DNA的电化学研究

本文对ＤＮＡ与电极的相互作用，ＤＮＡ的电化学反应，ＤＮＡ与其它分子相互作用的电化学研究和ＤＮＡ的电化学分析等方面的研究进展作了归纳和评述。     

罗丹明B—β—环糊精衍生物探针型主—客体分子相互识别？…

应用光谱法研究了生物大分子探针型主体分子罗丹明Ｂ－β－环糊精衍生物与ＤＮＡ的相互作用及温度对该探针特性的影响，探讨了相应的主体分子与ＤＮＡ分子相互作用的方式，嵌插作用能力大小以及温度对主体分子含客体分子时的影响，进一步研究了探针型主－客体分子相互识别作用及作用能力的大小，探讨了主－客体分子相互识别作用的机制。     

核酸分子嵌入剂

求文对核酸分子嵌入剂在核酸的识别、分离及分析中的应用，嵌入剂在特效新药设计及对核酸序列的特异位点裂解方面的新成就进行了评述。讨论了嵌入剂与溶液中ＤＮＡ及固定于ＮＣ膜上的单链ＤＮＡ的作用机理，引用参考文献３２篇。     

用盐酸阿霉素作为嵌入剂石墨电极伏安法识别测定DNA片段的研究

用盐酸阿霉素作为嵌入剂石墨电极伏安法识别测定ＤＮＡ片段的研究方禹之,刘盛辉,何品刚（华东师范大学化学系,上海,２０００６２）关键词ＤＮＡ,嵌入剂,盐酸阿霉素,伏安法核酸分子杂交技术是近年来发展起来的检测ＤＮＡ分子的一种重要手段,目前主要采用的放射性同...     

在石墨电极上脱氧核糖核酸与米托蒽醌嵌入作用的电化学研究

本文研究了单链ＤＮＡ分子在石墨电上的固定方法，采用核酸分子杂交技术，使具有电化学活性的米托蒽酯嵌入ＤＮＡ分子双螺旋结构的碱基对中，在电极上形成ｄｓＤＮＡ－ＭＳ层，通过伏安法研究ＤＮＡ分子和ＭＸ相互作用的电化学行为。     

3—羟基—4—甲氧基肉桂酸——基体辅助激光解吸电离质谱法测定DNA的有 …

报家长在体辅助激光解吸电离质谱法（ＭＡＬＤＩ－ＭＳ）测定ＤＮＡ分子的一种有效基体３－羟基－４－甲氧基肉桂酸。实验发现该基体对ＤＮＡ分子解吸和电离效率高,对ＤＮＡｄ（Ｔ）１０分子离子峰的分辨率为５５５１．４倍,噪比为１１．８。３－羟基－４－甲氧基肉桂酸是ＭＡＬＤＩ－ＭＳ法测定ＤＮＡ分子的一个可供选择使用有效基体。     

3-羟基-4-甲氧基肉桂酸--基体辅助激光解吸电离质谱法测定DNA的有效基体

报道用基体辅助激光解吸电离质谱法（ ＭＡＬＤＩ－ ＭＳ） 测定ＤＮＡ 分子的一种有效基体３－ 羟基－ ４ － 甲氧基肉桂酸。 实验发现该基体对ＤＮＡ 分子解吸和电离效率高, 对ＤＮＡｄ（ Ｔ） １０ 分子离子峰的分辨率为５ ５５１ ．４ , 信噪比为１１ ．８ 。３ － 羟基－ ４ － 甲氧基肉桂酸是ＭＡＬＤＩ－ ＭＳ 法测定ＤＮＡ 分子的一个可供选择使用有效基体。     

吩嗪染料与DNA分子相互作用的紫外-可见光谱研究

在对ＤＮＡ分子的研究中发现，一些小分子不仅可作为生物探针，还可成为以ＤＮＡ为靶目标的抗肿瘤（癌）药物的母体，如吖啶等．小分子物质与ＤＮＡ分子的非共价键力作用将改变ＤＮＡ分子构型，破坏其模板作用．本文在研究吩嗪染料——中性红（ＮｅｕｔｒａｌＲｅｄ，ＮＲ...     

