Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

The binding of adenosine(5')tetraphospho(5')adenosine to calf thymus histones measured by non-equilibrium dialysis.

ABSTRACT: Binding of adenosine(5')tetraphospho(5')adenosine (Ap4A) to histones of calf thymus was investigated by non-equilibrium dialysis. Histone H1 interacts with the dinucleotide via two strong sites and competes with Mg2+ ions. Intrinsic dissociation constants were 1.6 +/- 0.1 microM and 11 +/- 1 microM for zero and 0.4 mm-Mg2+ concentration respectively. Binding of poly(dT) and of other nucleotides to histone H1 was measured in an [3H]Ap4A-competition assay. The tendency to form complexes among nucleotides was highest for bisnucleoside tetraphosphates and decreased in the order poly(dT) greater than or equal to Ap4A approximately Gp4G greater than Ap4 much greater than Ap3A approximately Ap5A greater than or equal to ATP, GTP and dTTP. The co-ordination complex derived from Ap4A and cis-diammine-dichloroplatinum(II) was not reactive. The other histones of calf thymus also bound Ap4A with affinities decreasing in the order H4 approximately H3 greater than H1 greater than H2b greater than H2a. Ap4A stimulated the exchange of histone H1 between nucleosomes, but this effect was referred to ionic strength. It did not bind to assembled nucleosomes. Binding of Ap4A to histone H1 was decreased by salt (NaCl). At physiological saline concentration the value of the dissociation constant is commensurable with the value of the Ap4A concentration in the nucleus and thus indicative of complex-formation in vivo.

SUBMITTER: Just G

PROVIDER: S-EPMC1148332 | biostudies-other | 1987 Sep

REPOSITORIES: biostudies-other

ACCESS DATA

Json Xml

Similar Datasets

Cysteine in calf-thymus histones.

Project description:1. Calf-thymus histones contain cysteine, which is present almost entirely in the arginine-rich fraction F3 to the extent of about 1mole in 15000g. weight of the histone. 2. The cysteine in fraction F3 is readily available to thiol reagents and the protein yields an approximately equivalent amount of cysteic acid on oxidation with performic acid.

| S-EPMC1264744 | biostudies-other

Sedimentation equilibrium and other physicochemical studies on the lysine-rich fraction of calf thymus histones.

Project description:1. The lysine-rich fraction (Ia+Ib, or f1) of calf thymus histones was isolated as the sulphate by acid extraction. 2. Sedimentation-equilibrium measurements with interference optics showed that this fraction was monodisperse with a molecular weight of 19500+/-2000. 3. The ;apparent molecular weight' calculated from the sedimentation-equilibrium studies varied markedly with concentration. The large second virial coefficient implied by such variation was attributed to the very high charge/mass ratio of this relatively small protein. Estimates of the charge were made from the values of this virial coefficient. 4. The very large value of the virial coefficient explains anomalies in the earlier reports of the molecular weight of this histone and also why the z-average molecular weight can appear to be lower than the weight-average molecular weight. 5. The differences of the specific refractive increments, and the partial specific volumes, between dialysed and undialysed solutions of this histone fraction could also be attributed to its high molecular charge, which was estimated from these differences and agreed, within the expected limits, with the value deduced from the second virial coefficient. 6. Sedimentation-velocity measurements combined with the known molecular weight imply that lysine-rich histone has a high frictional ratio and an extended shape. Optical-rotatory-dispersion measurements indicated that it had a low helical content.

| S-EPMC1187204 | biostudies-other

N-Terminal acetyl-peptides from two calf thymus histones.

Project description:1. The same N-terminal peptide was isolated from two major calf thymus histone fractions, F2al and F2a2. 2. The structure of the peptides is N-acetylseryl-glycyl-arginine, and the yields account for most of the N-acetyl groups previously found in these histones. 3. Some other peptides not giving a ninhydrin reaction were also investigated.

| S-EPMC1198638 | biostudies-other

A FRACTIONATION OF THE HISTONES OF GROUP F2A FROM CALF THYMUS.

