Wyniki wyszukiwania - Biblioteka Nauki

1

Synthesis, characterization and biological activities of homo-binuclear Cu(II) and Zn(II) complexes derived from 2-hydroxy-5-methyl-1,3-benzenedicarboxaldehyde derivatives

100%

Raman N. , Sakthivel A. , Jeyamurugan R.

Open Chemistry

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2010

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tom 8

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nr 1

96-107

EN

Few novel binuclear Schiff base metal complexes [M2LCl3], where M = Cu(II) and Zn(II); L= 2,6-bis-({2-[(3-hydroxy-4-nitrobenzylidene)amino]ethylimino}methyl)-4-methylphenol (BHEM), 2,6-bis-({2-[(3,4-dimethoxybenzylidene)amino]ethylimino} methyl)-4-methylphenol (BDEM) and 2,6-bis-({2-[(2,3,5-trichlorobenzylidene)amino]ethylimino}methyl)-4-methylphenol (BTEM), have been synthesized and characterized by analytical and spectral data. The data suggest that BHEM/BDEM/BTEM ligands afford square-pyramidal/distorted square-pyramidal geometry on metalation with Zn(II)/Cu(II). The binding behaviour of these complexes with DNA has been investigated using electronic absorption spectroscopy as well as viscosity and voltammetric measurements; the results show that they interact with DNA through intercalating way. From the DNA cleavage study of these complexes, investigated by gel electrophoresis, we found that they efficiently cleave supercoiled pUC19 DNA in the presence of a reducing agent (3-mercaptopropionic acid) and on irradiation with UV light of 360 nm wavelength. The mechanism reveals that singlet oxygen (1O2) plays a significant role in the photo cleavage. The superoxide dismutase (SOD) mimetic activity of the synthesized complexes demonstrates that most of the complexes have promising SOD-mimetic activity. The antimicrobial study indicates that the complexes inhibit the growth of bacteria and fungi more than the free ligands. [...]

2

Organoruthenium(II) thiosemicarbazone complexes: synthesis, spectral characterization, DNA binding and DNA cleavage studies

100%

Raja G. , Jayabalakrishnan C.

Open Chemistry

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2013

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tom 11

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nr 6

1010-1018

EN

A series of new ruthenium(II) complexes were synthesized with Schiff bases derived from salicylaldehyde / o-hydroxyacetophenone/ o-vanillin / 2-hydroxy-1-naphthaldehyde with thiosemicarbazide and acetyl furan. They are characterized by elemental analysis, IR, electronic, 1H NMR, 13C NMR and mass spectral studies. The elemental analysis suggests the stoichiometry to be 1:1 (metal:ligand). Four of these complexes were tested for its binding with CT-DNA using absorption spectroscopic studies and two of these complexes exhibit efficient DNA cleavage activity. [...]

3

Methyl-CPG-binding protein 2 [MECP2]: role in development and gene expression

100%

Stratling W. H. , Yu F. , Thiesen J. , Buschdorf J.

Cellular and Molecular Biology Letters

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2000

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tom 05

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nr 2

4

In vitro DNA binding of purified CcpA protein from Lactococcus lactis IL1403

88%

Kowalczyk M. , Borcz B. , Płochocka D. , Bardowski J.

Acta Biochimica Polonica

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2007

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tom 54

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nr 1

71-78

EN

During this study His-tagged CcpA protein purified under native conditions to obtain a biologically active protein was used for molecular analysis of CcpA-dependent regulation. Using electrophoretic mobility shift assays it was demonstrated that CcpA of L. lactis can bind DNA in the absence of the HPr-Ser-P corepressor and exhibits DNA-binding affinity for nucleotide sequences lacking cre sites. However, purified HPr-Ser-P protein from Bacillus subtilis was shown to slightly increase the DNA-binding capacity of the CcpA protein. It was also observed that CcpA bound to the cre box forms an apparently more stable complex than that resulting from unspecific binding. Competition gel retardation assay performed on DNA sequences from two PEP:PTS regions demonstrated that the ybhE, bglS, rheB, yebE, ptcB and yecA genes situated in these regions are most probably directly regulated by CcpA.

5

Synthesis, DNA-binding and antiproliferative activity of N-(Nitrogen heterocyclic) norcantharidin acylamide acid

88%

Zhu W.-Z. , Hu R.-D. , Lin Q.-Y. , Wang X.-X. , Zheng X.-L.

