scholarly journals Spectrophotometric Studies on the Thermodynamics of the ds-DNA Interaction with Irinotecan for a Better Understanding of Anticancer Drug-DNA Interactions

2013 ◽  
Vol 2013 ◽  
pp. 1-8 ◽  
Author(s):  
Reza Hajian ◽  
Tan Guan Huat
Keyword(s):  
Dna Binding ◽  
Binding Constant ◽  
Double Helix ◽  
Dna Interaction ◽  
High Concentration ◽  
Competitive Reaction ◽  
Spectrophotometric Methods ◽  
Enthalpy And Entropy Changes ◽  
The One ◽  
Ct Dna

The ds-DNA binding properties of irinotecan (CPT-11) including binding constant, thermodynamic parameter, and thermal denaturation (Tm) have been systematically studied by spectrophotometric methods. The binding of CPT-11 to ds-DNA is quite strong as indicated by its remarkable hypochromicity and equilibrium binding constant (Kb). The van't Hoff plot of 1/Tversus ln Kbsuggests that the CPT-11 binds endothermically to ct-DNA which is characterized by large positive enthalpy and entropy changes. According to the polyelectrolyte theory, the charge release (Z), when ct-DNA interacts with CPT-11, is +0.98, which corresponds very well to the one positive charge carried by CPT-11. TheKbat a low concentration of salt is dominated by electrostatic interaction (98.5%) while that at a high concentration of salt is weakly controlled by nonelectrostatic processes (19.0%). A moderate stabilization of the double helix ds-DNA occurs when CPT-11 binds to ds-DNA as indicated by the increase inTmof ct-DNA by approximately 15°C in the presence of CPT-11. The CPT-11 is stabilized by intercalation in the DNA (binding constant,K[irinotecan-DNA] = 5.8 × 104 mol−1 L) and displaces the NR dye from the NR-DNA complex (K[NR-DNA] = 2.7 × 104 mol−1 L) in a competitive reaction.

scholarly journals DNA Interaction and DNA Cleavage Studies of a New Platinum(II) Complex Containing Aliphatic and Aromatic Dinitrogen Ligands

2011 ◽  
Vol 2011 ◽  
pp. 1-10 ◽  
Author(s):  
Nahid Shahabadi ◽  
Soheila Kashanian ◽  
Maryam Mahdavi ◽  
Noorkaram Sourinejad
Keyword(s):  
Dna Cleavage ◽  
Helical Structure ◽  
Dna Interaction ◽  
Van Der Waals Interactions ◽  
Double Helical Structure ◽  
Intercalative Mode ◽  
Physico Chemical ◽  
Calf Thymus ◽  
Enthalpy And Entropy Changes ◽  
Ct Dna

A new Pt(II) complex, [Pt(DIP)(LL)](NO3)2(in which DIP is 4,7-diphenyl-1,10-phenanthroline and LL is the aliphatic dinitrogen ligand,N,N-dimethyl-trimethylenediamine), was synthesized and characterized using different physico-chemical methods. The interaction of this complex with calf thymus DNA (CT-DNA) was investigated by absorption, emission, circular dichroism (CD), and viscosity measurements. The complex binds to CT-DNA in an intercalative mode. The calculated binding constant,Kb, was  M−1. The enthalpy and entropy changes of the reaction between the complex and CT-DNA showed that the van der Waals interactions and hydrogen bonds are the main forces in the interaction with CT-DNA. In addition, CD study showed that phenanthroline ligand insert between the base pair stack of double helical structure of DNA. It is remarkable that this complex has the ability to cleave the supercoiled plasmid.

Synthesis, Characterization, DNA Binding, and Photocleavage of [Ru(bpy)2(MFIP)]2+ and [Ru(phen)2(MFIP)]2+

2008 ◽  
Vol 61 (9) ◽  
pp. 725 ◽  
Author(s):  
Lifeng Tan ◽  
Sheng Zhang ◽  
Xiaohua Liu ◽  
Yue Xiao
Keyword(s):  
Mass Spectrometry ◽  
Dna Binding ◽  
1H Nmr Spectroscopy ◽  
Binding Properties ◽  
Experimental Conditions ◽  
Spectrophotometric Methods ◽  
Calf Thymus ◽  
Pbr322 Dna ◽  
Ct Dna ◽  
Dna Binding Properties