人的基因组及DNA序列分析──过去、现去及将来（上）

人的基因组研究已成为生命科学前沿领域中最热门的课题之一。ＤＮＡ序列分析是基因组研究的关键技术．本文对人的基因组分析及其对ＤＮＡ序列分析的要求进行了论述．对ＤＮＡ序列分析方法如板凝胶电泳自放射显影法、板凝胶电泳激光荧光法、毛细管电泳激光荧光法、阵列毛细管凝胶电泳激光荧光法。超薄层板在胶电泳激光荧光法作了详细评论．并对正在开发的不用凝胶电泳分离的直接测序新技术和新方法，如质谱法、原子探针法（扫描隧道显微镜、原子力显微镜）、杂交法、流动单分子荧光检测法等进行了评论。     

DNA芯片技术与脱氧核糖核酸序列分析

人类基因组计划的实施,有力地促进了ＤＮＡ序列分析技术的发展。ＤＮＡ芯片综合运用了固相合成化学、照相平版印制技术以及激光共聚焦扫描等技术,能够同时扫描分析多基因乃至基因组,可广泛应用于基因的多态性分析、基因定位、表达水平的监测以及遗传病的诊断等领域,是对传统的ＤＮＡ分析技术的一次重大突破。本文介绍了ＤＮＡ芯片技术的基本原理并对其应用作一简要综述。     

Is DNA's rigidity dominated by electrostatic or nonelectrostatic interactions?

Double-stranded DNA is among the stiffest biopolymers, whose bending propensity crucially influences many vital biological processes. It is not fully understood which among the two most likely forces, electrostatic self-repulsion or the compressive base pair stacking, plays a dominant role in determining the DNA's unique rigidity. Different theoretical and experimental studies led so far to contradictory results on this issue. In this Communication, we address this important question by means of Molecular Dynamics (MD) simulations using both atomistic and coarse-grained force fields. Using two independent sets of calculations, we found that electrostatic and nonelectrostatic effects play a comparable role in maintaining DNA's stiffness. Our findings substantially differ from predictions of existing theories for DNA rigidity and may indicate that a new conceptual understanding needs to be developed.     

Nucleic acid based molecular devices

In biology, nucleic acids are carriers of molecular information: DNA's base sequence stores and imparts genetic instructions, while RNA's sequence plays the role of a messenger and a regulator of gene expression. As biopolymers, nucleic acids also have exciting physicochemical properties, which can be rationally influenced by the base sequence in myriad ways. Consequently, in recent years nucleic acids have also become important building blocks for bottom-up nanotechnology: as molecules for the self-assembly of molecular nanostructures and also as a material for building machinelike nanodevices. In this Review we will cover the most important developments in this growing field of nucleic acid nanodevices. We also provide an overview of the biochemical and biophysical background of this field and the major "historical" influences that shaped its development. Particular emphasis is laid on DNA molecular motors, molecular robotics, molecular information processing, and applications of nucleic acid nanodevices in biology.     

Engineering DNA-based functional materials

While DNA is a genetic material, it is also an inherently polymeric material made from repeating units called nucleotides. Although DNA's biological functions have been studied for decades, the polymeric features of DNA have not been extensively exploited until recently. In this tutorial review, we focus on two aspects of using DNA as a polymeric material: (1) the engineering methods, and (2) the potential real-world applications. More specifically, various strategies for constructing DNA-based building blocks and materials are introduced based on DNA topologies, which include linear, branched/dendritic, and networked. Different applications in nanotechnology, medicine, and biotechnology are further reviewed.     

IDENTIFICATION OF ULTRAVIOLET-INDUCED THYMINE DIMERS IN DNA BY ABSORBANCE MEASUREMENTS

Abstract— The irradiation of native DNA's by ultraviolet radiation of different wave lengths changes their absorption spectra. The changes are similar to those found for the formation of dimers between adjacent thymines in polynucleotide chains. The decreases in absorbance at 270 mµ produced by 280 mµ irradiation are reversed to a large extent by subsequent 239 mµ irradiation. The magnitude of the absorbance changes produced by large doses of 280 mµ correspond to the formation of dimers between approximately 50 per cent of all the TT sequences in the DNA. An incident dose of 100 erg/mm² of 280 mµ radiation forms about one dimer per molecule of calf thymus DNA of molecular weight 6 times 10⁶. The irradiation of heat-denatured DNA produces larger absorbance changes than are observed in native DNA. The absorbance changes in denatured DNA arise in part from a heat-reversible reaction, presumably involving cytidine, part from the formation of thymine dimers, and part from some unknown photoproducts. The reversal of thymine dimers by short wave length irradiation does not pioduce an equivalent change in the melting temperature of the DNA.     