Open Chemistry

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2009

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tom 7

|

nr 3

569-575

EN

Two novel norcantharidin acylamide acids (HL1=N-pyrimidine norcantharidin acylamide acid, C12H13N3O4; HL2=N-pyridine norcantharidin acylamide acid, C13H14N2O4) were synthesized by a reaction of norcantharidin(NCTD) with 2-aminopyrimidine and 2-aminopyridine, respectively. Their structures were characterized by elemental analysis, IR, UV and 1 H NMR. Fluorescence titration and viscosity measurements indicated that HL1, HL2 and HL3 (HL3=N-phenyl norcantharidin acylamide acid, C14H15NO4) can bind calf thymus DNA via partial intercalation. The liner Stern-Volmer quenching constant Ksv values for HL1, HL2 and HL3 were 2.05 × 104 L mol−1, 1.15 × 104 L mol−1 and 8.30×103 L mol−1, respectively. Two compounds containing heterocycle of HL1 and HL2 have been found to cleave pBR322 plasmid DNA at physiological pH and temperature. The test of antiproliferation activity showed that the compounds had moderate to strong antiproliferative ability against the tested cell lines except of HL3 against the SMMC7721 cell line. The results indicated that the heterocycle attached to the norcantharidin was favorable to antiproliferative activity. This result was consistent with the DNA binding experiment. [...]

6

Aza and diaza bioisosteric anthracene-9,10-diones as antitumor agents

88%

Krapcho A. P. , Maresch M. J. , Hacker M. P. , Menta E. , Oliva A. , Giuliani F. C. , Spinelli S.

Acta Biochimica Polonica

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1995

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tom 42

|

nr 4

EN

Synthetic routes to aza and diaza bioisosteres related to the anthracene-9,10-dione, mitoxantrone, have been developed. The antitumor properties of these chemotypes are compared with those exhibited by the corresponding carbocyclic analogues. The sensitivity of the expressed cytotoxicities on the position(s) of the nitrogen atom(s) are discussed in terms of potential cellular targets. Several analogues show potential for clinical evaluations.

7

The impaired transcription factor AP-1 DNA binding activity in lymphocytes derived from subjects with some symptoms of premature ageing

88%

Sikora E. , Radziszewska E. , Kmiec T. , Maslinska D.

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nr 2

XX

The study of human disorders known as premature aging syndromes may provide insight into the mechanisms of cellular senescence. The main feature of cellular senescence in vitro is cessation of cell proliferation. Down syndrome (DS) and neuronal ceroid-lypofuscinosis (NCL) are clinically characterized by the premature onset of numerous features normally associated with human aging. Phytohemagglu- tinin stimulated lymphocytes derived from DS subjects showed a statistically significant diminished proliferation capacity in comparison with lymphocytes derived from NCL and healthy individuals. We demonstrated, by applying the electrophoretic mobility shift assay, slightly impaired AP-1 DNA binding activity in NCL lymphocytes and strong in DS ones. Our results showed that the same molecular mechanisms of proliferation cessation could exist in fibroblasts characterized by replicative senescence and in lymphocytes derived from individuals with premature aging syndromes (Down).

8

Hexahistidine [His6]-tag dependent protein dimerization: a cautionary tale

75%

Wu J. , Filutowicz M.

Acta Biochimica Polonica

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1999

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tom 46

|

nr 3

EN

Nickel nitrilotriacetic acid (Ni2+-NTA) immobilization of hexahistidine (His6) tagged proteins has become one of the most commonly used methods of affinity chromatography. Perhaps the greatest utility of this protein purification method stems from the general belief that His-tagged proteins (comprised of His6) are little affected in their activities or efficiencies, while alterations in specificity are unexpected. Although this is certainly true in many instances, we present a case in which the biochemical properties of proteins being studied were fundamentally altered due to the presence of His-tags. We carried out these studies using variants of the π30.5 protein of plasmid R6K, a DNA binding protein which negatively regulates plasmid replication. π30.5 can bind DNA containing a target sequence (TGAGR) arranged either asymmetrically (direct repeats) in the g origin, or symmetrically in inverted half-repeats (IR˘s) in the operator of its own gene, pir. Importantly, dimers of p protein bind to an IR; this property allows researchers to quickly assess whether different regulatory variants of p proteins exhibit altered dimerization properties. For example, π30.5 containing a single amino acid substitution, F107S (π20030.5), has been shown to be monomeric in solution and dimers were not observed bound to IR˘s. Here we demonstrate that the presence of a His-tag partially restores the ability of π20030.5 to dimerize in solution and bind to an IR in dimeric form. This report sends an important message that (other) proteins containing His-tags may differ from their wild type counterparts in dimerization/oligomerization properties.

