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1.
Biochim Biophys Acta Gene Regul Mech ; 1867(3): 195050, 2024 Jul 17.
Article in English | MEDLINE | ID: mdl-39029558

ABSTRACT

Armadillo repeat-containing proteins (ARMCs) are a large family found throughout eukaryotes, which play prominent roles in cell adhesion, signaling and cytoskeletal regulation. The ARMC6 protein is highly conserved in primates, including humans, but to date does not have a clear function beyond initial hints of a link to cancer and telomerase activity. We report here in vitro experiments showing ARMC6 binding to DNA promoter sequences from several cancer-related genes (e.g., EGFR, VEGF and c-MYC), and also to the telomeric RNA repeat (TERRA). ARMC6 binding activity appears to recognize G-quadruplex motifs, which are being increasingly implicated as structure-based protein binding sites in chromosome maintenance and repair. In vivo investigation of ARMC6 function revealed that when this protein is overexpressed in human cell lines, there is different expression of genes connected with oncogenic pathways and those implicated in downstream non-canonical telomerase pathways (e.g., VEGF, hTERT, c-MYC, ESM1, MMP3). ARMC6 is already known to interact with human shelterin protein TRF2 and telomerase. The protein binds G-quadruplex structures and does so preferentially to RNA over DNA. As such, this protein may be an example of how a non-canonical nucleic acid structural motif allows mediation between gene regulation and telomeric chromatin rearrangement pathways.

2.
Int J Mol Sci ; 23(1)2021 Dec 26.
Article in English | MEDLINE | ID: mdl-35008657

ABSTRACT

A series of 1,3,5-triazinyl aminobenzenesulfonamides substituted by aminoalcohol, aminostilbene, and aminochalcone structural motifs was synthesized as potential human carbonic anhydrase (hCA) inhibitors. The compounds were evaluated on their inhibition of tumor-associated hCA IX and hCA XII, hCA VII isoenzyme present in the brain, and physiologically important hCA I and hCA II. While the test compounds had only a negligible effect on physiologically important isoenzymes, many of the studied compounds significantly affected the hCA IX isoenzyme. Several compounds showed activity against hCA XII; (E)-4-{2-[(4-[(2,3-dihydroxypropyl)amino]-6-[(4-styrylphenyl)amino]-1,3,5-triazin-2-yl)amino]ethyl}benzenesulfonamide (31) and (E)-4-{2-[(4-[(4-hydroxyphenyl)amino]-6-[(4-styrylphenyl)amino]-1,3,5-triazin-2-yl)amino]ethyl}benzenesulfonamide (32) were the most effective inhibitors with KIs = 4.4 and 5.9 nM, respectively. In addition, the compounds were tested against vancomycin-resistant Enterococcus faecalis (VRE) isolates. (E)-4-[2-({4-[(4-cinnamoylphenyl)amino]-6-[(4-hydroxyphenyl)amino]-1,3,5-triazin-2-yl}amino)ethyl]benzenesulfonamide (21) (MIC = 26.33 µM) and derivative 32 (MIC range 13.80-55.20 µM) demonstrated the highest activity against all tested strains. The most active compounds were evaluated for their cytotoxicity against the Human Colorectal Tumor Cell Line (HCT116 p53 +/+). Only 4,4'-[(6-chloro-1,3,5-triazin-2,4-diyl)bis(iminomethylene)]dibenzenesulfonamide (7) and compound 32 demonstrated an IC50 of ca. 6.5 µM; otherwise, the other selected derivatives did not show toxicity at concentrations up to 50 µM. The molecular modeling and docking of active compounds into various hCA isoenzymes, including bacterial carbonic anhydrase, specifically α-CA present in VRE, was performed to try to outline a possible mechanism of selective anti-VRE activity.


Subject(s)
Anti-Bacterial Agents/pharmacology , Antineoplastic Agents/pharmacology , Carbonic Anhydrase Inhibitors/pharmacology , Sulfonamides/pharmacology , Vancomycin-Resistant Enterococci/drug effects , Antineoplastic Agents/therapeutic use , Carbonic Anhydrase I/antagonists & inhibitors , Carbonic Anhydrase II/antagonists & inhibitors , Carbonic Anhydrase IX/antagonists & inhibitors , Carbonic Anhydrases/drug effects , HCT116 Cells , Humans , Molecular Docking Simulation , Molecular Dynamics Simulation , Neoplasms/drug therapy , Structure-Activity Relationship
3.
Molecules ; 24(11)2019 May 31.
Article in English | MEDLINE | ID: mdl-31159174

