Spectral studies of the binding of lucigenin,a bisacridinium derivative,with double-helix DNA

The non-covalent binding of the cationic reagent lucigenin to DNA has been investigated by spectroscopic methods. Results from absorption, circular dichroism, and fluorescence studies revealed that lucigenin could intercalate into the helix of DNA. Polarization and melting studies provided further evidence of the intercalation binding of lucigenin with DNA. The binding constant was obtained by varying the DNA concentration while keeping the concentration of lucigenin constant. It was of the order of 10(4) mol(-1) L in DNA base pairs. The experiment also showed that electrostatic interaction played a significant role in the intercalation of lucigenin with DNA. It is suggested that lucigenin can be intercalated into the interior of the DNA double helix because it is initially attracted by the anionic DNA. This research offers a new intercalation functional group for DNA-targeted drug design.     

Molecular aspects on the interaction of phenosafranine to deoxyribonucleic acid: Model for intercalative drug-DNA binding

The mode, mechanism and energetics of interaction of phenosafranine, the planar, cationic and rigid phenazium dye to calf thymus DNA was investigated from absorption, fluorescence, circular dichroism, isothermal titration calorimetry, thermal melting, and viscosity. The study revealed non-cooperative binding of the dye to DNA with an affinity in the range (3.81-4.22) × 10⁵ M⁻¹ as observed from diverse techniques and obeying neighbor exclusion principle. The stoichiometry of binding was characterized to be one phenosafranine molecule per two base pairs. The binding was characterized by strong stabilization of DNA against thermal strand separation, large intrinsic circular dichroic changes of DNA by itself and the generation of induced circular dichroism for the optically inactive phenosafranine molecules. Hydrodynamic and fluorescence quenching studies revealed strong evidence that the phenosafranine molecules are intercalated between every alternate base pairs of calf thymus DNA. Isothermal titration calorimetry studies suggested that the binding was exothermic and favoured by both negative enthalpy and positive entropy changes. This study for the first time presents the complete molecular aspects and energetics of phenosafranine complexation to DNA as model for intercalative drug-DNA interaction.     

具有抗癌活性的新型硒杂环化合物的合成及其与牛血清蛋白的相互作用

合成了一种新的硒二唑衍生物4-(苯并[c][1,2,5]硒二唑-6-yl)苯-1,2-二氨基(BSBD).研究了其抗肿瘤活性,结果发现BSBD具有很好的抗癌活性,特别对Neuro-2a小鼠脑神经瘤细胞表现出很好的选择性.关于作用机制的研究发现,BSBD可呈剂量效应的诱导肿瘤细胞中Sub-G1凋亡峰的累积、染色质固缩及凋亡小体的形成,说明诱导细胞凋亡是BSBD发挥抗肿瘤活性的主要机制.进而应用紫外-可见吸收光谱、荧光光谱法、傅里叶红外光谱、圆二色光谱法研究了其与牛血清白蛋白(BSA)的相互作用.采用位点结合模型公式和热力学公式计算了结合常数、结合位点数及结合力类型,并用紫外-可见吸收光谱、红外光谱和圆二色光谱技术探讨了硒杂环化合物对牛血清白蛋白构象的影响.结果表明:BSBD能有效淬灭牛血清白蛋白的荧光强度,其猝灭机理为静态猝灭,主要作用力类型是氢键和范德华力.而同步荧光、紫外-吸收示差光谱、红外光谱和圆二色光谱都进一步证明了BSBD与BSA结合后,改变了BSA的内部结构.     

Chlorobenzylidine-calf thymus DNA interaction II: circular dichroism and nuclear magnetic resonance studies

The binding of chlorobenzylidine to calf thymus DNA has been studied in detail by means of circular dichroism (CD), nuclear magnetic resonance (1H NMR), viscosimetry and denaturation temperature (Tm). Chlorobenzylidine is found to intercalate between base pairs of DNA as evidence by: (1) induced circular dichroism; (2) broadened 1H NMR signals; (3) enhanced viscosity; and (4) increased denaturation temperature of the DNA helix. In addition, Scatchard plot from CD titration data gives a binding constant of 2.6 x 10(4) M(-1) and a binding site size of 4 base pairs at 25 degrees C. Matrix rank analysis shows that there are three main components contributing to the observed CD spectra. The nuclear magnetic resonance experiment shows that the planar aromatic ring of tetrahydroberberine group in chlorobenzylidine intercalates between the base pairs of DNA when chlorobenzylidine is bound to DNA.     