9

Effects of distortions by A-tracts of promoter B-DNA spacer region on the kinetics of open complex formation by Escherichia coli RNA polymerase

75%

Kolasa I. K. , Lozinski T. , Wierzchowski K. L.

Acta Biochimica Polonica

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2003

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tom 50

|

nr 4

EN

A-tracts in DNA due to their structural morphology distinctly different from the canonical B-DNA form play an important role in specific recognition of bacterial upstream promoter elements by the carboxyl terminal domain of RNA polymerase a subunit and, in turn, in the process of transcription initiation. They are only rarely found in the spacer promoter regions separating the -35 and -10 recognition hexamers. At present, the nature of the protein-DNA contacts formed between RNA polymerase and promoter DNA in transcription initiation can only be inferred from low resolution structural data and mutational and crosslinking experiments. To probe these contacts further, we constructed derivatives of a model Pa promoter bearing in the spacer region one or two An (n = 5 or 6) tracts, in phase with the DNA helical repeat, and studied the effects of thereby induced perturbation of promoter DNA structure on the kinetics of open complex (RPo) formation in vitro by Escherichia coli RNA polymerase. We found that the overall second-order rate constant ka of RPo formation, relative to that at the control promoter, was strongly reduced by one to two orders of magnitude only when the A-tracts were located in the nontemplate strand. A particularly strong 30-fold down effect on ka was exerted by nontemplate A-tracts in the -10 extended promoter region, where an involvement of nontemplate TG (-14, -15) sequence in a specific interaction with region 3 of tf-sub-unit is postulated. A-tracts in the latter location caused also 3-fold slower isomerization of the first closed transcription complex into the intermediate one that precedes formation of RPo, and led to two-fold faster dissociation of the latter. All these findings are discussed in relation to recent structural and kinetic models of RPo formation.

10

Expression and purification of 6xHis-tagged DNA binding domains of functional ecdysteroid receptor from Drosophila melanogaster

75%

Rusin A. , Niedziela-Majka A. , Rymarczyk G. , Ozyhar A.

Acta Biochimica Polonica

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1996

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tom 43

|

nr 4

EN

Two members of the nuclear receptor superfamily, EcR and UltTaspiracle (Usp) heterodimerize to form a functional receptor for 20-hydroxyecdysone — the key ecdysteroid controlling induction and modulation of morphogenetic events through Drosophila development. In order to study aspects of receptor function and ultimately the structural basis of the ecdysteroid receptor-DNA interaction, it is necessary to produce large quantities of purified EcR and Usp DNA-binding domains. Toward this end, we have expressed the EcR DNA-binding domain and the Usp DNA-binding domain as proteins with an affinity tag consisting of six histidine residues (6xHis-EcRDBD and 6xHis-UspDBD, respectively) using the expression vector pQE-30. Under optimal conditions, elaborated in this study, bacteria can express the recombinant 6xHis-EcRDBD to the levels of 11% of total soluble proteins and the 6xHis-UspDBD to the levels of 16%. Both proteins were purified to homogeneity from the soluble protein fraction using combination of ammonium sulphate fractionation and affinity chromatography on Ni-NTA agarose. The gel mobility shift experiments demonstrated that the purified 6xHis-EcRDBD and the 6xHis-UspDBD interact specifically with an 20-hydroxyecdysone response element from the promoter region of the hsp 27 Drosophila gene.

11

Identification of the DNA binding element of the human ZNF300 protein

63%

Qiu H. , Xue L. , Gao L. , Shao H. , Wang D. , Guo M. , Li W.

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tom 13

|

nr 3

391-403

EN

The human ZNF300 gene is a member of the KRAB/C2H2 zinc finger gene family, the members of which are known to be involved in various developmental and pathological processes. Here, we show that the ZNF300 gene encodes a 68-kDa nuclear protein that binds DNA in a sequence-specific manner. The ZNF300 DNA binding site, C(t/a)GGGGG(c/g)G, was defined via a random oligonucleotide selection assay, and the DNA binding site was further confirmed by electrophoretic mobility shift assays. A potential ZNF300 binding site was found in the promoter region of the human IL-2Rβ gene. The results of electrophoretic mobility shift assays indicated that ZNF300 bound to the ZNF300 binding site in the IL-2Rβ promoter in vitro. Transient co-transfection assays showed that ZNF300 could activate the IL-2Rβ promoter, and that the activation was abrogated by the mutation of residues in the ZNF300 binding site. Identifying the DNA binding site and characterizing the transcriptional regulation property of ZNF300 would provide critical insights into its potential as a transcriptional regulator.

12

Mitochondria as oxidative signalling organelles in T-cell activation: physiological role and pathological implications

63%

Kaminski M. M. , Roth D. , Krammer P. H. , Gulow K.