ABSTRACT

Expansions of trinucleotide repeats (TNRs) are associated with genetic disorders such as Friedreich's ataxia. The tumor suppressor p53 is a central regulator of cell fate in response to different types of insults. Sequence and structure-selective modes of DNA recognition are among the main attributes of p53 protein. The focus of this work was analysis of the p53 structure-selective recognition of TNRs associated with human neurodegenerative diseases. Here, we studied binding of full length p53 and several deletion variants to TNRs folded into DNA hairpins or loops. We demonstrate that p53 binds to all studied non-B DNA structures, with a preference for non-B DNA structures formed by pyrimidine (Py) rich strands. Using deletion mutants, we determined the C-terminal DNA binding domain of p53 to be crucial for recognition of such non-B DNA structures. We also observed that p53 in vitro prefers binding to the Py-rich strand over the purine (Pu) rich strand in non-B DNA substrates formed by sequence derived from the first intron of the frataxin gene. The binding of p53 to this region was confirmed using chromatin immunoprecipitation in human Friedreich's ataxia fibroblast and adenocarcinoma cells. Altogether these observations provide further evidence that p53 binds to TNRs' non-B DNA structures.


Subject(s)
DNA/chemistry , DNA/metabolism , Friedreich Ataxia/genetics , Friedreich Ataxia/metabolism , Nucleic Acid Conformation , Trinucleotide Repeat Expansion , Trinucleotide Repeats , Tumor Suppressor Protein p53/metabolism , Gene Expression , Humans , Protein Binding , Protein Interaction Domains and Motifs , Pyrimidines , Recombinant Proteins , Tumor Suppressor Protein p53/chemistry
4.
PLoS One ; 11(12): e0167439, 2016.
Article in English | MEDLINE | ID: mdl-27907175

ABSTRACT

Triplex DNA is implicated in a wide range of biological activities, including regulation of gene expression and genomic instability leading to cancer. The tumor suppressor p53 is a central regulator of cell fate in response to different type of insults. Sequence and structure specific modes of DNA recognition are core attributes of the p53 protein. The focus of this work is the structure-specific binding of p53 to DNA containing triplex-forming sequences in vitro and in cells and the effect on p53-driven transcription. This is the first DNA binding study of full-length p53 and its deletion variants to both intermolecular and intramolecular T.A.T triplexes. We demonstrate that the interaction of p53 with intermolecular T.A.T triplex is comparable to the recognition of CTG-hairpin non-B DNA structure. Using deletion mutants we determined the C-terminal DNA binding domain of p53 to be crucial for triplex recognition. Furthermore, strong p53 recognition of intramolecular T.A.T triplexes (H-DNA), stabilized by negative superhelicity in plasmid DNA, was detected by competition and immunoprecipitation experiments, and visualized by AFM. Moreover, chromatin immunoprecipitation revealed p53 binding T.A.T forming sequence in vivo. Enhanced reporter transactivation by p53 on insertion of triplex forming sequence into plasmid with p53 consensus sequence was observed by luciferase reporter assays. In-silico scan of human regulatory regions for the simultaneous presence of both consensus sequence and T.A.T motifs identified a set of candidate p53 target genes and p53-dependent activation of several of them (ABCG5, ENOX1, INSR, MCC, NFAT5) was confirmed by RT-qPCR. Our results show that T.A.T triplex comprises a new class of p53 binding sites targeted by p53 in a DNA structure-dependent mode in vitro and in cells. The contribution of p53 DNA structure-dependent binding to the regulation of transcription is discussed.


Subject(s)
DNA-Binding Proteins/genetics , DNA/genetics , Transcriptional Activation/genetics , Tumor Suppressor Protein p53/genetics , Binding Sites , DNA/chemistry , DNA-Binding Proteins/chemistry , Humans , Nucleic Acid Conformation , Nucleotide Motifs/genetics , Plasmids/genetics , Promoter Regions, Genetic , Regulatory Sequences, Nucleic Acid/genetics , Sequence Deletion/genetics , Tumor Suppressor Protein p53/chemistry
5.
Biosci Rep ; 36(5)2016 10.
Article in English | MEDLINE | ID: mdl-27634752

ABSTRACT

G-quadruplexes are four-stranded nucleic acid structures that are implicated in the regulation of transcription, translation and replication. Genome regions enriched in putative G-quadruplex motifs include telomeres and gene promoters. Tumour suppressor p53 plays a critical role in regulatory pathways leading to cell cycle arrest, DNA repair and apoptosis. In addition to transcriptional regulation mediated via sequence-specific DNA binding, p53 can selectively bind various non-B DNA structures. In the present study, wild-type p53 (wtp53) binding to G-quadruplex formed by MYC promoter nuclease hypersensitive element (NHE) III1 region was investigated. Wtp53 binding to MYC G-quadruplex is comparable to interaction with specific p53 consensus sequence (p53CON). Apart from the full-length wtp53, its isolated C-terminal region (aa 320-393) as well, is capable of high-affinity MYC G-quadruplex binding, suggesting its critical role in this type of interaction. Moreover, wtp53 binds to MYC promoter region containing putative G-quadruplex motif in two wtp53-expressing cell lines. The results suggest that wtp53 binding to G-quadruplexes can take part in transcriptional regulation of its target genes.