NETROPSIN: INTERACTION WITH ULTRAVIOLET IRRADIATED DNA

Abstract—Ultraviolet irradiation of double-stranded DNA reduces the circular dichroism (i < 300 nm) induced when the basic peptide antibiotic netropsin (Nt) is added to DNA subsequent to thc irradiation compared to the CD induced by the same concentrations of Nt added to unirradiated DNA. Nt is known to bind to A T base pairs in duplex DNA but will not bind to single-stranded DNA. The reduction in the maximum induced CD observed with saturating concentrations of Nt is a linear function of the concentration of pyrimidine dimers which. along with other dinucleotide photoproducts. form short disrupted regions in duplex DNA. The decrease in the CD of Nt bound to irradiated DNA could be due to elimination of potential Nt sites in the vicinity of a dimer. reduction in the average magnitude of the CD of Nt bound near a dimer or various combinations of these effects. In addition there is a reduction in the average binding constant for Nt bound to irradiated DNA compared to unirradiated DNA suggesting that formation of dinucleotide photoproducts either tends to preferentially eliminate the tighter binding sites or that tighter sites are converted to weaker ones. A simple model suggests that no more than one-third to one-half of the pyrimidine dimcrs formed in DNA completely eliminate a Nt site.     

Neomycin-neomycin dimer: an all-carbohydrate scaffold with high affinity for AT-rich DNA duplexes

A dimeric neomycin-neomycin conjugate 3 with a flexible linker, 2,2'-(ethylenedioxy)bis(ethylamine), has been synthesized and characterized. Dimer 3 can selectively bind to AT-rich DNA duplexes with high affinity. Biophysical studies have been performed between 3 and different nucleic acids with varying base composition and conformation by using ITC (isothermal calorimetry), CD (circular dichroism), FID (fluorescent intercalator displacement), and UV (ultraviolet) thermal denaturation experiments. A few conclusions can be drawn from this study: (1) FID assay with 3 and polynucleotides demonstrates the preference of 3 toward AT-rich sequences over GC-rich sequences. (2) FID assay and UV thermal denaturation experiments show that 3 has a higher affinity for the poly(dA)·poly(dT) DNA duplex than for the poly(dA)·2poly(dT) DNA triplex. Contrary to neomycin, 3 destabilizes poly(dA)·2poly(dT) triplex but stabilizes poly(dA)·poly(dT) duplex, suggesting the major groove as the binding site. (3) UV thermal denaturation studies and ITC experiments show that 3 stabilizes continuous AT-tract DNA better than DNA duplexes with alternating AT bases. (4) CD and FID titration studies show a DNA binding site size of 10-12 base pairs/drug, depending upon the structure/sequence of the duplex for AT-rich DNA duplexes. (5) FID and ITC titration between 3 and an intramolecular DNA duplex [d(5'-A(12)-x-T(12)-3'), x = hexaethylene glycol linker] results in a binding stoichiometry of 1:1 with a binding constant ～10(8) M(-1) at 100 mM KCl. (6) FID assay using 3 and 512 hairpin DNA sequences that vary in their AT base content and placement also show a higher binding selectivity of 3 toward continuous AT-rich than toward DNA duplexes with alternate AT base pairs. (7) Salt-dependent studies indicate the formation of three ion pairs during binding of the DNA duplex d[5'-A(12)-x-T(12)-3'] and 3. (8) ITC-derived binding constants between 3 and DNA duplexes have the following order: AT continuous, d[5'-G(3)A(5)T(5)C(3)-3'] > AT alternate, d[5'-G(3)(AT)(5)C(3)-3'] > GC-rich d[5'-A(3)G(5)C(5)T(3)-3']. (9) 3 binds to the AT-tract-containing DNA duplex (B* DNA, d[5'-G(3)A(5)T(5)C(3)-3']) with 1 order of magnitude higher affinity than to a DNA duplex with alternating AT base pairs (B DNA, d[5'-G(3)(AT)(5)C(3)-3']) and with almost 3 orders of magnitude higher affinity than a GC-rich DNA (A-form, d[5'-A(3)G(5)C(5)T(3)-3']).     

