两种卤代荧光素与DNA作用荧光特性的研究

对四溴荧光素(TBF)、四氯四溴荧光素(TTF)两种卤代荧光素与DNA作用的荧光特性进行了研究,结果表明：TBF和TTF的最大λ_ex/λ_em为518/540 nm和540/560 nm,DNA的存在会使TBF和TTF的荧光强度发生变化;荧光猝灭实验和偏振实验表明：TBF与DNA的作用方式可能是沟槽键合和嵌插作用,而TTF 嵌插在了DNA碱基对之间;盐效应实验表明：溶液离子强度的大小会影响TBF和TTF与DNA的作用;荧光法测得TBF和TTF与DNA的结合常数为1×106和2×106 L·mol-1,结合位点数为0.62和0.16。     

Deoxyribonucleic Acid and Bovine Serum Albumin Interaction with the Asymmetric Schiff Base Ligand and Its Molybdenum (VI) Complex: Multi Spectroscopic and Molecular Docking Studies

The interaction of an asymmetric Schiff base ligand derived from allylamine and 2,3-dihydroxybenzaldehyde and its molybdenum (VI) complex with deoxyribonucleic acid (DNA) and bovine serum albumin (BSA) were studied using spectroscopic and molecular docking methods. The spectroscopic results revealed that the DNA and BSA affinity for binding the Mo(VI) complex is greater than its ligand. Furthermore, the molecular docking calculations showed that H-bond, hydrophobic, π-π and π-cation interactions had the dominant roles in the stability of the compound-BSA complexes. The DNA interaction results suggested that the compounds interacted with DNA by the groove binding mechanism.     

Investigation on the interaction of glipizide with bovine hemoglobin by spectroscopy and molecular docking

This study aims to investigate the interaction between glipizide and bovine hemoglobin using fluorescence quenching, circular dichroism spectroscopy in various temperatures (293, 303, and 310?K) and molecular docking methods. The results demonstrated that glipizide could cause strong fluorescence quenching of bovine hemoglobin by a dynamic quenching mechanism, during which the hydrophobic interaction played a dominant role in this system. The order of magnitude of binding constant is 10⁴, and the number of binding site in the system was close to 1. It also showed that tyrosine residues and tryptophan residues were both involved in the binding of glipizide with bovine hemoglobin, and was closer to the later. Circular dichroism spectra revealed that the conformation of bovine hemoglobin was changed during the binding reaction. The interaction of the system was studied by both spectroscopic method and molecular docking simulation, and the conclusions are consistent.     

Interaction Mechanism of Trp-Arg Dipeptide with Calf Thymus DNA

The interaction between Trp-Arg dipetide (WR) and calf thymus DNA (ctDNA) in pH 7.4 Tris-HCl buffer was investigated by multi-spectroscopic techniques and molecular modeling. The fluorescence spectroscopy and UV absorption spectroscopy indicated that WR interacted with ctDNA in a minor groove binding mode and the binding constant was 4.1?×?10³. The ionic strength effect and single-stranded DNA (ssDNA) quenching effect further verified the minor groove binding mode. Circular dichroism spectroscopy (CD) was employed to measure the conformation change of ctDNA in the presence of WR. The molecular modeling results illustrated that electrostatic interaction and groove binding coexisted between them and the hydrogen bond and Van der Waals were main acting forces. All the above methods can be widely used to investigate the interaction of peptide with nucleic acids, which contributes to design the structure of new and efficient drugs.

Study on the spectral behavior of four fluorescent dyes and their interactions with nucleic acid by the luminescence method

The spectral characteristics of four fluorescent dyes: tetrabromofluorescein (TBF), tetrachlorotetrabromofluorescein (TTF), lissamine rhodamine RB 200 (LSR) and methylene violet (MV) were studied by fluorescence and paper substrate room temperature phosphorescence (PS-RTP) methods. The factors affected the luminescence were investigated including pH value, paper substrate and drying conditions, etc. The fluorescence polarizations and PS-RTP lifetimes of these compounds were obtained. The intensity of fluorescence and phosphorescence of TBF and TTF increased in the presence of DNA. Contrarily, that of LSR and MV decreased. The fluorescence quenching and polarization studies indicate that TTF, LSR and MV intercalate into DNA base pairs. In addition, the interaction of TBF with DNA is the comprehensive interaction of two modes: intercalation and groove binding. It was also found that ionic strength could affect the binding of fluorescent dyes and DNA.     