Development of capillary array DNA sequencers for genome analysis

Massive analysis of biological molecules is being successfully applied to elucidate various biological phenomena using techniques of molecular science. This new era was initiated by the Human Genome Project, which was supported by the development of various automated tools including DNA sequencers and DNA chips. A small project led by Akiyoshi Wada in Japan triggered the development of automated DNA analysis instruments. As one of the members of the project, the author has been engaged in developing DNA analyzers including capillary array DNA sequencers. Here, the principles and development of the main technologies related to capillary array DNA sequencers, which contributed to the completion of the Human Genome Project, are reviewed. © 2010 The Japan Chemical Journal Forum and Wiley Periodicals, Inc. Chem Rec 10: 000–000; 2010: Published online in Wiley InterScience ( www.interscience.wiley.com ) DOI 10.1002/tcr.200900010     

毛细管电泳DNA片段多态性分析

对毛细管筛分电泳在ＤＮＡ片段多态性分析中的应用作了较为详细的论述,还对ＤＮＡ片段多态性研究的意义和作用进行了讨论。     

Vibrational dynamics of DNA: IV. Vibrational spectroscopic characteristics of A-, B-, and Z-form DNA's

Linear and nonlinear IR spectroscopic studies of nucleic acids can provide crucial information on solution conformations of DNA double helix and its complex with other molecules. Carrying out density functional theory calculations of A-, B-, and Z-form DNA's, the authors obtained vibrational spectroscopic properties as well as coupling constants between different basis modes. The vibrational couplings that determine the extent of exciton delocalization are strongly dependent on DNA conformation mainly because the interlayer distance between two neighboring base pairs changes with respect to the DNA conformation. The Z-DNA has comparatively small interlayer vibrational coupling constants so that its vibrational spectrum depends little on the number of base pairs, whereas the A-DNA shows a notable dependency on the size. Furthermore, it is shown that a few distinctively different line shape changes in both IR and two-dimensional IR spectra as the DNA conformation changes from B to A or from B to Z can be used as marker bands and characteristic features distinguishing different DNA conformations.     

Development and characterization of on-chip biopolymer membranes

In lab-on-a-chip applications, filtration is currently performed prior to sample loading or through pre-cast membranes adhered to the substrate. These membranes cannot be patterned to micrometer resolution, and their adhesion may be incompatible with the fabrication process or may introduce contaminants. We have developed an on-chip separation process using a biocompatible polymer that can be patterned and has controllable molecular rejection properties. We spun cast cellulose acetate (CA) membranes directly onto silicon wafers. Characterization of the molecular flux across the membrane showed that molecular weight and charge are major factors contributing to the membranes' rejection characteristics. Altering casting conditions such as polymer concentration in the casting solution and the quenching-bath composition and/or temperature allowed control of the molecular weight cut-off (MWCO). Three MWCOs; 300, 350, and 700 Da have been achieved for non-linear molecules. Molecular shape is also very important as much higher molecular weight single-stranded DNA was electrophoresed across the membranes while heme with a similar negative charge density was rejected. This was due to DNA's small molecular cross section. This is an important result because heme inhibits polymerase chain reactions (PCR) reducing the detection and characterization of DNA from blood samples.     

Fluorescence resonance energy transfer in dye-labeled DNA

We present the results of molecular modeling of dye-labeled, double-stranded DNA. The structural information obtained from the simulations are used as input to an analysis of energy transfer in this system. The simulations reveal the nature of the interaction between a pair of fluorophores and DNA. The donor, tetramethylrhodamine, TMR, attached to the 5′-end of DNA with a six-carbon tether, interacts primarily with DNA's minor groove, but occasionally stacks against the DNA base pairs. The acceptor, Cy5, attached to the opposite strand at positions n (n = 7, 12, 14, 16, 19, 24, 27), binds in the major groove in two distinct locations on the upper and lower part of the groove. We analyzed in detail the dye-to-dye distances, dipole orientation factors and fluorescence resonance energy transfer (FRET) rates. Tests of the validity of the Förster model were conducted using the transition density cube (TDC) method, which provides the exact Coulombic interaction within a certain model chemistry. Our studies show that the use of long tethers does not guarantee rotational freedom of the dyes, as intended in the experiments. Instead, the tethers allow Cy5 to bind in two different geometries, which causes a large uncertainty in the dye-to-dye distances. Our results also show significant fluctuation in the orientation factor, κ², which, together with uncertainty in dye-to-dye distances, cause considerable uncertainty in interpreting FRET measurements. We suggest that molecular modeling, combined with the TDC method, provides a useful tool in designing and interpreting FRET experiments.