Effect of the ortho Modification of Azobenzene on the Photoregulatory Efficiency of DNA Hybridization and the Thermal Stability of its cis Form

We synthesized various azobenzenes methylated at their ortho positions with respect to the azo bond for more effective photoregulation of DNA hybridization. Photoregulatory efficiency, evaluated from the change of T_m (ΔT_m) induced by trans–cis isomerization, was significantly improved for all ortho‐modified azobenzenes compared with non‐modified azobenzene due to the more stabilized trans form and the more destabilized cis form. Among the synthesized azobenzenes, 4‐carboxy‐2′,6′ ‐ dimethylazobenzene ( 2′,6′‐Me‐Azo ), in which two ortho positions of the distal benzene ring with respect to carboxyl group were methylated, exhibited the largest ΔT_m, whereas the newly synthesized 2,6‐Me‐Azo (4‐carboxy‐2,6‐dimethylazobenzene), which possesses two methyl groups on the two ortho positions of the other benzene ring, showed moderate improvement of ΔT_m. Both NMR spectroscopic analysis and computer modeling revealed that the two methyl groups on 2′,6′‐Me‐Azo were located near the imino protons of adjacent base pairs; these stabilized the DNA duplex by stacking interactions in the trans form and destabilized the DNA duplex by steric hindrance in the cis form. In addition, the thermal stability of cis‐ 2′,6′‐Me‐Azo was also greatly improved, but not that of cis‐ 2,6‐Me‐Azo . Solvent effects on the half‐life of the cis form demonstrated that cis‐to‐trans isomerization of all the modified azobenzenes proceeded through an inversion route. Improved thermal stability of 2′,6′‐Me‐Azo but not 2,6‐Me‐Azo in the cis form was attributed to the retardation of the inversion process due to steric hindrance between lone pair electrons of the π orbital of the nitrogen atom and the methyl group on the distal benzene ring.     

RNA-templated single-base mutation detection based on T4 DNA ligase and reverse molecular beacon

A novel RNA-templated single-base mutation detection method based on T4 DNA ligase and reverse molecular beacon (rMB) has been developed and successfully applied to identification of single-base mutation in codon 273 of the p53 gene. The discrimination was carried out using allele-specific primers, which flanked the variable position in the target RNA and was ligated using T4 DNA ligase only when the primers perfectly matched the RNA template. The allele-specific primers also carried complementary stem structures with end-labels (fluorophore TAMRA, quencher DABCYL), which formed a molecular beacon after RNase H digestion. One-base mismatch can be discriminated by analyzing the change of fluorescence intensity before and after RNase H digestion. This method has several advantages for practical applications, such as direct discrimination of single-base mismatch of the RNA extracted from cell; no requirement of PCR amplification; performance of homogeneous detection; and easily design of detection probes.     

Detection of T4 DNA ligase using a solid-state electrochemiluminescence biosensing switch based on ferrocene-labeled molecular beacon

A solid-state electrochemiluminescence (ECL) biosensing switch based on special ferrocene-labeled molecular beacon (Fc-MB) has been successfully developed for T4 DNA ligase detection. Such special switch system consisted of two main parts, an ECL substrate and an ECL intensity switch. The ECL substrate was made by modifying the complex of Au nanoparticle and Ruthenium (II) tris-(bipyridine) (Ru(bpy)₃²⁺-AuNPs) onto Au electrode. A molecular beacon labeled by ferrocene as the ECL intensity switch. The molecular beacon is designed with special base sequence, which could combine with its target biomolecule via the reaction of the repair and recombination of nucleic acids by DNA ligase. During the reaction, the molecular beacon opened its stem-loop, and the labeled Fc was consequently kept away from the ECL substrate. Such structural change resulted in an obvious increment in ECL intensity due to the decreased Fc quenching effect to the ECL substrate. The analysis results are sensitive and specific.     