Subject(s)
DNA-Binding Proteins/genetics , G-Quadruplexes , Proto-Oncogene Proteins c-myc/genetics , Tumor Suppressor Protein p53/genetics , Circular Dichroism , DNA/genetics , DNA-Binding Proteins/metabolism , Gene Expression Regulation , HCT116 Cells , Humans , Promoter Regions, Genetic/genetics , Protein Binding , Proto-Oncogene Proteins c-myc/metabolism , Tumor Suppressor Protein p53/metabolism
6.
Bioconjug Chem ; 27(9): 2089-94, 2016 09 21.
Article in English | MEDLINE | ID: mdl-27479485

ABSTRACT

Nucleotides, 2'-deoxyribonucleoside triphosphates (dNTPs), and DNA probes bearing reactive chloroacetamido group linked to nucleobase (cytosine or 7-deazadaenine) through a propargyl tether were prepared and tested in cross-linking with cysteine- or histidine-containing peptides and proteins. The chloroacetamide-modifed dNTPs proved to be good substrates for DNA polymerases in the enzymatic synthesis of modified DNA probes. Modified nucleotides and DNA reacted efficiently with cysteine and cysteine-containing peptides, whereas the reaction with histidine was sluggish and low yielding. The modified DNA efficiently cross-linked with p53 protein through alkylation of cysteine and showed potential for cross-linking with histidine (in C277H mutant of p53).


Subject(s)
Acetamides/chemistry , DNA/chemistry , Nucleotides/chemistry , Peptides/chemistry , Proteins/chemistry , Cysteine/chemistry , Electron Transport , Histidine/chemistry , Models, Molecular , Nucleic Acid Conformation , Protein Conformation
7.
Biochimie ; 128-129: 83-91, 2016.
Article in English | MEDLINE | ID: mdl-27422117

ABSTRACT

The tumor suppressor protein p53 is a key factor in genome stability and one of the most studied of DNA binding proteins. This is the first study on the interaction of wild-type p53 with guanine quadruplexes formed by the human telomere sequence. Using electromobility shift assay and ELISA, we show that p53 binding to telomeric G-quadruplexes increases with the number of telomeric repeats. Further, p53 strongly favors G-quadruplexes folded in potassium over those formed in sodium, thus indicating the telomeric G-quadruplex conformational selectivity of p53. The presence of the quadruplex-stabilizing ligand, N-methyl mesoporphyrin IX (NMM), increases p53 recognition of G-quadruplexes in potassium. Using deletion mutants and selective p53 core domain oxidation, both p53 DNA binding domains are shown to be crucial for telomeric G-quadruplex recognition.


Subject(s)
DNA/chemistry , G-Quadruplexes , Telomere/chemistry , Tumor Suppressor Protein p53/chemistry , Base Sequence , Binding Sites/genetics , Binding, Competitive , Circular Dichroism , DNA/genetics , DNA/metabolism , Electrophoretic Mobility Shift Assay , Enzyme-Linked Immunosorbent Assay , Humans , Mesoporphyrins/chemistry , Mutation , Oligonucleotides/chemistry , Oligonucleotides/genetics , Oligonucleotides/metabolism , Potassium/chemistry , Protein Binding , Tandem Repeat Sequences/genetics , Telomere/genetics , Telomere/metabolism , Tumor Suppressor Protein p53/genetics , Tumor Suppressor Protein p53/metabolism
8.
Chemistry ; 21(45): 16091-102, 2015 Nov 02.
Article in English | MEDLINE | ID: mdl-26377361

ABSTRACT

N-(3-Azidopropyl)vinylsulfonamide was developed as a new bifunctional bioconjugation reagent suitable for the cross-linking of biomolecules through copper(I)-catalyzed azide-alkyne cycloaddition and thiol Michael addition reactions under biorthogonal conditions. The reagent is easily clicked to an acetylene-containing DNA or protein and then reacts with cysteine-containing peptides or proteins to form covalent cross-links. Several examples of bioconjugations of ethynyl- or octadiynyl-modified DNA with peptides, p53 protein, or alkyne-modified human carbonic anhydrase with peptides are given.