Interaction of Antitumor Drug Aclacinomycin‐A with DNA and Its Specific Sequence Site

Through UV and fluorescence spectrophotometries, the interaction of aclacinomycin‐A (ACM‐A) with DNA and its specific sequence have been investigated with the aid of circular dichroism spectrophotometry and differential pulse voltammetry method. The results demonstrated that ACM‐A was capable of intercalating DNA double helix, the π‐π electronic overlapping between π‐electrons of ACM‐A and base pair of DNA stabilized the ACM‐A‐DNA adduct, and through electrostatic interaction, the trisaccharide interacted with the minor groove of DNA owing to an amino group at C(3′). Electrochemical and spectroelectrochemical studies revealed that the original form of ACM‐A had higher affinity for DNA than the reduction form in which the trisaccharide group at C(7) was lost. According to the results obtained in this paper, ACM‐A showed preference for AT base pairs of the deoxyribonucleic acid duplex, and it was apt to interact with cytosine and thymine rather than the adenine of oligonucleotide.     

Multispectroscopic studies of the interaction of calf thymus DNA with the anti-viral drug, valacyclovir

The present study investigated the binding interaction between an antiviral drug, valacyclovir and calf thymus DNA (CT-DNA) using emission, absorption, circular dichroism, viscosity and DNA melting studies. In fluorimetric studies, thermodynamic enhancement constant (K(D)) and bimolecular enhancement constant (K(B)) were calculated at different temperatures and demonstrated that fluorescence enhancement is not initiated by a dynamic process, but instead by a static process that involves complex DNA formation in the ground state. Further, the enthalpy and entropy of the reaction between the drug and CT-DNA showed that the reaction is exothermic and enthalpy-favored. In addition, detectable changes in the circular dichroism spectrum of CT-DNA in the presence of valacyclovir indicated conformational changes in the DNA double helix following interaction with the drug. All these results prove that this antiviral drug interacts with CT-DNA via an intercalative mode of binding.     

Entropy driven binding of the alkaloid chelerythrine to polyadenylic acid leads to spontaneous self-assembled structure formation

The binding thermodynamics and interaction of the putative anticancer alkaloid chelerythrine with polyadenylic acid were investigated by isothermal titration calorimetry, absorption and fluorescence spectroscopy, circular dichroism, differential scanning calorimetry and thermal melting experiments. The equilibrium binding constant was evaluated to be of the order of 10⁷ M⁻¹. Strong positive entropic and favorable enthalpic contributions to the binding were revealed. The binding affinity was enhanced within (10 to 100) mM Na⁺ concentration. Circular dichroism spectra confirmed that the increase in entropy change was caused by a strong conformational change in the RNA polynucleotide. Absorption and circular dichroism melting studies revealed that chelerythrine binding induced self-assembled duplex structure formation in poly(A) molecules resulting in a cooperative melting profile. This was further confirmed from differential scanning calorimetry data. The intercalation binding of the alkaloid involved strong energy transfer from the polynucleotide bases to the bound alkaloid molecules. The remarkably high entropy driven binding of the alkaloid induced spontaneous self-assembled structure formation in poly(A) and the associated binding affinity is the highest so far reported for a small molecule binding to poly(A).     

钌-菲罗啉卟啉的合成及与DNA的相互作用

以5-(4-羟基苯基)-10,15,20-三苯基卟啉和钌-菲罗啉衍生物为原料, 合成了3个两亲性钌-菲罗啉卟啉化合物, 并通过核磁共振波谱、红外光谱、紫外-可见光谱、质谱和元素分析等对化合物的结构进行了确证. 采用紫外-可见光谱、 荧光发射光谱和圆二色光谱考察了目标化合物与ct-DNA的相互作用, 研究了它们与DNA的结合模式. 实验结果表明, Por1, Por2和Por3与DNA的结合常数分别为1.46×10⁵, 2.75×10⁵和5.69×10⁵ L/mol. 此外, 在不同DNA浓度下, Por1和Por2与DNA的结合模式为插入模式和外部结合模式共存, Por3与DNA的结合模式主要为自堆积的外部键合和静电作用. 结果表明, 钌-菲罗啉卟啉化合物是新型的光动力治疗试剂.     

First ruthenium organometallic complex of antibacterial agent ofloxacin. Crystal structure and interactions with DNA

An organometallic ruthenium complex of quinolone antibacterial agent ofloxacin, [(η(6)-p-cymene)RuCl(O,O-oflo)]·2.8H(2)O (1·2.8H(2)O), was isolated, and its crystal structure was determined. In this "piano-stool" complex, quinolone is bidentately coordinated to the metal through the ring carbonyl and one of the carboxylic oxygen atoms. Interactions of the title complex with DNA were studied by spectroscopic methods [electronic, fluorescence, and circular dichroism (CD)] and atomic force microscopy (AFM). It was established that the electrostatic attraction between the ruthenium complex and DNA in a solution is important for binding because interactions were observed only in a solution with low ionic strengths. An induced-CD (ICD) signal was observed in a solution of DNA and the title complex, which proves interaction between ruthenium and macromolecules. Competitive binding between cisplatin and 1 to DNA revealed that cisplatin prevents binding of 1. Our experiments revealed that binding of the title complex to DNA occurs also if guanine N7 is protonated. AFM has shown that the title complex provokes DNA shrinkage. Preliminary biological tests have also been performed.     

