Primary photoprocesses in cationic 5,10,15,20-meso-tetrakis(4-N-methylpyridiniumyl)porphyrin and its transition metal complexes bound with nucleic acids

2003 ◽  
Vol 07 (11) ◽  
pp. 766-774 ◽  
Author(s):  
Vladimir S. Chirvony
Keyword(s):  
Excited States ◽  
Transition Metal Complexes ◽  
Photophysical Properties ◽  
Binding Mode ◽  
Axial Ligand ◽  
Guanosine Monophosphate ◽  
Groove Binding ◽  
Base Pairs ◽  
Excited Complex ◽  
Groove Binding Mode

Photophysical properties of meso-tetrakis(4-N-methylpyridiniumyl)porphyrin ( TMpyP 4) and its metallocomplexes M (II) TMpy P4 ( M = Zn , Cu , Ni , Co ) bound to natural DNA and synthetic poly-, oligo- and mononucleotides are considered with a primary emphasis placed upon intermolecular interaction of the photoexcited porphyrins with the nearest environment. Quenching of the fluorescent S 1 (but not triplet T 1) state due to guanine to porphyrin electron transfer is observed for TMpyP 4 intercalated between GC base pairs of the double-strand helixes, whereas in the case of TMpyP 4 complexed with guanosine monophosphate (GMP) both S 1 and T 1 states of the porphyrin are quenched. Furthermore, a dependence of the efficiency of TMpyP 4 triplet state quenching by the dissolved molecular oxygen from air on the porphyrin localization enables one to readily distinguish porphyrin groove binding mode from intercalation. Excited states of the TMpyP 4 complexes with transition metals, in spite of their very short lifetimes, also interact with nucleic acid components by means of an axial ligand binding/release to/from the metal. A possible structure of the five-coordinate excited complex (“exciplex”) formed in case of CuTMpyP 4 groove binding to some single- and double-strand polynucleotides is discussed.

Metal-to-Ligand Charge Transfer Excited States in π-Conjugated Systems

2001 ◽  
Vol 665 ◽  
Author(s):  
Yiting Li ◽  
C. Ed Whittle ◽  
Keith A. Walters ◽  
Kevin D. Ley ◽  
Kirk S. Schanze
Keyword(s):  
Optical Properties ◽  
Charge Transfer ◽  
Excited States ◽  
Transition Metal Complexes ◽  
Transient Absorption ◽  
Photophysical Properties ◽  
Transient Absorption Spectroscopy ◽  
Conjugated Oligomers ◽  
Conjugated Systems ◽  
Ligand Charge Transfer

ABSTRACTThis paper overviews recent work that examined the optical properties of mono-disperse, PPE-based π-conjugated oligomers that contain a 2,2-bipyridine-5,5'-diyl metal coordinating unit. The photophysical properties of the free oligomers and metallated oligomers that contain the -Ru(bpy)22+ and -Re(CO)3Cl transition metal complexes coordinated to the bpy-diyl unit have been characterized by absorption, photoluminescence and transient absorption spectroscopy. In addition, we report the photophysics of a novel organometallic “square” that features “sides” consisting of a PPE-type π-conjugated oligomer and “corners” that consist of (dbubpy)PtII(acetylide)2 units (where dbubpy = 4,4'-di-tert-butyl-2,2'-bipyridine).

scholarly journals Theoretical Study of Sequence Selectivity and Preferred Binding Mode of Psoralen with DNA

2007 ◽  
Vol 2007 ◽  
pp. 1-5 ◽  
Author(s):  
Patricia Saenz-Méndez ◽  
Rita C. Guedes ◽  
Daniel J. V. A. dos Santos ◽  
Leif A. Eriksson
Keyword(s):  
Molecular Dynamics ◽  
Theoretical Study ◽  
Binding Mode ◽  
Minor Groove Binding ◽  
Binding Modes ◽  
Groove Binding ◽  
Base Pairs ◽  
Sequence Selectivity ◽  
Molecular Dynamics Methods ◽  
Low Efficiency

Psoralen interaction with two models of DNA was investigated using molecular mechanics and molecular dynamics methods. Calculated energies of minor groove binding and intercalation were compared in order to define a preferred binding mode for the ligand. We found that both binding modes are possible, explaining the low efficiency for monoadduct formation from intercalated ligands. A comparison between the interaction energy for intercalation between different base pairs suggests that the observed sequence selectivity is due to favorable intercalation in 5′-TpA in (AT)n sequences.