Subject(s)
Alkynes/chemistry , Azides/chemistry , Carbonic Anhydrases/chemistry , DNA/chemistry , Indicators and Reagents/chemistry , Peptides/chemistry , Sulfhydryl Compounds/chemistry , Sulfonamides/chemistry , Vinyl Compounds/chemistry , Biological Phenomena , Carbonic Anhydrases/metabolism , Catalysis , Click Chemistry , Copper/chemistry , Cycloaddition Reaction , DNA/metabolism , Humans , Peptides/metabolism
9.
Int J Mol Sci ; 16(2): 3163-77, 2015 Jan 30.
Article in English | MEDLINE | ID: mdl-25647416

ABSTRACT

A study of the effects of salt conditions on the association and dissociation of wild type p53 with different ~3 kbp long plasmid DNA substrates (supercoiled, relaxed circular and linear, containing or lacking a specific p53 binding site, p53CON) using immunoprecipitation at magnetic beads is presented. Salt concentrations above 200 mM strongly affected association of the p53 protein to any plasmid DNA substrate. Strikingly different behavior was observed when dissociation of pre-formed p53-DNA complexes in increased salt concentrations was studied. While contribution from the p53CON to the stability of the p53-DNA complexes was detected between 100 and 170 mM KCl, p53 complexes with circular DNAs (but not linear) exhibited considerable resistance towards salt treatment for KCl concentrations as high as 2 M provided that the p53 basic C-terminal DNA binding site (CTDBS) was available for DNA binding. On the contrary, when the CTDBS was blocked by antibody used for immunoprecipitation, all p53-DNA complexes were completely dissociated from the p53 protein in KCl concentrations≥200 mM under the same conditions. These observations suggest: (a) different ways for association and dissociation of the p53-DNA complexes in the presence of the CTDBS; and (b) a critical role for a sliding mechanism, mediated by the C-terminal domain, in the dissociation process.


Subject(s)
Plasmids/metabolism , Salts/pharmacology , Tumor Suppressor Protein p53/metabolism , Nucleic Acid Conformation , Plasmids/chemistry , Potassium Chloride/pharmacology , Protein Binding/drug effects
10.
Chem Sci ; 6(1): 575-587, 2015 Jan 01.
Article in English | MEDLINE | ID: mdl-28970873

ABSTRACT

New redox labelling of DNA by an azido group which can be chemically transformed to nitrophenyltriazole or silenced to phenyltriazole was developed and applied to the electrochemical detection of DNA-protein interactions. 5-(4-Azidophenyl)-2'-deoxycytidine and 7-(4-azidophenyl)-7-deaza-2'-deoxyadenosine nucleosides were prepared by aqueous-phase Suzuki cross-coupling and converted to nucleoside triphosphates (dNTPs) which served as substrates for incorporation into DNA by DNA polymerase. The azidophenyl-modified nucleotides and azidophenyl-modified DNA gave a strong signal in voltammetric studies, at -0.9 V, due to reduction of the azido function. The Cu-catalyzed click reaction of azidophenyl-modified nucleosides or azidophenyl-modified DNA with 4-nitrophenylacetylene gave nitrophenyl-substituted triazoles, exerting a reduction peak at -0.4 V under voltammetry, whereas the click reaction with phenylacetylene gave electrochemically silent phenyltriazoles. The transformation of the azidophenyl label to nitrophenyltriazole was used for electrochemical detection of DNA-protein interactions (p53 protein) since only those azidophenyl groups in the parts of the DNA not shielded by the bound p53 protein were transformed to nitrophenyltriazoles, whereas those covered by the protein were not.