The new ligand 2-(5-methyl-furan-2-yl)imidazo[4,5-f][1, 10]phenanthroline (MFIP) and its complexes [Ru(bpy)2(MFIP)]2+ 1 (bpy = 2,2′-bipyridine) and [Ru(phen)2(MFIP)]2+ 2 (phen = 1,10-phenanthroline) were synthesized and characterized by elemental analysis, mass spectrometry, and 1H NMR spectroscopy. The DNA binding properties of the two complexes were investigated by different spectrophotometric methods and viscosity measurements. The results suggest that both complexes bind to calf thymus DNA (CT-DNA) through intercalation, and both complexes can enantioselectively interact with CT-DNA. The Λ enantiomers of both complexes are slightly predominant for binding to CT-DNA over the Δ enantiomer. When irradiated at 400 nm, the two complexes promote the photocleavage of pBR322 DNA, and complex 2 cleaves DNA more effectively than complex 1 under comparable experimental conditions. Furthermore, mechanism studies reveal that singlet oxygen (1O2) plays a significant role in the photocleavage.

DNA-Binding and Photocleavage Behaviour of [Ru(bpy)2(MDPZ)]2+

2008 ◽  
Vol 61 (5) ◽  
pp. 376 ◽  
Author(s):  
Lifeng Tan ◽  
Hui Chao ◽  
Junjie Fei ◽  
Guojun Su ◽  
Sheng Zhang ◽  
...  
Keyword(s):  
Mass Spectrometry ◽  
Nmr Spectroscopy ◽  
Dna Binding ◽  
1H Nmr Spectroscopy ◽  
Luminescent Probe ◽  
Binding Properties ◽  
Spectrophotometric Methods ◽  
Molecular Light Switch ◽  
Ct Dna ◽  
Dna Binding Properties

The new ligand MDPZ (MDPZ = 7,7′-methylenedioxyphenyldipyrido[3,2-a:2′,3′-c]-phenazine and its RuII complex [Ru(bpy)2(MDPZ)]2+ (phen = 1,10-phenanthroline) was synthesized and characterized by elemental analysis, mass spectrometry, and 1H NMR spectroscopy. The DNA-binding properties of [Ru(bpy)2(MDPZ)]2+ were investigated by different spectrophotometric methods and viscosity measurements. The results suggest that the complex binds to CT-DNA through intercalation, and can enantioselectively interact with CT-DNA. Although the [Ru(bpy)2(MDPZ)]2+ complex does not show the characteristics of a molecular ‘light switch’ for DNA, [Ru(phen)2(MDPZ)]2+ may serve as a sensitive luminescent probe for DNA. Also, when irradiated at 365 nm, the complex promotes the photocleavage of pBR 322 DNA.

DNA Binding of Iron(II)-Phenanthroline Complexes: Effect of Methyl Substitution on Thermodynamic Parameters

2008 ◽  
Vol 63 (1) ◽  
pp. 37-46 ◽  
Author(s):  
◽  
Naoki Yoshiokab ◽  
Hidenari Inoueb
Keyword(s):  
Free Energy ◽  
Dna Binding ◽  
Thermodynamic Parameters ◽  
Binding Constant ◽  
Binding Free Energy ◽  
Hydrogen Atoms ◽  
Methyl Substitution ◽  
Total Binding ◽  
Electrostatic Binding ◽  
Ct Dna

The influence of methyl substitution on the thermodynamic parameters for the binding of [Fe(DMP)3]2+ and [Fe(TMP)3]2+ (DMP = 4,7-dimethyl-1,10-phenanthroline, TMP = 3,4,7,8-tetramethyl- 1,10-phenanthroline) to calf thymus DNA (ct-DNA) has been studied by determining their equilibrium binding constants (Kb) at various salt concentrations and temperatures. Kb of the iron(II) complexes to ct-DNA decreases with the salt concentration in the solution, suggesting considerable electrostatic interaction in the ct-DNA binding of the iron(II) complexes. In contrast, Kb of the DNA binding increases with temperature, indicating that the DNA binding reaction of the complex is endothermic and entropically driven. The evaluation of the non-electrostatic binding constant (K0t) based on polyelectrolyte theory has revealed that the K0t portions of the total binding constant (Kb) are relatively large and reach 46.4% for [Fe(DMP)3]2+ at [Na+] = 0.075 M and 43.9% for [Fe(TMP)3]2+ at [Na+] = 0.100 M. The contribution of non-electrostatic binding free energy (ΔG0t ) to total binding free energy change (ΔG0) is extremely large, i. e. > 90% for both iron(II) complexes at [Na+] = 0.05 M, suggesting that the stabilization of the DNA binding is mainly contributed from the non-electrostatic process. The effect of methyl substitution on electrostatic (ΔG0pe) and non-electrostatic (ΔG0t ) binding free energy changes has been systematically evaluated using the quantity of ΔΔG0pe and ΔΔG0t relative to that of the parent iron(II) complex, [Fe(phen)3]2+. The results indicate that the substitution of hydrogen atoms in the phen ligand by methyl groups decreases slightly the electrostatic binding free energy changes, but tremendously increases the non-electrostatic ones to yield net binding free energy changes which are more favorable for the ct-DNA binding.

