新型咪唑并邻菲罗啉衍生物对人端粒G-四链体相对于双螺旋DNA的选择性识别

G-四链体DNA是抗肿瘤药物研究开发的重要靶点,选择性识别并稳定G-四链体DNA的化合物是潜在的抗肿瘤药物.文章利用紫外可见吸收滴定,荧光滴定,CD光谱以及荧光共振能量转移熔点实验(FRET-melring)研究了三个基于邻菲罗啉的新型衍生物(A,B和C)与人端粒G-四链体DNA的相互作用.结果表明三个化合物通过末端堆积方式与G四链体DNA相互作用,结合常数(K)约为106 mol-1·L.当浓度为3 μmol·L-1时,化合物A,B和C分别使G四链体DNA熔点温度增加(△Tm)16.2,10.5和10.9℃.而且在10倍过量双螺旋DNA存在下均能选择性识别并稳定G-四链体结构.     

药根碱与DNA G-四链体的相互作用研究

DNA单链(PS2.M)在K~+存在下可被诱导形成G-四链体。文章利用圆二色谱(CD)以及核磁共振光谱(NMR)表征了G-四链体的形成,并通过荧光滴定光谱、紫外滴定光谱以及核磁共振光谱研究了盐酸药根碱与G-四链体的相互作用。加入G-四链体后,药根碱在530nm处的荧光明显增强;紫外吸收光谱表现出减色和红移现象,说明药根碱可能堆积到G-四链体的尾部或者插入到G-四链体尾部的两个G-四分体之间形成夹心结构。由等摩尔连续变化法算出药根碱和DNA的结合比为1∶1,利用Scatchard方程计算出二者的结合常数为3.12×10~6 L/mol、结合位点为0.98。实验表明:盐酸药根碱与G-四链体有很强的相互作用,药根碱可以稳定DNA的G-四链体结构,二者的作用模式可能为末端堆积。     

呫吨酮衍生物的合成及与G-四链体作用的研究

以邻羟基苯甲酸和间苯三酚为原料,通过一步法合成了1,3-二羟基咕吨酮,再经醚化、取代、季铵化反应得到化合物d,用IR、NMR、MS、元素分析等进行结构测定和表征,利用圆二色(CD)光谱和变温紫外-可见(UV-Vis)光谱研究了化合物d与G-四链体DNA的相互作用.CD光谱表明化合物d能诱导端粒DNA片段d[G3(T2AG3)3]形成反平行型的G-四链体结构;变温UV-Vis光谱显示化合物d使相应G-四链体DNA的Tm们值增加约6℃,表明化合物d同时起到稳定G-四链体的作用.     

邻菲罗啉衍生物与人端粒G-四链体DNA的相互作用及细胞活性研究

通过紫外可见吸收滴定,荧光滴定和聚合酶链反应停止分析(PCR stop assay)方法研究了3个邻菲罗啉衍生物1-3与人端粒G-四链体DNA在包含100mmol·L-1 KCl的磷酸缓冲体系中的相互作用,并用MTT法研究了化合物对人肝癌细胞HepG2增殖的影响.结果表明:这三个化合物都能与G-四链体相互作用并显著稳定其结构,结合常数约为1×106 mol-1·L;同时这些化合物能在微摩尔浓度抑制HepG2细胞增殖.     

多芳基咪唑CPD的合成及与G-四链体相互作用研究

以4-氟苯甲醛为起始原料，通过安息香缩合反应、氧化反应、亲核取代反应以及Debus-Radziszewski咪唑合成反应等步骤，合成得到了多芳基咪唑CPD.¹H NMR、¹³C NMR和HRMS确证其结构.紫外光谱实验和荧光光谱实验研究表明CPD对部分G-四链体具有一定的荧光识别作用，特别是可以识别c-myc G-四链体.单链DNA、双链DNA均不能使CPD的荧光产生增强，表现出较好的选择性.分子对接结果表明：CPD能堆积在G-四分体上，两条胺基侧链深入到G-四链体的负电性沟槽中，发生静电吸引作用，导致原有的分子构象发生变化，因而发射出荧光.     