11.
Biochem Biophys Res Commun ; 456(1): 29-34, 2015 Jan 02.
Article in English | MEDLINE | ID: mdl-25446071

ABSTRACT

Site-specific DNA recognition and binding activity belong to common attributes of all three members of tumor suppressor p53 family proteins: p53, p63 and p73. It was previously shown that heavy metals can affect p53 conformation, sequence-specific binding and suppress p53 response to DNA damage. Here we report for the first time that cadmium, nickel and cobalt, which have already been shown to disturb various DNA repair mechanisms, can also influence p63 and p73 sequence-specific DNA binding activity and transactivation of p53 family target genes. Based on results of electrophoretic mobility shift assay and luciferase reporter assay, we conclude that cadmium inhibits sequence-specific binding of all three core domains to p53 consensus sequences and abolishes transactivation of several promoters (e.g. BAX and MDM2) by 50µM concentrations. In the presence of specific DNA, all p53 family core domains were partially protected against loss of DNA binding activity due to cadmium treatment. Effective cadmium concentration to abolish DNA-protein interactions was about two times higher for p63 and p73 proteins than for p53. Furthermore, we detected partial reversibility of cadmium inhibition for all p53 family members by EDTA. DTT was able to reverse cadmium inhibition only for p53 and p73. Nickel and cobalt abolished DNA-p53 interaction at sub-millimolar concentrations while inhibition of p63 and p73 DNA binding was observed at millimolar concentrations. In summary, cadmium strongly inhibits p53, p63 and p73 DNA binding in vitro and in cells in comparison to nickel and cobalt. The role of cadmium inhibition of p53 tumor suppressor family in carcinogenesis is discussed.


Subject(s)
Cadmium/chemistry , Cobalt/chemistry , DNA-Binding Proteins/chemistry , DNA/chemistry , Membrane Proteins/chemistry , Nickel/chemistry , Nuclear Proteins/chemistry , Tumor Suppressor Proteins/chemistry , Cell Line, Tumor , Dithiothreitol/chemistry , Edetic Acid/chemistry , Humans , Metals/chemistry , Metals, Heavy/chemistry , Protein Binding , Protein Structure, Tertiary , Transcriptional Activation , Tumor Protein p73 , Tumor Suppressor Protein p53/chemistry
12.
Anal Chim Acta ; 828: 1-8, 2014 May 30.
Article in English | MEDLINE | ID: mdl-24845809

ABSTRACT

Electrochemical biosensors have the unique ability to convert biological events directly into electrical signals suitable for parallel analysis. Here we utilize specific properties of constant current chronopotentiometric stripping (CPS) in the analysis of protein and DNA-protein complex nanolayers. Rapid potential changes at high negative current intensities (Istr) in CPS are utilized in the analysis of DNA-protein interactions at thiol-modified mercury electrodes. P53 core domain (p53CD) sequence-specific binding to DNA results in a striking decrease in the electrocatalytic signal of free p53. This decrease is related to changes in the accessibility of the electroactive amino acid residues in the p53CD-DNA complex. By adjusting Istr and temperature, weaker non-specific binding can be eliminated or distinguished from the sequence-specific binding. The method also reflects differences in the stabilities of different sequence-specific complexes, including those containing spacers between half-sites of the DNA consensus sequence. The high resolving power of this method is based on the disintegration of the p53CD-DNA complex by the electric field effects at a negatively charged surface and fine adjustment of the millisecond time intervals for which the complex is exposed to these effects. Picomole amounts of p53 proteins and DNA were used for the analysis at full electrode coverage but we show that even 10-20-fold smaller amounts can be analyzed. Our method cannot however take advantage of very low detection limits of the protein CPS detection because low I(str) intensities are deleterious to the p53CD-DNA complex stability at the electrode surface. These data highlight the utility of developing biosensors offering novel approaches for studying real-time macromolecular protein dynamics.


Subject(s)
Biosensing Techniques , DNA/analysis , DNA/chemistry , Electrochemical Techniques , Tumor Suppressor Protein p53/analysis , Tumor Suppressor Protein p53/chemistry , Electrodes , Humans , Mercury/chemistry , Sulfhydryl Compounds/chemistry
13.
Biopolymers ; 101(4): 428-38, 2014 Apr.
Article in English | MEDLINE | ID: mdl-24037480

ABSTRACT

For mimicking macromolecular crowding of DNA quadruplexes, various crowding agents have been used, typically PEG, with quadruplexes of micromolar strand concentrations. Thermal and thermodynamic stabilities of these quadruplexes increased with the concentration of the agents, the rise depended on the crowder used. A different phenomenon was observed, and is presented in this article, when the crowder was the quadruplex itself. With DNA strand concentrations ranging from 3 µM to 9 mM, the thermostability did not change up to ∼2 mM, above which it increased, indicating that the unfolding quadruplex units were not monomolecular above ∼2 mM. The results are explained by self-association of the G-quadruplexes above this concentration. The ΔG(°) 37 values, evaluated only below 2 mM, did not become more negative, as with the non-DNA crowders, instead, slightly increased. Folding topology changed from antiparallel to hybrid above 2 mM, and then to parallel quadruplexes at high, 6-9 mM strand concentrations. In this range, the concentration of the DNA phosphate anions approached the concentration of the K(+) counterions used. Volume exclusion is assumed to promote the topological changes of quadruplexes toward the parallel, and the decreased screening of anions could affect their stability.


