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。     

分子计算机的研究进展*

研制分子计算机也许是突破传统半导体电子计算机发展极限的唯一出路。本文简述了最近十年分子计算机的研究进展, 重点讨论了DNA 计算机和生物分子计算机的研究成果, 并对可能为人类提供思考和尝试范本的生物活细胞中蛋白质的各种计算机制的研究给予了充分的关注。引用了43篇文献。     

DNA折纸术研究进展

DNA折纸术是近年来提出的一种全新的DNA自组装的方法,是DNA纳米技术与DNA自组装领域的一个重大进展。与传统的DNA自组装技术不同,DNA折纸术通过将一条长的DNA单链（通常为基因组DNA）与一系列经过设计的短DNA片段进行碱基互补,能够可控地构造出高度复杂的纳米图案或结构,在新兴的纳米领域中具有广泛的潜在应用。本文在介绍DNA折纸术相关原理的基础上,就DNA折纸术的起源、发展及其在DNA芯片、纳米元件与材料等领域的潜在应用进行了概述,探讨了DNA折纸术未来可能的发展方向。     

光控DNA可逆杂交/解链及其应用

通过光敏分子与DNA相互作用,可以实现光控DNA杂交与解链,这种光控DNA有望成为下一代DNA功能构筑材料和纳米机械能量输入模式。本文总结了可逆光控DNA杂交/解链的各种途径及其作用机理,并分析其使用条件和光控效果。已有实验结果的对比和归纳表明,从DNA骨架上楔入含侧链偶氮苯官能团的单元,通过顺反异构实现DNA双链解链与杂交的可逆光控最具应用潜力,并且仍有一定的改进空间。本文介绍了这种骨架楔入偶氮苯光控DNA材料在纳米技术和生物技术方面的应用,并对其进一步的研究方向进行了展望。     

基于生物芯片的核酸凝胶电泳仪

为克服传统平板凝胶电泳法操作步骤繁琐,实验时间长,以及采用紫外光源可能对人体造成伤害等缺陷,该文研制了一种基于电泳芯片的快速凝胶电泳仪,仅需DNA点样于电泳芯片后,将电泳芯片置于该电泳仪便可实现DNA样品快速分离及实时在线成像检测。以20、50、100 bp DNA ladder为检测对象,在仪器内对其分离效果进行验证及优化,其最佳电泳条件为电压100 V/cm,琼脂糖质量分数分别为2. 5%、1. 0%、1. 4%。结果表明在14 min内可以实现3种DNA样品的高效分离,DNA迁移距离与分子量的相关系数均高于0. 9,且该仪器具有较高的稳定性。     

DNA步行者在检测传感中的应用

DNA步行者（DNA Walker）是一种基于化学能布朗运动的人工模拟机器,由构象迁移和链置换反应驱动,在纳米轨道上实现物质的检测运输。基于DNA Walker的生物传感器是一种集生物和纳米技术于一体的新型高效传感器,在食品安全检测、生物传感等领域有巨大的应用潜力。本文介绍了DNA Walker的发展现状,并通过讨论,系统概述了DNA Walker传感器的设计原理及其在检测传感中的应用。总结了DNA Walker传感器的性能优势和所面临的挑战,并对该技术的研究前景进行了展望。     

DNA与两性表面活性剂相互作用研究

本文综述了DNA与两性表面活性剂相互作用的研究进展,主要介绍了利用荧光显微镜、动静态光散射、相图及浊度等方法对DNA与两性表面活性剂相互作用的观察与形成复合物的表征。由于两性表面活性剂所具有的独特性质,可以实现在特定pH范围通过静电作用诱导DNA构象发生线圈状向小球状的不连续转变,并可通过调节溶液pH值、离子强度等实现对DNA-两性表面活性剂复合物的稳定性的调控。DNA与两性表面活性剂相互作用形成的复合物在非病毒基因载体研究方面具有潜在的应用价值。     

DNA分子器件*

DNA不仅是一种重要的生物遗传物质,而且可以在生命科学以外的领域,尤其是在信息科学、材料科学中发挥重要作用.作为重要的部件,DNA分子器件的研究引起了科学家们的注意.本文对DNA分子器件的发展以及DNA分子器件的实现和应用前景及不足进行了较详尽的评述.     

