Electrochemical DNA Hybridization Detection Using DNA Cleavage

We report the new method for detection of DNA hybridization using enzymatic cleavage. The strategy is based on that S1 nuclease is able to specifically cleave only single strand DNA, but not double strand DNA. The capture probe DNA, thiolated single strand DNA labeled with electroactive ferrocene group, was immobilized on a gold electrode. After hybridization of target DNA of complementary and noncomplementary sequences, nonhybridized single strand DNA was cleaved using S1 nuclease. The difference of enzymatic cleavage on the modified gold electrode was characterized by cyclic voltammetry and differential pulse voltammetry. We successfully applied this method to the sequence‐selective discrimination between perfectly matched and mismatched target DNA including a single‐base mismatched target DNA. Our method does not require either hybridization indicators or other exogenous signaling molecules which most of the electrochemical hybridization detection systems require.     

Recognition of hairpin DNA from coil DNA by electrospray mass spectrometry with annealing strategy

This research presented an annealing strategy to identify hairpin DNA from coil DNA with the same base composition but different arrangements using electrospray mass spectrometry(ESI-MS).A series of single-stranded DNA were annealed with their complementary sequences,respectively.All the five pairs of hairpin DNA and coil DNA were unambiguously distinguished by ESIMS with annealing strategy.This research offers a potential method to probe the DNA structure by comparing with mass spectral characteristics.     

基于纳米金胶标记DNA探针的电化学DNA传感器研究

以纳米金胶为标记物,将其标记于人工合成的5-端巯基修饰的寡聚核苷酸片段上,制成了具有电化学活性的金胶标记DNA电化学探针;在一定条件下,使其与固定在玻碳电极表面的靶序列进行杂交反应,利用ssDNA与其互补链杂交的高度序列选择性和极强的分子识别能力,以及纳米金胶的电化学活性,实现对特定序列DNA片段的电化学检测以及对DNA碱基突变的识别.     

Electrochemical strategy for sensing DNA methylation and DNA methyltransferase activity

The present work demonstrates a novel signal-off electrochemical method for the determination of DNA methylation and the assay of methyltransferase activity using the electroactive complex [Ru(NH₃)₆]³⁺ (RuHex) as a signal transducer. The assay exploits the electrostatic interactions between RuHex and DNA strands. Thiolated single strand DNA1 was firstly self-assembled on a gold electrode via Au–S bonding, followed by hybridization with single strand DNA2 to form double strand DNA containing specific recognition sequence of DNA adenine methylation MTase and methylation-responsive restriction endonuclease Dpn I. The double strand DNA may adsorb lots of electrochemical species ([Ru(NH₃)₆]³⁺) via the electrostatic interaction, thus resulting in a high electrochemical signal. In the presence of DNA adenine methylation methyltransferase and S-adenosyl-l-methionine, the formed double strand DNA was methylated by DNA adenine methylation methyltransferase, then the double strand DNA can be cleaved by methylation-responsive restriction endonuclease Dpn I, leading to the dissociation of a large amount of signaling probes from the electrode. As a result, the adsorption amount of RuHex reduced, resulting in a decrease in electrochemical signal. Thus, a sensitive electrochemical method for detection of DNA methylation is proposed. The proposed method yielded a linear response to concentration of Dam MTase ranging from 0.25 to 10 U mL⁻¹ with a detection limit of 0.18 U mL⁻¹ (S/N = 3), which might promise this method as a good candidate for monitoring DNA methylation in the future.     

Miniaturised isotachophoresis of DNA

This paper presents the findings of a feasibility study investigating the behaviour of DNA under conditions of miniaturised isotachophoresis. An electrolyte system comprising a leading electrolyte of 5mM perchloric acid at pH 6.0 and a terminating electrolyte of 10mM gallic acid was devised and used to perform isotachophoresis of DNA containing samples on a miniaturised poly(methyl methacrylate) device. Under such conditions it was found that no separation of DNA fragments was observed with the substance migrating instead as a single isotachophoretic zone. Whilst such a result shows the method is unsuitable for analysis DNA it offers significant potential as a means of sample preparation for subsequent analysis using another method. This is because the single zone of DNA formed is preconcentrated to a constant concentration governed by the leading ion and is separated from all species with different effective electrophoretic mobilities.     

DNA/羟基磷灰石杂化膜修饰电极用于研究DNA与量子点的相互作用

首次利用溶胶-凝胶一步法制备了纳米多孔羟基磷灰石(HAp)-DNA杂化膜修饰玻碳电极,HAp优良的生物相容性和独特的吸附性可以将DNA固定在HAp多孔薄膜上,而DNA的大分子结构对HAp膜起到稳定剂的作用.采用循环伏安法和交流阻抗法系统地研究了电极表面固定DNA的稳定性以及固定的DNA与非电活性核壳型量子点CdTe/C...     