Specific recognition of human telomeric G-quadruplex DNA with small molecules and the conformational analysis by ESI mass spectrometry and circular dichroism spectropolarimetry

Electrospray ionization mass spectrometry (ESI-MS) was utilized to investigate the binding affinity and stoichiometry of small molecules with human telomeric G-quadruplex DNA. The binding-affinity order obtained for the (AGGGTT)(4) quadruplex was: Tel01>ImImImbetaDp>PyPyPygammaImImImbetaDp. The specific binding of Tel01 and PyPyPygammaImImImbetaDp in one system consisting of human telomeric G-quadruplex and duplex DNA was observed directly for the first time. This revealed that PyPyPygammaImImImbetaDp has a binding specificity for the duplex DNA, whereas Tel01 selectively recognizes the G-quadruplex DNA. Moreover, both ESI-MS and circular dichroism (CD) spectra indicated that Tel01 favored the formation and stabilization of the antiparallel G-quadruplex, and a structural transition of the (AGGGTT)(4) sequence from a coexistence of parallel and antiparallel G-quadruplexes to a parallel G-quadruplex induced by annealing.     

Spectroscopic Investigation on the Binding of the Antitumoral Pd(II) Complex to Human Serum Albumin

The interaction of human serum albumin (HSA) with 1,10‐phenanthroline‐ethyldithiocarbamatopalladium(II) nitrate complex, [Pd(phen)(Et‐dtc)]NO₃, has been studied by using absorption, fluorescence and circular dichroism spectroscopic measurements. UV‐Vis studies imply that The peptide strands of protein molecules extended more (denatured) upon the addition of Pd(II) complex. This process is spontaneous and exothermic. A fluorescence quenching reaction of Pd(II) complex and HSA was observed and quenching mechanism was suggested as static quenching according to Stern‐Volmer equation. The number of binding sites (n) and apparent association constant (K_A) were calculated using fluorescence quenching data. The circular dichroism results revealed the conformational changes in secondary structure of protein upon its interaction with Pd(II) complex. In these interaction studies, several thermodynamic and binding parameters are also determined which may provide deeper insights into structural changes induced by an antitumor Pd(II) complex on the protein as the metal complex side effects.     

A temperature-dependent interaction of neutral red with calf thymus DNA

Neutral red (NR) is used as a probe to study the temperature and concentration dependent interaction of a cationic dye with nucleic acid. A temperature-dependent interaction of NR with calf thymus DNA (CT DNA) has been studied by differential pulse voltammetry (DPV), UV-Visible absorption, circular dichroism (CD) and fluorescence spectroscopy. The experimental results of increasing peak current, changes in the UV-Visible absorption and fluorescence spectra of NR and decreasing the induced circular dichroism (ICD) intensity show that (i) the binding mode of NR molecules is changed from intercalating into DNA base pairs to aggregating along the DNA double helix and (ii) the orientation of NR chromophore in DNA double helix is also changed with the temperature.     

巯嘌呤金属配合物与小牛胸腺DNA的作用

用溴化乙锭为探针研究了巯嘌呤(mercaptopurine, MP)金属配合物与小牛胸腺 DNA的作用机制，探讨了其作用模式，即巯嘌呤与DNA是非嵌插结合，巯嘌呤金属酴 物与DNA之间的作用为静电方式和一定的嵌入方式。并求得巯嘌呤金属配合物与 DNA的结合常数。     

三联吡啶-萘酰亚胺二元化合物的合成及其与DNA的相互作用

本文合成了两种三联吡啶修饰的萘酰亚胺化合物NPI1和NPI2,并利用紫外-可见吸收光谱(UV-Vis)、圆二色光谱(CD)、荧光共振能量转移(FRET)等方法研究了它们与双链CT DNA和Htelo G-四链体DNA的相互作用。实验结果表明,化合物NPI1和NPI2对G-四链体DNA具有很好的结合能力和选择性,溶液中的碱金属离子种类和萘酰亚胺基团上的取代基对NPI1和NPI2与DNA的作用有很大的影响。在含K+的缓冲液中,NPI2与G-四链体的结合常数达到1.06×108 L/mol,是与双链CT DNA结合常数的268倍。圆二色谱结果表明在不含碱金属离子的溶液中,NPI1和NPI2可诱导Htelo DNA形成反平行结构G-四链体。Autodock分子对接模拟表明NPI1和NPI2可以通过堆积作用、静电作用、氢键等作用方式与G-四链体结合,使得它们对G-四链体具有很高亲和性(Ka>107 L/mol)。     