Multiple Spectroscopic,Docking and Cytotoxic Study of a Synthesized 2,2′ Bipyridin Phenyl Isopentylglycin Pt(II) Nitrate Complex: Human Serum Albumin and Breast Cancer Cell Line of MDA-MB231 as Targets

In the present study, the biological activities of a new synthesized Pt(II)-complex, 2,2′ bipyridinphenyl isopentylglycin Pt(II) nitrate was investigated via its interaction with the most important blood carrier protein of human serum albumin (HSA), using fluorescence and Far-UV circular dichroism (CD) spectroscopic techniques and also molecular docking. Moreover, cytotoxicity activity of the complex was studied against breast cancer cell line of MDA MB231 using 3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyltetrazolium bromide (MTT) assay. The Pt(II)-complex has a strong ability to quench the intrinsic fluorescence of HSA through a static quenching mechanism. According fluorescence quenching data, the binding parameters of the interaction were calculated and showed that hydrophobic interaction has an important role. The molecular docking results in coherent with fluorescence measurements illustrated that Pt(II) complex can bind to HSA at one position that located in the hydrophobic cavity of groove between drug site I and II. Also, experimental data on driving force in binding site was confirmed whereas theoretical results demonstrated Pt(II) complexinteract to HSA by hydrophobic interaction. Far-UV-CD results showed that Pt(II)-complex induced an increasing in the content of α-helical structure of the protein and stabilized it. Also, MTT assay represented growth inhibitory effect of the complex toward the breast cancer cell line.     

Binding Studies of Isoxsuprine Hydrochloride to Calf Thymus DNA Using Multispectroscopic and Molecular Docking Techniques

In the present work, the interaction of Isoxsuprine (ISX) with Calf thymus DNA (ct-DNA) under physiological conditions (Tris–HCl buffer of pH 7.4) was investigated by using electronic absorption, circular dichroism, viscosity, electrochemical studies, fluorescence techniques, salt effect studies and computational studies. Competitive fluorimetric studies with Hoechst 33258 have shown that ISX exhibit the ability to displace the DNA-bound Hoechst 33258, indicating that it binds to ct-DNA in strong competition with Hoechst 33258 for the minor groove binding. Furthermore, the resulting data showed that ISX cannot displace methylene blue or acridine orange, which are the common intercalator molecules. The viscosity of ct-DNA solution was almost unchanged on addition of ISX and circular dichroism (CD) spectra of ct-DNA showed small changes in the presence of ISX which is in agreement with groove binding mode of interaction. Thus all above studies showed that the ISX drug binds to ct-DNA in a groove binding mode.The salt-effect studies showed the non-electrostatic nature of binding of ISX to ct-DNA. Moreover, molecular docking results support the above experimental data and suggest that ISX prefers to bind on the minor groove of ct-DNA.     

分子对接和荧光光谱法研究槲皮素与β-葡萄糖苷酶的相互作用

结合分子对接法和光谱法,研究了槲皮素与β-葡萄糖苷酶的相互作用及作用机理。首先利用AutoDock 4.2软件对β-葡萄糖苷酶与槲皮素、竞争性抑制剂对硝基苯-β-D-巯基葡萄糖的分子对接分别进行研究,然后采用荧光光谱法研究了槲皮素与β-葡萄糖苷酶的结合反应,并测定了结合常数。结果表明：这种相互作用使β-葡萄糖苷酶发生内源荧光猝灭,属于静态猝灭机制。通过计算得到槲皮素与β-葡萄糖苷酶在17,27和37 ℃下结合常数分别为4.36×104,4.04×104和3.18×104 L·mol-1。氢键和疏水作用对槲皮素与β-葡萄糖苷酶的结合起重要作用,也存在静电作用力。分子对接研究和荧光光谱实验两者相互补充,可从理论和实验两方面协同研究槲皮素与β-葡萄糖苷酶之间的相互作用。     

