Effect of buffer flow on DNA separation in a microfabricated electrophoresis system

An adequate buffer reservoir is one essential component of an electrophoresis system, providing current carrying ions and maintaining constant pH. In a microfabricated DNA separation system with on-chip electrodes, the amount of buffer used is limited by the design of the device; the buffer continuity can be easily disturbed by the production of bubbles. Continuously flowing 1 x Tris-borate-EDTA (TBE) buffer over the electrodes at the cathodic end solves both problems. This flow increases the resolution for ssDNA primer separations (21 and 25 bases) to a maximum value of 1.4 within a distance of 1.2 cm, about four times higher than that without flow. Similar improvement has been achieved for dsDNA separation (20 bp ladder; BioRad) at a distance of only 0.4 cm, giving baseline resolution for bands from 20 to 240 bp. We have also investigated the effect of buffer concentration on resolution, and no similar improvement can be obtained by merely increasing the buffer concentration without flow.     

Immobilization of Chymotrypsin on Silica Beads Based on High Affinity and Specificity Aptamer and Its Applications

Aptamers with high affinity and specificity to targets, bring new approaches to immobilizing proteins or enzymes. In this work, a group of single-stranded DNA aptamers specific for chymotrypsin were obtained by SELEX method in vitro. After investigation and characterization of all aptamers, AptC.1 (abbreviation for the aptamer with the highest affinity for chymotrypsin) was selected and grafted onto silica matrix with the help of glutaraldehyde as linker, and used subsequently to immobilize chymotrypsin. Specifically, it is shown in experiment that, 12.65 µg of chymotrypsin could be immobilized on 10 mg of AptC.1-Silica in 10 mM pH 8.0 borate solutions, and the activity of immobilized enzyme was not inhibited. Bovine serum albumin, myoglobin and cytochrome c were introduced to investigate the enzymatic performance of prepared immobilized chymotrypsin reactor. All these results demonstrated that aptamer could serve as a potential medium for the immobilization of proteins or enzymes.     

Silicon nanowires as field-effect transducers for biosensor development: A review

The unique electronic properties and miniaturized dimensions of silicon nanowires (SiNWs) are attractive for label-free, real-time and sensitive detection of biomolecules. Sensors based on SiNWs operate as field effect transistors (FETs) and can be fabricated either by top–down or bottom–up approaches. Advances in fabrication methods have allowed for the control of physicochemical and electronic properties of SiNWs, providing opportunity for interfacing of SiNW-FET probes with intracellular environments. The Debye screening length is an important consideration that determines the performance and detection limits of SiNW-FET sensors, especially at physiologically relevant conditions of ionic strength (>100 mM). In this review, we discuss the construction and application of SiNW-FET sensors for detection of ions, nucleic acids and protein markers. Advantages and disadvantages of the top–down and bottom–up approaches for synthesis of SiNWs are discussed. An overview of various methods for surface functionalization of SiNWs for immobilization of selective chemistry is provided in the context of impact on the analytical performance of SiNW-FET sensors. In addition to in vitro examples, an overview of the progress of use of SiNW-FET sensors for ex vivo studies is also presented. This review concludes with a discussion of the future prospects of SiNW-FET sensors.     

Advances in aptameric biosensors designed to detect toxic contaminants from food,water, human fluids,and the environment

Detection of toxic small molecule contaminants with sensitivity, accuracy, and specificity is a challenging task. Traditionally used HPLC and mass spectrometry-based assays suffer from several drawbacks, including lengthy sample preparation, heavy instrumentation, and the need for expert technicians. Specific, measurable, accurate, robust, and time-saving (SMART) biosensors are needed to detect toxic substances. Aptamers provide unique opportunities for the rapid development of SMART biosensors to meet above challenges. Since aptamers are short nucleotide sequences; they are easy for chemical synthesis and functional modifications. Aptamers acquire specific molecule recognition potential through unique chemical bonding, including H-bonds, pi-pi, van der Waals, and hydrophobic interactions. For the discovery of aptamers, the SELEX process is used. Recently, efforts have been made to develop aptamers to detect toxic small molecules like antibiotics, pesticides, insecticides, pollutants, toxins, and allergens. Aptamer technology is a promising tool for analyzing these chemicals from diverse matrices. This review provides an update on advances in nucleic acid-based aptameric sensors for molecular diagnostics of toxic chemical from food, water, human fluids, and the environment.     

老鼠Tet1蛋白能氧化单链脱氧核糖核酸上的5-甲基胞嘧啶到5-羟甲基胞嘧啶和5-羧基胞嘧啶(英文)

5-甲基胞嘧啶在哺乳动物细胞中具有广泛的作用.而它被双脱氧家族Tet蛋白氧化所得的产物5-羟甲基胞嘧啶、5-醛基胞嘧啶和5-羧基胞嘧啶也被证明在细胞发育和5-甲基胞嘧啶动态平衡调控中具有关键的作用.已有的研究结果表明,Tet蛋白能够识别双链DNA上的5-甲基胞嘧啶,并将其氧化成5-羟甲基胞嘧啶、5-醛基胞嘧啶和5-羧基胞嘧啶.我们通过质谱仪检测发现,老鼠Tet1蛋白的DNA结合结构域还能识别和氧化单链DNA上的5-甲基胞嘧啶.这一发现暗示我们,Tet蛋白家族不但具有已经发现的氧化双链DNA上5-甲基胞嘧啶的功能,还有可能作用于DNA的复制及转录,甚至具有氧化单链RNA上对应的甲基修饰碱基的能力.     

