Entanglement complexity of lattice ribbons

We consider a discrete ribbon model for double-stranded polymers where the ribbon is constrained to lie in a three-dimensional lattice. The ribbon can be open or closed, and closed ribbons can be orientable or nonorientable. We prove some results about the asymptotic behavior of the numbers of ribbons withn plaquettes, and a theorem about the frequency of occurrence of certain patterns in these ribbons. We use this to derive results about the frequency of knots in closed ribbons, the linking of the boundary curves of orientable closed ribbons, and the twist and writhe of ribbons. We show that the centerline and boundary of a closed ribbon are both almost surely knotted in the infinite-n limit. For an orientable ribbon, the expectation of the absolute value of the linking number of the two boundary curves increases at least as fast as n, and similar results hold for the twist and writhe.     

Interactions of DNA with graphene and sensing applications of graphene field-effect transistor devices: A review

Graphene field-effect transistors (GFET) have emerged as powerful detection platforms enabled by the advent of chemical vapor deposition (CVD) production of the unique atomically thin 2D material on a large scale. DNA aptamers, short target-specific oligonucleotides, are excellent sensor moieties for GFETs due to their strong affinity to graphene, relatively short chain-length, selectivity, and a high degree of analyte variability. However, the interaction between DNA and graphene is not fully understood, leading to questions about the structure of surface-bound DNA, including the morphology of DNA nanostructures and the nature of the electronic response seen from analyte binding. This review critically evaluates recent insights into the nature of the DNA graphene interaction and its affect on sensor viability for DNA, small molecules, and proteins with respect to previously established sensing methods. We first discuss the sorption of DNA to graphene to introduce the interactions and forces acting in DNA based GFET devices and how these forces can potentially affect the performance of increasingly popular DNA aptamers and even future DNA nanostructures as sensor substrates. Next, we discuss the novel use of GFETs to detect DNA and the underlying electronic phenomena that are typically used as benchmarks for characterizing the analyte response of these devices. Finally, we address the use of DNA aptamers to increase the selectivity of GFET sensors for small molecules and proteins and compare them with other, state of the art, detection methods.     

Quartz crystal microbalance immunosensor for the detection of antibodies to double-stranded DNA

We report the development of a novel quartz crystal microbalance immunosensor with the simultaneous measurement of resonance frequency and motional resistance for the detection of antibodies to double-stranded DNA (dsDNA). The immobilization of poly(l-lysine) and subsequent complexation with DNA resulted in formation of a sensitive dsDNA-containing nanofilm on the surface of a gold electrode. Atomic force microscopy has been applied for the characterization of a poly(l-lysine)–DNA film. After the blocking with bovine serum albumin, the immunosensor in flow-injection mode was used to detect the antibodies to dsDNA in purified protein solutions of antibodies to dsDNA and to single-stranded DNA, monoclonal human immunoglobulin G, DNase I and in blood serum of patients with bronchial asthma and systemic lupus erythematosus. Experimental results indicate high sensitivity and selectivity of the immunosensor. In memoriam Prof. Victor G. Vinter     

Influence of Environmental Parameters on the Stability of the DNA Molecule

Fluctuations in viscosity within the cell nucleus have wide limits. When a DNA molecule passes from the region of high viscosity values to the region of low values, open states, denaturation bubbles, and unweaving of DNA strands can occur. Stabilization of the molecule is provided by energy dissipation—dissipation due to interaction with the environment. Separate sections of a DNA molecule in a twisted state can experience supercoiling stress, which, among other things, is due to complex entropic effects caused by interaction with a solvent. In this work, based on the numerical solution of a mechanical mathematical model for the interferon alpha 17 gene and a fragment of the Drosophila gene, an analysis of the external environment viscosity influence on the dynamics of the DNA molecule and its stability was carried out. It has been shown that an increase in viscosity leads to a rapid stabilization of the angular vibrations of nitrogenous bases, while a decrease in viscosity changes the dynamics of DNA: the rate of change in the angular deviations of nitrogenous bases increases and the angular deformations of the DNA strands increase at each moment of time. These processes lead to DNA instability, which increases with time. Thus, the paper considers the influence of the external environment viscosity on the dissipation of the DNA nitrogenous bases’ vibrational motion energy. Additionally, the study on the basis of the described model of the molecular dynamics of physiological processes at different indicators of the rheological behavior of nucleoplasm will allow a deeper understanding of the processes of nonequilibrium physics of an active substance in a living cell to be obtained.     

