Browse
Submit Data
Databases
API
Help

Dataset Information

17 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Binding of cationic bis-porphyrins linked with p- or m-xylylenediamine and their zinc(II) complexes to duplex DNA.

ABSTRACT: Spectroscopic, viscometric, and molecular docking analysis of binding of cationic bis-porphyrins linked with p- or m-xylylenediamine (H(2)pXy and H(2)mXy) and their zinc(II) complexes (ZnpXy and ZnmXy) to duplex DNA are described. H(2)pXy and H(2)mXy bound to calf thymus DNA (CTDNA) stronger than unichromophoric H(2)TMPyP, and showed exciton-type induced circular dichroism spectra of their Soret bands. The H(2)TMPyP-like units of the metal-free bis-porphyrins did not intercalate into CTDNA, and thus the binding mode is outside binding with intramolecular stacking. ZnpXy showed favorable binding to A.T over G.C region, and should lie in the major groove of A.T region.

SUBMITTER: Ishikawa Y

PROVIDER: S-EPMC6245075 | biostudies-literature | 2008 Dec

REPOSITORIES: biostudies-literature

ACCESS DATA

Json Xml

Publications

Binding of cationic bis-porphyrins linked with p- or m-xylylenediamine and their zinc(II) complexes to duplex DNA.

Ishikawa Yoshinobu Y Yamakawa Naoki N Uno Tadayuki T

Molecules (Basel, Switzerland) 20081215 12

Spectroscopic, viscometric, and molecular docking analysis of binding of cationic bis-porphyrins linked with p- or m-xylylenediamine (H(2)pXy and H(2)mXy) and their zinc(II) complexes (ZnpXy and ZnmXy) to duplex DNA are described. H(2)pXy and H(2)mXy bound to calf thymus DNA (CTDNA) stronger than unichromophoric H(2)TMPyP, and showed exciton-type induced circular dichroism spectra of their Soret bands. The H(2)TMPyP-like units of the metal-free bis-porphyrins did not intercalate into CTDNA, and ...[more]

PMID: 19078853

Similar Datasets

Binding Interactions of Zinc Cationic Porphyrin with Duplex DNA: From B-DNA to Z-DNA.

Project description:Recognition of unusual left-handed Z-DNA by specific binding of small molecules is crucial for understanding biological functions in which this particular structure participates. Recent investigations indicate that zinc cationic porphyrin (ZnTMPyP4) is promising as a probe for recognizing Z-DNA due to its characteristic chiroptical properties upon binding with Z-DNA. However, binding mechanisms of the ZnTMPyP4/Z-DNA complex remain unclear. By employing time-resolved UV-visible absorption spectroscopy in conjunction with induced circular dichroism (ICD), UV-vis, and fluorescence measurements, we examined the binding interactions of ZnTMPyP4 towards B-DNA and Z-DNA. For the ZnTMPyP4/Z-DNA complex, two coexisting binding modes were identified as the electrostatic interaction between pyridyl groups and phosphate backbones, and the major groove binding by zinc(II) coordinating with the exposed guanine N₇. The respective contribution of each mode is assessed, allowing a complete scenario of binding modes revealed for the ZnTMPyP4/Z-DNA. These interaction modes are quite different from those (intercalation and partial intercalation modes) for the ZnTMPyP4/B-DNA complex, thereby resulting in explicit differentiation between B-DNA and Z-DNA. Additionally, the binding interactions of planar TMPyP4 to DNA were also investigated as a comparison. It is shown that without available virtual orbitals to coordinate, TMPyP4 binds with Z-DNA solely in the intercalation mode, as with B-DNA, and the intercalation results in a structural transition from Z-DNA to B-ZNA. These results provide mechanistic insights for understanding ZnTMPyP4 as a probe of recognizing Z-DNA and afford a possible strategy for designing new porphyrin derivatives with available virtual orbitals for the discrimination of B-DNA and Z-DNA.

| S-EPMC5979451 | biostudies-literature

<i>meso</i>-Thiophenium Porphyrins and Their Zn(II) Complexes: A New Category of Cationic Photosensitizers.

Project description:A new category of cationic meso-thiophenium porphyrins are introduced as possible alternatives to the popular meso-pyridinium porphyrins. Combinations of cationic porphyrins bearing meso-2-methylthiophenium and meso-4-hydroxyphenyl moieties T2(OH)2M (A2B2 type) and T(OH)3M (AB3 type) along with their zinc(II) complexes T2(OH)2MZn and T(OH)3MZn, are reported. The increase in the number of thienyl groups attached to the meso-positions of the porphyrin derivatives (A2B2 frame) has been shown to impart longer fluorescence lifetimes and stronger photocytotoxicity toward A549 lung cancer cells, as evident with T2(OH)2M and its corresponding diamagnetic metal complex T2(OH)2MZn. The photoactivated T2(OH)2MZn imparts an early stage reactive oxygen species (ROS) upregulation and antioxidant depletion in A549 cells and contributes to the strongest oxidative stress-induced cell death mechanism in the series. The DFT calculations of the singlet-triplet energy gap (ΔE) of all the four hydrophilic thiophenium porphyrin derivatives establish the potential applicability of these cationic photosensitizers as PDT agents.

| S-EPMC7549270 | biostudies-literature

Organoplatinum(II) Complexes Self-Assemble and Recognize AT-Rich Duplex DNA Sequences.

