Effect of mono-/divalent metal ions on the conductivity characteristics of DNA solutions transferring through a microfluidic channel

Interactions between deoxyribonucleic acid(DNA) and metal ions are vital for maintaining life functions, however,there are still unsolved questions about its mechanisms. It is of great practical significance to study these issues for medical chip design, drug development, health care, etc. In this investigation, the conductivity properties of λ-DNA solutions with mono-/divalent metal ions(Na+, K^(+), Mg^(2+), and Ca^(2+)) are experimentally studied as they are electrically driven through a 5 μm microfluidic channel. Experimental data indicate that the conductivities of λ-DNA solutions with metal ions(M+/M2+) basically tend to reduce firstly and then increase as the voltage increases, of which the turning points varied with the metal ions. When the voltage surpasses turning points, the conductivity of λ-DNA-M+solutions increases with the concentration of metal ions, while that of λ-DNA-M^(2+)solutions decrease. Moreover, the conductivity of λ-DNA-M^(2+)solutions is always smaller than that of λ-DNA-M+solutions, and with high-concentration M^(2+), it is even smaller than that of the λ-DNA solution. The main reasons for the above findings could be attributed to the polarization of electrodes and different mechanisms of interactions between metal ions and λ-DNA molecules. This investigation is helpful for the precise manipulation of single DNA molecules in micro-/nanofluidic space and the design of new biomedical micro-/nanofluidic sensors.

Synthesis, Crystal Structure and DNA Binding Studies of a Nickel(II) Complex with 2-Aminomethylbenzimidazole and Demethylcantharate

A new mixed-ligand nickel（Ⅱ） complex, [Ni（L）（DCA）（H2O）]·2H2O （L = C8H9N3, 2-aminomethyl-benzimidazole, DCA2- = 7-oxabicyclo[2,2,1]heptane-2,3-dicarboxylate, demethylcantharate, C8H8O5）, has been synthesized and characterized. The structure of the complex was determined by single-crystal X-ray diffraction. It is of monoclinic system, space group P21/c with a = 7.7211（7）, b = 12.0799（12）, c = 19.7867（19）, β = 100.390（6）°, V = 1815.2（3） nm3, Dc = 1.625 g·cm-3, Ζ = 4, F（000） = 928, R = 0.0314 and wR = 0.0822. In addition, the interaction between the complex and DNA was studied by means of fluorescence spectra and viscosity. The results indicate that the complex binds to DNA by the mode of partial intercalation with the Stern-Volmer constants Ksv of 3.81 × 104 mol·L-1.

Synthesis, Structure, and DNA Binding of a Platinum(Ⅱ) Complex Based on the 3,4,5-Trimethoxy-phenyl-1H-imidazo[4,5-f][1,10]phenanthroline

A new platinum（Ⅱ） complex of [Pt（chda）（3,4,5-triopip）]Cl·2H2O（1） based on 3,4,5-trimethoxy-phenyl-1 H-imidazo[4,5-f][1,10]phenanthroline（3,4,5-triopip） has been synthesized by hydrothermal methods and its consequences are characterized by elemental analysis, IR, single-crystal X-ray diffraction, UV-Vis absorption and fluorescent spectrum. The UV-Vis absorption studies reveal that the molecule undergoes considerable interaction with the nucleic acid. In this mononuclear structure, the platinum adopts a four-coordinated square planar geometry, which may favor the intercalation between the neighboring bases of the G-quadruplex（G4） DNA.

Interaction of DNA with aromatic hydrocarbons fraction in atmospheric particulates of Xigu District of Lanzhou,China

Voluminously epidemiological studies show that the relationships exist between the air pollution and human health and cancer. Aromatic hydrocarbons （AHs） in air form a large class of organic pollutants, which are widely in environment and many of them are known to be carcinogenic and/or mutagenic and contribute to ambient air pollution. In the past decades, bioassays mainly have been used to evaluate the toxicity of chemical mixtures in atmospheric particulates or aqueous environment. However, it is well known that the covalent complexes formed by carcinogens with DNA may be exert negative results in bioassay. So the main aim of this paper is to develop an evaluation method of toxicity effects of chemical mixtures in atmospheric particulates from chemical standpoint. In this study, the in vitro interaction of the AHs with DNA was investigated by absorption, fluorescence and resonance light scattering （RLS） spectroscopic techniques. The results showed that the AHs in the atmospheric particulates could combine with calf thymus DNA （ctDNA） and herring sperm DNA （hsDNA） without being activated or metabolized by organism, respectively. Intercalation may be present in the mechanism of interaction. The binding constants of the AHs with ctDNA and hsDNA were 2.5x102 and 2.0x103, respectively, which indicated that the interaction of the AHs with hsDNA is stronger than that with ctDNA. In addition, the relationships of dose-effect between the total mole concentration of chemical components and the ability of binding ctDNA and hsDNA were confirmed. This research made it possible to study the toxicity effects of chemical mixtures in atmospheric particulates by chemical method. It is believed that the composition and contents of unknown AHs and the interaction of DNA with AHs in atmospheric particulates of Xigu District of Lanzhou City, China are first reported in the past twenty years.

