An ab initio study of the conformational preferences of Hoechst 33258 in gas-phase and aqueous solution environments

A quantum mechanical study of the conformational preferences of Hoechst 33258, a synthetic minor groove-binding drug, has been performed in both gas-phase and aqueous solution. Gas-phase calculations were performed at the HF/6-31G(d) and MP2/6-31G(d) levels of theory, whereas calculations in the aqueous solution phase were performed using the PCM model with the 6-31G(d) basis set. The molecule was divided into three fragments, which were submitted to a systematic and detailed conformational study. The results clearly indicate that Hoechst 33258 does not adopt a planar conformation in either the gas-phase or aqueous solution. Thus, a folded conformation is not induced by binding of the molecule to DNA, but is an intrinsic property of the compound. Received: 3 March 1998 / Accepted: 29 May 1998 / Published online 19 August 1998     

Improved Fluorometric DNA Determination Based on the Interaction of the DNA/Polycation Complex with Hoechst 33258

When DNA is mixed with the cationic polyelectrolyte poly(diallyldimethyl ammonium chloride) (PDDA), the DNA/PDDA complex is formed instantaneously at room temperature. This complex is much more efficient in enhancing the fluorescence of Hoechst 33258 (H 33258) than DNA alone. Based on the interaction of H 33258 with the DNA/PDDA complex, a new fluorescence assay for DNA is described. At pH 7.3 in Tris-HCl buffered solution, the DNA/PDDA complex causes a sharp enhancement in fluorescence intensity of H 33258. Simultanously, the emission maximum wavelength of H 33258 blueshifts from 490nm to 450nm, while the excitation redshifts from 345 to 350nm. The calibration graphs for calf thymus DNA (ctDNA) and herring sperm DNA (hsDNA) are both linear up to 5.0µgmL^–1 when the concentration of H 33258 and PDDA are fixed at 1.5×10^–6 and 1.6×10^–5molL^–1, respectively. The method is specific for native DNA. The 3 detection limits for ctDNA and hsDNA are 1.8 and 5.6ngmL^–1, respectively, i.e. much lower than in the presence of H 33258 alone. Four synthetic samples were determined satisfactorily. This method can also be developed to investigate the formation and the nature of the complexes between DNA and polycations, which have recently been widely applied in some fields such as genetic engineering and gene therapy.     

Electrochemical and Spectroscopic Studies on the Interaction of Malachite Green with DNA and Its Application

The interaction of malachite green (MG) with double‐stranded DNA (dsDNA) in pH 7.0 Britton–Robinson (B–R) buffer solution was investigated by electrochemical and spectrophotometric methods. Within the potential scan range of ?1.0 to +1.5 V (vs. SCE), MG has two oxidative peaks at 0.547 V and 0.833 V and one reductive peak at 0.362 V on cyclic voltammogram at the scan rate of 0.20 V/s. After the addition of dsDNA into the MG solution, the oxidative peak current at 0.547 V decreases obviously. The electrochemical parameters, such as the charge transfer coefficient (α), the surface reaction rate constant (k_s) and the diffusion coefficient (D), were calculated and compared between in the absence and presence of dsDNA. The results show that these parameters of MG after adding dsDNA have greatly changed, which indicates that an electrochemical active complex was formed. The interaction mechanisms of MG with dsDNA are discussed in some details from the electrochemistry and UV‐vis spectrophotometry. The reduction of the peak current of MG after adding dsDNA was further used for the quantification of dsDNA by differential pulse voltammetry (DPV). The linear range for dsDNA is in the range of 10.0–100.0 μg/mL with the linear regression equation as Δi_p (μA)=0.065+0.0096 C (μg/mL) and the detection limit of 6.0 μg/mL (3σ). The influences of coexisting substances were investigated and artificial samples were determined with satisfactory results.     

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.     

Voltammetric Behavior of Antileukemia Drug Glivec. Part II – Redox Processes of Glivec Electrochemical Metabolite

Glivec is a newly developed drug that belongs to the class of 2‐phenylaminopyrimidine. It is a potent inhibitor of ABL‐kinase, the main clinical manifestation of chronic myelogenous leukemia (CML). Based on its activity on CML, glivec is undergoing extensive evaluation for its activity against other tumor types. Detection and quantitation of glivec in biological fluids or cells is thus very important. The antileukemia drug glivec undergoes oxidation at glassy carbon electrodes and involves the formation of an oxidation product, P_glivec. The adsorption of P_glivec at the GCE surface yields a compact monolayer allowing an electrochemical study of this compound adsorbed at the GCE surface. The reversible redox reaction of the adsorbed P_glivec is pH dependent and occurs with the transfer of 2 electrons and 2 protons. The surface standard potential and the rate constant of the heterogeneous electrochemical reaction were calculated using cyclic voltammetry to be E^θ′=+180 mV and k=15.5 s^?1, respectively. The total surface concentration of adsorbed P_glivec is 2.5×10^?12 mol cm^?2. The analytical determination of glivec was carried out by differential pulse voltammetric measurement of the anodic peak current corresponding to either the oxidation peak of glivec or the oxidation peak of P_glivec adsorbed on the GCE surface. The limits of detection of glivec and adsorbed P_glivec based on three times the noise level are 3.3×10^?8 M and 2.9×10^?10 M, respectively.     