Project description:The specific recognition of AT-rich DNA sequences opens up the door to promising diagnostic and/or therapeutic strategies against gene-related diseases. Here, we demonstrate that amphiphilic PtII complexes of the type [Pt(dmba)(N∧N)]NO3 (dmba = N,N-dimethylbenzylamine-κN, κC; N∧N = dpq (3), dppz (4), and dppn (5)) recognize AT-rich oligonucleotides over other types of DNA, RNA, and model proteins. The crystal structure of 4 shows the presence of significant π-stacking interactions and a distorted coordination sphere of the d8 PtII atom. Complex 5, containing the largest π-conjugated ligand, forms supramolecular assemblies at high concentrations under aqueous environment. However, its aggregation can be promoted in the presence of DNA at concentrations as low as 10 μM in a process that "turns on" its excimer emission around 600 nm. Viscometry, gel electrophoresis, and theoretical calculations demonstrate that 5 binds to minor groove when self-assembled, while the monomers of 3 and 4 intercalate into the DNA. The complexes also inhibit cancer cell growth with low-micromolar IC50 values in 2D tissue culture and suppress tumor growth in 3D tumor spheroids with a multicellular resistance (MCR) index comparable to that of cisplatin.

| S-EPMC8456496 | biostudies-literature

Tris-(2-pyridyl)-pyrazolyl Borate Zinc(II) Complexes: Synthesis, DNA/Protein Binding and In Vitro Cytotoxicity Studies.

Project description:Zn(II) complexes bearing tris[3-(2-pyridyl)-pyrazolyl] borate (Tppy) ligand (1-3) was synthesized and examined by spectroscopic and analytical tools. Mononuclear [TppyZnCl] (1) has a Zn(II) centre with one arm (pyrazolyl-pyridyl) dangling outside the coordination sphere which is a novel finding in TppyZn(II) chemistry. In complex [TppyZn(H2O)][BF4] (2) hydrogen bonding interaction of aqua moiety stabilizes the dangling arm. In addition, solution state behaviour of complex 1 confirms the tridentate binding mode and reactivity studies show the exogenous axial substituents used to form the [TppyZnN3] (3). The complexes (1-3) were tested for their ability to bind with Calf thymus (CT) DNA and Bovine serum albumin (BSA) wherein they revealed to exhibit good binding constant values with both the biomolecules in the order of 104-105 M-1. The intercalative binding mode with CT DNA was confirmed from the UV-Visible absorption, viscosity, and ethidium bromide (EB) DNA displacement studies. Further, the complexes were tested for in vitro cytotoxic ability on four triple-negative breast cancer (TNBC) cell lines (MDA-MB-231, MDA-MB-468, HCC1937, and Hs 578T). All three complexes (1-3) exhibited good IC50 values (6.81 to 16.87 μM for 24 h as seen from the MTS assay) results which indicated that these complexes were found to be potential anticancer agents against the TNBC cells.

| S-EPMC8659194 | biostudies-literature

Comparison of the Binding Geometry of Free-Base and Hexacoordinated Cationic Porphyrins to A- and B-Form DNA.

Project description:Although the transition from B-DNA to the A-form is essential for many biological concerns, the properties of this transition have not been resolved. The B to A equilibrium can be analyzed conveniently because of the significant changes in circular dichroism (CD) and absorption spectrum. CD and linear dichroism (LD) methods were used to examine the binding of water-soluble meso-tetrakis(N-methylpyridinium-4-yl)porphyrin (TMPyP) and its derivatives, Co-TMPyP, with B- and A-calf thymus DNA. B- to A-transitions occurred when the physiological buffer was replaced with a water-ethanol mixture (∼80 v/v %), and the fluorescence emission spectra of TMPyP bound to DNA showed a different pattern under ethanol-water conditions and water alone. The featureless broad emission bands of TMPyP were split into two peaks near at 658 and 715 nm in the presence of DNA under an aqueous solution. In the case of an ethanol-water system, however, the emission bands are split in two peaks near at 648 and 708 nm and 656 and 715 nm with and without DNA, respectively. This may be due to a change in the solution polarity. On the basis of the CD and LD data, TMPyP interacts with B-DNA via intercalation at a low ratio under a low ionic strength, 1 mM sodium phosphate. On the other hand, the interaction with A-DNA (80 v/v % ethanol-water system) occurs in a nonintercalating manner. This difference might be because the structural conformations, such as the groove of A-DNA, are not as deep as in B-DNA and the bases are much more tilted. In the case of Co-TMPyP, porphyrin binds preferably via an outside self-stacking mode with B- and A-DNA.

| S-EPMC6641412 | biostudies-literature

Bis(imidazole-?N)bis-(nitrato-?O)zinc(II).

