Continuing damage to rat retinal DNA during darkness following light exposure

The damaging effects of visible light on the mammalian retina can be detected as functional, morphological or biochemical changes in the photoreceptor cells. Although previous studies have implicated short-lived reactive oxygen species in these processes, the termination of light exposure does not prevent continuing damage. To investigate the degenerative processes persisting during darkness following light treatment, rats were exposed to 24 h of intense visible light and the accumulation of DNA damage to restriction fragments containing opsin, insulin 1 or interleukin-6 genes was measured as single-strand breaks (ssb) on alkaline agarose gels. With longer dark treatments all three DNA fragments showed increasing DNA damage. Treatment of rats with the synthetic antioxidant dimethylthiourea prior to light exposure reduced the initial development of alkali-sensitive strand breaks and allowed significant repair of all three DNA fragments. The time course of double-strand DNA breaks was also examined in specific genes and repetitive DNA. Nucleosomal DNA laddering was evident immediately following the 24 h light treatment and increased during the subsequent dark period. The increase in the intensity of the DNA ladder pattern suggests a continuation of enzymatically mediated apoptotic processes triggered during light exposure. The protective effects of antioxidant suggests that the light-induced DNA degradative process includes both early oxidative reactions and enzymatic processes that continue after cessation of light exposure.     

Modified DNA aptamer that binds the (R)-isomer of a thalidomide derivative with high enantioselectivity

A thalidomide-binding aptamer was produced by systematic evolution of ligands by exponential enrichment from a library of non-natural DNA in which thymidine had been replaced with a modified deoxyuridine bearing a cationic functional group via a hydrophobic methylene linker at the C5 position. The additional functional group in the modified DNA aptamer could improve stability against nucleases and increase the binding affinity to thalidomide. The selected aptamer could recognize thalidomide enantioselectively, although a racemic thalidomide-attached gel was used for the selection. Surface plasmon resonance and fluorescence titration studies revealed that the selected modified DNA aptamer and a truncated version bound with an (R)-thalidomide derivative with high enantioselectivity, but not with the (S)-form. The modified group in the DNA aptamer is indispensable for the interaction with thalidomide, as the corresponding natural type DNA bearing the same base sequence showed no binding affinity with (R)- nor (S)-thalidomide. Computational sequence analysis suggested that the selected apatamer (108 mer) could fold into a three-way junction structure; however, truncation of this aptamer (31 mer) revealed that the thalidomide-binding site is a hairpin-bulge region that is a component of one of the arms of the three-way junction structure. The Kd value of the truncated 31 mer aptamer for binding with the (R)-thalidomide derivative was 1.0 microM estimated from fluorescence titration study. The aptamer that can recognize a single enantiomer of thalidomide will be useful as a biochemical tool for the analysis and study of the biological action of thalidomide enantiomers.     

Stability and selectivity of unnatural DNA with five-membered-ring nucleobase analogues

In an effort to develop an orthogonal third base pair for the storage of genetic information, thiophene and furan heterocycles have been examined as nucleobase analogues. The stability of the unnatural bases was evaluated in duplex DNA paired opposite other unnatural bases as well as opposite the natural bases. Several unnatural base pairs are identified that are both reasonably stable and strongly selective against mispairing with native bases. These results expand the potential nucleobase analogues with which the genetic alphabet may be expanded to include five-membered-ring heterocycles.     

空壳纳米金修饰的新型DNA传感器

利用新型材料金纳米空球, 通过层层修饰的技术, 分别将壳聚糖、空壳纳米金、L-半胱氨酸、细胞色素c以及ssDNA探针修饰到玻碳电极表面, 制备了一种新型的DNA生物传感器. 以紫外及透射电子显微镜(TEM)表征了空壳纳米金, 以循环伏安法、阻抗谱图等电化学方法研究了传感器的特性, 通过原子力显微镜方法观察了该DNA生物传感器不同层之间的形态差异. 结果表明, 该修饰电极所吸附的ssDNA探针为1.672×10^―10 mol•cm^－2. 在指示剂柔红霉素的帮助下, DNA探针可与互补的DNA进行杂交, 借此以微分脉冲伏安法测定DNA.     