光谱法研究有机农药污染物与DNA的相互作用

利用紫外光谱、荧光光谱及圆二色谱(CD)等光谱方法研究了有机农药敌敌畏(DDVP)、乐果(DIM)、氧化乐果(OME)及生物农药申嗪霉素的有效成分吩嗪-1-羧酸(PCA)与端粒脱氧核糖核酸(DNA)间的相互作用。 结果表明,有机农药分子可能主要以嵌入模式与DNA结合,DDVP、DIM、OME以及PCA与端粒DNA之间的表观结合常数分别为：1.17×106、1.48×106、4.52×105和1.80×106 L/mol,与DNA结合能力的大小顺序为PCA＞DIM＞DDVP＞OME。 这些有机农药分子明显不利于DNA双螺旋结构的稳定性。 有机农药分子的嵌入削弱了DNA碱基对之间的π-π堆积作用,对DNA的二级结构有一定的影响,使得DNA的双螺旋结构变得松散。     

Interaction of an antidepressant buzepide methiodide with DNA immobilized on the glassy carbon electrode

In the present study, a DNA-biosensor was prepared using immobilization technique to investigate the interaction between an antidepressant, buzepide methiodide (BZP) and calf thymus DNA. BZP showed a quasireversible peak in Britton-Robinson (BR) buffer of pH 5 at bare glassy carbon electrode (GCE). At DNA modified GCE, the peak potential of BZP was observed to be shifted towards positive potential revealing intercalative mode of binding. The binding constant and stoichiometry between DNA and BZP are calculated to be 1.908×10(5)M(-1) and 0.982, respectively. The spectroscopic techniques viz., spectrofluorescence and UV-vis absorption have also been employed to understand the interaction between BZP and DNA. The results serve as a reference for the interaction of BZP with DNA base pairs in the natural environment of living cells.     

DNA-interaction studies of a copper(II) complex containing ceftobiprole drug using molecular modeling and multispectroscopic methods

Abstract

The interaction of the [Cu(cef)(phen)Cl₂] complex with calf-thymus DNA (ct-DNA) at physiological pH was investigated by UV-visible spectrophotometry, fluorescence measurement, dynamic viscosity measurements, circular dichroism spectroscopy, and molecular modeling. UV-vis spectra showed 5?nm bathochromic shift of the absorption band at 270?nm along with significant hypochromicity for the absorption band of the complex. The binding constant obtained of UV-vis (1?×?10⁵ M^?1) is more in keeping with intercalators and suggests this binding mode. Moreover, thermodynamic parameters indicated that hydrogen bond and van der Waals interactions play main roles in the binding of [Cu(cef)(phen)Cl₂] to ct-DNA. In addition, [Cu(cef)(phen)Cl₂]-DNA docked model is in approximate correlation with the experimental results.     

Microcalorimetry and spectroscopic studies on the binding of dye janus green blue to deoxyribonucleic acid

The interaction of the phenazinium dye janus green blue (JGB) with deoxyribonucleic acid was investigated using isothermal titration calorimetry and thermal melting experiments. The calorimetric data were supplemented by spectroscopic studies. Calorimetry results suggested the binding affinity of the dye to DNA to be of the order of 10⁵ M^?1. The binding was predominantly entropy driven with a small negative favorable enthalpy contribution to the standard molar Gibbs energy change. The binding became weaker as the temperature and salt concentration was raised. The temperature dependence of the standard molar enthalpy changes yielded negative values of standard molar heat capacity change for the complexation revealing substantial hydrophobic contribution in the DNA binding. An enthalpy–entropy compensation behavior was also observed in the system. The salt dependence of the binding yielded the release of 0.69 number of cations on binding of each dye molecule. The non-polyelectrolytic contribution was found to be the predominant force in the binding interaction. Thermal melting studies revealed that the DNA helix was stabilized against denaturation by the dye. The binding was also characterized by absorbance, resonance light scattering and circular dichroism spectral measurements. The binding constants from the spectral results were close to those obtained from the calorimetric data. The energetic aspects of the interaction of the dye JGB to double-stranded DNA are supported by strong binding revealed from the spectral data.