DNA分子组装体研究进展*

DNA分子组装体在基因治疗、电子转移、分子器件和纳米材料构筑等方面具有很强的应用前景.本文对近几年来DNA分子组装体的研究作了评述.     

分子逻辑器件研究进展

分子器件具有尺寸小、设计合成可控、存储量大、反应速度快、人工智能等诸多优点,是当今化学、物理和材料等领域研究最为重要的一个交叉领域.综述了近些年来分子逻辑器件领域的研究进展.介绍了各种类型的分子逻辑门、半(加)减法器、分子逻辑线路以及DNA分子和固态分子计算.最后提出了分子器件存在的问题并展望了其应用前景.     

"分子梳"研究进展

“分子梳”是DNA被可移动的气-液界的均匀拉直,该技术涉及两个过程:DNA分子末端与基底表面的特异性结合和移动的气-液界面对DNA分子的均匀拉直。该技术在构建纳米材料/结构,研究DNA转录和复制,绘制基因物理图谱等方面得到了应用。预计“分子梳”技术将在以下方面取得进展:以拉直的DNA为模板构建纳米器件和纳米材料;用于基因突变的临床检测;结合原子力显微术(AFM),建立“原子力显微术原位杂交”技术以替代荧光原位杂交。     

含对溴苯基的新型DNA切割剂的合成及活性研究

人工合成的光引发活性 DNA切割剂在化学、生物学和医药等领域中具有重要的学术意义和潜在的应用价值 [1,2 ] .DNA切割分子可以在光的引发下切割 DNA,它的优点在于对体系从时间和空间上进行控制 .目前已经成功地合成出芳香族卤化物、醌类、金属络合物、 C60 衍生物等多种光引发活性 DNA切割剂 .将 DNA识别分子与光切割分子相连 ,则可以合成具有识别功能的光引发活性 DNA切割分子 .卤代苯基是一类重要的光活性基团 ,在紫外光引发下 ,生成苯基自由基切割 DNA[3 ] .偏端霉素是含有 3个吡咯环的寡聚酰胺 ,它是一种天然的抗肿瘤抗生素 ,…     

DNA与其靶向分子相互作用研究进展

DNA与其靶向分子相互作用的研究不仅对阐述一些抗肿瘤、抗病毒药物及致癌物的作用机理,而且对进一步指导人工核酸酶的合成及DNA高级结构研究等方面的工作都具有重要意义.本文着重评述了近年来不同结构类型的DNA靶向分子与DNA相互作用研究方面的进展.     

基于核酸框架的分子机器

分子机器是一种由分子构建的微型设备,在受到适当的刺激如光、温度、pH或电磁场时,它能够在分子水平上执行类似宏观机器的机械运动.然而,分子机器的研究仍面临着许多技术挑战,包括如何精确控制分子机器的运动,如何构建大规模的分子机器系统等.作为有潜力的分子自组装技术,利用DNA纳米技术可以构建复杂的刺激响应纳米机器并精确调控其在分子水平的运动.本文中,我们简单介绍了DNA纳米技术的组装原理,综述了响应DNA链置换、光、热、pH和电场等不同类型刺激的核酸框架分子机器,并探讨了它们在药物递送、构建三维等离子体光学器件以及作为生物分子标尺等方面的应用.     

金属卟啉对杂环及DNA分子识别研究进展

介绍了近几年国内外关于组装金属卟啉对杂环分子、DNA碱基以及RNA的分子识别的研究进展, 并简述了本课题组对金属卟啉与杂环及药物分子复合物的理论研究工作. 金属卟啉广泛存在于自然界和生物体中, 此识别过程对研究和模拟生命体中各种细胞之间的相互作用具有重要意义. 组装后的金属卟啉可通过轴向配位、氢键及π-π堆积作用等识别杂环分子. 金属卟啉对DNA的识别主要有四种作用方式, 而金属卟啉对DNA以及RNA分子的识别主要靠疏水作用力、静电力以及自堆叠作用. 卟啉阳离子与DNA的结合位点受主体侧链取代基的空间结构影响. 金属卟啉对药物分子的识别靠配位键和氢键进行, 以配位键结合的复合物通常具有更高的结合能.     