Electrochemical Studies of the Recognition Interaction of Rhodamine B with DNA

The recognition interaction of rhodamine B (RB) with DNA was studied in pH 7.5 Britton-Robinson (B-R) buffer solution by electrochemical techniques. An irreversible oxidation peak at glassy carbon electrode was obtained at 0.92V (vs. SCE). After the addition of DNA into the RB solution, the peak current of RB decreased apparently without the shift of peak potential. The electrochemical parameters such as the charge transfer coefficient α and the electrode reaction standard rate constant ks of RB in the absence and presence of DNA were determined, which did not change, indicating that a non-electroactive complex was formed, so the concentration of RB in the solution decreased and the peak current decreased correspondingly.     

农药异丙威与小牛胸腺DNA的作用研究

在生理酸度条件下,采用紫外光谱和荧光光谱法研究异丙威与小牛胸腺DNA的作用表明:DNA对异丙威的荧光有明显的猝灭作用,属于静态猝灭方式;K4[Fe(CN)6]猝灭试验发现DNA对异丙威有明显的保护作用,离子强度的改变对异丙威和异丙威-DNA体系的荧光均无明显影响;异丙威的加入使DNA的熔点升高,并且异丙威能够竞争置换EB与DNA的结合位点。上述实验也表明,异丙威以嵌插方式作用于DNA的结合位点,有可能通过形成DNA加合物的形式造成DNA损伤,从而最终导致基因突变。     

二茂铁与DNA作用的表面电化学研究

在研究碳纳米管电极上二茂铁电化学性质的基础上,应用二茂铁修饰电极和DNA修饰电极研究了二茂铁与小牛胸腺DNA的相互作用。结果表明,修饰电极上的二茂铁都呈现一对明显的氧化还原峰,二茂铁修饰电极与DNA的作用表现为氧化还原峰电流减小,与溶液中的两者作用情况类似,而DNA修饰电极与二茂铁的作用则表现为氧化还原峰电流增大。扫描电镜结果也证实了两种修饰电极上的二茂铁与DNA间的作用。此外,还讨论了二茂铁与DNA间的作用模式。     

尼古丁与DNA相互作用的电化学研究

用线性扫描伏安法、循环伏安法及光谱法研究了尼古丁与DNA在0.2 mol/LpH 6.0的H2C2O4缓冲溶液中的相互作用。研究结果显示,随着DNA的加入,尼古丁峰电流降低,峰电位正移,说明尼古丁是以嵌入形式与DNA结合,生成了一种结合比为2∶1的非电活性化合物,结合常数β为1.56×109。并用多种电化学方法求得了电极过程的动力学参数。     

DNA与维生素B2相互作用的电化学研究

研究了维生素 B2 与 DNA在 p H4.5 6条件下相互作用的电化学行为。DNA的存在能导致维生素 B2 氧化还原峰电流降低 ,峰电位基本不变。通过测定 DNA引入前后的一些电化学参数 ,推测维生素 B2 与 DNA在该条件下结合生成了一种非电活性的超分子化合物。针对该类型体系 ,推导出一系列方程求得该超分子化合物的组成为 1∶ 1 ,结合常数β =6.0 2× 1 0     

Direct Detection of DNA and DNA‐Ligand Interaction by Impedance Spectroscopy

In this work we present an impedimetric detection system for DNA‐ligand interactions. The sensor system consists of thiol‐modified single‐stranded DNA chemisorbed to gold. Impedance measurements in the presence of the redox system ferri‐/ferrocyanide show an increase in charge transfer resistance (R_ct) after hybridisation of a complementary target. Different amounts of capture strands, used for gold electrode modification, result in surface coverages between 3 and 15 pmol/cm² ssDNA. The relative change in R_ct upon hybridisation increases with increasing amount of capture probe on the electrode from 1.5‐ to 4.5‐fold. Impedimetric detection of binding events of a metal‐intercalator ([Ru(phen)₃]²⁺) and a groove binder (spermine) to double‐stranded DNA is demonstrated. Binding of [Ru(phen)₃]²⁺ and spermine exhibits a decrease in charge transfer resistance. Here, the ligand’s interaction leads to electrostatic shielding of the negatively charged DNA backbone. The impedance changes have been evaluated in dependence on the concentration of both DNA binders. Furthermore, the association of a single‐stranded binding protein (SSBP) is found to cause an increase in charge transfer resistance only when incubated with single‐stranded DNA. The specific binding of an anti‐dsDNA antibody to the dsDNA‐modified electrode surface decreases in contrast the interfacial impedance.     

