scholarly journals Identification of Binding Mode of a Platinum (II) Complex, (DIP), and Calf Thymus DNA

2011 ◽  
Vol 2011 ◽  
pp. 1-7 ◽  
Author(s):  
Nahid Shahabadi ◽  
Soheila Kashanian ◽  
Azadeh Fatahi
Keyword(s):  
Melting Temperature ◽  
Double Helix ◽  
Spectral Characteristics ◽  
Binding Mode ◽  
Calf Thymus Dna ◽  
Specific Viscosity ◽  
Pt Complex ◽  
Calf Thymus ◽  
Double Helix Structure ◽  
Dna Double Helix

The Pt(II) complex, PtCl2(DIP) (DIP = chelating dinitrogen ligand: 4,7-diphenyl-1,10-phenanthroline), was synthesized and characterized by elemental analysis (CHN) and NMR and UV-vis techniques. The binding of this complex to calf thymus DNA was investigated using various physicochemical methods such as spectrophotometric, circular dichroism, spectrofluorometric, melting temperature, and viscosimetric techniques. Upon addition of the complex, important changes were observed in the characteristic UV-Vis bands (hyperchromism) of calf thymus DNA (CT-DNA): increase in melting temperature, sharp increase in specific viscosity of DNA, and induced CD spectral changes. Also the fluorescence spectral characteristics and interaction of Pt complex with DNA have been studied. Pt bound to DNA showed a marked decrease in the fluorescence intensity. The results show that both the complex and the NR molecules can intercalate competitively into the DNA double-helix structure. The experimental results show that the mode of binding of the this complex to DNA is classical intercalation.

Viscometric Studies on the Stability of DNA-Proflavine Complex

1972 ◽  
Vol 27 (11) ◽  
pp. 1385-1387 ◽  
Author(s):  
G. C. Das ◽  
N. N. Das Gupta
Keyword(s):  
Double Helix ◽  
Thermal Stabilization ◽  
Binding Mode ◽  
Stable Configuration ◽  
P Value ◽  
Binding Modes ◽  
Specific Viscosity ◽  
Complex Variation ◽  
The Stability ◽  
Dna Double Helix

Viscometric technique has been used to estimate the relative contributions of strong and weak binding modes towards thermal stabilization of the Proflavine-DNA complex. Variation of the ratio of the specific viscosity of the dye-bound DNA to that of the DNA solution (η′sp/η sp) with different dye to DNA-phosphate ratios (D/P) shows that the saturation is attained at D/P value of about 0.2. This effect is more pronounced at lower ionic strengths. Heat-induced helix-coil transition curves at different D/P values at a fixed ionic strength of the buffer reveal a gradual shift towards higher temperature with the increase of D/P and levelling off at D/P of about 0.22. It is suggested that only the strong binding mode causes thermal stabilization of the DNA double helix and the double helix having all the possible intercalating sites saturated by the dye molecules attains the most stable configuration.

Binding of an anionic fluorescent probe with calf thymus DNA and effect of salt on the probe–DNA binding: a spectroscopic and molecular docking investigation

RSC Advances ◽  
2014 ◽  
Vol 4 (108) ◽  
pp. 63549-63558 ◽  
Author(s):  
Saptarshi Ghosh ◽  
Pronab Kundu ◽  
Bijan Kumar Paul ◽  
Nitin Chattopadhyay
Keyword(s):  
Molecular Docking ◽  
Dna Binding ◽  
Fluorescent Probe ◽  
Binding Mode ◽  
Docking Studies ◽  
Calf Thymus Dna ◽  
Molecular Docking Studies ◽  
Biologically Relevant ◽  
Calf Thymus

Binding mode of biologically relevant anionic probe, ANS, with ctDNA is divulged from spectroscopic and molecular docking studies.

