色氨酸标记的GCN4单体肽与DNA位点的分子识别

酵母转录激活因子GCN4调控细胞中氨基酸的生物合成, 是典型的含bZIP结构域的DNA结合蛋白.本文合成了天然蛋白GCN4的碱性区（226-252）, 并在其N末端引入色氨酸残基W, 做为单体肽GCN4-W.圆二色(CD)实验表明, 突变后的单体肽仍能序列特异性识别DNA结合位点AP-1和ATF/CREB.用荧光滴定方法获得了GCN4-W与DNA位点结合形成复合物的表观解离常数.     

分子极性在DNA-蛋白质识别过程中的作用——对λ阻遏蛋白-操纵基因体系的研究

本文证明λ阻遏蛋白的电荷分布显示,分子的静电极性可能加速蛋白质向DNA分子的非特异性结合.分布于阻遏蛋白分子前26个残基的一片正电荷区可能提供一个非特异性结合面.此外,在许多DNA-蛋白质特异性识别过程中,蛋白质以二聚体为活力单位与DNA结合.这很可能也是由于有利于静电作用的缘故。     

多溴联苯醚与人血清白蛋白相互作用的表面等离子体共振及分子对接

采用表面等离子体共振(SPR)技术,在模拟生理条件下实时动态研究了8种典型多溴联苯醚(PBDEs)与人血清白蛋白(HSA)相互作用的动力学和热力学行为.通过分子对接模拟研究了PBDEs与HSA相互作用的分子机制,探讨了不同PBDEs与蛋白的结合模式及作用力.动力学实验结果表明, PBDEs中溴原子的个数和取代位置对相互作用有规律性的影响.溴原子通过改变PBDEs分子与HSA作用过程中的解离速率来影响其亲和力,溴原子个数越多, PBDEs与HSA作用的亲和力越强;而取代基位置则影响PBDEs与HSA作用结合速率的快慢,同分异构体中间位取代溴的亲和力大于邻位取代溴.分子对接结果显示, 8种PBDEs主要结合于HSA的Site I位点,但结合位点周边氨基酸残基类型的差异影响了结合力.范德华力和氢键对结合能的贡献远大于静电力.     

苝酰亚胺受体的聚集形态对有机太阳电池中激子过程与电子传输的影响（英文）

末端烷基链分叉位置对苝酰亚胺(PBI)线性二联体的堆积模式具有显著影响,进而影响激子过程与载流子传输.二联体两端烷基链分叉位点紧靠苝酰亚胺能够抑制分子长程有序堆积,形成具有较少能量陷阱的无定形聚集态;而两端烷基链分叉位点远离苝酰亚胺则导致多种聚集结构共存,分子间强π-π相互作用位点成为能量陷阱.结果表明, PBI受体的聚集方式对有机太阳电池的性能产生重要影响,需要尽量减少活性层中的多种聚集结构共存以免引起激子解离受限以及载流子传输迟滞.     

"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。     

二芳基乙烯衍生物与DNA结合的分子动力学研究

基于分子动力学方法, 对2种旋转异构的二芳基乙烯(DTE, dithienylethene)衍生物(DTE1和DTE2)与不同分子结构DNA结合过程的热力学与动力学特征进行模拟, 结果发现, DTE1, DTE2与DNA分子采用小凹槽结合(MiGB)的模式结合时所需能量最低, 存在的分子间库仑能与范德华相互作用能最小, 说明该结合模式最稳定; 由于空间位阻作用, 互为旋转异构体的2个DTE衍生物与DNA作用表现出截然不同的结合行为, DNA对DTE衍生物具有明显的对映异构体选择性; DTE衍生物与DNA分子作用位点的选择性直接与构成位点的碱基对相关.     

电喷雾质谱法研究天然产物小分子识别人类端粒G-四链体及复合物的热稳定性

利用电喷雾质谱(ESI-MS)研究了12种天然产物小分子与人类端粒G-四链体结构的非共价相互作用和识别功能, 比较了不同小分子与人类端粒G-四链体的结合强弱, 发现了一种新的识别小分子——防己诺林碱对人类端粒G-四链体有很好的结合. 通过质谱升温实验比较了小分子结合对G-四链体热稳定性的影响, 防己诺林碱的结合使G-四链体的离子的解离温度(T1/2)上升到200 ℃. 利用分子模拟对G-四链体DNA与小分子结合的模式以及稳定性进行了探讨, 给出了防己诺林碱可能的结合位点和结合模式, Autodock计算出来的结合能约为-31.5 kJ·mol-1. 同原来的平面型分子不同, 防己诺林碱是一类新型结构的分子, 为设计合成新型G-四链体识别分子提供了新的结构模型.     