A ruthenium nitrosyl that rapidly delivers NO to proteins in aqueous solution upon short exposure to UV light

Two Ru(III) complexes, [Ru(PaPy(3))(Cl)](BF(4)) (2) and [Ru(PaPy(3))(NO)](BF(4))(2) (3) (PaPy(3)H = N,N'-bis(2-pyridylmethyl)amine-N-ethyl-2-pyridine-2-carboxamide), have been synthesized and characterized by spectroscopy and X-ray diffraction. Nitrosyl complex 3 has been prepared by passage of purified NO gas to the hot methanolic solution of the chloro derivative 2. Complex 3 exhibits nu(NuOmicron) stretching frequency at 1899 cm(-)(1) indicating a [Ru-NO](6) configuration. Clean (1)H NMR spectra of 3 in D(2)O and CD(3)CN confirm the S = 0 ground state. When an aqueous solution of [Ru(PaPy(3))(NO)](BF(4))(2) is exposed to low intensity UV light, it rapidly loses NO and forms [Ru(PaPy(3))(H(2)O)](2+). This reaction can be conveniently used to transfer NO to proteins such as myoglobin (Mb) and cytochrome c oxidase. The NO transfer reaction is clean and occurs upon short exposure to light.     

Aminoethylprolyl peptide nucleic acids (aepPNA): chiral PNA analogues that form highly stable DNA:aepPNA2 triplexes

[formula: see text] The replacement of the glycyl component in the peptide nucleic acid (PNA) backbone by a prolyl unit bearing a nucleobase leads to the aminoethylprolyl (aep) PNAs, which are chiral and cationic. The homooligomeric aepPNA binds to complementary DNA sequences with high affinity and sequence specificity, forming highly stable triplexes.     

Sequencing of antisense DNA analogues by capillary gel electrophoresis with laser-induced fluorescence detection

A method using capillary gel electrophoresis with laser-induced fluorescence detection is described which permits complete sequence determination of antisense DNA analogues of unknown sequence. This method, originally created as a tool to confirm the sequence of antisense oligonucleotides being developed as therapeutic drugs, utilizes data collected under a range of experimental conditions described by the Ogston model as applied to gel electrophoresis. A linear relationship independent of experimental conditions between the relative electrophoretic migration time and the oligonucleotide base number was observed and is shown to be consistent with a simplified version of this model and can be used to facilitate the sequence determination.     

Optically high transparency and light color of organosoluble fluorinated polyamides with bulky xanthene pendent groups

New fluorinated polyamides were prepared directly from a diamine, 9,9‐bis[4‐(2‐trifluoromethyl‐4‐aminophenoxy)phenyl]xanthene ( BTFAPX ) with various aromatic dicarboxylic acid chlorides by low‐temperature polycondensation. The polymers were produced with moderate‐to‐high inherent viscosities of 0.65–1.01 dl/g while the weight‐average molecular weight and number‐average molecular weight were in the range of 69,000–82,000 and 39,000–43,000, respectively. Nearly all the polymers were readily soluble in amide‐type polar aprotic solvents [e.g. N, N‐dimethylacetamide (DMAc) and N‐methyl‐2‐pyrrolidinone], and even in less polar solvents such as dimethyl sulfoxide and pyridine, and afforded transparent, light‐colored, and flexible films upon casting from DMAc solvent. The polymers showed glass transition temperatures between 235 and 284°C, and 10% weight loss temperatures ranging from 495 to 532°C and 476 to 510°C in nitrogen and air, respectively, and char yields higher than 55% at 800°C in nitrogen. All polymers were amorphous and their films exhibited tensile strengths of 64–95 MPa, elongations at break of 6–9%, and tensile moduli of 1.9–2.5 GPa. These polymers had dielectric constants ranging from 3.65 to 4.03 (100 Hz), low‐moisture absorption in the range of 0.56–1.14%, and high transparency with an ultraviolet–visible absorption cut‐off wavelength in the 334–372 nm range. Copyright © 2010 John Wiley & Sons, Ltd.     