Enzyme‐Regulated Activation of DNAzyme: A Novel Strategy for a Label‐Free Colorimetric DNA Ligase Assay and Ligase‐Based Biosensing

The DNA nick repair catalyzed by DNA ligase is significant for fundamental life processes, such as the replication, repair, and recombination of nucleic acids. Here, we have employed ligase to regulate DNAzyme activity and developed a homogeneous, colorimetric, label‐free and DNAzyme‐based strategy to detect DNA ligase activity. This novel strategy relies on the ligation‐trigged activation or production of horseradish peroxidase mimicking DNAzyme that catalyzes the generation of a color change signal; this results in a colorimetric assay of DNA ligase activity. Using T4 DNA ligase as a model, we have proposed two approaches to demonstrate the validity of the DNAzyme strategy. The first approach utilizes an allosteric hairpin‐DNAzyme probe specifically responsive to DNA ligation; this approach has a wide detection range from 0.2 to 40 U mL^?1 and a detection limit of 0.2 U mL^?1. Furthermore, the approach was adapted to probe nucleic acid phosphorylation and single nucleotide mismatch. The second approach employs a “split DNA machine” to produce numerous DNAzymes after being reassembled by DNA ligase; this greatly enhances the detection sensitivity by a signal amplification cascade to achieve a detection limit of 0.01 U mL^?1.     

Accumulated detection of ethidium bromide using a UV-irradiated DNA film modified electrode and its application for electrochemical detection of an environmental pollutant

In this study, DNA was first fabricated on a glassy carbon electrode by UV-irradiation. Through this process, water-soluble DNA was converted into insoluble materials, and a stable DNA film formed on the electrode. Ethidium bromide (EtBr), a typical model substance for harmful chemicals having planer structure, was used as an electroactive intercalator. This allowed our group to investigate the electrochemical and accumulative behaviors of the intercalator in UV-irradiated DNA film on the electrode. The UV-irradiated, DNA film-modified electrode (UV-DNA-FE) made it possible to accumulate electroactive EtBr on the electrode and detect it after accumulation. The modified electrode was used to detect dibenzofuran (DBF) as an environmental pollutant. The measurements were successfully obtained by focusing on the variation of the electrode response of EtBr, based on the competitive reaction between EtBr and DBF for the intercalating sites of DNA. The results indicated the possibility of using UV-DNA film as a sensing mechanism.     

基于分子信标实时监测大肠杆菌DNA连接酶催化的DNA连接过程

报道了一种对DNA连接过程进行实时监测的方法,利用分子信标核酸探针作为DNA连接反应的模板和检测探针,实时监测了 E.coli DNA连接酶催化的DNA连接反应,克服了传统的凝胶电泳技术操作复杂、周期长及无法实时监测DNA连接过程的缺点,为核酸连接过程的实时监测和连接酶催化机理的研究提供了更为丰富的信息.在此基础上,发展了一种快速、准确测定 E.coli DNA连接酶的方法,线性响应范围为4.0×10^-6～2.0×10^-4U/μL,检测下限为4.0×10^-6U/μL.     

Solution Structure of a Parallel-Stranded Oligoisoguanine DNA Pentaplex Formed by d(T(iG)(4) T) in the Presence of Cs(+) Ions

What a pentaplexing situation: Isoguanine (iG) is an isomer of guanine, where the positions of the C2 amino group and the C6 carboxy group are swapped. iG can self-assemble into pentads in the presence of alkali metal cations. Cs(+) ions were found to stabilize a pentaplex of d(T(iG)(4) T). Solution NMR studies of this pentaplex in the presence of Cs(+) ions (or Na(+) , K(+) , Rb(+) , or NH(4) (+) cations) demonstrate its stability and structure.     

New mixed ligand complexes of ruthenium(II) that incorporate a modified phenanthroline ligand: Synthesis, spectral characterization and DNA binding

The hexafluorophosphate and chloride salts of two ruthenium(II) complexes, viz. [Ru(phen)(ptzo)₂]² and [Ru(ptzo)₃]²⁺, where ptzo = 1,10-phenanthrolino[5,6-e]1,2,4-triazine-3-one (ptzo) — a new modified phenanthroline (phen) ligand, have been synthesised. These complexes have been characterised by infrared, UV-Vis, steady-state emission and¹H NMR spectroscopic methods. Results of absorption and fluorescence titration as well as thermal denaturation studies reveal that both thebis- and tris-complexes of ptzo show moderately strong affinity for binding with calf thymus (CT) DNA with the binding constants being close to 10⁵M^-1 in each case. An intercalative mode of DNA binding has been suggested for both the complexes. Emission studies carried out in non-aqueous solvents and in aqueous media without DNA reveal that both [Ru(phen)(ptzo)₂]²⁺ and [Ru(ptzo)₃]²⁺ are weakly luminescent under these solution conditions. Successive addition of CT DNA to buffered aqueous solutions containing [Ru(phen)(ptzo)₂]²⁺results in an enhancement of the emission. These results have been discussed in the light of the dependence of the structure-specific deactivation processes of the MLCT state of the metallo-intercalator with the characteristic features of its DNA interaction. In doing so, attempts have been made to compare and contrast its properties with those of the analogous phenanthroline-based complexes including the ones reported by us previously.     