Molecular interaction of silybin with hyaluronidase: A spectroscopic and molecular docking study

In this study, the molecular interaction of silybin with hyaluronidase was investigated by spectroscopic methods and molecular docking. It was found that silybin had strong ability to quench the intrinsic fluorescence of hyaluronidase by a static quenching procedure. The binding constants were obtained at three temperatures (293, 298, and 310 K). The results of synchronous fluorescence and three-dimensional fluorescence and molecular docking showed that silybin bound into the hyaluronidase cavity site and the binding of silybin to hyaluronidase could induce micro-environmental and conformational changes in hyaluronidase, which resulted in the reduced hyaluronidase activity. The thermodynamic parameter analysis and molecular docking experiments revealed that all types of non-covalent interaction, including hydrogen bonding interaction, van der Waals forces, hydrophobic interaction, and electrostatic interaction were present in the binding process of silybin with hyaluronidase. The results obtained here will provide direct evidence at a molecular level to understand the mechanism of the inhibitory effect of silybin against hyaluronidase.     

分子对接和荧光光谱法研究槲皮素与β-葡萄糖苷酶的相互作用

结合分子对接法和光谱法,研究了槲皮素与β-葡萄糖苷酶的相互作用及作用机理.首先利用AutoDock 4.2软件对β-葡萄糖苷酶与槲皮素、竞争性抑制剂对硝基苯-β-D-琉基葡萄糖的分子对接分别进行研究,然后采用荧光光谱法研究了槲皮素与β-葡萄糖苷酶的结合反应,并测定了结合常数.结果表明:这种相互作用使β-葡萄糖苷酶发生内...     

光谱法研究普利沙星与小牛胸腺DNA的结合作用

利用紫外光谱,荧光光谱及流体动力学方法,研究了普利沙星与小牛胸腺DNA的作用机理。讨论了不同浓度普利沙星与DNA作用的紫外光谱,荧光光谱,磷酸盐效应以及离子强度对两者相互作用的影响,测量了DNA的热变性温度和粘度。从紫外光谱图上看出DNA发生了明显的减色效应, 说明普利沙星可能与DNA发生作用。普利沙星的荧光光谱发生了有规律的猝灭,最大发射峰发生红移, 猝灭常数为3.1×104 L·mol-1, 为静态猝灭,表明普利沙星与DNA结合生成了二元复合物。磷酸盐效应表明普利沙星与DNA的磷酸基团不发生静电作用。普利沙星引起了DNA的热变性温度略微升高(≤7℃)和DNA粘度略微下降, 表明普利沙星与DNA之间不存在插入作用, 只是在DNA的外部发生沟槽作用。     

山姜素与脱氧核糖核酸的相互识别研究

应用荧光光谱法及紫外-可见光谱法研究了生理条件下(pH 7.4)山姜素(ALP)与DNA分子之间的相互识别。考察了不同温度下(25,32和39 ℃),DNA对山姜素荧光猝灭情况。实验发现, DNA能猝灭山姜素的内源性荧光,随着温度的升高,荧光猝灭常数K_SV逐渐减小(K_SV分别为3.288×103, 2.923×103和2.467×103 L·mol-1),并且DNA对山姜素的猝灭速率常数K_q要大于药物小分子与生物大分子之间的最大扩散所控制的碰撞猝灭常数,得出DNA对山姜素的荧光猝灭是单一的静态猝灭过程。DNA与山姜素相互作用紫外-可见光谱显示,DNA不能使得山姜素的吸收峰发生减色效应和红移现象,而山姜素也不能使溴化乙锭-DNA体系的荧光强度及最大荧光峰位置发生变化,即山姜素不和溴化乙锭竞争与DNA的结合位点。DNA热变性实验发现,解链DNA对山姜素的荧光猝灭程度要大于正常DNA的猝灭程度,由此推断山姜素与DNA不存在嵌插作用。同时,I-离子效应和盐效应表明,山姜素与DNA之间主要以沟槽模式相结合。     

