Substituent effects on the binding of ethidium and its derivatives to natural DNA

The binding of eight ethidium derivatives to short (approximately 35 base-pair), random sequence DNA has been investigated using 1H-NMR. At 35 degrees C, all drugs cause upfield shifts of the DNA imino proton resonances characteristic of intercalative binding to DNA, but the line shapes vary significantly with the nature of the drug. The results confirm our previous proposal that removal of the amino group at position-3, but not at position-8, on the parent ethidium shortens the lifetime of the intercalative state (less than 1-2 ms at 35 degrees C). These results suggest that hydrogen-bonding interactions with the 3-NH2 group are involved in stabilization of the drug-DNA complex or that changes in charge distribution that accompany removal of the 3-NH2 group reduce the complex stability. The magnitude of the shift of the drug-DNA spectra indicates a slight preference for binding of the drugs adjacent to G X C base-pairs.     

机械阻断神经管的闭合影响爪蟾神经管辐射状切入及神经嵴细胞定向迁移(英文)

神经管闭合缺陷 (NTDs)是一种严重的先天畸形疾病,在新生儿中有千分之一的发病率。神经管融合前后,多种组织参与形态发生运动。神经管一经融合,神经嵴细胞就会向背侧中线方向产生单极突出并向此方向迁移形成神经管的顶部。与此同时,神经管从腹侧开始发生辐射状切入以实现单层化。在此,我们在非洲爪蟾的移植体中机械阻断神经管的闭合以检测其细胞运动及随后的图式形成。结果显示神经管闭合缺陷的移植体不能形成单层化的神经管,并且神经嵴细胞滞留在侧面区域不能向背侧中线迁移,而对神经前体标记基因的检测显示神经管的背腹图式形成并未受到影响。以上结果表明神经管的融合对于辐射状切入和神经嵴细胞向背侧中线方向的迁移过程是必需的,而对于神经管的沿背腹轴方向的图式形成是非必需的。     

Direct electron transfer of hemoglobin in layered alpha-zirconium phosphate with a high thermal stability

A heme protein hemoglobin (Hb) was reacted with preexfoliated layered alpha-zirconium phosphate (alpha-ZrP) platelets. An X-ray diffraction (XRD) pattern of small range showed that the exfoliated alpha-ZrP platelets reassembled after the addition of Hb molecules, with the protein intercalated between the layers. UV-Vis and Fourier transform infrared (FTIR) spectra analysis displayed that no significant denaturation occurred to the intercalated protein. The bioactivity of Hb was also investigated by testing the electrochemical properties of the Hb/alpha-ZrP composite. Results showed that the intercalation of Hb into the layered material not only improved the thermal stability of Hb but also enhanced the direct electron transfer ability between protein molecules and electrode. The protein still showed bioactivity after treatment at a temperature as high as 85 degrees C. A pair of well-defined redox peaks at approximately -0.37 and -0.32V was observed on the cyclic voltammograms (CVs) of the Hb/alpha-ZrP composite modified electrode, and the electrode reactions showed a surface-controlled process with a single proton transfer. The resultant biosensor constructed by the Hb/alpha-ZrP composite displayed an excellent response to the reduction of hydrogen peroxide (H(2)O(2)) with good reproducibility.     

Crystal structure of chartreusin derivative A132

The crystal structure of chartreusin derivative A132 (benzilidene chartreusin) has been determined by single-crystal X-ray diffraction. The space group is C2 with unit cell dimensions, a=18.482(4), b=8.749(3), c=43.906(2) A, beta=94.87(2) degrees, and the structure was refined to R-factors of 0.2365 (6585 all unique reflections) and 0.087 (2914 reflections with F(o)>4 sigma(F(o))) by a full-matrix least-squares method. There are two molecules in an asymmetric unit. Both molecules have similar structures, which are favorable to bind with DNA in the minor groove. A modeling study of the A132-DNA complex based on the X-ray structures suggests that the sugar moiety of A132 may play an important role in recognizing the sequence of DNA base pairs.     