金属核酸酶及寡聚酰胺与双链DNA分子对接模式的理论研究

采用分子对接软件AutoDock分别研究了金属核酸酶、寡聚酰胺与DNA对接模式. 研究结果表明, 金属核酸酶、寡聚酰胺与DNA对接结果与实验数据吻合得较好. 在金属核酸酶与DNA的对接中, 最优构型都是金属核酸酶对接在DNA的小沟内. 随着中心金属上电荷的增加, 最大对接能呈现上升趋势. 尤其是配体体积较小的金属核酸酶, 最佳对接位点受中心金属上电荷影响较大, 即随着中心金属上电荷的从少到多, 最佳对接位点呈现多样化的趋势. 在柔性分子寡聚酰胺与双链DNA分子的对接中, 分子随DNA小沟的柔性变形是对接结合的关键. 其最佳的结合物位点也都是在DNA的小沟内, 其对接结果与晶体结构一致.     

人血清白蛋白与氨基酸对映异构体的差异性识别研究

以人血清白蛋白为识别主体,利用表面等离子体共振(SPR)技术实时研究了其与5种氨基酸对映异构体相互作用过程中的动态行为。实验结果显示,每种氨基酸分子的L-和D-型异构体在与人血清白蛋白作用过程中均存在明显的动力学差异。动力学数据分析表明,虽然各种氨基酸的L-和D-型异构体与人血清白蛋白作用的结合速率常数、解离速率常数无统一规律,但在解离平衡常数或结合平衡常数上有一致性。每种氨基酸的L-型异构体与人血清白蛋白的亲和力均大于D-型,这表明人血清白蛋白在与氨基酸对映异构体作用的过程中基于手性识别作用而产生了明显的差异性结合。     

高通量虚拟筛选CDK2/Cyclin A2靶点抑制剂

CDK2/Cyclin A2复合蛋白的异常表达与乳腺癌、 口腔癌、 食管鳞状细胞癌的发生密切相关. CDK2/ Cyclin A2复合蛋白的活性位点不同于CDK2单体. 至今临床上尚无靶向此复合蛋白的药物分子. 针对CDK2/Cyclin A2复合蛋白, 以实验报道的10个抑制剂分子构建药效团模型, 通过药物体外药代动力学（ADME）、 Docking、 聚类分析、 毒性预测, 从DrugBank, ChEMBL和TCM@Taiwan 3个数据库约90万组数据中进行高通量虚拟筛选, 进一步进行MD模拟、 MM/PBSA结合自由能计算、 能量分解和平均非共价作用(aNCI)分析, 筛选出3个抑制效果优于阳性实验药Roscovitine的先导分子: DrugBank-2004, DrugBank-583和ChEMBL-7122. 与CDK2蛋白相比, CDK2/Cyclin A2复合蛋白结合位点空间变大, 先导分子与Lys33, Asp86, Lys129和Asp145残基之间的排斥作用有所降低, 导致结合自由能更大.     

Fluorescence study of DNA binding and bending by EcoRI DNA methyltransferase

We have applied fluorescence anisotropy and fluorescence resonance energy transfer (FRET) techniques to study the interaction between EcoRI DNA methyltransferase (M.EcoRI) and its target DNA in solution. Upon binding with M.EcoRI, the dsDNA containing GAATTC bends to flip out the second adenine for methylation. The binding affinity of M.EcoRI to two dsDNA fragments (20 and 38 bp) was studied with fluorescence anisotropy. Their binding constants at different temperatures from 20 to 40 degrees C were obtained, and the thermodynamic parameters of binding were derived. The results showed that M.EcoRI had a higher binding affinity to the short dsDNA strand than to the long one, and its binding to DNA was primarily entropy-driven. By labeling the 5' ends of the 20-bp dsDNA with two fluorescent dyes, fluorescein (FAM) and tetramethylrhodamine (TMR), we were able to monitor the enhanced TMR fluorescence in the presence of M.EcoRI. The end-to-end distance of the dsDNA determined from the FRET efficiency was changed from 72.4 to 63.4 A, and the DNA bending angle was estimated as 57.8 degrees .     