Spectroscopic and Electrochemical Studies of the Interaction Between Fuchsin Basic and DNA

Introduction DNAbiosensorsareacompletelynewtypeoftech nologicalconceptionsbyusingspecificaffinitybetween mattersinlivingbeingstodistinguishdirectlyand quicklysequence specificDNA[1].Withtherapidde velopmentofgeneticengineering,oneofthekeyissues needtobere…     

Biosensor for Hepatitis B Virus DNA PCR Product and Electrochemical Study of the Interaction of Di(2,2′‐bipyridine)osmium(III) with DNA

The strategy for electrochemical detection of HBV DNA PCR product (181 bps) was designed by covalently immobilizing single‐stranded HBV DNA on preoxidized glassy carbon electrode surface. The immobilization of single stranded DNA was verified by AC impedance spectra. The following hybridization reaction on surface was evidenced by electrochemical methods using [Os(bpy)₂Cl₂]⁺ as an electroactive indicator. The interactions of [Os(bpy)₂Cl₂]⁺ with calf thymus single and double stranded DNA immobilized on preoxidized glassy carbon electrodes were studied. [Os(bpy)₂Cl₂]⁺ could bind preferentially to the duplex DNA by intercalating to base pairs. The intrinsic binding constant of [Os(bpy)₂Cl₂]⁺ with calf thymus DNA was calculated to be 1.21×10⁴ M^?1. Using [Os(bpy)₂Cl₂]⁺ as an electrochemical hybridization indicator, the HBV DNA sensor has been used to detect qualitatively target HBV DNA in solution with high sensitivity and selectivity.     

Electrochemical and Spectroscopic Study of the Interaction of Indirubin with DNA

The interaction of indirubin with DNA was studied by differential pulse voltammetry (DPV) and linear sweep voltammetry (LSV) at the bare or DNA‐modified electrode and UV‐vis or IR spectra. As a result of intercalating of this drug into the double helical structure of DNA, the DPV of indirubin shows that peak potentials shift and peak currents decrease with the addition of DNA. UV‐vis spectra exhibits that the absorption intensity of indirubin at 538.7 nm^?1 decreases, which indicates that the anticancer herbal drug indirubin binds DNA. In addition, IR‐spectra of DNA and DNA‐indirubin adduct imply indirubin interacts with the phosphate groups of DNA by hydrogen bond or electrostatic interaction. Under our experiment conditions, the decrease of peak current is proportional to DNA concentration, which can be applied to estimate DNA concentration. The results indicate that the herbal drug indirubin can interfere with the DNA by intercalating into the double helix of DNA and interacting with the phosphate groups of DNA.     

Interaction of zanamivir with DNA and RNA: Models for drug–DNA and drug–RNA bindings

Zanamivir (ZAN) is the first of a new generation of influenza virus-specific drugs known as neuraminidase inhibitors, which acts by interfering with life cycles of influenza viruses A and B. It prevents the virus spreading infection to other cells by blocking the neuraminidase enzyme present on the surface of the virus. The aim of this study was to examine the stability and structural features of calf thymus DNA and yeast RNA complexes with zanamivir in aqueous solution, using constant DNA or RNA concentration (12.5 mM) and various zanamivir/polynucleotide (P) ratios of 1/20, 1/10, 1/4, and 1/2. FTIR and UV–visible spectroscopy are used to determine the drug external binding modes, the binding constant and the stability of zanamivir–DNA and RNA complexes in aqueous solution. Structural analysis showed major interaction of zanamivir with G-C (major groove) and A-T (minor groove) base pairs and minor perturbations of the backbone PO₂ group with overall binding constants of K_{zanamivir–DNA} = 1.30 × 10⁴ M⁻¹ and K_{zanamivir–RNA} = 1.38 × 10⁴ M⁻¹. The drug interaction induces a partial B to A-DNA transition, while RNA remains in A-conformation.     

Factors Affecting DNA–DNA Interstrand Cross‐Links in the Antiparallel 3′–3′ Sense: A Comparison with the 5′–5′ Directional Isomer