双核钌配合物与c-myc G-四链体DNA的键合性能

通过紫外可见吸收光谱和荧光光谱滴定、Job plot、圆二色光谱、聚合酶链式扩增反应(PCR)、显色反应以及FRET实验,研究了苯酚基双核钌配合物与c-myc G-四链体DNA(c-myc Pu27和c-myc Pu22)之间的相互作用. 结果表明,配合物对c-myc Pu27和c-myc Pu22 DNA都有较强结合,键合常数分别为6.21 × 10⁷ L/mol 和2.33×10⁶ L/mol,键和模式为沟槽结合,键合物质的量比为2∶1;配合物在浓度为4 μmol/L(c-myc Pu27)、6 μmol/L(c-myc Pu22)时,可完全抑制PCR扩增产物生成,表明其能够诱导c-myc DNA形成G-四链体结构. 此外,配合物可使F27T和F22T的熔解温度分别升高13 ℃和12 ℃,且在双链DNA存在时F27T和F22T的熔解温度几乎没有变化,表明其对c-myc G-四链体DNA具有显著的稳定性及选择性.     

基于分子生物技术的DNA计算系统

为解决DNA计算模型随机初始化过程存在的问题,提出数据初始化模型,保证了初始数据的完整性,减少了计算过程中参与筛选的DNA链的数量,提高了计算精度。针对生物实验反应时间较长,活性DNA材料成本高的现状,开发了仿生DNA计算系统,通过仿真实验解决了哈密顿问题。     

利用过氧化物模拟酶催化化学发光法检测钾离子

K+存在时,富含鸟嘌呤(Guanine)的特定序列单链DNA会发生构象变化形成G-四联体结构,从而能够与氯化血红素(hemin)结合生成具有过氧化物酶活性的模拟酶,对鲁米诺-H2O2化学发光体系具有强的催化作用.据此,提出了利用G-四联体-hemin-鲁米诺-H2O2化学发光体系测定K+的新方法.探讨了DNA浓度,he...     

人体细胞中发现四螺旋DNA结构

据物理学家组织网近日报道，DNA双螺旋结构早已为人熟知，而英国剑桥大学科学家21日在《自然一化学》杂志上发表的论文显示，四螺旋DNA结构，即G-四联体同样存在于人类基因组中。它们形成的区域具有丰富的乌嘌呤基础构件，因此通常缩写为“G”。     

核糖核苷酸还原酶研究

核糖核苷酸还原酶广泛存在于各种生物中,是生物体内唯一的催化4种核糖核苷酸还原、生成相应的脱氧核糖核苷酸的酶。该酶是DNA合成和修复的关键酶和限速酶,对细胞的增殖和分化起着调控作用。不同生物中的RR根据其结合的金属辅助因子不同而分类。虽然不同类型RR之间的氨基酸序列相似性很低,但它们有十分相似的三级结构的活性中心和相同的催化功能。RR分子中包含2个变构位点,即酶活性中心和底物特异结合位点。活性中心通过生物有机自由基的作用催化核糖核苷酸还原;底物特异结合位点通过变构作用调控4种dNTPs在细胞内的平衡。因此,该酶不仅是研究DNA合成与修复、细胞增殖与分化及癌症的治疗与抗癌药物开发的重要靶点,同时也是研究酶的结构与功能以及酶的催化机理等的重要工具。本文总结了该酶的种类与分布、结构特征、催化机理及作为抗癌药物开发靶点等方面的研究进展。     

Circular dichroism spectroscopic studies on structures formed by telomeric DNA sequences in vitro

Telomere plays an important role in cellular processes, such as cell aging, death and carcinogenisis. Having special sequences, it can form quadruplex structure in vitro. Circular dichroism (CD) spectroscopic studies show that TTAGGG, (TTAGGG)2 and (TTAGGG)4 can all form quadruplex in vitro and exist mainly as parallel quadruplex without metal ions. Both K+ and Na+ can stabilize the tetrameric structure and facilitate the forming of anti-parallel conformation. Furthermore, the conformations of quadruplex can also be affected by sequence length, the nature and concentration of metal ions.     