DNA-binding, photocleavage and anti-cancer activity of tin(IV) corrole

2018 ◽  
Vol 22 (09n10) ◽  
pp. 739-750 ◽  
Author(s):  
An-Na Xie ◽  
Zhao Zhang ◽  
Hua-Hua Wang ◽  
Atif Ali ◽  
Dong-Xu Zhang ◽  
...  
Keyword(s):  
Dna Binding ◽  
Binding Mode ◽  
Calf Thymus Dna ◽  
Free Base ◽  
Docking Analysis ◽  
Calf Thymus ◽  
Anti Cancer ◽  
Active Intermediate ◽  
Dna Scission ◽  
Cancer Activity

A new tin(IV) corrole, 5,10,15-tris(4-methoxycarbonylphenyl) corrole tin(IV) (1-Sn) was synthesized and characterized. The DNA binding, photocleavage and anti-cancer activity were studied and compared with its free-base. The interaction of 1-Sn and its free-base 1 with calf thymus DNA had been investigated by spectroscopic methods, viscosity measurements and molecular docking analysis. The results revealed that 1-Sn and 1 could interact with calf thymus DNA via an outside groove binding mode. Furthermore, although 1 displayed no photonuclease activity, 1-Sn exhibited good photonuclease activity as indicated by agarose gel electrophoresis, and superoxide anion might be the active intermediate for the DNA scission. Finally, 1 was nontoxic but 1-Sn displayed cytotoxicity towards A549 tumor cell lines.

scholarly journals Fluorescence and Molecular Simulation Studies on the Interaction between Imidazolium-Based Ionic Liquids and Calf Thymus DNA

Processes ◽  
2019 ◽  
Vol 8 (1) ◽  
pp. 13
Author(s):  
Khairulazhar Jumbri ◽  
Mohd Azlan Kassim ◽  
Normawati M. Yunus ◽  
Mohd Basyaruddin Abdul Rahman ◽  
Haslina Ahmad ◽  
...  
Keyword(s):  
Ionic Liquids ◽  
Double Helix ◽  
Structural Features ◽  
Docking Studies ◽  
Calf Thymus Dna ◽  
Valuable Insight ◽  
Screening Model ◽  
Calf Thymus ◽  
A Minor ◽  
Insight Into

This work presents a molecular level investigation on the nature and mode of binding between imidazolium-based ionic liquids (ILs) ([Cnbim]Br where n = 2, 4, 6) with calf thymus DNA. This investigation offers valuable insight into the mechanisms of interactions that can affect the structural features of DNA and possibly cause the alteration or inhibition of DNA function. To expedite analysis, the study resorted to using molecular docking and COnductor like Screening MOdel for Real Solvents (COSMO-RS) in conjunction with fluorescence spectroscopic data for confirmation and validation of computational results. Both the fluorescence and docking studies consistently revealed a weak interaction between the two molecules, which corresponded to the binding energy of a stable docking conformation in the range of −5.19 to −7.75 kcal mol−1. As predicted, the rod-like structure of imidazolium-based ILs prefers to bind to the double-helix DNA through a minor groove. Interestingly, the occurrence of T-shape π-π stacking was observed between the amine group in adenine that faces the aromatic ring of imidazole. In addition, data of COSMO-RS for the interaction of individual nucleic acid bases to imidazolium-based ILs affirmed that ILs showed a propensity to bind to different bases, the highest being guanine followed by cytosine, thymine, uracil, and adenine.

scholarly journals Affinity studies of hypocrellin B and mono-cysteine substituted hypocrellin B with CT-DNA using spectroscopic methods

2005 ◽  
Vol 19 (5,6) ◽  
pp. 259-266 ◽  
Author(s):  
Shaohua Wei ◽  
Jiahong Zhou ◽  
Yuying Feng ◽  
Deyin Huang ◽  
Xuesong Wang ◽  
...  
Keyword(s):  
Deoxyribonucleic Acid ◽  
Double Helix ◽  
Cd Spectroscopy ◽  
Base Stacking ◽  
Calf Thymus ◽  
Visible Spectra ◽  
Hypocrellin B ◽  
Uv Visible ◽  
Dna Double Helix ◽  
Ct Dna

