Characterization of DNA Intercalator Bound to Calf Thymus DNA：Ionic Strength and pH Value Effects

By means of circular dichroism(CD) spectrum coupled with UV-Vis and fluorescence spectra,the binding model of DNA intercalator A1{4-(2-diethylamino-ethylamino)-8-oxo-8H-acenaphtho[1,2-b]pyrrole-9-carbonitrile} to calf thymus(CT) DNA was investigated,depending on the values of R(R is defined as the ratio of the concentration of A1 to CT DNA base pairs) and different outer factors.Molecules A1 were intercalated into the CT DNA base pairs in different orientations in the intercalation pocket at a lower R value...     

Topologically-Interlocked Minicircles as Probes of DNA Topology and DNA-Protein Interactions

DNA minicircles exist in biological contexts, such as kinetoplast DNA, and are promising components for creating functional nanodevices. They have been used to mimic the topological features of nucleosomal DNA and to probe DNA-protein interactions such as HIV-1 and PFV integrases, and DNA gyrase. Here, we synthesized the topologically-interlocked minicircle rotaxane and catenane inside a frame-shaped DNA origami. These minicircles are 183 bp in length, constitute six individual single-stranded DNAs that are ligated to realize duplex interlocking, and adopt temporary base pairing of single strands for interlocking. To probe the DNA-protein interactions, restriction reactions were carried out on DNAs with different topologies such as free linear duplex or duplex constrained inside origami and free or topologically-interlocked minicircles. Except the free linear duplex, all tested structures were resistant to restriction digestion, indicating that the topological features of DNA, such as flexibility, curvature, and groove orientation, play a major role in DNA-protein interactions.     

用盐酸阿霉素作为嵌入剂石墨电极伏安法识别测定DNA片段的研究

用盐酸阿霉素作为嵌入剂石墨电极伏安法识别测定ＤＮＡ片段的研究方禹之,刘盛辉,何品刚（华东师范大学化学系,上海,２０００６２）关键词ＤＮＡ,嵌入剂,盐酸阿霉素,伏安法核酸分子杂交技术是近年来发展起来的检测ＤＮＡ分子的一种重要手段,目前主要采用的放射性同...     

A Supercharged Fluorescent Protein as a Versatile Probe for Homogeneous DNA Detection and Methylation Analysis

Supercharged proteins are a new class of functional proteins with exceptional stability and potent ability to deliver bio‐macromolecules into cells. As a proof‐of‐principle, a novel application of supercharged proteins as a versatile biosensing platform for nucleic acid detection and epigenetics analysis is presented. Taking supercharged green fluorescent protein (ScGFP) as the signal reporter, a simple turn‐on homogenous method for DNA detection has been developed based on the polyionic nanoscale complex of ScGFP/DNA and toehold strand displacement. This assay shows high sensitivity and potent ability to detect single‐base mismatch. Furthermore, combined with bisulfite conversion, this ScGFP‐based assay was further applied to analyze site‐specific DNA methylation status of genomic DNA extracted from real human colon carcinoma tissue sample with ultrahigh sensitivity (4 amol methylated DNA).     

Multinuclear Non‐Heme Iron Complexes for Double‐Strand DNA Cleavage

Bleomycin mimics : Efficient oxidative double‐strand DNA cleavage has been achieved with multinuclear non‐heme iron complexes (see scheme). These complexes therefore represent model compounds that mimic the mode of action of the anti‐tumor drug bleomycin.

     

Molecular Characterization of DNA Double Strand Breaks with Tip‐Enhanced Raman Scattering

DNA double strand breaks (DSBs) are deadly lesions that can lead to genetic defects and cell apoptosis. Techniques that directly detect DNA DSBs include scanning electron microscopy, atomic force microscopy (AFM), and fluorescence based approaches. While these techniques can be used to identify DSBs they provide no information on the molecular events occurring at the break. Tip‐enhanced Raman scattering (TERS) can provide molecular information from DNA at the nanoscale and in combination with AFM provides a new way to visualize and characterize the molecular structure of DSBs. DSBs result from cleavage at the 3’‐ and 5’‐bonds of deoxyribose upon exposure to UVC radiation based on the observation of P? O? H and methyl/methylene deformation modes enhanced in the TERS spectra. It is hypothesized that strand fragments are hydrogen‐terminated at the lesion, indicating the action of free radicals during photon exposure.     