聚氨酯分子印章的制备和表征

“软平板印刷”微结构制备技术为微米和亚微米器件的制备提供了一条新的途径 [1] ,已被电子学家和材料学家所应用 ,近年来进入了生物学领域[2 ] .本实验室将这一方法与生物分子电子学相结合 ,提出了用于 DNA芯片在片合成的分子印章法 [3,4 ] .分子印章法的实质是接触压印与组合化学相结合的固相界面反应 .聚二甲氧基硅氧烷 ( PDMS)是一种软印刷的优良材料 [5] ,但是由于其疏水性和较差的机械性能 ,必须对其进行改性才能用来制备 DNA分子印章 [6 ] .　　聚氨酯作为一种功能材料 ,由于分子中交替的软、硬链段及其不同的热动力学性能而形成…     

弹性竿模型下超螺旋DNA分子的构象研究

采用弹性竿模型 (Elasticrodmodel) ,用MonteCarlo方法对DNA分子的构象进行研究 .通过计算发现 ,DNA分子的能量是由弯曲势能EB 和扭转势能ET 两部分组成 ,通常EB 比ET 大一至两个数量级 .同时给出了均方回转半径与链长之间的关系为〈R2g〉 =1 1 69 5 -3 5×n +0 0 2 5×n2 ,它体现了DNA分子结构的特点 .验证了公式Lk=Wr+Tw ,得出Lk与Wr比较接近的结论 ,考虑DNA分子的构型 ,意味着DNA分子容易被弯曲而不易被扭转 ,但随着连接系数的增加 ,DNA被扭转的几率也在增加 .这为分析DNA分子的结构特征提供了一种新方法     

生物分子功能化碳纳米管

利用生物分子功能化碳纳米管,使其具备生物相容性和特殊的识别功能并引入生物体系是一项极具应用潜力的研究.如何利用不同种类的生物分子功能化碳纳米管则是该领域须解决的一个关键问题.本文综述了利用生物分子酶、蛋白质、氨基酸、肽螺旋、DNA功能化碳纳米管的最新研究进展,重点介绍了碳纳米管侧壁与端口的DNA功能化以及碳纳米管的DNA填充,并对DNA功能化碳纳米管在生物传感器、电化学检测及DNA操纵碳纳米管自组装方面的应用作了阐述.     

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。     

生物大分子自组装膜及其应用研究进展

本文主要介绍了酶，蛋白质、DNA等生物大分子自组装膜的研究进展，并对生物大分子膜在生物传感器，分子器件，高效催化材料，医用生物材料等方面的应用前景进行了展望。     

用于毛细管电泳DNA分离的合成聚合物*

毛细管电泳的无胶筛分方法在DNA片段分离、DNA 测序方面取得了显著的成绩并已成功应用于人类基因组计划.该法是在毛细管柱中充入一定浓度和组成的线性高分子溶液,利用其对样品组分电泳迁移时的阻滞作用,按分子量大小对DNA等生物大分子进行筛分分离分析.因此,聚合物筛分介质的类型、组成和性质会显著影响分离效果.近年来,由于受到基因组计划的影响,出现了许多用于DNA片段分离和DNA测序的水溶性高分子聚合物,并取得很大进展.本文按照均聚物和共聚物的分类,综述了作为筛分介质的各种合成聚合物及其应用效果,并简要介绍了有关的筛分理论和分离的评价指标.     

Δ-和Λ-[Ru(bpy)2(HPIP)2+两种异构体对小牛胸腺DNA不同键合速率的CD光谱证明

Wilson[1]于1997年发表了关于DNA导电性的评论性文章, 介绍了各种学派的观点. 争论焦点在于DNA是否为导体. 将两种配合物键合于DNA作为接头, 通过研究电子转移可确定DNA是否为导线, 其中配合物和DNA键合模式是研究的关键. Barton[2]和Norden[3]均认为2+ 配合物能强烈插入DNA中. 我们[4]曾从改变辅助配体角度出发, 研究2+和DNA的作用, 结果证明2+具有更强的插入能力, 并结合文献把键合模式归纳为3类, 即静电键合、沟面键合和插入键合[5]. 最近, 我们报道了新体系2+/DNA/2+(bpy=2,2′-bipyridine), 其中2+和2+均可插入DNA中. 2+是光诱导电子给予体, 2+是电子接受体, 荧光光谱证明前者的电子通过DNA中的π电子转移给后者, 导致后者荧光猝灭, 结果支持DNA是导线的观点[6]. 2+中的PIP芳香环和DNA碱基芳环组成π电子的堆积力[7], 从而增强了对DNA的插入能力.     