Archivum Immunologiae et Therapiae Experimentalis

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2013

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tom 61

|

nr 5

13

A new division of bacterial UvrA homologues

63%

Marszalkowska M. , Bil M. , Kreft L. , Olszewski M.

BioTechnologia. Journal of Biotechnology Computational Biology and Bionanotechnology

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2013

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tom 94

|

nr 1

14

The role of WRKY transcription factors in plants

63%

Grzechowiak M.

BioTechnologia. Journal of Biotechnology Computational Biology and Bionanotechnology

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2014

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tom 95

|

nr 3

15

Effect of reversed orientation and length of An.Tn DNA binding sequences in the -35 and spacer domains of a consensus-like Escherichia coli promoter on its strength in vivo and gross structure of the open complex in vitro

63%

Lozinski T. , Wierzchowski K. L.

Acta Biochimica Polonica

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1996

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tom 43

|

nr 1

EN

In continuation of an earlier study (Łoziński ct at., 1991 Nucleic Acids Res. 19, 2947-2953) a series of consensus-like E. coli promoters with bending An Tn sequences of different length (n = 3-8) and orientation in the -35 and spacer domains was constructed, cloned into the plasmid pDS3 and their strength in vivo measured in relation to an internal transcriptional standard. Gel mobilities of free DNA restriction fragments carrying these promoters and of open transcriptional complexes with cognate RNA polymerase were determined by polyacrylamide gel electrophoresis and the gross structure of the complexes interpreted in terms of the theoretically predicted superstructure of DNA restriction fragments. The results obtained together with those reported earlier show that bending of the DNA helix axis immediately upstream of the -35 domain generally lowers the promoter strength in vivo and brings about shortening of the mean square end-to-end distance between free DNA ends in the open complex in vitro. T4Í-34...-37) and Ts(-34...-38) tracts located in the nontemplate DNA strand had the largest and comparable effect on the promoter strength, while the As T5 (-37...-41) sequence in either orientation (As tract in the template or nontemplate strand) exerted a much smaller effect. Promoters with the spacer bent by about 40° but in different directions, by two An (n = 5 or 6) tracts aligned in phase with the B-DNA repeat and located either in the template or nontemplate strands, had somewhat lower strength in vivo but the gross geometry of the respective open complexes was the same as that of a control promoter with straight spacer. Implications of these findings are discussed in connection with the existing model of E. coli transcriptional open complex.

16

Binding of SPXK- and APXK-peptide motifs to At-rich DNA. Experimental and theoretical studies

63%

Brzeski J. , Grycuk T. , Lipkowski A. W. , Rudnicki W. , Lesyng B. , Jerzmanowski A.

Acta Biochimica Polonica

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1998

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tom 45

|

nr 1

EN

The binding properties of the SPXK- and APXK-type peptides to the AT-rich DNA fragments of different length were studied by measuring the competition of peptides with Hoechst 33258 dye for DNA binding and by the gel shift assay analysis. In parallel to the experimental studies, molecular modeling techniques were used to analyze possible binding modes of the SPXZ and APXK motifs to the AT-rich DNA. The results of the competition measurements and gel shift assays suggest that serine at the i-1 position (i is proline) can be replaced by alanine without affecting the binding properties of the motif. Thus, the presence of the conserved serine in this motif in many DNA-binding proteins is probably not dictated by structural requirements. Based on the results of molecular modeling studies we propose that the binding mode of the SPXK- type motifs to the AT-rich DNA resembles closely that between the N-terminal arm of the homeodomain and DNA. This model confirms that serine in the SPXK motifs is not essential for the DNA binding. The model also indicates that if X in the motif is glutamic acid, this residue is probably protonated in the complex with DNA.

17

The properties of plant [Cucurbita pepo] nuclear matrix preparations are strongly affected by the preparation method

63%

Rzepecki R.