三聚氰胺对DNA潜在损伤作用的研究

在生理酸度条件下(pH 7.4),采用溴化乙锭(EB)为荧光探针的荧光光谱法、I-离子荧光猝灭效应、DNA熔点和粘度效应等手段,研究了三聚氰胺与DNA的相互作用。随着DNA的加入,三聚氰胺的荧光强度明显减小而且三聚氰胺能够猝灭DNA-EB复合物的荧光,说明三聚氰胺能够竞争置换EB而与DNA作用;三聚氰胺的加入使得DNA的粘度增大,DNA-EB的熔点降低;DNA的加入减小了I-对三聚氰胺荧光的猝灭程度。三聚氰胺以嵌插方式作用于DNA的亲核位点,意味着三聚氰胺进入生物体后有可能通过形成DNA加合物的形式造成DNA损伤,从而最终导致基因突变。     

(E)-2-乙氧基乙基-2-氰基-3-((4-(2,4-二氟苯氧基)苄基)氨基)-3-甲氧基丙烯酸酯对超螺旋质粒DNA的特异性切割(英文）

研究了一种新型丙烯酸酯 (E)-2-乙氧基乙基-2-氰基-3-((4-(2,4-二氟苯氧基)苄基)氨基)-3-甲氧基丙烯酸酯(MAZ)对超螺旋pUC19 DNA的定点切割作用。利用紫外吸收、荧光光谱、凝胶电泳和DNA测序技术研究其核酸切割特异性。紫外吸收光谱的红移和减色效应,以及静态荧光淬灭表明MAZ与DNA的作用属于典型的插入模式。不仅如此,凝胶电泳条带的变化以及DNA测序结果表明DNA的定点切割是通过DNA双链的分步水解完成。     

DNA‐Computer — Superrechner der Zukunft?: Chemie und Informatik

A new method for utilizing the outstanding qualities of natural information systems has been developed. The data processing elements of the computers consist of desoxyribonucleic acid (DNA). DNA computers facilitate tridimensional and parallel information processing. Due to the numerous parallel chemical reactions, a DNA computer can master problems which can not be solved with conventional electronic computers. DNA computers offer many possibilities. Since a DNA computer can simulate any given Turing machine computation, a DNA computer is able to execute every program.     

Connectable DNA Logic Gates: OR and XOR Logics

Modern computer processors are based on semiconductor logic gates connected to each other in complex circuits. This study contributes to the development of a new class of connectable logic gates made of DNA in which the transfer of oligonucleotide fragments as input/output signals occurs upon hybridization of DNA sequences. The DNA strands responsible for a logic function form associates containing immobile DNA four‐way junction structures when the signal is high and dissociate into separate strands when the signal is low. A basic set of logic gates (NOT, AND, and OR) was designed. Two NOT gates, two AND gates, and an OR gate were connected in a network that corresponds to an XOR logic function. The design of the logic gates presented here may contribute to the development of the first biocompatible molecular computer.     

Solvating,manipulating, damaging,and repairing DNA in a computer

This work highlights four different topics in modeling of DNA: (i) the importance of water and ions together with the structure and function of DNA; the hydration structure around the ions appears to be the determining factor in the ion coordination to DNA, as demonstrated in the results of our MD simulations; (ii) how MD simulations can be used to simulate single molecule manipulation experiments as a complement to reveal the structural dynamics of the studied biomolecules; (iii) how damaged DNA can be studied in computer simulations; and (iv) how repair of damaged DNA can be studied theoretically. © 2006 Wiley Periodicals, Inc. Int J Quantum Chem, 2007     

An assembling strategy for DNA cages with minimum strands

DNA polyhedra are artificial cage-like architectures based on interlocked and interlinked DNA double-strands. Using fewer strands to construct DNA cages shows an important role in the design of single-stranded DNA molecules. However, construction methods for DNA polyhedra from topological perspective remains not well understood. In this study, we theoretically propose an assembling strategy for DNA polyhedra with minimum strands based on computer algorithm. The results show that this efficient method could search DNA polyhedra with fewer strands faster. Our research provides new insights into design and synthesis for DNA polyhedra with required topological structures.     

