Spatially Controllable DNA Condensation by a Water‐Soluble Supramolecular Hybrid of Single‐Walled Carbon Nanotubes and β‐Cyclodextrin‐Tethered Ruthenium Complexes

A supramolecular hybrid is prepared by the supramolecular surface modification of single‐walled carbon nanotube (SWCNT) with cationic β‐cyclodextrin‐tethered ruthenium complexes through a spacer molecule that contains both an adamantane and a pyrene moiety. By employing the supramolecular hybrid, spatially controllable DNA condensation along the SWCNT skeleton is achieved by anchoring cationic ruthenium complexes on the surface. Furthermore, because of the unique physiological properties of SWCNTs, the cationic supramolecular hybrid can be used as a nonviral gene delivery system with the ruthenium complexes as a fluorescent probe to monitor uptake of DNA by cells.     

Quantitative study of stereospecific binding of monoclonal antibody to anti-benzo(a)pyrene diol epoxide-N-dG adducts by capillary electrophoresis immunoassay

The stereospecific binding of monoclonal antibody (mAb) 8E11 to anti-benzo(a)pyrene diol epoxide (BPDE)-dG adducts in single nucleoside, long oligonucleotide, and genomic DNA were quantitatively evaluated using noncompetitive and competitive capillary electrophoresis (CE) immunoassays. Two single-stranded TMR-BPDE-90mers containing a single anti-BPDE-dG adduct with defined stereochemistry and a fluorescent label at 5′-end were used as fluorescent probes for competitive CE immunoassay. To quantitatively evaluate the binding affinity through competitive CE immunoassays, a series of equations were derived according to the binding stoichiometry. The binding of mAb 8E11 to trans-(+)-anti-BPDE-dG displays strongest affinity (K_b: 3.57 × 10⁸ M⁻¹) among all four investigated anti-BPDE-dG mononucleoside adducts, and the cis-(−)-anti-BPDE-dG displays lowest affinity (K_b: 1.14 ×10⁷ M⁻¹). The binding of monoclonal antibody (mAb) 8E11 to BPDE-dG adducts in long DNA (90mer) preferentially forms the complex with a stoichiometry of 1:1, and that mAb 8E11 displays a slightly higher affinity with trans-(+)-anti-BPDE-90mers (K_b: 6.36 ± 0.54 × 10⁸ M⁻¹) than trans-(−)-anti-BPDE-90mers (K_b: 4.52 ± 0.52 × 10⁸ M⁻¹). The mAb 8E11 also displays high affinity with BPDE-dG adducts in genomic DNA (K_b: 3.74 × 10⁸ M⁻¹), indicating its promising applications for sensitive immuno-detection of BPDE-DNA adducts in genomic DNA.     

Parallel Detection of Different DNA Sequences on One Gold Electrode

Motivated by the potential of electrochemical techniques to analyze hybridization events fast and in a simple and cost‐effective way we present here a detection system allowing a parallel electrochemical DNA analysis. For this purpose different probe DNA strands have been immobilized on one electrode. By the use of two different target DNA sequences, both marked with the redox active methylene blue, we can show that hybridization with the complementary probe sh“NA strands can occur without steric hindrance. Each target has been recognized down to 3nM with a very high specificity of the sensor. In addition, we can detect two different ssDNA targets labeled with different redox active molecules, methylene blue and ferrocene, on one sensor surface simultaneously.     