Dialing in color with rare earth metals: facile photoluminescent production of true white light

Combining polymeric architectures with metal ions produces hybrid materials with extremely rich properties. We are studying polymers containing terpyridine in the side chain. In this report, the chelation of lanthanide ions, Eu³⁺, Tb³⁺, and Dy³⁺ resulted in metal functionalized copolymers that exhibited excellent emission of red, green, and blue light respectively. The polymer architecture easily allows incorporation of all three colors into the material, which leads to the facile production of true white light in solution or the solid state. Quantum efficiencies for the polymer systems were determined. The white light system had an efficiency of 5%. Various combinations of colors were achieved from the basic RBG colors by simply varying the metal ion ratios in the polymer backbone. This easy tuning of the color makes these systems attractive. Copyright © 2007 John Wiley & Sons, Ltd.     

An efficient RNA-cleaving DNA enzyme that synchronizes catalysis with fluorescence signaling

DNA enzymes are single-stranded DNA molecules with catalytic capabilities that are isolated from random-sequence DNA libraries by "in vitro selection". This new class of catalytic biomolecules has the potential of being used as unique molecular tools in a variety of innovative applications. Here we describe the creation and characterization of an RNA-cleaving autocatalytic DNA, DEC22-18, that uniquely links chemical catalysis with real-time fluorescence signaling capability in the same molecule. A trans-acting DNA molecule, DET22-18, was also developed from DEC22-18 that behaves as a true enzyme with a k(cat) of approximately 7 min(-1)-a rate constant that is the second largest ever reported for a DNA enzyme. It cleaves a chimeric RNA/DNA substrate at the lone RNA linkage surrounded by a closely spaced fluorophore-quencher pair-a unique structure that permits the synchronization of the chemical cleavage with fluorescence signaling. DET22-18 has a stem-loop structure and can be conjugated with DNA aptamers to form allosteric deoxyribozyme biosensors.     

A new Os,Rh bimetallic with O2 independent DNA cleavage and DNA photobinding with red therapeutic light excitation

Many Ru and Os systems display photoactive (3)MLCT states. Systems activated by therapeutic window light in the absence of O(2) remain elusive. [(bpy)(2)Os(dpp)RhCl(2)(phen)](3+) photobinds and photocleaves DNA under red light in an oxygen independent manner, due to molecular design involving one Os chromophore coupled to a photoactive cis-Rh(III)Cl(2) moiety.     

UV-B exposure causes DNA damage and changes in protein expression in northern pike (Esox lucius) posthatched embryos

The ongoing anthropogenically caused ozone depletion and climate change has increased the amount of biologically harmful UV-B radiation, which is detrimental to fish in embryonal stages. The effects of UV-B radiation on the levels and locations of DNA damage manifested as cyclobutane pyrimidine dimers (CPDs), heat shock protein 70 (HSP70) and p53 protein in newly hatched embryos of pike were examined. Pike larvae were exposed in the laboratory to current and enhanced doses of UV-B radiation. UV-B exposure caused the formation of CPDs in a fluence rate-dependent manner, and the CPDs were found deeper in the tissues with increasing fluence rates. UV-B radiation induced HSP70 in epidermis, and caused plausible p53 activation in the brain and epidermis of some individuals. Also at a fluence rate occurring in nature, the DNA damage in the brain and eyes of pike and changes in protein expression were followed by severe behavioral disorders, suggesting that neural molecular changes were associated with functional consequences.     

