should partially contribute to the AP nanocavity-specific fluorescence, as opposed to the solvent effect . Due to the strong binding with the AP nanocavity, PAL will find wide applications in the DNA damage recognition and sensor development.