采用纳米金和双链探针比色检测单碱基突变

将链置换的高度特异性与纳米金凝聚变色的光学特性相结合,设计了一种新型的单碱基突变比色检测方法。本方法直接采用纳米金作为比色报告基团,以两个末端均带有巯基的双链DNA为特异捕获探针,利用互补序列和单碱基突变序列对双链探针置换能力的差异,实现了对单碱基突变的检测。本检测方法直观、快速、简便、成本低,pmol级的样品无需仪器就可以观察到颜色的变化。     

电化学法研究苯磺酰类5-氟尿嘧啶衍生物与双链和G-四链DNA的相互作用

本文以自组装法制得的双链DNA（ds．DNA）和G-四链体DNA（G4-DNA）修饰的金电极为工作电极,以Fe（CN）63-／4-为电活性指示剂,采用循环伏安法和微分脉冲伏安法研究了非电活性苯磺酰类5-氟尿嘧啶衍生物与ds-DNA和G4．DNA的相互作用．实验结果表明：苯磺酰类5-氟尿嘧啶与ds-DNA或G4．DNA的结合常数与苯环上邻、对位取代基的得失电子能力密切相关,强吸电子基团取代有利于苯磺酰类5-氟尿嘧啶选择性结合G-四链体DNA．     

采用电活性标记物N-(2-乙基-二茂铁)马来酰亚胺检测与表面固定的 一致性双链DNA特异性作用的p53蛋白质

建立了电化学检测表面固定捕获的野生型p53蛋白质的方法. 首先在金电极表面形成巯基化的单链DNA探针/己硫醇(HT)混合自组装膜, 随后巯基化的单链DNA探针与溶液中序列匹配的靶点DNA杂交, 所形成的一致性双链DNA捕获溶液中的野生型p53蛋白质. p53分子表面的半胱氨酸残基采用巯基特异性试剂N-(2-乙基-二茂铁)马来酰亚胺(Fc-Mi)进行衍生. 通过检测二茂铁的电化学信号来指示p53与一致性双链DNA之间的特异性相互作用. p53蛋白质与双链DNA的键合程度取决于双链DNA的序列. 该方法可检测的p53最低浓度为1.33 nmol•L－1.     

Analytical applications of Raman spectroscopy

In this article interaction of transition metal complexes with DNA and its applications in electrochemical DNA biosensors as hybridization indicator or electroactive marker of DNA are reviewed. Special emphasis has been given to the efforts for the development of new transition metal complexes and their interaction to DNA. DNA and polymers covalently conjugated with transition metal complexes were also reviewed.     

Study of interactions between actinomycin D and oligonucleotides by microchip electrophoresis and ESI-MS

In the present study, the interactions between actinomycin D (ActD) and single stranded DNA (ssDNA) 5′-CGTAACCAACTGCAACGT-3′ and a duplex stranded DNA (dsDNA) with this sequence were investigated by microchip-based non-gel sieving electrophoresis and electrospray ionization mass spectrometry (ESI-MS). The ssDNA was designed according to the conserved regions of open reading frame 1b (replicase 1B) following the Tor 2 SARS genome sequence of 15611-15593. The binding constants of the interactions between ActD and ssDNA/dsDNA were (8.3 ± 0.32) × 10⁶ M⁻¹ (ssDNA) and (2.8 ± 0.02) × 10⁵ M⁻¹ (dsDNA), respectively, calculated from microchip electrophoresis via Scatchard plot. The binding stoichiometries were 1:1 (single/1ActD molecule) and 1:2 (duplex/2ActD molecules) calculated from microchip electrophoresis, and the results were further verified by ESI-MS. The results obtained by these two methods indicated that ActD bound much more tightly to ssDNA used in this work than dsDNA. Furthermore, this is shown that the microchip-based non-gel sieving electrophoresis method is a rapid, highly sensitive and convenient method for the studies of interactions between DNA and small molecule drugs.     

5-N-甲基苯并呋喃［3,2-b］喹啉衍生物的合成及其作为DNA嵌插剂的光谱学研究

以生物碱白叶藤碱为出发点,依据生物电子等排体原则,设计了5-N-甲基苯并呋喃[3,2-b]喹啉母体,并参考安吖啶结构特征,合成了一系列5-N-甲基苯并呋喃喹啉的11-位苯胺衍生物,通过波谱手段确认其结构。运用紫外-可见光谱法和分子对接测定了衍生物与DNA的结合常数K和对接分数。紫外光谱实验中,衍生物与小牛胸腺DNA结合后吸收峰出现减色效应和红移现象;离子强度实验排除了表面结合模式的可能性;结合EB置换实验和分子模拟的结果,可初步推断作用模式为嵌插作用。