Subject(s)
DNA/chemistry , G-Quadruplexes , Telomere/chemistry , Circular Dichroism , Densitometry , Electrophoresis, Polyacrylamide Gel , Entropy , Humans , Microscopy, Atomic Force , Spectrophotometry, Ultraviolet
14.
Angew Chem Int Ed Engl ; 52(40): 10515-8, 2013 Sep 27.
Article in English | MEDLINE | ID: mdl-23939933

ABSTRACT

Bioorthogonal covalent cross-linking of DNA-binding proteins (p53) to DNA was achieved through novel DNA probes bearing a reactive vinylsulfonamide (VS) group. The VS-modified dCTP served as building block for polymerase synthesis of modified DNA, which was readily conjugated with cysteine-containing peptides and proteins by Michael addition.


Subject(s)
Acrylamide/chemistry , DNA/chemistry , Proteins/chemistry , Sulfonamides/chemistry , Vinyl Compounds/chemistry , Acrylamide/chemical synthesis , Cross-Linking Reagents/chemistry , DNA/chemical synthesis , DNA-Directed DNA Polymerase/chemistry , Ethylenes/chemistry , Models, Molecular , Proteins/metabolism , Sulfonamides/chemical synthesis , Sulfonic Acids/chemistry , Vinyl Compounds/chemical synthesis
15.
PLoS One ; 8(3): e59567, 2013.
Article in English | MEDLINE | ID: mdl-23555710

ABSTRACT

Hot spot mutant p53 (mutp53) proteins exert oncogenic gain-of-function activities. Binding of mutp53 to DNA is assumed to be involved in mutp53-mediated repression or activation of several mutp53 target genes. To investigate the importance of DNA topology on mutp53-DNA recognition in vitro and in cells, we analyzed the interaction of seven hot spot mutp53 proteins with topologically different DNA substrates (supercoiled, linear and relaxed) containing and/or lacking mutp53 binding sites (mutp53BS) using a variety of electrophoresis and immunoprecipitation based techniques. All seven hot spot mutp53 proteins (R175H, G245S, R248W, R249S, R273C, R273H and R282W) were found to have retained the ability of wild-type p53 to preferentially bind circular DNA at native negative superhelix density, while linear or relaxed circular DNA was a poor substrate. The preference of mutp53 proteins for supercoiled DNA (supercoil-selective binding) was further substantiated by competition experiments with linear DNA or relaxed DNA in vitro and ex vivo. Using chromatin immunoprecipitation, the preferential binding of mutp53 to a sc mutp53BS was detected also in cells. Furthermore, we have shown by luciferase reporter assay that the DNA topology influences p53 regulation of BAX and MSP/MST1 promoters. Possible modes of mutp53 binding to topologically constrained DNA substrates and their biological consequences are discussed.


Subject(s)
DNA, Superhelical/metabolism , Mutant Proteins/metabolism , Mutation , Tumor Suppressor Protein p53/metabolism , Binding Sites , Cell Line, Tumor , DNA, Superhelical/chemistry , Gene Expression Regulation/genetics , Humans , Intracellular Signaling Peptides and Proteins , Mutant Proteins/chemistry , Mutant Proteins/genetics , Plasmids/genetics , Promoter Regions, Genetic/genetics , Protein Binding , Protein Serine-Threonine Kinases/genetics , Substrate Specificity , Tumor Suppressor Protein p53/chemistry , Tumor Suppressor Protein p53/genetics , bcl-2-Associated X Protein/genetics
16.
Biochem Biophys Res Commun ; 433(4): 445-9, 2013 Apr 19.
Article in English | MEDLINE | ID: mdl-23501101

ABSTRACT

Cysteine oxidation and covalent modification of redox sensitive transcription factors including p53 are known, among others, as important events in cell response to oxidative stress. All p53 family proteins p53, p63 and p73 act as stress-responsive transcription factors. Oxidation of p53 central DNA binding domain destroys its structure and abolishes its sequence-specific binding by affecting zinc ion coordination at the protein-DNA interface. Proteins p63 and p73 can bind the same response elements as p53 but exhibit distinct functions. Moreover, all three proteins contain highly conserved cysteines in central DNA binding domain suitable for possible redox modulation. In this work we report for the first time the redox sensitivity of p63 and p73 core domains to a thiol oxidizing agent azodicarboxylic acid bis[dimethylamide] (diamide). Oxidation of both p63 and p73 abolished sequence-specific binding to p53 consensus sequence, depending on the agent concentration. In the presence of specific DNA all p53 family core domains were partially protected against loss of DNA binding activity due to diamide treatment. Furthermore, we detected conditional reversibility of core domain oxidation for all p53 family members and a role of zinc ions in this process. We showed that p63 and p73 proteins had greater ability to resist the diamide oxidation in comparison with p53. Our results show p63 and p73 as redox sensitive proteins with possible functionality in response of p53 family proteins to oxidative stress.