电化学研究亚甲蓝与DNA的相互作用

The interaction of small molecules with DNA is of interest because it is important in the design of new and more efficient drugs targeted to DNA. The metal complexes, natural antibiotics, and a lot of other planar heterocyclic cations, have been investigated for their DNA     

Circular dichroism spectroscopic studies on structures formed by telomeric DNA sequencesin vitro

Telomere plays an important role in cellular processes, such as cell aging, death and carcinogenisis. Having special sequences, it can form quadruplex structurein vitro. Circular dichroism (CD) spectroscopic studies show that TTAGGG, (TTAGGG)₂ and (TTAGGG)₄ can all form quadruplexin vitro and exist mainly as parallel quadruplex without metal ions. Both K⁺ and Na⁺ can stabilize the tetrameric structure and facilitate the forming of anti-parallel conformation. Furthermore, the conformations of quadruplex can also be affected by sequence length, the nature and concentration of metal ions.     

Crystal structure of parallel quadruplexes from human telomeric DNA

Telomeric ends of chromosomes, which comprise noncoding repeat sequences of guanine-rich DNA, are fundamental in protecting the cell from recombination and degradation. Disruption of telomere maintenance leads to eventual cell death, which can be exploited for therapeutic intervention in cancer. Telomeric DNA sequences can form four-stranded (quadruplex) structures, which may be involved in the structure of telomere ends. Here we describe the crystal structure of a quadruplex formed from four consecutive human telomeric DNA repeats and grown at a K(+) concentration that approximates its intracellular concentration. K(+) ions are observed in the structure. The folding and appearance of the DNA in this intramolecular quadruplex is fundamentally different from the published Na(+)-containing quadruplex structures. All four DNA strands are parallel, with the three linking trinucleotide loops positioned on the exterior of the quadruplex core, in a propeller-like arrangement. The adenine in each TTA linking trinucleotide loop is swung back so that it intercalates between the two thymines. This DNA structure suggests a straightforward path for telomere folding and unfolding, as well as ways in which it can recognize telomere-associated proteins.     

Quadruplex structure of Oxytricha telomeric DNA oligonucleotides.

The telomeres of most eukaryotes contain a repeating G-rich sequence with the consensus d(T/A)1-4G1-8, of which 12-16 bases form a 3' single-strand overhang beyond the telomeric duplex. It has been proposed that these G-rich oligonucleotides associate to form four-stranded structures from one, two or four individual strands and that these structures may be relevant in vivo. The proposed structures contain Hoogsteen base-paired G-quartets, precedent for which has been in the literature for many years. Here we use 1H NMR spectroscopy to study the conformations of the DNA oligonucleotides d(G4T4G4) (Oxy-1.5) and d(G4T4G4T4G4T4G4) (Oxy-3.5) which contain the Oxytricha telomere repeat (T4G4). We find that these molecules fold to form a symmetrical bimolecular and an intramolecular quadruplex, respectively. Both structures have four G-quartets formed from nucleotides that are alternately syn and anti along each strand. This arrangement differs from earlier models in which the strands are alternately all syn or all anti. The T4 loops in Oxy-1.5 are on opposite ends of the quadruplex and loop diagonally across the G-quartet, resulting in adjacent strands being alternately parallel and antiparallel.     

Telomeric DNA dimerizes by formation of guanine tetrads between hairpin loops

The telomeric ends of eukaryotic chromosomes are composed of simple repeating sequences in which one DNA strand contains short tracts of guanine residues alternating with short tracts of A/T-rich sequences. The guanine-rich strand is always oriented in a 5'-3' direction towards the end of the chromosome and is extended to produce a 3' overhang of about two repeating units in species where the telomeric terminus is known. This overhang has been implicated in the formation of several unusual intra-and intermolecular DNA structures, although none of these structures has been characterized fully. We now report that oligonucleotides encoding Tetrahymena telomeres dimerize to form stable complexes in solution. This salt-dependent dimerization is mediated entirely by the 3'-terminal telomeric overhang (TT-GGGGTTGGGG) and produces complexes in which the N7 position of every guanine in the overhangs is chemically inaccessible. We therefore propose that telomeric DNA dimerizes by hydrogen bonding between two intramolecular hairpin loops, to form antiparallel quadruplexes containing cyclic guanine base tetrads. These novel hairpin dimers may be important in telomere association and recombination and could also provide a general mechanism for pairing two double helices in other recombinational processes.     