Evidence of DNA-Ligand Binding with Different Modes Studied by Spectroscopy

The binding behavior of several fluorescence dyes to calf thymus DNA has been studied by absorption, fluorescence and atomic force microscopy (AFM), which could provide direct evidence of formation modes and the corresponding nanostructural features of the ligand-DNA complexes.

Synthesis, Crystal Structure and DNA Interaction Study of 3-(2-(3,5-Diphenyl-4,5-dihydropyrazol-1-yl)thiazol-4-yl)-2H-chromen-2-one

A new compound 3-（2-（3,5-diphenyl-4,5-dihydropyrazol-1-yl）thiazol-4-yl）-2Hchromen-2-one was synthesized by cyclocondensation of 3,5-diphenyl-4,5-dihydropyrazole-1-carbothioamide with 3-（2-bromoacetyl）-2H-chromen-2-one in ethanol at reflux for 2hrs. The compound was characterized by IR, 1H-NMR, 13C-NMR and single-crystal X-ray diffraction analysis. The newly synthesized compound（C27H19N3O2S） crystallizes in the triclinic system, space group P1 with a = 5.2476（6）, b = 18.289（2）, c = 23.115（3） , α = 93.546（7）, β = 94.715（6）, γ = 92.347（7）°, V = 2204.3（4）3, Z = 4, Mr = 449.51, crystal size = 0.38 mm × 0.22 mm × 0.16 mm,（I 2σ（I）） = 35317, 9736, 3785, Rint = 0.081,（Δρ）max = 0.19 and（Δρ）min = –0.24 e·-3. DNA interaction studies revealed that the target compound strongly interacts with DNA through an intercalation binding mode and the binding constant of the compound is 7.45 × 104 M-1.

Synthesis,Crystal Structure and DNA Interaction of a Chiral Platinum(Ⅱ)Complex with 2-(2,3-Dimethoxyphenyl)-1H-imidazo[4,5-f][1,10]phenanthroline

A new platinum（Ⅱ） complex of [Pt（chda）（2,3-dmopip）]Cl·H2O（1, chda = cyclohexan-ediamine, 2,3-dmopipH = 2-（2,3-dimethoxyphenyl）-1H-imidazo[4,5-f][1,10]phenanthroline） has been synthesized by hydrothermal methods and characterized by elemental analysis, IR, single-crystal X-ray diffraction, UV-vis and fluorescent spectrum. In complex 1, the platinum adopts a four-coordinated square planar geometry. The DNA-binding interaction has been investigated. The complex can bind to DNA by an intercalative mode, presenting high DNA-binding affinity.

Transcription's bubble under the influence of long-range interactions and helicoidal coupling

The influence of power-low long-range interactions （LRI） and helicoidal coupling （HC） on the properties of localized solitons in a DNA molecule when a ribonucleic acid polymerase （RNAP） binds to it at the physiological temperature is analytically and numerically investigated in this paper. We have made an analogy with the Heisenberg model Hamiltonian of an anisotropic spin ladder with ferromagnetic legs and anti-ferromagnetic rung coupling. When we limit ourselves to the second-order terms in the Taylor expansion, the DNA dynamics is found to be governed by a completely integrable nonlinear Schr？dinger （NLS） equation. In this case, results show that increasing the value of HC force or LRI parameter enhances the bubble height and reduces the number of base pairs which form the bubble. For the fourth-order terms in a Taylor expansion, results are closely resembling those of second-order terms, and are confirmed by numerical investigation. These results match with some experimental data and thus provide a better representation of the base pairs opening in DNA which is essential for the transcription process.

Synthesis,Crystal Structure and Bioactivity of a Pd(Ⅱ) Complex with Demethylcantharate and 2,2′-Bipyridine

A novel crystal with the molecular formula [Pd（DCA）（bipy）]2 [Pd（bipy）Cl2 ]·6.75H2O was formed by PdCl2 with disodium demethylcantharate （Na2 （DCA）,DCA2= 7-oxa-bicyclo[2.2.1]heptane-2,3-bicarboxylate） and 2,2-bipyidine （bipy） through the hydrothermal method.The complex was characterized by elemental analysis and infrared spectroscopy.The structure of the complex was determined by single-crystal X-ray diffraction,which is of triclinic system,space group P1 with a=13.6818（7）,b=14.8426（8）,c=15.0043（8）,α=97.319（3）,β=92.521（3）,γ=105.776（2）°,V=2898.4（3） 3,Dc=1.545 g·cm-3,Z=1,F（000）=1420,S=0.852,the final R=0.0525 and wR=0.1777 for 13634 observer reflections （I〉2σ（I））.The binding reaction of the complex with ct-DNA and bovine serum albumin （BSA） was studied by fluorescence spectroscopy.The results indicated that the complex binds to ct-DNA via the partial intercalation.The binding constant K A of the complex interaction with BSA was 3.98×10 5 L·mol-1 and one binding site would be formed.The antiproliferative activity of the complex against human hepatoma cells （SMMC7721） in vitro is much higher than that of Na 2 （DCA）.