NB-506, an indolocarbazole topoisomerase I inhibitor, binds preferentially to triplex DNA

A novel competition dialysis method was used to study the structural selectivity of the nucleic acid binding of NB-506, a promising indolocarbazole anticancer agent. A pronounced preference for NB-506 binding to the DNA triplex poly [dA]:(poly[dT])(2) was observed among potential binding to 12 different nucleic acid structures and sequences. Structures included in the assay ranged from single-stranded DNA, through a variety of right-handed DNA duplexes, to multistranded triplex and tetraplex forms. RNA and left-handed Z DNA were also included in the assay. The preferential binding to triplex was confirmed by UV melting experiments. The novel and unexpected structural selectivity shown by NB-506 may arise from a complementary shape between its extended aromatic ring system and the planar triplex stack.     

Two closely related nickel complexes have different effects on DNA damage and cell viability

Nickel is considered a weak carcinogen. It is known to interact with DNA and DNA-binding proteins. The ability of certain nickel compounds to cleave DNA has been exploited mainly for research purposes and less for developing new anticancer drugs. Here we compare the interactions of two closely related nickel complexes, [NiCR]2+ and [Ni(CR-2H)]2+, with DNA. CR stands for 2,12-dimethyl-3,7,11,17-tetraazabicyclo-[11.3.1]-heptadeca-1(17),2,11,13,15-pentaene. [NiCR]2+ has been used in the past as a structure-specific probe for RNA and DNA oligonucleotides in the presence of oxidizing agent but little is known about the biological effects of either complex. Our results show that [Ni(CR-2H)]2+ can damage DNA in vivo and in vitro in the absence of an added oxidizing agent and has an IC50 of 70 microM in human breast cancer cells whereas [NiCR]2+ and NiCl2 do not exhibit significant cytotoxicity. However, both [NiCR]2+ and [Ni(CR-2H)]2+ bind to the minor groove of double-stranded DNA.     

Structure analysis of hydrotalcite intercalated with pyrenetetrasulfonate; experiments and molecular modelling

The structure of pyrenetetrasulfonate intercalated with hydrotalcite, having the formula [Zn_0.68Al_0.32(OH)₂][(C₁₆H₆O₁₂S₄)_0.08 · x H₂O], was proposed based on molecular simulations combined with experimental data (X-ray powder diffraction, thermogravimetry). Calculations were done for samples kept at various relative humidities (0%, 84%, 98%). The appropriate models were selected from comparison of calculated and measured diffraction patterns. Modelling revealed the arrangement of pyrenetetrasulfonate anions, and the positions and the amount of water molecules in the interlayer space of the host structure. The results confirmed a large variability in the arrangement of the guest species. In the sample without water molecules (0% RH), pyrenetetrasulfonate anions formed a layer at the centre of the interlayer distance. For the sample kept at 84% RH, the anions formed two layers at the thirds of the interlayer. For the sample kept at 98% RH, the anions became tilted with respect to the layered double hydroxides (LDH) layers and are less organised. Water molecules were arranged in three distinct planes: one in the middle and two at the quarters of interlayer distance. The number of water molecules obtained by the modelling basically agrees with the water content as measured by thermogravimetry. Figure Pyrenetetrasulfonate was intercalated into hydrotalcite and equilibrated at various relative humidities. Structural analysis was performed using molecular simulations based on X-ray and thermogravimetric data     

Addressing the problems of base pairing and strand cyclization in template-directed synthesis: a case for the utility and necessity of 'molecular midwives' and reversible backbone linkages for the origin of proto-RNA

Nucleic acid synthesis is precisely controlled in living organisms by highly evolved protein enzymes. The remarkable fidelity of information transfer realized between template and product strands is the result of both the spatial selectivity of the polymerase active site for Watson-Crick base pairs at the point of nucleotide coupling and subsequent proof-reading mechanisms. In the absence of naturally derived polymerases, in vitro template-directed synthesis by means of chemically activated mononucleotides has proven remarkably inefficient and error-prone. Nevertheless, the spontaneous emergence of RNA polymers and their protein-free replication is frequently taken as a prerequisite for the hypothetical 'RNA world'. We present two specific difficulties that face the de novo synthesis of RNA-like polymers in a prebiotic (enzyme-free) environment: nucleoside base selection and intramolecular strand cyclization. These two problems are inherent to the assumption that RNA formed de novo from pre-existing, chemically-activated mononucleotides in solution. As a possible resolution to these problems, we present arguments and experimental support for our hypothesis that small molecules (referred to as 'molecular midwives') and alternative backbone linkages (under equilibrium control) facilitated the emergence of the first RNA-like polymers of life.