以乙二胺为手臂分子制备的DNA修饰电极及其伏安性能

Carboxyl was formed on the surface of glassy carbon electrode(GCE) by electrochemical oxidation. Ethylenediamine(En) was used as the arm molecule to link carboxyl with dsDNA using 1-ethyl-3-(3-dimethylaminopropyl)-carbodiimide hydrochloride (EDC) and N- hydroxysuccinimide (NHS) as the activators to prepare dsDNA modified electrode(dsDNA/En/GCE). It was shown that dsDNA couM be covalently immobilized on the surface of GCE. ssDNA modified electrode(ssDNA/En/GCE) was obtained via the thermal denaturation of dsDNA/En/GCE. The dsDNA/En/GCE and ssDNA/En/GCE were characterized by voltammetry with methylene blue(MB) as the indicator. The results indicated that the currents of the redox peaks of MB at ssDNA/En/GCE were larger than those at dsDNA/En/GCE, and the currents of the redox peaks at En/GCE were the smallest. The peak-currents of MB at the DNA modified electrode had good reproducibility after multi-denaturation and hybridization cycles.     

异咯嗪修饰富勒烯-聚丙烯酸的合成及其与DNA的相互作用

利用自由基聚合反应合成了聚丙烯酸修饰的富勒烯(C₆₀-PAA),进一步通过酯化反应将核黄素类似物6,7-二甲基-9-(2’-羟乙基)-异咯嗪(DHIX)与C₆₀-PAA共价连接,得到C₆₀-PAA-DHIX.利用傅立叶红外光谱(FT-IR)、核磁共振氢谱(¹HNMR)、紫外-可见吸收光谱(UV-Vis)、荧光光谱对产物的化学结构进行了表征.循环伏安法表明,C₆₀-PAA-DHIX中富勒烯基团的第一还原电位要高于DHIX基团的第一还原电位.ESR实验表明C₆₀-PAA-DHIX能与N,N-二甲基苯胺发生多步光诱导电子转移反应,即DHIX基团与N,N-二甲基苯胺发生光诱导电子转移生成DHIX负离子自由基(DHIX^-·),DHIX^-·能进一步将电子传递给富勒烯生成富勒烯负离子自由基.DNA熔解曲线、紫外-可见吸收光谱和荧光光谱结果表明,C₆₀-PAA-DHIX通过沟槽结合与CTDNA作用,而C₆₀-PAA与DNA的作用较弱.无氧条件下,C₆₀-PAA-DHIX具有比C₆₀-PAA更强的DNA光损伤能力.     

Identification of nuclear proteins that interact with platinum-modified DNA by photoaffinity labeling

Interactions between cellular proteins and cisplatin-modified DNA are important in determining the anticancer activity of the drug. To develop a general approach for identifying proteins that mediate cellular responses to cisplatin, photoreactive cisplatin analogues having a tethered benzophenone moiety were prepared and used to form the major 1,2-intrastrand platinum-DNA cross-links. Upon irradiation of the platinated DNA dissolved in a HeLa nuclear extract, the appended photolabile benzophenone group generates a highly reactive species that binds irreversibly to cellular proteins that interact with the probe. Several DNA-protein cross-linked adducts were identified that may function in the cellular processing of cisplatin-DNA adducts. Of these, PARP-1 had not previously been demonstrated directly to contact Pt-DNA cross-links in human cells.     

Determination of 1‐Naphthol with Denatured DNA–Modified Pretreated Glassy Carbon Electrode

Abstract

A highly sensitive electrochemical biosensor for the detection of trace amount of 1‐naphthol was designed. Acid‐denatured DNA were immobilized onto the pretreated glassy carbon electrode (GCE(ox)) surface. Two well‐defined oxidation peaks were observed on the denatured DNA‐modified GCE(ox) at about +0.80 V and +1.10 V (vs. Ag/AgCl) in 0.10‐M acetate buffer (pH 5.0). The peak current of the guanine residue decreased with increasing concentration of 1‐naphthol. The optimum experimental conditions for the detection of 1‐naphthol were explored, and the calibration was linear for 1‐naphthol in the range of 1.0×10^?8?1.1×10^?6 M, with a correlation coefficient of 0.998. The limit of detection (LOD) was 5.0×10^?9 M (S/N=3).     