DOTP versus DOTA as Ligands for Lanthanide Cations: Novel Structurally Characterized CeIV and CeIII Cyclen-Based Complexes and Clusters in Aqueous Solutions

The coordination and redox chemistry of aqueous Ce^IV/III macrocyclic compounds were studied by using the ligands DOTA and DOTP (1,4,7,10-tetraazacyclododecane-1,4,7,10-tetrayl)tetraacetic acid and 1,4,7,10-tetraazacyclododecane-1,4,7,10-tetra(methylene phosphonic acid), respectively). The hydrolysis tendency of the tetravalent cation in the presence of DOTA is shown to result in the formation of a highly ordered, fluorite-like [Ce^IV₆(O)₄(OH)₄(H₂O)₈(DOTAH)₄] oxo-hydroxo structure both in solution and in the solid state. The lifetime of the analogous species formed in the presence of DOTP was found to be much shorter. Spectroscopic measurements of the latter suggest its similarity to the former. Its gradual decomposition in solution leads to the accumulation of the in-cage complexes [Ce^IVDOTP] and [Ce^IIIDOTP(H₂O)], which were crystallographically characterized in this study. The redox energetics and spectroscopic characteristics for the transition between these two in-cage complexes in aqueous solutions were studied as well. Together with the crystallographic structures of the above-mentioned species, the in-cage [Ce^IVDOTA(H₂O)] complex structure is presented herein for the first time. An elaborative analysis of the X-ray crystallographic structural data obtained for the in-cage complexes studied herein and similar structures published previously suggests that hard-bonding cyclen-derived ligands are, counter-intuitively, better suited for encapsulating, and perhaps kinetically stabilize softer cations than harder ones with DOTP, marked as a possible adequate chelator for the study of the aqueous properties of Ln^II and Ac^III cations.     

Templated Formation of Discrete RNA and DNA:RNA Hybrid G‐Quadruplexes and Their Interactions with Targeting Ligands

G‐rich RNA and DNA oligonucleotides derived from the human telomeric sequence were assembled onto addressable cyclopeptide platforms through oxime ligations and copper‐catalyzed azide‐alkyne cycloaddition (CuAAc) reactions. The resulting conjugates were able to fold into highly stable RNA and DNA:RNA hybrid G‐quadruplex (G4) architectures as demonstrated by UV, circular dichroism (CD), and NMR spectroscopic analysis. Whereas rationally designed parallel RNA and DNA:RNA hybrid G4 topologies could be obtained, we could not force the formation of an antiparallel RNA G4 structure, thus supporting the idea that this topology is strongly disfavored. The binding affinities of four representative G4 ligands toward the discrete RNA and DNA:RNA hybrid G4 topologies were compared to the one obtained with the corresponding DNA G4 structure. Surface plasmon resonance (SPR) binding analysis suggests that the accessibility to G4 recognition elements is different among the three structures and supports the idea that G4 ligands might be shaped to achieve structure selectivity in a biological context.     

具有全新机理的DNA旋转酶抑制剂的筛选及抑菌活性

利用具有新机制的抗耐药菌DNA旋转酶抑制剂GSK299423与DNA旋转酶的晶体复合物(PDB code:2XCS)构建基于配体-受体复合物的药效团模型, 诱骗集(Decoy set)验证结果表明该药效团模型具有较强的活性识别能力. 将药效团模型与分子对接相结合用于筛选化合物库, 通过抑菌活性测定, 获得了具有抗多药耐药菌活性的DNA旋转酶抑制剂LTH02.     

Syntheses of bifunctional molecules containing [12]aneN3 and carbazol moieties as effective DNA condensation agents

Bifunctional molecules containing macrocyclic polyamine[12]aneN3 and carbazol units,1 4,have been efficiently synthesized and fully characterized.Through gel electrophoresis,atomic force microscopy,and dynamic light scattering experiments,compounds 3 and 4b bearing both[12]aneN3and carbazol moieties showed effective DNA condensation ability at the concentration of 80μM.Investigations from EB displacement fluorescence spectra,viscosity titration,and ionic strength effects revealed that the effective DNA condensation comes from the appropriate combination of carbazol and[12]aneN3units in the bifunctional molecules,and the DNA condensation process is reversible.The incorporation of triazole units in the molecules clearly reduced the cytotoxicity.     

Novel cyclen-based linear polymer as a high-affinity binding material for DNA condensation

A novel cyclen-based linear polyamine (POGEC) was designed and synthesized from the reaction between 1,3-propanediol diglycidyl ether and 1,7-bis(diethoxyphosphory)-1,4,7,10-tetraazacyclod- odecane. High-affinity binding between POGEC and DNA was demonstrated by agarose gel electrophoresis and scanning electron microscopy (SEM). Moreover, the formed POGEC/DNA complex (termed polyplex) could be disassociated to release the free DNA through addition of the physiological concentration of NaCl solution. Fluorescence spectrum was used to measure the high-affinity binding and DNA condensation capability of POGEC. Circular dichroism (CD) spectrum indicates that the DNA conformation did not change after binding to POEGC. Supported by the National Natural Science Foundation of China (Grant Nos. 20725206 and 20732004), Specialized Research Fund for the Doctoral Program of Higher Education, and Scientific Fund of Sichuan Province for Outstanding Young Scientist     

Initial DNA Interactions of the Binuclear Threading Intercalator Λ,Λ‐[μ‐bidppz(bipy)4Ru2]4+: An NMR Study with [d(CGCGAATTCGCG)]2