Project description:1. The calf-thymus histone group F2a has been separated into two subfractions by stepwise precipitation with acetone from acid solution. 2. Carboxymethyl-cellulose and dextran-gel column chromatography and a method involving dialysis against ethanol have also given the subfractions, but the acetone-hydrochloric acid method has proved to be the most practicable. 3. The two subfractions differ significantly in their amino acid composition and in the pattern of peptides obtained by tryptic digestion. Both fractions have a very low content of N-terminal amino acids and contain acetyl groups.

| S-EPMC1206417 | biostudies-other

Non-equilibrium pronucleus histones require gametal factor Lsm1 induced major satellite RNA decay

Project description:The development of a multicellular organism with various organs and tissues is a complex but highly concerted process, in which cells acquire different identities through exquisite spatiotemporal regulations called cell fate decision. Here, we Lsm1 targets non-coding major satellite RNAs in mouse zygote, which is required for the non-equilibrium epigenetic modification, especially H3K9me3 establishment during early embryo development.

2022-07-05 | GSE179556 | GEO

Interaction of 6 mercaptopurine with calf thymus DNA--deciphering the binding mode and photoinduced DNA damage.

Project description:DNA is one of the major intracellular targets for a wide range of anticancer and antibiotic drugs. Elucidating the binding between small molecules and DNA provides great help in understanding drug-DNA interactions and in designing of new and promising drugs for clinical use. The ability of small molecules to bind and interfere with DNA replication and transcription provides further insight into how the drugs control the expression of genes. Interaction of an antimetabolite anticancer drug 6 mercaptopurine (6MP) with calf thymus DNA was studied using various approaches like UV-visible spectroscopy, fluorescence spectroscopy, CD, viscosity and molecular docking. UV-visible spectroscopy confirmed 6MP-DNA interaction. Steady state fluorescence experiments revealed a moderate binding constant of 7.48 × 10(3) M(-1) which was consistent with an external binding mode. Competitive displacement assays further confirmed a non-intercalative binding mode of 6MP which was further confirmed by CD and viscosity experiments. Molecular docking further revealed the minimum energy conformation (-119.67 kJ/mole) of the complex formed between DNA and 6MP. Hence, the biophysical techniques and in-silico molecular docking approaches confirmed the groove binding/electrostatic mode of interaction between 6MP and DNA. Further, photo induced generation of ROS by 6MP was studied spectrophotometrically and DNA damage was assessed by plasmid nicking and comet assay. There was a significant increase in ROS generation and consequent DNA damage in the presence of light.

| S-EPMC3981731 | biostudies-literature

Study of the Binding Interaction between Wortmannin and Calf Thymus DNA: Multispectroscopic and Molecular Docking Studies.

Project description:IntroductionWortmannin (WTN) is a steroid metabolite that inhibits phosphatidylinositol 3-kinase and other signaling pathways. Structurally, the WTN consists of a cyclopentanophenanthrene-like structure with several oxygen-rich moieties which have the potential to interact with deoxyribonucleic acid (DNA) molecules.MethodsWe aim to evaluate the WTN and calf thymus DNA (ct-DNA) interaction with molecular docking using the AutoDock 4.2 software. UV and fluorescence spectroscopy and viscosity techniques were performed to confirm the in silico analysis.ResultsMolecular docking showed that the WTN interacted with ct-DNA via hydrogen bonds at guanine-rich sequences. The number of hydrogen bonds between the WTN and DNA was 1-2 bonds (average 1.2) per WTN molecule. The in silico binding constant was 2 × 103 M-1. UV spectroscopy showed that the WTN induced a hyperchromic feature without wavelength shifting. The WTN and DNA interaction led to quenching of DNA-emitted fluorescence. The different concentrations of WTN had no effect on DNA viscosity. Taken together, our results demonstrated WTN interacts with DNA in the nonintercalating mode, which is considered as a new mechanism of action.ConclusionThese results suggest that the WTN may exert its biological effects, at least in part, via interaction with DNA.

| S-EPMC6949734 | biostudies-literature

Conformation and Rheological Properties of Calf-Thymus DNA in Solution.