Two-dimensional densely packed DNA nanostructure derived from DNA complexation with a low-generation poly(amidoamine) dendrimer

One of the keys for using deoxyribonucleic acid (DNA) as a nanomaterial relies on how the individual DNA chain can be aligned and how a multitude of DNA chains can be packed into ordered nanostructures. Here we present a simple method for constructing a 2-D densely packed DNA nanostructure using the electrostatic complex of DNA with a poly(amidoamine) (PAMAM) dendrimer of generation two. Ordered DNA arrays are formed by drop-casting an aqueous solution containing positively overcharged complexes onto mica followed by a prolonged incubation. During the incubation, the complexes tend to adsorb onto the negatively charged mica surface through electrostatic attraction. The rodlike complexes organize to form ordered arrays to increase the surface density of the adsorbed complexes and hence the attractive free energy of adsorption. The densely packed nanostructure obtained here is distinguished from the previously reported spheroid or toroid structure derived from DNA complexations with the higher-generation dendrimers.     

Optimization of DNA hybridization analysis on microarrays with colorimetric detection

A method of hybridization analysis on a DNA microarray using colorimetric detection on the basis of horseradish peroxidase has been developed. The effectiveness of the incorporation of biotin as a label in the DNA molecule in the PCR process is estimated and the conditions of hybridization of the biotin-labeled DNA with oligonucleotides immobilized on the surface of the array are optimized. The possibility of using the developed method is shown by the example of genotyping of CTX-M β-lactamases.     

长链DNA在金基底上的固定化和电化学标记

本文提出在金基底上用阳离子聚电解质———聚二烯丙基二甲基胺氯化物 (poly(dial lyldimethylammoniumchloride) ,PDDA)自组装膜固定长链DNA的方法 ,用DiffuseReflectanceIn frared ,XPS和STM技术进行表征 ,并对DNA杂交进行电化学标记     

酸性条件下的DNA构象变化加速DNA变性解链

调控DNA的变性解链过程是DNA扩增与检测的关键步骤。对于传统的热循环DNA扩增策略,由于变温过程中热量分布不均一以及变温速度慢等不利因素,会直接影响DNA变性解链过程,从而降低DNA检测放大的效果、延长检测的时长。因此,探索快速、高效的调控DNA变性解链的方法具有重要的研究意义。本文发展了以胞嘧啶在酸性条件下的质子化反应为基础,通过改变溶液的pH值,来诱导DNA构象在Watson-Crick（WC）碱基对与Hoogsteen（HG）碱基对之间的分子构象转换,从而实现精准、快速、高效的DNA变性解链调控目标。结果表明,相较于传统的温控方法,pH调控方法能显著提高DNA变性的速率约6倍以上。本文发现pH调控方法通过降低双链DNA的反应焓约160 kJ/mol,从而提高双链DNA变性速率和效率。该方法具有用于DNA信号放大与检测等相关应用的潜力。     

Bioconjugated nanoparticles for DNA protection from cleavage

We have developed a novel method to protect DNA from cleavage using bioconjugated nanoparticles. Positively charged amino-modified silica nanoparticles have been directly prepared using water-in-oil microemulsion. Plasmid DNA can be easily enriched onto the positively charged nanoparticle surface, and the DNA strands are well protected from enzymatic cleavage. When incubated with nuclease enzyme for enzymatic cleavage, free plasmid DNA strands are completely cleaved, while those on the nanoparticle surfaces are intact. Our results clearly demonstrate unique properties of nanomaterials when combined with biomolecules. Our simple bionanotechnology will be highly useful in DNA separation, manipulation, and detection, and possibly in genetic engineering and gene therapy, as plasmid DNA can be protected in cellular environments without any change in its property.     

Complex Reconfiguration of DNA Nanostructures

Nucleic acids have been used to create diverse synthetic structural and dynamic systems. Toehold‐mediated strand displacement has enabled the construction of sophisticated circuits, motors, and molecular computers. Yet it remains challenging to demonstrate complex structural reconfiguration in which a structure changes from a starting shape to another arbitrarily prescribed shape. To address this challenge, we have developed a general structural‐reconfiguration method that utilizes the modularly interconnected architecture of single‐stranded DNA tile and brick structures. The removal of one component strand reveals a newly exposed toehold on a neighboring strand, thus enabling us to remove regions of connected component strands without the need to modify the strands with predesigned external toeholds. By using this method, we reconfigured a two‐dimensional rectangular DNA canvas into diverse prescribed shapes. We also used this method to reconfigure a three‐dimensional DNA cuboid.     