Newly replicated DNA is associated with DNA topoisomerase II in cultured rat prostatic adenocarcinoma cells

DNA topoisomerases have been proposed to function in a variety of genetic processes in both prokaryotes and eukaryotes. Here, we have assessed the role of DNA topoisomerase II in mammalian DNA replication by determining the proximity of newly synthesized DNA to covalent enzyme-DNA complexes generated by treating cultured rat prostatic adenocarcinoma cells with teniposide. Teniposide (VM-26), an epipodophyllotoxin, is known to interact with mammalian DNA topoisomerase II so as to trap the enzyme in a covalent complex with DNA. We have found that the teniposide-induced trapping of such complexes requires MgCl2, is stimulated by ATP and is inhibited by novobiocin. The formation of covalent complexes seems to be reversible on removal of teniposide. Furthermore, analysis of the covalent complexes formed between 3H-thymidine pulse-labelled DNA and topoisomerase II following teniposide treatment reveals a direct association of the enzyme with nascent DNA fragments. Our results suggest that DNA topoisomerase II may interact with newly replicated daughter DNA molecules near DNA replication forks in mammalian cells.     

Measurement of anomalously high hydration of (dA)n.(dT)n double helices in dilute solution

Different DNA sequences have different physical properties, which seem to be important for their biological function. In particular, (dA)n.(dT)n has many unusual features, which include resistance to conformational changes in a variable chemical environment, an unusual thermodynamics of interaction with ligands, and the inability to reassociate into nucleosomes. Short A.T base-pair runs also play a critical role in DNA bending. It is believed that hydration of DNA is an important factor in determining the physical chemical and biological properties of different regions of DNA. Until now, however, it has not been possible to study the details of the hydration of DNA in dilute solution with sufficient sensitivity and precision. Moreover, it was not known if different base sequences differ in the extent of their hydration. Indirect evidence that (dA)n.(dT)n can be hydrated to a greater extent than other DNA sequences may be inferred from a recent study of the binding of drugs to polynucleotides. Here we used a novel high-precision technique measuring ultrasonic velocity to obtain direct estimates of the extent of hydration of various oligo- and polynucleotides in dilute solution. We report that different DNA sequences differ in their hydration, and that (dA)n.(dT)n in particular has an anomalously high level of hydration.     

金属离子与DNA碱基对间相互作用的理论研究

在B3LYP 6-31G(d,p)水平,全优化Li+、Na+、K+、Cu+、Mg2+、Ca2+、Cu2+、Zn2+、Cd2+、Ba2+、Hg2+(Cd2+、Ba2+和Hg2+用有效实势(ECP)方法处理)与鸟嘌呤(G)-胞嘧啶(C)碱基对配合物的气相结构,通过相互作用能和能量分解分析得出配合物的稳定性顺序和内在规律以及其作用机制和影响因素;后采用Onsager模型,计算在水溶液(ε=78.39)中的单点能量,讨论溶剂效应对各配合物相互作用能及各能量分解项的影响.通过分析表明主族金属离子与GC碱基对间的作用以静电相互作用为主,而副族金属离子与GC对间相互作用中共价作用的成份较大,甚至还可能占主导作用,这可能是配合物间性质及变化规律差异的根源.电荷布居及轨道分析结果均与上述结论一致.     

Direct measurement of electrical transport through DNA molecules

Attempts to infer DNA electron transfer from fluorescence quenching measurements on DNA strands doped with donor and acceptor molecules have spurred intense debate over the question of whether or not this important biomolecule is able to conduct electrical charges. More recently, first electrical transport measurements on micrometre-long DNA 'ropes', and also on large numbers of DNA molecules in films, have indicated that DNA behaves as a good linear conductor. Here we present measurements of electrical transport through individual 10.4-nm-long, double-stranded poly(G)-poly(C) DNA molecules connected to two metal nanoelectrodes, that indicate, by contrast, large-bandgap semiconducting behaviour. We obtain nonlinear current-voltage curves that exhibit a voltage gap at low applied bias. This is observed in air as well as in vacuum down to cryogenic temperatures. The voltage dependence of the differential conductance exhibits a peak structure, which is suggestive of the charge carrier transport being mediated by the molecular energy bands of DNA.