From Intercalation to Groove Binding: Switching the DNA-Binding Mode of Isostructural Transition-Metal Complexes

2014 ◽  
Vol 20 (11) ◽  
pp. 3089-3096 ◽  
Author(s):  
Haslina Ahmad ◽  
Ashley Wragg ◽  
Will Cullen ◽  
Claire Wombwell ◽  
Anthony J. H. M. Meijer ◽  
...  
Keyword(s):  
Dna Binding ◽  
Transition Metal ◽  
Metal Complexes ◽  
Transition Metal Complexes ◽  
Binding Mode ◽  
Groove Binding

scholarly journals Binding of BRACO19 to a Telomeric G-Quadruplex DNA Probed by All-Atom Molecular Dynamics Simulations with Explicit Solvent

Molecules ◽  
2019 ◽  
Vol 24 (6) ◽  
pp. 1010 ◽  
Author(s):  
Babitha Machireddy ◽  
Holli-Joi Sullivan ◽  
Chun Wu
Keyword(s):  
Molecular Dynamics ◽  
Binding Energy ◽  
Free Ligand ◽  
Binding Mode ◽  
Dna Duplex ◽  
Telomeric Dna ◽  
Groove Binding ◽  
Relative Population ◽  
G Quadruplex ◽  
Groove Binding Mode

Although BRACO19 is a potent G-quadruplex binder, its potential for clinical usage is hindered by its low selectivity towards DNA G-quadruplex over duplex. High-resolution structures of BRACO19 in complex with neither single-stranded telomeric DNA G-quadruplexes nor B-DNA duplex are available. In this study, the binding pathway of BRACO19 was probed by 27.5 µs molecular dynamics binding simulations with a free ligand (BRACO19) to a DNA duplex and three different topological folds of the human telomeric DNA G-quadruplex (parallel, anti-parallel and hybrid). The most stable binding modes were identified as end stacking and groove binding for the DNA G-quadruplexes and duplex, respectively. Among the three G-quadruplex topologies, the MM-GBSA binding energy analysis suggested that BRACO19′s binding to the parallel scaffold was most energetically favorable. The two lines of conflicting evidence plus our binding energy data suggest conformation-selection mechanism: the relative population shift of three scaffolds upon BRACO19 binding (i.e., an increase of population of parallel scaffold, a decrease of populations of antiparallel and/or hybrid scaffold). This hypothesis appears to be consistent with the fact that BRACO19 was specifically designed based on the structural requirements of the parallel scaffold and has since proven effective against a variety of cancer cell lines as well as toward a number of scaffolds. In addition, this binding mode is only slightly more favorable than BRACO19s binding to the duplex, explaining the low binding selectivity of BRACO19 to G-quadruplexes over duplex DNA. Our detailed analysis suggests that BRACO19′s groove binding mode may not be stable enough to maintain a prolonged binding event and that the groove binding mode may function as an intermediate state preceding a more energetically favorable end stacking pose; base flipping played an important role in enhancing binding interactions, an integral feature of an induced fit binding mechanism.

Interaction of Methylene Blue with Synthetic Polynucleotide Poly(dA)-Poly(dT)

2018 ◽  
Vol 13 (01) ◽  
pp. 29-36 ◽  
Author(s):  
Marine A. Parsadanyan ◽  
Ara P. Antonyan ◽  
Poghos O. Vardevanyan ◽  
Hakob E. Sngryan
Keyword(s):  
Methylene Blue ◽  
Binding Site ◽  
Binding Constant ◽  
Binding Mode ◽  
Groove Binding ◽  
Base Pairs ◽  
Strong Binding ◽  
Synthetic Polynucleotide ◽  
Strong Mode

The interaction of methylene blue (MB) with poly(dA)-poly(dT) has been studied. It was revealed that MB binds to this polynucleotide by strong and weak modes. It was shown that the strong binding mode of MB is realized by semi-intercalation. Apart from the strong mode, this ligand binds to AT-sequences by weak electrostatic modes as well. Values of the binding constant [Formula: see text] and number of base pairs [Formula: see text] per binding site of MB for the mentioned modes were determined. It was shown that at the interaction with AT sequences MB does not behave itself as a groove binding compound.