Subject(s)
DNA-Binding Proteins/chemistry , Nuclear Proteins/chemistry , Tumor Suppressor Protein p53/chemistry , Tumor Suppressor Proteins/chemistry , Base Sequence , Cysteine/chemistry , DNA/chemistry , DNA-Binding Proteins/chemical synthesis , Diamide/chemistry , Dithiothreitol/chemistry , Edetic Acid/chemistry , Electrophoresis, Agar Gel , Electrophoretic Mobility Shift Assay , Humans , Nuclear Proteins/chemical synthesis , Oxidation-Reduction , Protein Interaction Mapping , Protein Structure, Tertiary , Tumor Protein p73 , Tumor Suppressor Protein p53/chemical synthesis , Tumor Suppressor Proteins/chemical synthesis , Zinc/chemistry
17.
Cell Cycle ; 11(17): 3290-303, 2012 Sep 01.
Article in English | MEDLINE | ID: mdl-22894900

ABSTRACT

The molecular mechanisms underlying mutant p53 (mutp53) "gain-of-function" (GOF) are still insufficiently understood, but there is evidence that mutp53 is a transcriptional regulator that is recruited by specialized transcription factors. Here we analyzed the binding sites of mutp53 and the epigenetic status of mutp53-regulated genes that had been identified by global expression profiling upon depletion of endogenous mutp53 (R273H) expression in U251 glioblastoma cells. We found that mutp53 preferentially and autonomously binds to G/C-rich DNA around transcription start sites (TSS) of many genes characterized by active chromatin marks (H3K4me3) and frequently associated with transcription-competent RNA polymerase II. Mutp53-bound regions overlap predominantly with CpG islands and are enriched in G4-motifs that are prone to form G-quadruplex structures. In line, mutp53 binds and stabilizes a well-characterized G-quadruplex structure in vitro. Hence, we assume that binding of mutp53 to G/C-rich DNA regions associated with a large set of cancer-relevant genes is an initial step in their regulation by mutp53. Using GAS1 and HTR2A as model genes, we show that mutp53 affects several parameters of active transcription. Finally, we discuss a dual mode model of mutp53 GOF, which includes both stochastic and deterministic components.


Subject(s)
Gene Expression Regulation, Neoplastic/genetics , Regulatory Elements, Transcriptional/physiology , Transcription, Genetic/genetics , Tumor Suppressor Protein p53/metabolism , Binding Sites/genetics , Cell Cycle Proteins/genetics , Cell Cycle Proteins/metabolism , Cell Line, Tumor , Chromatin Immunoprecipitation , GPI-Linked Proteins/genetics , GPI-Linked Proteins/metabolism , Gene Expression Profiling , Guanosine/metabolism , Humans , Mutation/genetics , Polymerase Chain Reaction , Receptor, Serotonin, 5-HT2A/genetics , Receptor, Serotonin, 5-HT2A/metabolism , Regulatory Elements, Transcriptional/genetics , Tumor Suppressor Protein p53/genetics
18.
Bioinformatics ; 27(18): 2510-7, 2011 Sep 15.
Article in English | MEDLINE | ID: mdl-21791534

ABSTRACT

MOTIVATION: Current methods for identification of potential triplex-forming sequences in genomes and similar sequence sets rely primarily on detecting homopurine and homopyrimidine tracts. Procedures capable of detecting sequences supporting imperfect, but structurally feasible intramolecular triplex structures are needed for better sequence analysis. RESULTS: We modified an algorithm for detection of approximate palindromes, so as to account for the special nature of triplex DNA structures. From available literature, we conclude that approximate triplexes tolerate two classes of errors. One, analogical to mismatches in duplex DNA, involves nucleotides in triplets that do not readily form Hoogsteen bonds. The other class involves geometrically incompatible neighboring triplets hindering proper alignment of strands for optimal hydrogen bonding and stacking. We tested the statistical properties of the algorithm, as well as its correctness when confronted with known triplex sequences. The proposed algorithm satisfactorily detects sequences with intramolecular triplex-forming potential. Its complexity is directly comparable to palindrome searching. AVAILABILITY: Our implementation of the algorithm is available at http://www.fi.muni.cz/lexa/triplex as source code and a web-based search tool. The source code compiles into a library providing searching capability to other programs, as well as into a stand-alone command-line application based on this library. CONTACT: lexa@fi.muni.cz SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.