Cathodic adsorptive stripping voltammetric behaviour of guanine in the presence of copper at the static mercury drop electrode

The cathodic adsorptive electrochemical behavior of guanine in the presence of some metal ions at the static mercury drop electrode was investigated. A 1.0×10⁻³ mol l⁻¹ NaOH or a 2.0×10⁻² mol l⁻¹ Hepes buffer at pH 8.0 solutions were used as supporting electrolytes. The reduction peak potential for guanine was found to be around −0.15 V, which is very close to the mercury reduction wave. A new peak appears at −0.60 V in the presence of copper or at −1.05 V in the presence of zinc. A square wave voltammetric procedure for electroanalytical determination of guanine in 2.0×10⁻² mol l⁻¹ Hepes buffer at pH 8.0 containing 1.6×10⁻⁵ mol l⁻¹of copper ions, was developed. An accumulation potential of −0.15 V during 270 s for the prior adsorption of guanine at the electrode surface was used. The response of the system was found to be linear in the range of guanine concentration from 6.62×10⁻⁸ to 1.32×10⁻⁷ mol l⁻¹ and the detection limit was 7.0×10⁻⁹ mol l⁻¹. The influence of DNA bases such as adenine, cytosine and thymine was also examined. Cyclic voltammetry was used to characterize the interfacial and redox mechanism.     

Magnetic beads as versatile tools for electrochemical DNA and protein biosensing

Magnetic beads (MBs) are versatile tools in the separation of nucleic acids, proteins and other biomacromolecules, their complexes and cells. In this article recent application of MBs in electrochemical biosensing and particularly in the development of DNA hybridization sensors is reviewed. In these sensors MBs serve not only for separation but also as a platform for optimized DNA hybridization. A hybridization event is detected separately at another surface, which is an electrode. The detection is based either on the intrinsic DNA electroactivity or on various kinds of DNA labeling, including chemical modification, enzyme tags, nanoparticles, electroactive beads, etc., greatly amplifying the signals measured. In addition to DNA hybridization, other kinds of biosensing in combination with MBs, such as DNA-protein interactions, are reviewed.     

Modeling ssDNA electrophoretic migration with band broadening in an entangled or cross-linked network

We use a coarse-grained model proposed by Graham and Larson based on the temporary network model by Schieber et al.. [1] to simulate the electrophoretic motion of ssDNA and corresponding band broadening due to dispersion. With dimensionless numbers reflecting the experimental physical properties, we are able to simulate ssDNA behavior under weak to moderate electric field strengths for chains with 8-50 entanglements per chain ( approximately 1000-8500 base pairs), and model smoothly the transition from reptation to oriented reptation. These results are fitted with an interpolation equation, which allows the user to calculate dimensionless mobilities easily from input parameters characterizing the gel matrix, DNA molecules, and field strengths. Dimensionless peak widths are predicted from mobility fluctuations using the central limit theorem and the assumption that the mobility fluctuations are Gaussian. Using results from previous studies of ssDNA physical properties (effective charge xiq and Kuhn step length b(K)) and sieving matrix properties (pore size or tube diameter a), we give scaling factors to convert the dimensionless values to "real" experimental values, including the mobility, migration distance, and time. We find that the interpolation equation fits well the experimental data of ssDNA mobilities and peak widths, supporting the validity of the coarse-grained model. The model does not account for constraint release and hernia formation, and assumes that the sieving network is a homogeneous microstructure with no temperature gradients and no peak width due to injection. These assumptions can be relaxed in future work for more accurate prediction.     

ssDNA-QDs/GO multicolor fluorescence system for synchronous screening of hepatitis virus DNA

Viral hepatitis is a common infectious disease caused by five viruses (hepatitis virus A, B, C, D, and E). Given the diversity of hepatitis virus, rapid screening and accurate typing of viral hepatitis are the prerequisites for hepatitis therapy. Here, a multicolor fluorescence system was constructed by combining with the multi-color fluorescence properties of CdSe/ZnS quantum dots (QDs, emission wavelengths: 525 nm, 585 nm and 632 nm) and the broad-spectrum fluorescence quenching performance of GO. Taking advantage of the specific recognition of ssDNA modified CdSe/ZnS QDs to target hepatitis virus DNA, the constructed system could effectively distinguish hepatitis A virus DNA (HAV-DNA), hepatitis B virus DNA (HBV-DNA), and hepatitis C virus DNA (HCV-DNA) in a homogeneous solution. Based on the different adsorption property of GO for ssDNA and dsDNA, the fluorescence Forster resonance energy transfer (FRET) process between ssDNA modified QDs and GO could be regulated. The fluorescence signal of the constructed system presented a sensitive response to HAV-DNA, HBV-DNA, and HCV-DNA content in the range of 1.0–192 nM, 8.0–192 nM, and 1.0–128 nM, respectively. The limit of detection for HAV-DNA, HBV-DNA, and HCV-DNA is 0.46 nM, 1.53 nM, and 0.58 nM. The constructed system can be used to screen hepatitis virus DNA in real samples, which provides an alternative strategy for rapid screening and diagnosis of viral hepatitis.