DNA纳米技术的研究及应用*

以纳米材料为标志的纳米技术研究已掀起高潮,并已经渗入到包括生物医学在内的诸多学科。作为生物大分子之一的脱氧核糖核酸（DNA）由于具有独特的理化性质,被广泛用于构造各种纳米结构、生物器件和仿生构件。目前DNA纳米技术已成为分子生物学和纳米科学中最为活跃的研究领域,它为纳米器件的制作提供了一种新技术、新方法,对分子级电子元件的研究具有深远的意义,在DNA计算机、纳米生物机械及基因治疗等方面占有一席之地,成为生物化学中一个极具生命力的科学前沿。作者在自己工作的基础上,跟踪国际前沿技术对DNA纳米技术的研究进展及应用作了较为详细的评述。     

Programming the Nucleation of DNA Brick Self‐Assembly with a Seeding Strand

Recently, the DNA brick strategy has provided a highly modular and scalable approach for the construction of complex structures, which can be used as nanoscale pegboards for the precise organization of molecules and nanoparticles for many applications. Despite the dramatic increase of structural complexity provided by the DNA brick method, the assembly pathways are still poorly understood. Herein, we introduce a “seed” strand to control the crucial nucleation and assembly pathway in DNA brick assembly. Through experimental studies and computer simulations, we successfully demonstrate that the regulation of the assembly pathways through seeded growth can accelerate the assembly kinetics and increase the optimal temperature by circa 4–7 °C for isothermal assembly. By improving our understanding of the assembly pathways, we provide new guidelines for the design of programmable pathways to improve the self‐assembly of DNA nanostructures.     

Programming the Nucleation of DNA Brick Self-Assembly with a Seeding Strand

Recently, the DNA brick strategy has provided a highly modular and scalable approach for the construction of complex structures, which can be used as nanoscale pegboards for the precise organization of molecules and nanoparticles for many applications. Despite the dramatic increase of structural complexity provided by the DNA brick method, the assembly pathways are still poorly understood. Herein, we introduce a “seed” strand to control the crucial nucleation and assembly pathway in DNA brick assembly. Through experimental studies and computer simulations, we successfully demonstrate that the regulation of the assembly pathways through seeded growth can accelerate the assembly kinetics and increase the optimal temperature by circa 4–7 °C for isothermal assembly. By improving our understanding of the assembly pathways, we provide new guidelines for the design of programmable pathways to improve the self-assembly of DNA nanostructures.     

阿达玛变换显微图象分析(Ⅱ)──荧光衰减对图象和定量分析数据的影响

采用计算机模拟的方法,系统地考察了试样的荧光衰减对阿达玛变换图象和定量分析数据的影响,并把阿达玛变换显微图象分析仪用于细胞内DNA的定量分析,得到了满意的结果。     

Modelling CreA protein–DNA recognition determinants. A molecular dynamics study of fully charged CreA–DNA model in water

CreA, the negative regulator mediating carbon catabolism repression in Aspergillus nidulans, is a protein that contains a DNA-binding domain comprising two zinc finger motifs. A 3D model for the CreA–G4 (5′-GCGGGGGCGT-3′) complex is constructed on the basis of the structure of the Zif268–DNA crystal complex [Science 252 (1991) 809] and using similarity analysis and computer assisted modelling techniques. The CreA–G4 model was then subjected to a set of molecular dynamics (MD) studies. Based on our previous nano second long Zif268–DNA MD simulation, a 170 ps long trajectory was deemed sufficient to test possible DNA–protein interactions. A screening of the static model and of the trajectory was performed for protein amino acids, nucleotide bases, phosphates backbone and water molecules mediating protein–DNA contacts. Energy, root mean square deviation (RMSD), principal inertial moment and distances were analysed. For this time span, the stability shown in fluctuation patterns reveals the presence of a complex behaving in a manner similar to Zif268–DNA.

An unambiguous characterisation of the amino acids involved in DNA-binding was obtained. These results could contribute towards the establishment of a code of protein–DNA recognition for this class of DNA-binding motifs.