Thermodynamics of interaction of meso-tetra-(4N-oxyethylpyridyl) porphyrin and its Cu(II)- and Co(II)- containing derivatives with A and B forms of DNA

2017 ◽  
Vol 21 (11) ◽  
pp. 731-738
Author(s):  
Ani A. Avetisyan ◽  
Ishkhan V. Vardanyan ◽  
Yeva B. Dalyan
Keyword(s):  
Ionic Strength ◽  
Spectral Data ◽  
Binding Constant ◽  
Binding Mode ◽  
Water Soluble ◽  
Binding Mechanism ◽  
Groove Binding ◽  
Low Ionic Strength ◽  
Circular Dichroïsm ◽  
Groove Binding Mode

The interaction of water soluble meso-tetra-(4N-oxyethylpyridyl) porphyrin (TOEPyP4) and its Cu(II)- and Co(II)-containing derivatives (CuTOEPyP4 and CoTOEPyP4) with A and B forms of DNA at low ionic strength was studied via UV-vis spectrophotometry and Circular Dichroism. It is shown that the binding constant of TOEPyP4 and CuTOEPyP4 with A–DNA is two times larger than with B–DNA, and the binding constant of CoTOEPyP4 does not depend on the form of DNA. The thermodynamical analysis based on spectral data indicates the preferable entropic character of porphyrins binding with both forms of DNA. This result shows that at low ionic strength the external groove binding mode is a preferred binding mechanism of these porphyrins with both forms of DNA.

Synthesis, Characterization, DNA-Binding Study of C15H12O4N2 and its Lanthanide Complexes

2013 ◽  
Vol 749 ◽  
pp. 516-520
Author(s):  
Chao Chao Song ◽  
Xiang Rong Liu ◽  
Shun Sheng Zhao ◽  
Jun Wang ◽  
Jing Wen Ren ◽  
...  
Keyword(s):  
Dna Binding ◽  
Ir Spectroscopy ◽  
Elemental Analysis ◽  
Lanthanide Complexes ◽  
Binding Mode ◽  
Binding Study ◽  
Groove Binding ◽  
Groove Binding Mode

A new series complexes of Ln nitrate with H2L, where Ln stands for La, Ce, Pr, Nd, Sm, Eu, Gd, Tb, Dy, Ho, Er, Yb, and H2L is 2-carboxybenzaldehyde- (4-hydroxy) benzoylhydrazone, were synthesized. Elemental analysis and IR spectroscopy were used to characterize and found that the complexes were Ln (HL)2(NO3)·4EtOH·4H2O type. The binding mode of complexes with CTDNA was investigated by UV-Vis titration and emission titration, suggesting that the complexes bind with CTDNA in a non-covalent groove binding mode.

The magnetic properties, DNA/HSA binding and nuclease activity of manganese N-confused porphyrin

2016 ◽  
Vol 20 (05) ◽  
pp. 624-638 ◽  
Author(s):  
Su-Hong Peng ◽  
Biao-Biao Lv ◽  
Atif Ali ◽  
Jia-Min Wang ◽  
Xiao Ying ◽  
...  
Keyword(s):  
Nuclease Activity ◽  
Binding Mode ◽  
Active Species ◽  
Zero Field ◽  
Zero Field Splitting ◽  
Groove Binding ◽  
Binding Properties ◽  
Calf Thymus ◽  
Ct Dna ◽  
Groove Binding Mode

The first oxidative cleavage of DNA by manganese [Formula: see text]-confused porphyrin [chloro(2-aza-2-methyl-5,10,15,20-tetrakis([Formula: see text]-chlorophenyl)-21-carbaporphyrin)manganese(III), 1] using H2O2 as oxidant agent and its magnetic, calf thymus DNA(ct-DNA)- and human serum albumin (HSA) binding properties were investigated. The magnitude of the axial (D) zero-field splitting for the mononuclear Mn(III) center in 1 was determined to be approximately 2.71 cm[Formula: see text] by paramagnetic susceptibility measurements. The DNA- and HSA binding experimental results showed that 1 bound to ct-DNA via an outside groove binding mode and the hydrophobic cavity located in subdomain IIA of HSA with the binding constant of 4.144 × 105 M[Formula: see text] and [Formula: see text] 106 M[Formula: see text], respectively. Thermodynamic parameters revealed that both DNA- and HSA binding were spontaneous process. The main driven forces were the hydrogen bond and van der Waals for the former, but hydrophobic interaction for the latter, which were further confirmed by molecular docking modeling. Manganese [Formula: see text]-confused porphyrin 1 could cleave the supercoiled plasmid DNA efficiently in the presence of hydrogen peroxide. Hydroxyl radical ([Formula: see text]OH) was found the active species for oxidative damage of DNA.

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