Binuclear polypyridine ruthenium compounds have been shown to slowly intercalate into DNA, following a fast initial binding on the DNA surface. For these compounds, intercalation requires threading of a bulky substituent, containing one Ru^II, through the DNA base‐pair stack, and the accompanying DNA duplex distortions are much more severe than with intercalation of mononuclear compounds. Structural understanding of the process of intercalation may greatly gain from a characterisation of the initial interactions between binuclear Ru^II compounds and DNA. We report a structural NMR study on the binuclear Ru^II intercalator Λ,Λ‐B (Λ,Λ‐[μ‐bidppz(bipy)₄Ru₂]⁴⁺; bidppz=11,11′‐bis(dipyrido[3,2‐a:2′,3′‐c]phenazinyl, bipy = 2,2′‐bipyridine) mixed with the palindromic DNA [d(CGCGAATTCGCG)]₂. Threading of Λ,Λ‐B depends on the presence and length of AT stretches in the DNA. Therefore, the latter was selected to promote initial binding, but due to the short stretch of AT base pairs, final intercalation is prevented. Structural calculations provide a model for the interaction: Λ,Λ‐B is trapped in a well‐defined surface‐bound state consisting of an eccentric minor‐groove binding. Most of the interaction enthalpy originates from electrostatic and van der Waals contacts, whereas intermolecular hydrogen bonds may help to define a unique position of Λ,Λ‐B. Molecular dynamics simulations show that this minor‐groove binding mode is stable on a nanosecond scale. To the best of our knowledge, this is the first structural study by NMR spectroscopy on a binuclear Ru compound bound to DNA. In the calculated structure, one of the positively charged Ru²⁺ moieties is near the central AATT region; this is favourable in view of potential intercalation as observed by optical methods for DNA with longer AT stretches. Circular dichroism (CD) spectroscopy suggests that a similar binding geometry is formed in mixtures of Λ,Λ‐B with natural calf thymus DNA. The present minor‐groove binding mode is proposed to represent the initial surface interactions of binuclear Ru^II compounds prior to intercalation into AT‐rich DNA.     

Novel fluorene/fluorenone DNA and RNA binders as efficient non-toxic ds-RNA selective fluorescent probes

A series of structurally similar 1-substitued heteroaryl fluorene derivatives were prepared in a simple single step reaction, oxidized to fluorenones and then both, fluorenes and fluorenones, were methylated to enhance the solubility and increase the affinity to DNA/RNA. Interactions of both, fluorene and fluorenone analogues with various ds-DNA, ds-RNA revealed strong ds-DNA/RNA binding, and various thermal stabilization effects. Most intriguingly, some fluorene derivatives showed opposite fluorescence change (increase for ds-RNA and decrease for ds-DNA), which was not previously reported for any fluorene analogue. CD experiments along with other methods support ds-DNA minor groove binding and major groove ds-RNA binding. All compounds showed negligible interaction with G-quadruplex DNA. Very low cell cytotoxicity of studied compounds combined with very efficient cellular uptake makes these fluorescent dyes safe for laboratory applications. Moreover, especially compounds which show opposite fluorescence response to ds-DNA and ds-RNA, are promising lead compounds for further studies aimed toward ds-RNA-specific fluorescence markers.     

Synthesis,Characterization, DNA Binding Properties,and Antioxidant Activity of Novel Copper(II) and Zinc(II) Complexes with Bis(pyrrol‐2‐yl‐methylamine) Ligands

Three novel ligands H₄Lⁿ (n = 1–3) and their copper(II) and zinc(II) complexes were prepared and characterized on the basis of elemental analyses, molar conductivity, ¹H NMR, UV/Vis, and IR spectroscopy as well as mass spectrometry. DNA binding properties of the ligands and their complexes were investigated by absorption spectroscopy, ethidium bromide displacement experiments, and viscosity measurements. The experimental results indicate that the new ligands and their complexes can bind to DNA and the binding affinities of the complexes are higher than those of the ligands. In addition, the antioxidant activity of the ligands and complexes was determined by superoxide and hydroxyl radical scavenging methods in vitro, indicating that the complexes exhibit more effective antioxidant activity than the ligands alone.     

A Metal–Organic Framework/DNA Hybrid System as a Novel Fluorescent Biosensor for Mercury(II) Ion Detection

Mercury(II) ions have emerged as a widespread environmental hazard in recent decades. Despite different kinds of detection methods reported to sense Hg²⁺, it still remains a challenging task to develop new sensing molecules to replenish the fluorescence‐based apparatus for Hg²⁺ detection. This communication demonstrates a novel fluorescent sensor using UiO‐66‐NH₂ and a T‐rich FAM‐labeled ssDNA as a hybrid system to detect Hg²⁺ sensitively and selectively. To the best of our knowledge, it has rarely been reported that a MOF is utilized as the biosensing platform for Hg²⁺ assay.