Project description:The title complex, [Zn(NO(3))(2)(C(3)H(4)N(2))(2)], contains a Zn(II) centre with a slightly distorted tetra-hedral coordination environment, involving two N atoms from imidazole ligands and two O atoms from nitrate anions. The imino NH groups participate in inter-molecular N-H?O hydrogen bonds.

| S-EPMC2970476 | biostudies-literature

Bis(dimethyl sulfoxide-?O)bis(saccharinato-?N)-zinc(II).

Project description:The title compound, [Zn(C(7)H(4)N(2)O(3)S)(2)(C(2)H(6)OS)(2)], is a neutral four-coordinate complex with a tetra-hedral geometry. The metal atom is surrounded by the two dimethyl sulfoxide (DMSO) ligands, each coordinating through the O atom, and two anionic saccharinate (1,1,3-trioxo-2,3-dihydro-1?(6),2-benzo-thia-zol-2-ide) ligands coordinating through the N atom. The tetra-hedral geometry is slightly distorted as is evident from the N-Zn-N bond angle of 113.85?(6)°, the O-Zn-O bond angle of 98.92?(6)° and O-Zn-N bond angles of 116.96?(6) and 103.93?(6)°. The Zn-N bond lengths are 1.9742?(15) and 2.0025?(16)?Å. The Zn-O bond lengths are 1.9806?(14)?Å and 1.9468?(14)?Å. The DMSO ligand coordinates through the lone pair of electrons on the O atom, as can be seen from the Zn-O-S bond angle of 131.30?(8)°.

| S-EPMC3238599 | biostudies-literature

Bis(?-5-nitro-2-oxidobenzoato)bis-[triaqua-zinc(II)].

Project description:The title complex mol-ecule, [Zn(2)(C(7)H(3)NO(5))(2)(H(2)O)(6)], is a centrosymmetric dimer containing two zinc(II) cations with distorted octa-hedral geometries provided by the O atoms of three water mol-ecules and the two bridging bidentate 5-nitro-salicylate ligands. The separation between the metal centres in the dimer is 3.1790?(11)?Å. The crystal structure is stabilized by O-H?O hydrogen bonds, one of which intra-dimeric, linking the dimers into a three-dimensional network.

| S-EPMC2971764 | biostudies-literature

σ-GeH and Germyl Cationic Pt(II) Complexes.

Project description:The low electron count Pt(II) complexes [Pt(NHC')(NHC)][BArF] (where NHC is a N-heterocyclic carbene ligand and NHC' its metalated form) react with tertiary hydrogermanes HGeR3 at room temperature to generate the 14-electron platinum(II) germyl derivatives [Pt(GeR3)(NHC)2][BArF]. Low-temperature NMR studies allowed us to detect and characterize spectroscopically some of the σ-GeH intermediates [Pt(η2-HGeR3)(NHC')(NHC)][BArF] that evolve into the platinum-germyl species. One of these compounds has been characterized by X-ray diffraction studies, and the interaction of the H-Ge bond with the platinum center has been analyzed in detail by computational methods, which suggest that the main contribution is the donation of the H-Ge to a σ*(Pt-C) orbital, but backdonation from the platinum to the σ*(Ge-H) orbital is significant. Primary and secondary hydrogermanes also produce the corresponding platinum-germyl complexes, a result that contrasts with the reactivity observed with primary silanes, in which carbon-silicon bond-forming reactions have been reported. According to density functional theory calculations, the formation of Pt-Ge/C-H bonds is both kinetically and thermodynamically preferred over the competitive reaction pathway leading to Pt-H/C-Ge bonds.

| S-EPMC9949701 | biostudies-literature

Aspartate-Based CXCR4 Chemokine Receptor Binding of Cross-Bridged Tetraazamacrocyclic Copper(II) and Zinc(II) Complexes.

Project description:The CXCR4 chemokine receptor is implicated in a number of diseases including HIV infection and cancer development and metastasis. Previous studies have demonstrated that configurationally restricted bis-tetraazamacrocyclic metal complexes are high-affinity CXCR4 antagonists. Here, we present the synthesis of Cu(2+) and Zn(2+) acetate complexes of six cross-bridged tetraazamacrocycles to mimic their coordination interaction with the aspartate side chains known to bind them to CXCR4. X-ray crystal structures for three new Cu(2+) acetate complexes and two new Zn(2+) acetate complexes demonstrate metal-ion-dependent differences in the mode of binding the acetate ligand concomitantly with the requisite cis-V-configured cross-bridged tetraazamacrocyle. Concurrent density functional theory molecular modelling studies produced an energetic rationale for the unexpected [Zn(OAc)(H2 O)](+) coordination motif present in all of the Zn(2+) cross-bridged tetraazamacrocycle crystal structures, which differs from the chelating acetate [Zn(OAc)](+) structures of known unbridged and side-bridged tetraazamacrocyclic Zn(2+) -containing CXCR4 antagonists.

| S-EPMC5224883 | biostudies-literature

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

Tweets

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data