Cellular and Molecular Biology Letters

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2000

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tom 05

|

nr 2

EN

Nuclear matrices from White bush (Cucurbita pepo var. patisoniana) cell nuclei were isolated. Three different preparation methods were used. The methods were: I- the method of Berezney and Coffey [1] involving extraction of cell nuclei with 2M NaCl and Triton X-100 (called the “High Salt” method); II- the same with pre-treatment of cell nuclei with 0.5 mM CuSO4 (stabilisation step); III- the method of Mirkovitch et al. [2] involving lithium diiodosalicylate (LIS) extraction (called the “LIS” method). Each of the three methods was used in three variants of nucleic acid removal: restriction enzymes, endogenous nucleases and DN-ase I with RN-ase A digestion. Nuclear matrices were analysed for protein and DNA content, residual RNA and DNA synthesis activity, endonucleolytic activity and specific SAR DNA binding properties. The lowest protein and DNA content and endonucleolytic activity was found in nuclear matrices isolated by the “High Salt” method. It also had the lowest RNA and DNA synthesis and endonucleolytic activity. The highest protein and DNA content, and RNA and DNA synthesis and endonucleolytic activity was found in nuclear matrices isolated by the “LIS” method. When exogenous SAR DNA binding activity was compared, the highest was found in nuclear matrices isolated by the “High Salt” method while the lowest was in the “LIS” method preparation. Nuclear matrices isolated by the “High Salt” method with a stabilisation step always displayed average values of assayed parameters. These data indicate that the biological residual properties of a nuclear matrix preparation strongly depend on the method used.

18

Changes in DNA-binding activity of transcription factors in the differentiating bovine mammary gland

63%

Malewski T. , Gajewska M. , Zwierzchowski L.

Animal Science Papers and Reports

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2005

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tom 23

|

nr 2

EN

Our earlier studies carried out in silico demonstrated that different transcription factors have their putative binding sites in the 5’-flanking regions of bovine milk protein genes. Now we extended our study to include the experimental analysis of these transcription factors. This study on electrophoretic mobility shift assay (EMSA) of nuclear proteins derived from bovine mammary glands showed for the first time the presence there of CREB, NF-κB, Oct1 and Sp1 transcription factors. The pattern of DNA-protein complexes of Sp1 transcription factor significantly differed between virgin heifers and lactating cows. Transition from pregnancy to lactation was associated with changes in the DNAprotein binding patterns of NFI and Oct1 transcription factors.

PL

Wcześniejsze badania autorów prowadzone in silico wykazały obecność potencjalnych miejsc wiązania dla wielu czynników transkrypcyjnych w rejonach 5’-flankujących genów białek mleka. W obecnej pracy przedstawiono wyniki analizy poszerzonej o doświadczalne badanie wiązania tych czynników transkrypcyjnych z DNA. Stosując analizę EMSA z użyciem białek jądrowych gruczołu mlekowego bydła w różnych stadiach jego rozwoju, po raz pierwszy wykazano obecność w nim czynników transkrypcyjnych CREB, NF-κB, Oct1 i Sp1. Kompleksy DNA-białko czynnika transkrypcyjnego Sp1 wykazały różne wzory ruchliwości elektroforetycznej u dziewiczych i cielnych jałówek. Przejście od ciąży do laktacji wiązało się z dalszymi zmianami w kompleksach DNA-białko czynników transkrypcyjnych NFI i Oct1.

19

Binding of Escherichia coli integration host factor [IHF] to the origin segment of p15A plasmid

63%

Hiszczynska-Sawicka E. , Kur J.

Acta Biochimica Polonica

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1995

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tom 42

|

nr 1

EN

The integration host factor (IHF) is a sequence-specific, histone-like, multi-fun- ctional DNA-binding and -bending protein of Escherichia coli. Characterization and functional analysis of this protein has been carried out mainly in bacteriophage λ and other mobile genetic elements. In this paper we report data concerning the binding of IHF protein to the plasmid oripl5A region. IHF binds to the single site of the DNA fragment containing the oripl5A, as shown by the gel mobility shift assays and footprinting experiment. On the basis of the ihf consensus sequences published, we have been able to identify one sequence of putative ihf site into the oripl5A sequence with two mismatches in relation to the consensus sequence of Kur et al., 1989, Gene 81,1-15. One ihf binding site was also found in the oriColEl region sequence with three mismatches in relation to this consensus sequence.

20

DNA-nuclear matrix interactions analyzed by cross-linking reactions in intact nuclei from avian liver

63%

Ferraro A. , Eufemi M. , Cervoni L. , Altieri F. , Turano C.

Acta Biochimica Polonica

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1995

|

tom 42

|

nr 2

EN

To detect the interactions of DNA with the nuclear matrix proteins, DNA-protein cross-linkages were induced in intact nuclei from chicken liver by the use of ds-diammine dichloroplatinum. Methods have been devised for fast purification both of the proteins and of the DNA fragments involved in the cross-linked complexes. By Southern-Western blotting a number of matrix proteins isolated from the complexes have been shown to recognize specifically DNA sequences present in the cross-linked DNA fragments. This experimental approach not only allows to identify the nuclear matrix-DNA interactions existing in the nucleus before its disruption, but also provides a preparation of matrix proteins enriched in those species which are involved in such interactions and which can therefore be detected with high sensitivity.