Subject(s)
Algorithms , DNA/metabolism , Escherichia coli K12/genetics , Sequence Analysis, DNA/methods , Base Pair Mismatch , Base Sequence , DNA/chemistry , Genome , Humans , Inverted Repeat Sequences , Likelihood Functions , Nucleic Acid Conformation
19.
Anal Chim Acta ; 668(2): 166-70, 2010 Jun 04.
Article in English | MEDLINE | ID: mdl-20493293

ABSTRACT

In this paper we extend the application area of the label-free structure-sensitive electrochemical DNA sensing with mercury-based electrodes which is for the first time used, in combination with immunoprecipitation at magnetic beads (MB), for the probing of DNA interactions with tumor suppressor protein p53. The technique relies on capture of the p53-DNA complexes at MB via anti-p53 antibodies, followed by salt-induced dissociation of linear DNA from the complex and its voltammetric detection. Competitive binding of p53 to various plasmid DNA substrates, including lin or scDNAs with or without a specific target site, can easily be followed by ex situ electrochemical analysis of DNA recovered from the immunoprecipitated complexes. Compared to gel electrophoresis which is usually applied to analyze different plasmid DNA forms and their complexes with proteins, the electrochemical detection is faster and allows simpler quantitation of DNA containing free ends at submicrogram levels. We demonstrate applicability of the proposed technique to monitor different DNA-binding activities of wild type and mutant p53 proteins.


Subject(s)
Biosensing Techniques , Electrochemical Techniques , Immunoprecipitation , Tumor Suppressor Protein p53 , Animals , Binding Sites , Binding, Competitive , Biosensing Techniques/methods , DNA/metabolism , Electrochemical Techniques/methods , Electrodes , Electrophoresis, Agar Gel , Humans , Immunoprecipitation/methods , Magnetics , Mercury , Mice , Tumor Suppressor Protein p53/analysis , Tumor Suppressor Protein p53/genetics , Tumor Suppressor Protein p53/metabolism
20.
Cancer Genet Cytogenet ; 197(2): 107-16, 2010 Mar.
Article in English | MEDLINE | ID: mdl-20193843

ABSTRACT

Stable cell lines obtained by spontaneous immortalization might represent early stages of malignant transformation and be useful experimental models for studies of mechanisms of cancer development. The FHC (fetal human cells) cell line has been established from normal fetal colonic mucosa. Detailed characterization of this cell line and mechanism of spontaneously acquired immortality have not been described yet. Therefore, we characterized the FHC cell line in terms of its tumorigenicity, cytogenetics, and TP53 gene mutation analysis. FHC cells displayed capability for anchorage-independent growth in semisolid media in vitro and formed solid tumors after transplantation into SCID (severe combined immunodeficiency) mice. This tumorigenic phenotype was associated with hypotriploidy and chromosome number ranging from 66 to 69. Results of comparative genetic hybridization arrays showed that most chromosomes included regions of copy number gains or losses. Region 8q23 approximately 8q24.3 (containing, e.g., MYC proto-oncogene) was present in more than 20 copies per nucleus. Moreover, we identified mutation of TP53 gene in codon 273; triplet CGT coding Arg was changed to CAG coding His. Expression of Pro codon 72 polymorphic variant of p53 was also detected. Mutation of TP53 gene was associated with abolished induction of p21(Waf1/Cip1) and MDM-2 proteins and resistance to apoptosis after genotoxic treatment. Because of their origin from normal fetal colon and their relative resistance to the induction of apoptosis, FHC cells can be considered a valuable experimental model for various studies.


Subject(s)
Colon/physiology , Colonic Neoplasms/genetics , Colonic Neoplasms/pathology , Genes, p53 , Animals , Apoptosis/physiology , Carcinoembryonic Antigen/metabolism , Cell Adhesion/physiology , Cell Growth Processes/physiology , Cell Line, Transformed , Cell Transformation, Neoplastic/genetics , Cell Transformation, Neoplastic/pathology , Colon/cytology , Colon/metabolism , Comparative Genomic Hybridization , Cytogenetic Analysis/methods , DNA Damage , DNA Mutational Analysis/methods , Female , Fetus/cytology , HCT116 Cells , Humans , In Situ Hybridization, Fluorescence , Karyotyping , Keratins/metabolism , Mice , Mice, SCID , Neoplasm Transplantation , Phenotype , Proto-Oncogene Mas , Signal Transduction
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