One-step syntheses of alkyl glycosides and alkyl-substituted DNA oligomers by chemoselective glycosidations using DNA bases

The simple and practical synthesis of alkyl glycosides by novel chemoselective glycosidations using natural resources, DNA and RNA nucleosides, was realized, and the one-step synthesis of chemoselectively modified DNA oligomers using the glycosidation method was also demonstrated.     

利用荧光标记引物和DNA自动测序仪确定DNA的断裂位点

建立了利用荧光标记引物和DNA自动测序仪进行DNA断裂位点分析的新方法, 该方法简便易行、灵敏度高、重复性好、数据分析客观性强、结果可靠, 适用于各种因素造成的DNA断裂位点的分析.     

土霉素的电化学性质及其与DNA相互作用的研究

研究了土霉素在玻碳电极上的电化学行为。并利用电化学方法研究了土霉素与小牛胸腺DNA(ctDNA)的相互作用,DNA的存在能导致土霉素还原峰电流降低,峰电位正移,推测土霉素与DNA在该条件下以键合模式相互结合。紫外-可见吸收光谱的研究进一步确证了上述结果。     

Analysis of DNA adducts bases by capillary electrophoresis with amperometric detection.

We have developed a method for the detection of DNA adducts by combining capillary electrophoresis (CE) with the specificity of amperometric detection. Guanine is the most easily damaged base of the four normal DNA bases and many adducts of guanine have been found in DNA. These guanine adducts are often electrochemically active, while the normal bases with the exception of guanine are not. Therefore, CE with amperometric detection will be a promising method to study DNA damage. The four normal deoxynucleosides and two damaged deoxnucleosides N2-ethyldeoxyguanosine (N2-ethyl-dG) and 8-hydroxydeoxyguanosine (8-OH-dG), were completely separated by micellar electrokinetic chromatography (MEKC). Deoxyguanosine and the two damaged deoxynucleosides were identified using amperometric detection. The sensitivity of our system was comparable to that of UV detection. Analysis of DNA hydrolysis products was also performed briefly using this method.     

微囊藻属DNA电化学传感器的研制

利用自组装法将巯基修饰的DNA探针与6-巯基-1-己醇(MCH)固定到金电极表面,制备了微囊藻属特定DNA传感器,将该传感器与完全互补的微囊藻DNA序列、完全不互补序列,以及单碱基错配序列进行杂交,以Hoechst 33258为杂交指示剂,应用循环伏安法和线性扫描伏安法研究了该传感器对目标DNA的电化学检测行为.研究表明,当与完全互补DNA杂交后,Hoechst 33258氧化信号有明显的增强.实验对自组装时间、MCH浸泡时间及杂交液离子浓度进行了优化.结果表明,当自组装时间为90 min,MCH浸泡时间为1 h,杂交溶液中NaCl浓度为0.3 mol/L时,电化学信号最好.目标DNA的氧化峰电流值与其浓度在1×10~(-8) ～1×10~(-6) mol/L范围内呈良好的线性关系,检出限为8.1×10~(-9) mol/L.     

Metric representation of DNA sequences

A metric representation of DNA sequences is borrowed from symbolic dynamics. In view of this method, the pattern seen in the chaos game representation of DNA sequences is explained as the suppression of certain nucleotide strings in the DNA sequences. Frequencies of short nucleotide strings and suppression of the shortest ones in the DNA sequences can be determined by using the metric representation.     

Programmed‐Assembly System Using DNA Jigsaw Pieces

A novel method for assembling multiple DNA origami structures has been developed by using designed 2D DNA origami rectangles, so‐called “DNA jigsaw pieces” that have sequence‐programmed connectors. Shape and sequence complementarity were introduced to the concavity and convex connectors in the DNA rectangles for selective connection with the help of nonselective π‐stacking interactions between the side edges of the DNA jigsaw piece structures. Single DNA jigsaw piece units were assembled into unidirectional nanostructures with the correct alignment and uniform orientation. Three and five different DNA jigsaw pieces were assembled into predesigned and ordered nanostructures in a programmed fashion. Finally, three‐, four‐, and five‐letter words have been displayed by using this programmed DNA jigsaw piece system.     

Transfer-printing of highly aligned DNA nanowires

We developed a simple method of reproducibly creating highly aligned DNA nanowires without any surface modifications or special equipment. Stretched DNA molecules initially present on the PDMS sheet were transferred onto another surface using transfer-printing (TP). Fluorescent microscopic and atomic force microscopic images revealed that many DNA molecules were highly aligned on surfaces after TP. Furthermore, it was also possible to realize the two-dimensional assembly of DNA nanowires by repeating TP.