Prediction and analysis of binding affinities for chemically diverse HIV-1 PR inhibitors by the modified SAFE_p approach

One of the biggest challenges in the "in silico" screening of enzyme ligands is to have a protocol that could predict the ligand binding free energies. In our group we have developed a very simple screening function (referred to as solvent accessibility free energy of binding predictor, SAFE_p) which we have applied previously to the study of peptidic HIV-1 protease (HIV-1 PR) inhibitors and later to cyclic urea type HIV-1 PR inhibitors. In this work, we have extended the SAFE_p protocol to a chemically diverse set of HIV-1 PR inhibitors with binding constants that differ by several orders of magnitude. The resulting function is able to reproduce the ranking and in many cases the value of the inhibitor binding affinities for the HIV-1 PR, with accuracy comparable with that of costlier protocols. We also demonstrate that the binding pocket SAFE_p analysis can contribute to the understanding of the physical forces that participate in ligand binding. The analysis tools afforded by our protocol have allowed us to identify an induced fit phenomena mediated by the inhibitor and have demonstrated that larger fragments do not necessarily contribute the most to the binding free energy, an outcome partially brought about by the substantial role the desolvation penalty plays in the energetics of binding. Finally, we have revisited the effect of the Asp dyad protonation state on the predicted binding affinities.     

Applications of polymethacrylate-based monoliths in high-performance liquid chromatography

Monolithic columns were introduced in the early 1990s and have become increasingly popular as efficient stationary phases for most of the important chromatographic separation modes. Monoliths are functionally distinct from porous particle-based media in their reliance on convective mass transport. This makes resolution and capacity independent of flow rate. Monoliths also lack a void volume. This eliminates eddy dispersion and permits high-resolution separations with extremely short flow paths. The analytical value of these features is the subject of recent reviews. Nowadays, among other types of rigid macroporous monoliths, the polymethacrylate-based materials are the largest and most examined class of these sorbents. In this review, the applications of polymethacrylate-based monolithic columns are summarized for the separation, purification and analysis of low and high molecular mass compounds in the different HPLC formats, including micro- and large-scale HPLC modes.     

三核铜(Ⅰ/Ⅱ)配合物[Cu(en)_2]·[Cu(pht)_2]_2的合成、晶体结构及与DNA相互作用的研究

报道了多核铜配合物[Cu(en)_2]·[Cu(pht)_2]_2(Hpht:苯妥英,即5,5-二苯基-2,2-咪唑烷酮;en:乙二胺)的溶剂热合成、晶体结构及其与DNA的相互作用.该晶体属三斜晶系,P_1~-空间群,晶胞参数:a=0.8453(2)nm,b=1.1878(3)nm,c=1.5674(4)nm,a=101.197(3)°,β=97.690(3)°,γ=103.283(3)°,V=1.476(6)nm~3,D_c=1.480 g/cm~3,Z=1,F(000)=679,μ=1.139nm~(-1),R_1=0.0402,wR_2=0.0962[I>2σ(Ⅰ)],GOF=1.035.XPS和X射线单晶衍射数据显示该配合物分子由混价铜组成,包括两个一价铜和一个二价铜,其中每个Cu(Ⅰ)分别与两个苯妥英配体提供的氮原子配位,N-Cu(Ⅰ)-N的夹角为177°,一个Cu(Ⅱ)与六个配位原子配位(CuN_4O_2),形成一个稍变形八面体结构.配合物与DNA相互作用研究表明,该配合物主要是以插入方式与小牛胸腺DNA结合.     

Simple and sensitive fluorometric sensing of malachite green with native double-stranded calf thymus DNA as sensing material

A novel fluorometric sensing of malachite green is proposed in this paper. The native double-stranded calf thymus DNA was used as sensing material. In the presence of native double-stranded calf thymus DNA, malachite green could interact with the DNA, which resulted in a strong fluorescence emission. The fluorescent intensity was linear with malachite green concentration in the range of 4.0 × 10⁻¹⁰ − 1.8 × 10⁻⁷ g ml⁻¹ and the limit of detection was 2.0 × 10⁻¹⁰ g ml⁻¹. Before fluorescence measurement, the only required operation is the mixing of two solutions. So, this method is rather simple and rapid. The method is very safe for the analyst. Furthermore, the mechanism for fluorescence enhancing of native double-stranded calf thymus DNA on MG was proposed based on a series of experiments. The results suggest that the interaction between MG and calf thymus DNA is intercalation in nature.