基于线性荧光探针对T4 DNA连接酶的活性分析

利用线性荧光探针作为核酸连接反应的模板和信号分子, 通过实时监测荧光信号的降低来表征连接产物的生成过程, 从而建立了一种连续、简单且特异性高的T4 DNA连接酶活性分析的新方法, 检出限可达1.2 U/mL; 同时, 该方法还可用于快速考察金属离子和化学药物对酶促反应的影响. 实验结果表明, 该法不仅为灵敏、实时监测核酸连接反应提供了一种简便快捷的非同位素分析方法, 也为开展核酸连接酶活性分析、反应动力学机制探讨和药物快速筛选提供了一种新技术.     

肾上腺素在对氨基苯磺酸修饰玻碳电极上的电化学行为

采用电化学聚合法首次制备了对氨基苯磺酸修饰玻碳电极。实验表明,该修饰电极对肾上腺素(EP)有明显的电催化特性。在pH 7.6的磷酸盐缓冲溶液(PBS)中,抗坏血酸(AA)和EP在修饰电极上的电位分别为-0.124 V和0.192V。电位差达到300 mV,且在高浓度的AA的存在下可以实现对EP的测定。EP在该电极上检测的线性范围是5.0×10-7~1.0×10-4mol/L,检出限为3.6×10-8。此法已用于针剂样品的测定。     

Protein p53 Binding to Cisplatin‐modified DNA Targets Evaluated by Modification‐specific Electrochemical Immunoprecipitation Assay

Studies of protein interactions with chemically modified nucleic acids are of importance in various areas of biomolecular and biomedical research, including investigations of the binding of proteins important in medicine with DNA modified with drugs and diagnostic applications of modified DNAs in biosensing and bioanalysis. Chemical modification of DNA substrates with various species inside or outside specific protein binding sites can affect the protein‐DNA recognition. In this paper we present a simple electrochemical immunoprecipitation technique designed for evaluation of the effects of antitumor drug cisplatin on the p53‐DNA binding. The cisplatin‐DNA adducts are utilized as electroactive labels allowing a facile determination of the p53‐bound modified DNA. Effects observed using this technique accord with results of previous biochemical assays. This approach is potentially applicable in studies that deal with the influence of any electroactive DNA modifications on the protein‐DNA binding.     

聚铬黑T修饰电极检测亚硝酸盐的研究

利用电化学聚合法将铬黑T修饰到玻碳电极表面,制得聚铬黑T修饰电极。该修饰电极对亚硝酸盐的电化学氧化具有明显的催化作用,这种催化作用主要是由于聚铬黑T薄膜与带负电荷的亚硝酸盐离子的静电相互作用,导致亚硝酸盐离子富集在电极表面/溶液界面,显著增强了亚硝酸盐的氧化电流。电子传输系数α为0.735。选用0.85V作为工作电压,对亚硝酸盐进行安培检测,在0.05μmol/L～1.0 mmol/L和1.0～20.0 mmol/L两个浓度范围内呈现良好的线性关系,检测限达到0.01μmol/L。且该修饰电极有良好的重现性和稳定性。将该修饰电极用于泡菜中亚硝酸盐的测定,获得了满意的结果。     

On-line pre-concentration and UV determination of DNA fragments by dynamic coating capillary electrophoresis and its application to detection of genetically modified oilseed rape based on PCR

In this work, it was demonstrated that on-line pre-concentration and separation of DNA fragments within bared silica column by dynamic coating capillary electrophoresis and UV detection. The DNA fragments were pre-concentrated with long electrokinetic injecting time (99 s), peak height increased dramatically as a function of injection time, especially for shorter length DNA. The concentration sensitivity of DNA fragments can be improved from 20- to 100-fold relative to a normal injection (5 s). The electro-osmotic flow (EOF) and DNA-wall interactions within the capillary were eliminated effectively by dynamic coating method. Employing 0.5% poly(ethylene oxide) (PEO) in Tris-phosphate-EDTA (TBE) buffer as sieving matrix, DNA fragments, ranging from 11 to 657 bp, were separated within 20 min. The linear coefficient of linear relation between the migration and DNA length is 0.999. The DNA fragments amplified from transgenic oilseed rape by polymerase chain reaction (PCR) were separated and detected by this method, demonstrating the potential use of this method for effective DNA analysis and detection of genetically modified organisms (GMO).     