Probing the Binding Requirements of Modified Nucleosides with the DNA Nuclease SNM1A

SNM1A is a nuclease that is implicated in DNA interstrand crosslink repair and, as such, its inhibition is of interest for overcoming resistance to chemotherapeutic crosslinking agents. However, the number and identity of the metal ion(s) in the active site of SNM1A are still unconfirmed, and only a limited number of inhibitors have been reported to date. Herein, we report the synthesis and evaluation of a family of malonate-based modified nucleosides to investigate the optimal positioning of metal-binding groups in nucleoside-derived inhibitors for SNM1A. These compounds include ester, carboxylate and hydroxamic acid malonate derivatives which were installed in the 5′-position or 3′-position of thymidine or as a linkage between two nucleosides. Evaluation as inhibitors of recombinant SNM1A showed that nine of the twelve compounds tested had an inhibitory effect at 1 mM concentration. The most potent compound contains a hydroxamic acid malonate group at the 5′-position. Overall, our studies advance the understanding of requirements for nucleoside-derived inhibitors for SNM1A and indicate that groups containing a negatively charged group in close proximity to a metal chelator, such as hydroxamic acid malonates, are promising structures in the design of inhibitors.     

Ferrocenyl‐Modified DNA: Synthesis,Characterization and Integration with Semiconductor Electrodes

The ferrocenyl‐nucleoside, 5‐ethynylferrocenyl‐2′‐deoxycytidine ( 1 ) has been prepared by Pd‐catalyzed cross‐coupling between ethynylferrocene and 5‐iodo‐2′‐deoxycytidine and incorporated into oligonucleotides by using automated solid‐phase synthesis at both silica supports (CPG) and modified single‐crystal silicon electrodes. Analysis of DNA oligonucleotides prepared and cleaved from conventional solid supports confirms that the ferrocenyl‐nucleoside remains intact during synthesis and deprotection and that the resulting strands may be oxidised and reduced in a chemically reversible manner. Melting curve data show that the ferrocenyl‐modified oligonucleotides form duplex structures with native complementary strands. The redox potential of fully solvated ferrocenyl 12‐mers, 350 mV versus SCE, was shifted by +40 mV to a more positive potential upon treatment with the complement contrary to the anticipated negative shift based on a simple electrostatic basis. Automated solid‐phase methods were also used to synthesise 12‐mer ferrocenyl‐containing oligonucleotides directly at chemically modified silicon <111> electrodes. Hybridisation to the surface‐bound ferrocenyl‐DNA caused a shift in the reduction potential of +34 mV to more positive values, indicating that, even when a ferrocenyl nucleoside is contained in a film, the increased density of anions from the phosphate backbone of the complement is still dominated by other factors, for example, the hydrophobic environment of the ferrocene moiety in the duplex or changes in the ferrocene–phosphate distances. The reduction potential is shifted >100 mV after hybridisation when the aqueous electrolyte is replaced by THF/LiClO₄, a solvent of much lower dielectric constant; this is consistent with an explanation based on conformation‐induced changes in ferrocene–phosphate distances.     

Oxy-peptide nucleic acid with a pyrrolidine ring that is configurationally optimized for hybridization with DNA

Four stereoisomers of oxy-peptide nucleic acids containing ether linkages in the main chain and conformationally-restricted pyrrolidine rings (pyrrolidine-based oxy-PNA = POPNA) were newly synthesized and investigated for binding to DNA. cis-l-POPNA with 9 adenine bases formed the most stable hybrid with dT(9). The POPNA showed high sequence specificity similar to that of the Nielsen-type PNA and sharper melting behavior in hybridization with DNA than the Nielsen-type PNA.     

Label-free detection of sequence-specific DNA with multiwalled carbon nanotubes and their light scattering signals

A detection method for DNA sequence-specificity in a homogeneous medium is presented with multiwalled carbon nanotubes (MWCNTs) as optical probes on the basis of the measurements of light scattering signals. ssDNA can prevent MWCNTs from coagulation in electrolyte solution while dsDNA cannot, displaying different light scattering signals. With the light scattering signals, target DNA in the range of 8.6-86.4 nM could be detected and one base pair mismatch could be discriminated. The sequence specificity for the present method has been identified with PCR products.