Numerical study of DNA-functionalized microparticles and nanoparticles: explicit pair potentials and their implications for phase behavior

DNA-coated colloids have great potential for the design of complex self-assembling materials. In order to predict the structures that will form, knowledge of the interactions between DNA-functionalized particles is crucial. Here, we report results from Monte Carlo simulations of the pair-interaction between particles coated with single-stranded DNA sticky ends that are connected to the surface by relatively short and stiff surface tethers. We complement our calculations with a study of the interaction between two planar surfaces coated with the same DNA. Based on our simulations we propose analytical expressions for the interaction potentials. These analytical expressions describe the DNA-mediated interactions well for particle sizes ranging from tens of nanometers to a few micrometers and for a wide range of grafting densities. We find that important contributions to both the repulsive and attractive parts of the free energy come from purely entropic effects of the discrete tethered sticky ends. Per bond, these entropic contributions have a magnitude similar to the hybridization free energy of a free pair of sticky ends in solution and they can thus considerably change the effective sticky-end binding strength. Based on the calculated interaction potentials, we expect that stable gas-liquid separation only occurs for particles with radii smaller than a few tens of nanometers, which suggests that nanoparticles and micrometer-sized colloids will follow different routes to crystallization. Finally, we note that the natural statistical nonuniformities in the surface distribution of sticky ends lead to large variations in the binding strength. This phenomenon may compromise the reliability of tests that aim to detect specific DNA targets in diagnostics. In addition to guiding the design of novel self-assembling materials and gene-detection assays, the insights presented here could also shed more light on (multivalent) interactions in other systems with tethered binding groups, for instance in the areas of supramolecular chemistry or ligand-receptor mediated biorecognition.     

Bridging Ligand Length Controls AT Selectivity and Enantioselectivity of Binuclear Ruthenium Threading Intercalators

The slow dissociation of DNA threading intercalators makes them interesting as model compounds in the search for new DNA targeting drugs, as there appears to be a correlation between slow dissociation and biological activity. Thus, it would be of great value to understand the mechanisms controlling threading intercalation, and for this purpose we have investigated how the length of the bridging ligand of binuclear ruthenium threading intercalators affects their DNA binding properties. We have synthesised a new binuclear ruthenium threading intercalator with slower dissociation kinetics from ct‐DNA than has ever been observed for any ruthenium complex with any type of DNA, a property that we attribute to the increased distance between the ruthenium centres of the new complex. By comparison with previously studied ruthenium complexes, we further conclude that elongation of the bridging ligand reduces the sensitivity of the threading interaction to DNA flexibility, resulting in a decreased AT selectivity for the new complex. We also find that the length of the bridging ligand affects the enantioselectivity with increasing preference for the ΔΔ enantiomer as the bridging ligand becomes longer.     

Effects of DNA mismatches on binding affinity and kinetics of polymerase-DNA complexes as revealed by surface plasmon resonance biosensor

In this study, surface plasmon resonance (SPR) biosensor techniques were used to obtain quantitative information on the kinetics of the DNA and polymerase I (Klenow fragment) interaction. DNA duplexes containing different base compositions at the binding site were immobilized on the SPR sensor surface via biotin-streptavidin chemistry and the subsequent binding of the polymerase was measured in real time. Various kinetic models were tested and a translocation model was shown to provide the best fit for the binding and dissociation profiles. The results revealed that the enzyme binds to DNA at both the polymerase and the exonuclease domains with different association and dissociation rates as well as affinity constants, depending on the presence of mismatches near the primer 3'-end. Introduction of unpaired bases increases the DNA binding affinity towards the exonuclease domain and promotes the translocation of DNA from the polymerase site to the exonuclease site. The results also demonstrated that SPR biosensors may be used as a sensitive technique for studying molecular recognition events such as single-base discrimination involved in protein-DNA interaction.     