Analytical Techniques Used to Detect DNA Binding Modes of Ruthenium(II) Complexes with Extended Phenanthroline Ring

This review describes the analytical techniques used to detect DNA-probes such as Ru(II) complexes with hetero cyclic imidazo phenanthroline (IP) ligands. Studies on drug-DNA interactions are useful biochemical techniques for visualization of DNA both in vitro and in vivo. The interactions of small molecules that binds to DNA are mainly classified into two major classes, one involving covalent binding and another non-covalent binding. Covalent binding in DNA can be irreversible and may leads to inhibition of all DNA processes which subsequently leads to cell death. Usually, covalent interactions leads to permanent changes in the structure of nucleic acids. The non-covalent interaction of molecules with DNA can be due to electrostatic interaction, intercalation and groove binding. These interactions of DNA probes can be explored by various spectroscopic techniques viz. UV–visible, emission, emission quenching spectroscopy, viscosity and thermal denaturation measurements.     

Study on the Interaction of an Anthracycline Disaccharide with DNA by Spectroscopic Techniques and Molecular Modeling

This study was designed to examine the interaction of 4'-O-(a-L-Cladinosyl) daunorubicin (DNR-D5), a disaccharide anthracycline with calf thymus deoxyribonucleic acid (ctDNA) by UV/Vis in combination with fluorescence spectroscopy and molecular modeling techniques under physiological conditions (Britton-Robinson buffer solutions, pH?=?7.4). By the analysis of UV/Vis spectrum, it was observed that upon binding to ctDNA the anthraquinone chromophore of DNR-D5 could slide into the base pairs. Moreover, the large binding constant indicated DNR-D5 had a high affinity with ctDNA. At the same time, fluorescence spectra suggested that the quenching mechanism of the interaction of DNR-D5 to ctDNA was a static quenching type. The binding constants between DNR-D5 and ctDNA were calculated based on fluorescence quenching data at different temperatures. The negative ?G implied that the binding process was spontaneous, and negative ?H and negative ΔS suggested that hydrogen bonding force most likely played a major role in the binding of DNR-D5 to ctDNA. Moreover, the results obtained from molecular docking corroborate the experimental results obtained from spectroscopic investigations.     

光谱法结合分子对接模拟技术研究头孢他啶与胰蛋白酶的相互作用机理

本文主要通过荧光光谱法与分子对接技术研究了在298,303,310 K温度下头孢他啶(CFD)与胰蛋白酶(TRP)之间的作用机制。研究结果表明,CFD与TRP之间是通过1∶1的静态猝灭方式相互作用。依照双对数方程处理荧光猝灭数据得到了CFD与TRP作用的结合常数Ka和结合位点数n。通过热力学方程求得了不同温度下CFD与TRP作用的热力学参数。实验数据表明,它们之间的作用力主要是疏水作用和氢键作用,这与分子对接技术所得的结果是一致的。     

Fluorescence Investigation on the Interaction of a Prevalent Competitive Fluorescent Probe with Entomic Odorant Binding Protein

In recent years, one prevalent competitive fluorescent probe, N-phenyl-1-naphthylamine (1-NPN), was frequently utilized to measure the binding affinity of entomic odorant binding proteins (OBPs) with diverse plant volatiles or pheromones. Nevertheless, the details and model of the binding interaction are still largely unknown, although it is vital to investigate the physiological function of OBPs. Here we studied the binding interaction between 1-NPN and OBP2, a recombinant OBP from eastern honeybee, Apis cerana, by the combination of fluorescence quenching spectra, synchronous fluorescence spectra, ultraviolet spectra, circular dichroism spectra, and molecular docking. The Stern–Volmer curve of the fluorescence quenching of OBP2 by 1-NPN indicated it was a static quenching mechanism, and the binding constants and binding number were determined, respectively. Based on the Förster theory of nonradiation energy transfer (FRET), the binding distance was calculated, and the intrinsic fluorescent energy was predicted to transfer from the donor OBP2 to the acceptor 1-NPN. Synchronous fluorescence spectra and circular dichroism spectra were used to investigate the conformational change in binding progress. The thermodynamic parameters showed that the interaction was mainly driven by hydrophobic force, which was validated by the molecular docking; meanwhile, the binding mode was revealed and one hydrogen bond was found between the nitrogen atom of 1-NPN and Glu29 of OBP2.     