Regulable DNA–Protein Interactions in Vitro and Vivo at Epigenetic DNA Marks

5-Formyluracil(5fU)is a vital DNA marker that is widely distributed in the cells of organisms.A unique feature of 5fU is the possession of a potentially reactive aldehyde group in its structure that could realize addition and condensation reactions.However,the biological functional details of 5fU remain mostly elusive,especially,regarding its relatedness with proteins.In this current study,we show that 5fU bases have a strong affinity toward nucleosome core particles,and that could yield regulable DNA–protein conjugates(DPCs)via chemical interactions between amino and aldehyde groups,and reductants could be applied to stabilize or dissociate the interactions.Besides,we developed a photocaged method to exploit the relationship between 5fU and nucleosomes.Finally,by applying a combination of the existence of 5fU–histone interactions in vivo by ChIP analysis of histone H4 with liquid chromatography–mass spectrometry(LC–MS),we probed further,the DPCs’influence on nucleosome and enzyme.Collectively,our results showed that the 5fU–protein interactions increase the occupancy and stability of nucleosomes,affect enzyme recognition,and block DNA replication.These might imply that,in vivo,the DPCs between 5fU and nucleosome core particles might play a key role in 5fU-associated pathways such as DNA repair,transcriptional regulation,or development.

New DNA probe for studying cell membrane interactions

Subject Code:B05 With the support by the National Natural Science Foundation of China and the US National Institutes of Health,a team led by Dr.Tan Weihong(谭蔚泓)at Hunan University and the University of Florida reported a new DNA probe for studying cell membrane interactions,which was recently published

Synthesis,crystal structures of novel complexes of rare earth with norfloxacin,interaction with DNA and BSA

Three novel rare earth complexes [N（CH 3） 4 ][Ln（NF） 4 ]·6H 2 O（Ln=Nd（III）（1）,Sm（III）（2）,Ho（III）（3）） were synthesized using hydrothermal method from norfloxacin HNF=1-ethyl-6-fluoro-1,4-dihydro-4-oxo-7-（1-piperazinyl）-3-quinoline carboxylic acid,C 16 H 18 FN 3 O 3）,imidazole and rare earth nitrates.The complexes were characterized by elemental analysis,FT-IR,TG-DTG and X-ray single crystal diffraction.Each rare earth ion was eight-coordinated with carboxyl-O atoms and keto-O atoms from norfloxacin.Four of the norfloxacin ions acted as bidentate chelate group took part in the coordination with rare earth ion.The structures of complexes were tetragonal system with space group I4 1 /acd,which were allomerism.The interaction between complex 1 and DNA was studied by electronic absorption spectra and fluorescence spectroscopy.The binding interaction between the complex 1 and bovine serum albumin（BSA） was studied by fluorescence spectroscopy.The complex 1 bound to DNA by the mode of partial intercalation.Complex 1 had a strong ability to quench the fluorescence from BSA.The complex interaction was mainly a static quenching process with BSA together with formation of two binding sites.

Studies on the Interaction of Dinitratobis（phen） Cadmium Complex with DNA

DNA-binding properties of the dinitratobis（phen） cadmium complex [Cd（phen）2（NO3）2] （where phen = 1,10-phenanthroline） have been investigated with absorption titration, fluorescence spectroscopy, viscosity measurement, molecular modeling and density functional theory （DFT） calculations. The results indictate DNA-binding mode of the complex to be weak groove binding rather than partial intercalative interaction expected of the extended planar aromatic phen ring. In addition, the DNA cleavage study was carried out by gel electrophoresis experiment. The results showed that the complex both hardly cleaves pBR322 DNA in the absence and present ascorbate. So it is suggested that the formation of cadmium complex can decrease cadmium toxicity to some extents.

Characterization, Crystal Structure and Initial DNA Binding Interaction of Two Cu（Ⅱ） Complexes with 4,5-Diazafluoren-9-one

Two new complexes [Cu（dafo）2（en）]（ClO4）2·2H2O （en=NH2CH2CH2NH2） 1 and [Cu（dafo）2（dap）]（ClO4）2·2H2O [dap=NH2CH2CH（CH3）NH2] 2 （dafo=4,5-diazafluoren-9-one） have been synthesized and characterized by elemental analysis, IR and UV spectra. Meanwhile, the complex 1 has been characterized by single crystal X-ray diffraction analysis. The initial DNA binding interactions of the complexes 1 and 2 have been investigated by UV spectra, emission spectra and cyclic voltammogram. Concluding the results of three methods used to measure the interaction of complexes 1 and 2 with DNA, the action mode of the two complexes with DNA is intercalation, and character of ligands and steric effect may affect the interaction of the complexes with DNA.

lncRInter:A database of experimentally validated long non-coding RNA interaction

Non-coding regions are the major component of human genomes and the long non-coding RNA（IncRNA）is a class of pervasive genes located in noncoding regions（Morris and Mattick,2014）.IncRNAs play a wide range of regulatory roles in gene transcription,translation,epigenetic modification and protein function by interacting with different types of molecules including DNA,