The interaction of anticancer drug hypocrellin B (HB) and mono-cysteine substituted hypocrellin B (MCHB) with calf thymus deoxyribonucleic acid (CT-DNA) has been investigated using spectral methods. The results of UV–visible spectra showed that the HB and MCHB can intercalate into the base-stacking domain of the CT-DNA double helix. Further studies based on fluorescence spectroscopy and circular dichroism (CD) spectroscopy also supported the intercalation mechanism.

scholarly journals Synthesis of New Five Coordinated Copper(II) and Nickel(II) Complexes of L-Valine and Kinetic Study of Copper(II) with Calf Thymus DNA

2002 ◽  
Vol 9 (1-2) ◽  
pp. 81-90 ◽  
Author(s):  
Aijaz Ahmad Tak ◽  
Farukh Arjmand ◽  
Sartaj Tabassum
Keyword(s):  
Metal Ion ◽  
Binding Mode ◽  
Molar Conductance ◽  
Order Conditions ◽  
Calf Thymus Dna ◽  
First Order ◽  
Reversible Redox ◽  
Calf Thymus ◽  
Vis Spectroscopy ◽  
Kinetics Of

Five coordinated novel complexes of CuII and NiII have been synthesized from benzil and 1,3- diaminopropane-CuII/NiII complex and characterized by elemental analysis, i.r., n.m.r., e.p.r, molar conductance and u.v-vis, spectroscopy. The complexes are ionic in nature and exhibit pentaeoordinated geometry around the metal ion. The reaction kinetics of C25H36N5O2CuCl with calf thymus DNA was studied by u.v-vis, spectroscopy in aqueous medium. The complex after interaction with calf thymus DNA shows shift in the absorption spectrum and hypochromicity indicating an intercalative binding mode. The Kobs values have been calculated under pseudo-first order conditions. The redox behaviour of complex C25H36N5O2CuCl in the presence and in the absence of calf thymus DNA in the aqueous solution has been investigated by cyclic voltammetry. The cyclic voitammogram exhibits one quasi-reversible redox wave corresponding to CuII/CuI redox couple with E1/2 values of -0.377 and -0.237 V respectively at a scan rate of 0.1Vs-1 .On interaction with calf thymus DNA, the complex C25H36N5O2CuCl exhibits shifts in both Ep as well as in E1/2 values, indicating strong binding of the complex to the calf thymus DNA.

scholarly journals The Importance and Challenges for Analytical Chemistry in Proteomics Analysis

2021 ◽  
Vol 8 (10Years) ◽  
pp. 51-73
Author(s):  
Weliton Batiston ◽  
Emanuel Carrilho
Keyword(s):  
Analytical Chemistry ◽  
Double Helix ◽  
X Ray Diffraction ◽  
Proteomics Analysis ◽  
Linus Pauling ◽  
X Ray ◽  
Francis Crick ◽  
Double Helix Structure ◽  
The Right ◽  
Dna Double Helix

Although Linus Pauling had an exceptional scientific contribution to the study of chemical bonds, reported in his book The Nature of Chemical Bond, the lousy image he got for the X-ray diffraction drove him to an unstable structure with an unreal DNA triple helix publication. Oppositely, for the consecration of James Watson & Francis Crick, they had the opportunity to enter science history using the right image of X-ray to propose the famous DNA double helix structure correctly. This chapter of science is an excellent example of how analytical chemistry performance affects horizons and scientific advances. Today the complexity of the systems is more significant and understanding how all proteins truly work into cells and organisms is the current challenge from proteomics. Comprehending how analysis is carried out and how instruments work could promote new insights to improve the analytical performance in proteomics. Here we described an overview based on our expertise on the analytical chemistry toolkit for proteomics analysis: shotgun, bottom-up, middle-down, top-down, and native proteomics, and their inherent instrumentation technologies. In addition, a detailed discussion of the analytical figures of merit in proteomics analysis is provided. We also address the limitations in multidimensional liquid chromatography and tandem mass spectrometry platforms. Furthermore, we present some perspectives in bioinformatics, mathematical modeling simulations, and chemometrics tools, as well.

Sign in / Sign up

Export Citation Format

Share Document