DNA Computing Systems Activated by Electrochemically‐triggered DNA Release from a Polymer‐brush‐modified Electrode Array

An array of four independently wired indium tin oxide (ITO) electrodes was used for electrochemically stimulated DNA release and activation of DNA‐based Identity, AND and XOR logic gates. Single‐stranded DNA molecules were loaded on the mixed poly(N ,N ‐dimethylaminoethyl methacrylate) (PDMAEMA)/poly(methacrylic acid) (PMAA) brush covalently attached to the ITO electrodes. The DNA deposition was performed at pH 5.0 when the polymer brush is positively charged due to protonation of tertiary amino groups in PDMAEMA, thus resulting in electrostatic attraction of the negatively charged DNA. By applying electrolysis at −1.0 V(vs. Ag/AgCl reference) electrochemical oxygen reduction resulted in the consumption of hydrogen ions and local pH increase near the electrode surface. The process resulted in recharging the polymer brush to the negative state due to dissociation of carboxylic groups of PMAA, thus repulsing the negatively charged DNA and releasing it from the electrode surface. The DNA release was performed in various combinations from different electrodes in the array assembly. The released DNA operated as input signals for activation of the Boolean logic gates. The developed system represents a step forward in DNA computing, combining for the first time DNA chemical processes with electronic input signals.     

A sensitive DNA electrochemical biosensor based on magnetite with a glassy carbon electrode modified by muti-walled carbon nanotubes in polypyrrole

A novel sensitive electrochemical biosensor based on magnetite nanoparticle for monitoring DNA hybridization by using MWNT-COOH/ppy-modified glassy carbon electrode is described. In this new detection system, mercapatoacetic acid (RSH)-coated magnetite nanoparticles, capped with 5′-(NH₂) oligonucleotide, is used as DNA probe to complex 29-base polynucleotide target (a piece of human porphobilinogen deaminase PBGD promoter from 170 to 142). Target sequence hybridized with the probe results in the decrease of the reduction peak current of daunomycin connected with probe. The response of non-complementary sequence was almost the same as the blank, and the response of three-base mismatched sequence within 29-base polynucleotide was obviously distinguished from complementary sequence, which can easily identify point mutation of DNA. The equation of calibration plot is i_p (μA) = 0.8255 − 0.0847c_{target oligonucleotide} × 10¹³ in the range of 6.9 × 10⁻¹⁴ to 8.6 × 10⁻¹³ mol/L, and correlation coefficient is 0.9974. The detective limit is 2.3 × 10⁻¹⁴ mol/L of target oligonucleotide. This device can be optimized for the detection of complex sequence.     

Quantum Chemical Study of the Enzymatic Repair of T(6‐4)C/C(6‐4)T UV‐Photolesions by DNA Photolyases

Several strategies have evolved to repair one of the abundant UV radiation‐induced damages caused to DNA, namely the mutagenic pyrimidine (6‐4) pyrimidone photolesions. DNA (6‐4)‐photolyases are enzymes repairing these lesions by a photoinitiated electron transfer. An important aspect of a possible repair mechanism is its generality and transferability to different (6‐4) lesions. Therefore, previously suggested mechanisms for the repair of the T(6‐4)T lesion are here transferred to the T(6‐4)C and C(6‐4)T lesions and investigated theoretically using quantum chemical methods. Despite the different functional groups of the pyrimidine bases involved, a general valid molecular mechanism was identified, in which the initial step is an electron transfer coupled to a proton transfer from the protonated HIS365 to the N3^′ nitrogen of the 3^′ pyrimidine, followed by an intramolecular OH/NH₂ transfer in one concerted step, which does not require an oxetane/azetidine or isolated water/ammonia intermediate.     

Analysis of Diazofluorene DNA Binding and Damaging Activity: DNA Cleavage by a Synthetic Monomeric Diazofluorene

The lomaiviticins and kinamycins are complex DNA damaging natural products that contain a diazofluorene functional group. Herein, we elucidate the influence of skeleton structure, ring and chain isomerization, D‐ring oxidation state, and naphthoquinone substitution on DNA binding and damaging activity. We show that the electrophilicity of the diazofluorene appears to be a significant determinant of DNA damaging activity. These studies identify the monomeric diazofluorene 11 as a potent DNA cleavage agent in tissue culture. The simpler structure of 11 relative to the natural products establishes it as a useful lead for translational studies.