Protamine-DNA interaction

1978 ◽  
Vol 36 (2) ◽  
pp. 200-201
Author(s):  
D.P. Bazett-Jones ◽  
F.P. Ottensmeyer
Keyword(s):  
Small Volume ◽  
Double Helix ◽  
Dna Interaction ◽  
Dark Field ◽  
Sperm Head ◽  
Nuclear Proteins ◽  
Field Electron Microscopy ◽  
Dark Field Electron ◽  
Dna Double Helix ◽  
Positively Charged

Dark field electron microscopy has been used for the study of the structure of individual macromolecules with a resolution to at least the 5Å level. The use of this technique has been extended to the investigation of structure of interacting molecules, particularly the interaction between DNA and fish protamine, a class of basic nuclear proteins of molecular weight 4,000 daltons.Protamine, which is synthesized during spermatogenesis, binds to chromatin, displaces the somatic histones and wraps up the DNA to fit into the small volume of the sperm head. It has been proposed that protamine, existing as an extended polypeptide, winds around the minor groove of the DNA double helix, with protamine's positively-charged arginines lining up with the negatively-charged phosphates of DNA. However, viewing protamine as an extended protein is inconsistent with the results obtained in our laboratory.

scholarly journals Mechanism of NanR gene repression and allosteric induction of bacterial sialic acid metabolism

2021 ◽  
Vol 12 (1) ◽  
Author(s):  
Christopher R. Horne ◽  
Hariprasad Venugopal ◽  
Santosh Panjikar ◽  
David M. Wood ◽  
Amy Henrickson ◽  
...  
Keyword(s):  
Sialic Acid ◽  
Dna Binding ◽  
Protein Interactions ◽  
Acid Metabolism ◽  
Environmental Changes ◽  
Dna Interaction ◽  
Protein Protein Interactions ◽  
Nutrient Source ◽  
Cryo Electron Microscopy ◽  
Close Proximity

AbstractBacteria respond to environmental changes by inducing transcription of some genes and repressing others. Sialic acids, which coat human cell surfaces, are a nutrient source for pathogenic and commensal bacteria. The Escherichia coli GntR-type transcriptional repressor, NanR, regulates sialic acid metabolism, but the mechanism is unclear. Here, we demonstrate that three NanR dimers bind a (GGTATA)3-repeat operator cooperatively and with high affinity. Single-particle cryo-electron microscopy structures reveal the DNA-binding domain is reorganized to engage DNA, while three dimers assemble in close proximity across the (GGTATA)3-repeat operator. Such an interaction allows cooperative protein-protein interactions between NanR dimers via their N-terminal extensions. The effector, N-acetylneuraminate, binds NanR and attenuates the NanR-DNA interaction. The crystal structure of NanR in complex with N-acetylneuraminate reveals a domain rearrangement upon N-acetylneuraminate binding to lock NanR in a conformation that weakens DNA binding. Our data provide a molecular basis for the regulation of bacterial sialic acid metabolism.

scholarly journals High concentration Brownian coagulation in jet flow using two enhancement formulations

2012 ◽  
Vol 16 (5) ◽  
pp. 1519-1523
Author(s):  
Pei-Feng Lin ◽  
Di-Chong Wu ◽  
Ze-Fei Zhu
Keyword(s):  
Volume Fraction ◽  
Taylor Series Expansion ◽  
Expansion Method ◽  
High Volume ◽  
Jet Flow ◽  
High Concentration ◽  
Brownian Coagulation ◽  
Planar Jet ◽  
Ultra Fine Particle ◽  
The One

Ultra-fine particle coagulation by Brownian motion at high concentration in planar jet flow is simulated. A Taylor-Series Expansion Method of Moments is employed to solve the particle general dynamic equation. The volume fraction gets high value, very closes to that at the nozzle exit. As the vortex pairing develops, the high volume fraction region rolls out and mixes with the low value region. The enhancement factor given by Trzeciak et al. will be less than one at some specific outer positions, which seems to be less accurate than the one given by Heine et al.

Sign in / Sign up

Export Citation Format

Share Document