Detection of conformational and net charge differences in DNA-protein complexes by quantitative electrophoresis on polyacrylamide-agarose copolymer gels

The Galactosidase repressor (GalR) of Escherichia coli modulates the expression of the gal operon by binding to two DNA operators, OE and O1. The OE and O1 elements are 16 bp pallindromic DNA sequences, differing in four of the base pairs. OE and O1 DNA fragments, both free and complexed with repressor, were analyzed by "quantitative gel electrophoresis". By the criteria of that method, applied to the linear Ferguson plots of both DNA fragments and the linear ranges of those of the DNA-GalR complexes, it was shown that the apparent size of DNA increases upon repressor binding. Moreover, this size increase is greater for the complex with the O1 operator than for the complex with the OE operator in the case that GalR is located in the center of a 155 bp DNA fragment. This is not the case when GalR is located in a peripheral position. By contrast with their size differences, the centrally located GalR-O1 and GalR-OE complexes appear to possess indistinguishable net surface charge densities as judged from the intercepts with the mobility axis. The larger size of the complex with centrally located O1 fragment, as compared with that bearing the OE fragment, is interpreted as being due to bending of the DNA-protein complex, since an authentically bent fragment of a plasmid with bent upstream activator sequence also exhibits a larger slope of the Ferguson plot, and thus the larger size, than predicted on the basis of its DNA chain length (bp).(ABSTRACT TRUNCATED AT 250 WORDS)     

Short Optimally Capped Duplex DNA as Conformationally Restricted Analogue of B-DNA

We describe the synthesis of short double-stranded DNA fragments (see 4 and 13 ) which are capped on both ends by an optimally designed linker molecule. The new structures are stable with respect to hybrid dissociation and should have implications in physical studies involving double-stranded DNA as well as in the antisense area for the specific modulation of gene expressions.     

Kinetic discrimination of sequence-specific DNA-drug binding measured by surface plasmon resonance imaging and comparison to solution-phase measurements

We demonstrate the use of surface plasmon resonance (SPR) imaging for direct detection of small-molecule binding to surface-bound DNA probes. Using a carefully designed array surface, we quantitatively discriminate between the interactions of a model drug with different immobilized DNA binding sites. Specifically, we measure the association and dissociation intercalation rates of actinomycin-D (ACTD) to and from double-stranded 5'-TGCT-3' and 5'-GGCA-3' binding sites. The rates measured provide mechanistic information about the DNA-ACTD interaction; ACTD initially binds nonspecifically to DNA but exerts its activity by dissociating slowly from strong affinity sites. We observe a slow dissociation time of kd-1 = 3300 +/- 100 s for ACTD bound to the strong affinity site 5'-TGCT-3' and a much faster dissociation time (210 +/- 15 s) for ACTD bound weakly to the site 5'-GGCA-3'. These dissociation rates, which differ by an order of magnitude, determine the binding affinity for each site (8.8 x 10(6) and 1.0 x 10(6) M(-1), respectively). We assess the effect the surface environment has on these biosensor measurements by determining kinetic and thermodynamic constants for the same DNA-ACTD interactions in solution. The surface suppresses binding affinities approximately 4-fold for both binding sites. This suppression suggests a barrier to DNA-drug association; ACTD binding to duplex DNA is approximately 100 times slower on the surface than in solution.     

The use of ECD/ETD to identify the site of electrostatic interaction in noncovalent complexes

Electrostatic interactions play an important role in the formation of noncovalent complexes. Our previous work has highlighted the role of certain amino acid residues, such as arginine, glutamate, aspartate, and phosphorylated/sulfated residues, in the formation of salt bridges resulting in noncovalent complexes between peptides. Tandem mass spectrometry (MS) studies of these complexes using collision-induced dissociation (CID) have provided information on their relative stability. However, product-ion spectra produced by CID have been unable to assign specifically the site of interaction for the complex. In this work, tandem MS experiments were conducted on noncovalent complexes using both electron capture dissociation (ECD) and electron-transfer dissociation (ETD). The resulting spectra were dominated by intramolecular fragments of the complex with the electrostatic interaction site intact. Based upon these data, we were able to assign the binding site for the peptides forming the noncovalent complex.