Project description:Studies of DNA molecule behavior in aqueous solutions performed through different approaches allow assessment of the solute-solvent interactions and examination of the strong influence of conformation on its physicochemical properties, in the presence of different ionic species and ionic concentrations. Firstly, the conformational behavior of calf-thymus DNA molecules in TE buffer solution is presented as a function of temperature. Secondly, their rheological behavior is discussed, as well as the evidence of the critical concentrations, i.e., the overlap and the entanglement concentrations (C* and Ce, respectively) from steady state flow and oscillatory dynamic shear experiments. The determination of the viscosity in the Newtonian plateau obtained from flow curves η ( ) allows estimation of the intrinsic viscosity and the specific viscosities at zero shear when C[η] < 40. At end, a generalized master curve is obtained from the variation of the specific viscosity as a function of the overlap parameter C[η]. The variation of the exponent s obtained from the power law η~ -s for both flow and dynamic results is discussed in terms of Graessley's analysis. In the semi-dilute regime with entanglements, a dynamic master curve is obtained as a function of DNA concentration (CDNA > 2.0 mg/mL) and temperature (10 °C < T < 40 °C).

| S-EPMC6432584 | biostudies-literature

A Supramolecular Interaction of a Ruthenium Complex With Calf-Thymus DNA: A Ligand Binding Approach by NMR Spectroscopy.

Project description:Lawsone itself exhibits interesting biological activities, and its complexation with a metal center can improve the potency. In this context a cytotoxic Ru-complex, [Ru(law)(dppb)(bipy)] (law = lawsone, dppb = 1,4-bis(diphenylphosphino)butane and bipy = 2,2'-bipyridine), named as CBLAU, was prepared as reported. In this work, NMR binding-target studies were performed to bring to light the most accessible interaction sites of this Ru-complex toward Calf-Thymus DNA (CT-DNA, used as a model), in a similar approach used for other metallic complexes with anti-cancer activity, such as cisplatin and carboplatin. Advanced and robust NMR binding-target studies, among them Saturation Transfer Difference (STD)-NMR and longitudinal relaxometry (T1), were explored. The 1H and 31P -NMR data indicate that the structure of Ru-complex remains preserved in the presence of CT-DNA, and some linewidth broadening is also observed for all the signals, pointing out some interaction. Looking at the binding efficiency, the T1 values are highly influenced by the formation of the CBLAU-DNA adduct, decreasing from 11.4 s (without DNA) to 1.4 s (with DNA), where the difference is bigger for the lawsone protons. Besides, the STD-NMR titration experiments revealed a stronger interaction (KD = 5.9 mM) for CBLAU-DNA in comparison to non-complexed lawsone-DNA (KD = 34.0 mM). The epitope map, obtained by STD-NMR, shows that aromatic protons from the complexed lawsone exhibits higher saturation transfer, in comparison to other Ru-ligands (DPPB and bipy), suggesting the supramolecular contact with CT-DNA takes place by the lawsone face of the Ru-complex, possibly by a spatial ?-? stacking involving ?-bonds on nucleic acids segments of the DNA chain and the naphthoquinone group.

| S-EPMC6857657 | biostudies-literature

Relative binding affinities of integrin antagonists by equilibrium dialysis and liquid chromatography-mass spectrometry.

Project description:The integrin ?v?6 is a potential target for treatment of idiopathic pulmonary fibrosis (IPF). Equilibrium dialysis (ED) was investigated for its ability to report ligand binding in an ?v?6 inhibitor screening assay. As a preliminary experiment, an established peptidomimetic inhibitor of the integrin was dialyzed against ?v?6, and the fraction bound (f b) and percentage saturation determined by liquid chromatography-mass spectrometry (LC-MS) analysis. Quantitation of the inhibitor in the two chambers of the ED cartridge revealed an uneven distribution in the presence of ?v?6, corresponding to near saturation binding to the protein (93 ± 3%), while the control (without integrin) showed an equal partitioning of the inhibitor on either side of the dialysis membrane. A competitive ED assay with a 12 component mixture of antagonists was conducted, and the results compared with an established cell adhesion assay for quantifying ?v?6 inhibition of individual antagonists. Compounds clustered into three groupings: those with pIC 50 values between ca. 5.0 and 5.5, which possessed ED f b values indistinguishable from the controls, those with pIC 50s of 6.5 ± 0.2, which exhibited detectable integrin binding (f b 13-25%) in the ED assay, and a single compound of pIC 50 7.2 possessing an f b value of 38%. A good correlation between ED-derived f b and pIC 50 was observed despite the two assays utilizing quite different outputs. These results demonstrate that ED with LC-MS detection shows promise as a rapid ?v?6 integrin antagonist screening assay for mixtures of putative ligands.

| S-EPMC4329580 | 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