Spectroscopic and Binding Properties of Berberine to DNA and Its Application to DNA Detection

Berberine(BER) binds to the double helical DNA with a high affinity There is only a much smaller hypochromism and no shifts in the absorption spectra when BER binds to calf thymus DNA(CT DNA) The fluorescence yields increase dramatically when BER binds to DNA, with no shifts in the emission maximum. These spectral changes are in contrast to the behavior observed with many fluorescent intercalates Groove binding rather than intercalation was suggested to be the cause of these spectral changes. Consistent with groove binding, for polyamide anion quenching studies showed that the magnitude of K_sv of the bound BER was higher than that of the free BER. The addition of salt to the solution releases the DNA-bound drug action from the groove and causes a decrease in the fluorescence yield. The results of all above studies proved the groove binding of BER to DNA. The large fluorescence enhancements observed when BER binds to DNA and the poor fluorescence yield of BER in the absence of DNA can be used for sensitive detection of DNA The linear concentration range was 0–20μg/ml The limit of detection for CT DNA was 12 ng/ml     

染料木素酯化修饰物与ctDNA的相互作用

在pH7.2的Tris-HCl缓冲溶液中,采用紫外光谱和荧光光谱法研究了2种新型染料木素酯化修饰物,染料木素7-乙酰阿魏酸酯(GenA)和染料木素7,4′-二-乙酰阿魏酸酯(GenDA)与小牛胸腺DNA(ctDNA)的相互作用。随着ctDNA的加入,GenA与GenDA的紫外吸收和荧光光谱的强度均发生不同程度的降低。ctDNA对化合物的荧光猝灭为静态猝灭过程。在293K时化合物与ctDNA的结合常数分别为2.81×106L.mol-1和1.19×104L.mol-1。同时通过I-离子效应、离子强度、DNA熔点、粘度法等研究证实,在该实验条件下,GenA与ctDNA之间具有较强的作用,主要以嵌插方式结合;GenDA主要以沟槽方式与ctDNA作用。     

Study on the effect of protein on drug efficacy: cefonicid sodium–pepsin binding mechanism

The mechanism of interaction between cefonicid sodium and pepsin was investigated by various spectroscopic methods and molecular docking. Cefoncid sodium quenched the intrinsic fluorescence of pepsin at pH of 2.0 to form a new complex in a 1:1 binding mode driven by Van der Waals and hydrogen bonds. The mechanism of quenching was static. The results of molecular docking indicated that the cefonicid sodium-binding site was located in the active site of pepsin. The protein binding rates of cefonicid sodium in gastric juice was calculated and the binding model was established. It is concluded that cefonicid sodium is not suitable for oral administration.     

SYBR Green I: Fluorescence Properties and Interaction with DNA

In this study, we have investigated the fluorescence properties of SYBR Green I (SG) dye and its interaction with double-stranded DNA (dsDNA). SG/dsDNA complexes were studied using various spectroscopic techniques, including fluorescence resonance energy transfer and time-resolved fluorescence techniques. It is shown that SG quenching in the free state has an intrinsic intramolecular origin; thus, the observed >1,000-fold SG fluorescence enhancement in complex with DNA can be explained by a dampening of its intra-molecular motions. Analysis of the obtained SG/DNA binding isotherms in solutions of different ionic strength and of SG/DNA association in the presence of a DNA minor groove binder, Hoechst 33258, revealed multiple modes of interaction of SG inner groups with DNA. In addition to interaction within the DNA minor groove, both intercalation between base pairs and stabilization of the electrostatic SG/DNA complex contributed to increased SG affinity to double-stranded DNA. We show that both fluorescence and the excited state lifetime of SG dramatically increase in viscous solvents, demonstrating an approximate 200-fold enhancement in 100?% glycerol, compared to water, which also makes SG a prospective fluorescent viscosity probe. A proposed structural model of the SG/DNA complex is compared and discussed with results recently reported for the closely related PicoGreen chromophore.