DNA Aptamers are Functional Molecular Recognition Sensors in Protic Ionic Liquids

The function and structural changes of an AMP molecular aptamer beacon and its molecular recognition capacity for its target, adenosine monophosphate (AMP), was systematically explored in solution with a protic ionic liquid, ethylammonium nitrate (EAN). It could be proven that up to 2 M of EAN in TBS buffer, the AMP molecular aptamer beacon was still capable of recognizing AMP while also maintaining its specificity. The specificity was proven by using the guanosine monophosphate (GMP) as target; GMP is structurally similar to AMP but was not recognized by the aptamer. We also found that in highly concentrated EAN solutions the overall amount of double stranded DNA formed, as well as its respective thermal stability, diminished gradually, but surprisingly the hybridization rate (k_h) of single stranded DNA was significantly accelerated in the presence of EAN. The latter may have important implications in DNA technology for the design of biosensing and DNA‐based nanodevices in nonconventional solvents, such as ionic liquids.     

Differential DNA Recognitions of Benzimidazole Based Astemizole,Omeprazole, Lansoprazole,and Thiabendazole

Well known benzimidazole based drugs – astemizole, omeprazole, lansoprazole, and thiabendazole – are studied whether those can bind with two different oligonucleotides sequences or not. Molecular docking study and further molecular dynamics are employed to find out the capability of these drugs toward different DNA sequences. The substitution at N2 with different atoms/group or heterocyclic moieties favors the binding in the major groove of DNA in most of the cases. The substitutions at N1 beside N2 position clearly increase the binding possibility of astemizole as compared to the rest. Various functional possibilities of known drugs through DNA recognitions may be explored in drug repurposing purposes in virtue of present study.     

Functionalized Nanogap for DNA Read-Out: Nucleotide Rotation and Current-Voltage Curves

Functionalized nanogaps embedded in nanopores show a strong potential for enhancing the detection of biomolecules, their length, type, and sequence. This detection is strongly dependent on the features of the target biomolecules, as well as the characteristics of the sensing device. In this work, through quantum-mechanical calculations, we elaborate on representative such aspects for the specific case of DNA detection and read-out. These aspects include the influence of single DNA nucleotide rotation within the nanogap and the current-voltage (I-V) characteristics of the nanogap. The results unveil a distinct variation in the electronic current across the functionalized device for the four natural DNA nucleotides with the applied voltage. These also underline the asymmetric response of the rotating nucleotides on this applied voltage and the respective variation in the rectification ratio of the device. The electronic tunneling current across the nanogap can be further enhanced through the proper choice of an applied bias voltage. We were able to correlate the enhancement of this current to the nucleotide rotation dynamics and a shift of the electronic transmission peaks towards the Fermi level. This nucleotide specific shift further reveals the sensitivity of the device in reading-out the identity of the DNA nucleotides for all different configurations in the nanogap. We underline the important information that can be obtained from both the I-V curves and the rectification characteristics of the nanogap device in view of accurately reading-out the DNA information. We show that tuning the applied bias can enhance this detection and discuss the implications in view of novel functionalized nanopore sequencers.     

Chiral DNA Origami Nanotubes with Well‐Defined and Addressable Inside and Outside Surfaces

We report the design and assembly of chiral DNA nanotubes with well‐defined and addressable inside and outside surfaces. We demonstrate that the outside surface can be functionalised with a chiral arrangement of gold nanoparticles to create a plasmonic device and that the inside surface can be functionalised with a track for a molecular motor allowing transport of a cargo within the central cavity.     

基于钌多吡啶类配合物的DNA分子光开关及生物传感研究

DNA结构具有多态性,利用小分子化合物对不同结构的DNA分子进行识别及调控具有重要的生物学意义.本文主要针对近年来钌多吡啶配合物作为DNA分子光开关的研究进行综述,内容包括DNA分子光开关的机制,不同结构DNA的分子光开关,DNA分子光开关的开关循环控制策略和钌多吡啶类配合物及与纳米材料相结合作为生物传感器的研究.     

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.