Reported herein is a study of the unusual 3′–3′ 1,4‐GG interstrand cross‐link (IXL) formation in duplex DNA by a series of polynuclear platinum anticancer complexes. To examine the effect of possible preassociation through charge and hydrogen‐bonding effects the closely related compounds [{trans‐PtCl(NH₃)₂}₂(μ‐trans‐Pt(NH₃)₂{NH₂(CH₂)₆NH₂}₂)]⁴⁺ (BBR3464, 1 ), [{trans‐PtCl(NH₃)₂}₂(μ‐NH₂(CH₂)₆NH₂)]²⁺ (BBR3005, 2 ), [{trans‐PtCl(NH₃)₂}₂(μ‐H₂N(CH₂)₃NH₂(CH₂)₄)]³⁺ (BBR3571, 3 ) and [{trans‐PtCl(NH₃)₂}₂{μ‐H₂N(CH₂)₃‐N(COCF₃)(CH₂)₄}]²⁺ (BBR3571‐COCF₃, 4 ) were studied. Two different molecular biology approaches were used to investigate the effect of DNA template upon IXL formation in synthetic 20‐base‐pair duplexes. In the “hybridisation directed” method the monofunctionally adducted top strands were hybridised with their complementary 5′‐end labelled strands; after 24 h the efficiency of interstrand cross‐linking in the 5′–5′ direction was slightly higher than in the 3′–3′ direction. The second method involved “postsynthetic modification” of the intact duplex; significantly less cross‐linking was observed, but again a slight preference for the 5′–5′ duplex was present. 2D [¹H, ¹⁵N] HSQC NMR spectroscopy studies of the reaction of [¹⁵N]‐ 1 with the sequence 5′‐d{TATACATGTATA}₂ allowed direct comparison of the stepwise formation of the 3′–3′ IXL with the previously studied 5′–5′ IXL on the analogous sequence 5′‐d(ATATGTACATAT)₂. Whereas the preassociation and aquation steps were similar, differences were evident at the monofunctional binding step. The reaction did not yield a single distinct 3′–3′ 1,4‐GG IXL, but numerous cross‐linked adducts formed. Similar results were found for the reaction with the dinuclear [¹⁵N]‐ 2 . Molecular dynamics simulations for the 3′–3′ IXLs formed by both 1 and 2 showed a highly distorted structure with evident fraying of the end base pairs and considerable widening of the minor groove.     

Electrochemical DNA biosensor for the determination of benzo[a]pyrene–DNA adducts

The metabolites of the environmental pollutant, benzo[a]pyrene (BaP) are carcinogenic and mutagenic agents. Thus, the determination of additional products (adducts) of the interaction between DNA and BaP, attracts great interest in cancer research.

In this study, the determination of interaction between BaP and calf thymus double-stranded DNA (dsDNA) was performed by using differential pulse voltammetry (DPV) and constant current chronopotentiometric stripping analysis (PSA) in connection with carbon paste electrode (CPE) or glassy carbon electrode (GCE). As a result of interaction of BaP with dsDNA, the signal obtained from the oxidation of guanine decreased and a new adduct signal at a more positive potential appeared. This new peak is attributed to the formation of an adduct from the interaction of guanine with BaP. The chemically prepared anti-7,8,9,10-tetrahydrobenzo[a]pyrene-7,8-diol-9,10-epoxide (BPDE) adduct by using iodine oxidation was analyzed and the electrochemical signal of the adduct was observed. When the dsDNA modified GCE was immersed into various concentrations of BaP solution, the oxidation peak of guanine decreased and the adduct peak increased with the increasing BaP concentration. The partition coefficient was also obtained from the peak of BaP with dsDNA. The results revealed that the formation of adducts could be determined by using electrochemical DNA biosensors, which are fast, simple and cost-effective devices. Furthermore, this study promises that the analysis of other important adducts would benefit from the introduction of electrochemical methods.     

生物小分子与DNA相互作用的光谱及电化学研究进展

评述了生物小分子与DNA的作用方式及其相互作用的光谱及电化学研究方法.引用文献32篇.     

Spectroscopic and Spectroelectrochemical Studies of Interaction of Nile Blue with DNA

ＩｎｔｒｏｄｕｃｔｉｏｎＩｔｉｓｇｅｎｅｒａｌｌｙａｃｃｅｐｔｅｄｔｏｄａｙｔｈａｔｔｈｅｒｅａｒｅｔｈｒｅｅｋｉｎｄｓｏｆｂｉｎｄｉｎｇｍｏｄｅｌｓｆｏｒｓｍａｌｌｍｏｌｅｃｕｌｅｓｔｏＤＮＡ ,ｗｈｉｃｈｒｅｆｅｒｔｏｉｎｔｅｒｃａｌａｔｉｖｅｂｉｎｄｉｎｇ ,ｇｒｏｏｖｅｂｉｎｄｉｎｇａｎｄｅｌｅｃｔｒｏｓｔａｔｉｃｂｉｎｄｉｎｇ .Ｉｎｔｈｅｓｅｂｉｎｄｉｎｇｍｏｄｅｌｓ ,ｔｈｅｉｎｔｅｒ ｃａｌａｔｉｖｅｂｉｎｄｉｎｇｉｓｔｈｏｕｇｈｔａｓｔｏｂｅｔｈｅｓｔｒｏｎｇｅｓｔｂｉｎｄｉｎｇｂｅｃ…