Wyniki wyszukiwania

1

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

2

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.

Acta Biochimica Polonica

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1993

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tom 40

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nr 2

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).

3

DNA-binding properties and cytotoxicity of biscationic extended diphenylfurans derivatives: effects of the terminal basic side chains

88%

Bielawski K., Bielawska A., Wolczynski S.

Folia Histochemica et Cytobiologica. Supplement

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2001

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tom 39

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nr 1

4

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

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nr 4

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.

5

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

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nr 4

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.

6

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

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nr 3

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.

7

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

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nr 4

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.

8

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

9

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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

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nr 1

10

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.

Cellular and Molecular Biology Letters

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2008

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tom 13

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nr 3

391-403

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.

11

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

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nr 3

12

Plant heat shock transcription factors: positive and negative aspects of regulation

63%

Czarnecka-Verner E., Yuan C. X., Nover L., Scharf K. D., Gurley W. B.

Biological Bulletin of Poznań. Supplement

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1997

|

tom 34

13

Interference between DNA binding activities of AP-1 and GR transcription factors in rats thymocytes undergoing dexamethasone-induced apoptosis

63%

Sikora E., Rossini G. P., Grassilli E., Bellesia E., Salomoni P., Franceschi C.

Acta Biochimica Polonica

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1996

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tom 43

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nr 4

The early molecular events of glucocorticoid-induced apoptosis have been investigated by studying glucocorticoid receptor levels, as well as binding activities to GRE and AP-1 sequences, using nuclear extracts from dexamethasone (Dex)-treated rat thymocytes. When the time-course of glucocorticoid-receptor complexes in nuclei of thymocytes was evaluated by binding studies using the tritiated ligand, we found that nuclear accumulation of radioactive complexes occurred in the first hour of incubation, and was followed by a progressive decline. This trend was confirmed by immunoblotting of nuclear proteins using a monoclonal anti-glucocorticoid receptor antibody. When the kinetics of binding activity to AP-1 and GRE sequences were studied, using nuclear extracts prepared from Dex-treated thymocytes in gel shift assays, we found peaks at 1 and 2 h after Dex treatment, and a return to basal levels in the following hours. Binding specificity was proved by competition studies using non-radioactive sequences, including mutated AP-1. Unexpectedly, however, protein binding to GRE was better competed for by AP-1 sequence than by GRE itself. Data obtained using the super gel shift assay suggested that AP-l/Jun can be responsible for the high affinity for the GRE sequence. Thus, we report here for the first time that an interference between AP-1 and GR in the binding to DNA consensus sequences — previously described in other biological systems — also occurs during apoptosis induced by glucocorticoids in lymphoid cells.

14

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

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tom 42

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nr 2

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.

15

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

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nr 1

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.

16

Actinomycin D specifically inhibits the interaction between transcription factor Sp1 and its binding site

63%

Czyz M., Gniazdowski M.

Acta Biochimica Polonica

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1998

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tom 45

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nr 1

The mode of action of many anticancer drugs involves DNA interactions. We here examine the ability of actinomycin D to alter the specific binding of transcription factors Sp1 and NFκB to their DNA sequences. Employing an electrophoretic mobility shift assay, it is shown that actinomycin D inhibits complex formation between nuclear proteins present in the extracts from stimulated human umbilical vein endothelial cells and the Sp1-binding site. Actinomycin D is also able to induce disruption of preformed DNA-protein complexes, pointing to the importance of an equilibrium of three components: actinomycin D, protein and DNA for drug action. The effect of actinomycin D is sequence-specific, since no inhibition is observed for interaction of nuclear proteins with the NFκB binding site. The results support the view that DNA-binding drugs displaying high sequence-selectivity can exhibit distinct effects on the interaction between DNA and different DNA-binding proteins.

17

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

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.

18

Physiological state-dependent changes in transcription factor DNA-binding activities of the rabbit mammary gland

63%

Malewski T., Gajewska M., Zwierzchowski L.

Animal Science Papers and Reports

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2005

|

tom 23

|

nr 2

Our earlier studies carried out in silico demonstrated that different transcription factors have their putative binding sites in the 5’-flanking regions of rabbit milk protein genes. Now we extended his study to include the experimental analysis of the transcription factors. This study of electrophoretic mobility shift assay (EMSA) of nuclear proteins showed for the first time the presence of AP1, CREB, Myb, and Sp1 transcription factors in the rabbit mammary gland. The abundance of all transcription factors studied in the mammary gland changed during pregnancy-lactation-weaning cycle. The DNA-binding activity of the Myb transcription factor correlated well with the level of milk protein gene expression. The affinity of Myb to its binding sequence is methylation-dependent. One of CREspecific DNA-protein complexes was found only in nuclear protein from the lactating rabbits mammary gland. The amount of AP1 DNA-binding activity transiently decreased in the early involution. Transition from early to late involution was associated with the restoration of the AP1 activity, and with the decrease of the Myb and Sp1 protein-DNA binding activities.

19

Interaction of the Pisum sativum nuclear matrix proteins with SAR DNA

63%

Rzepecki R., Markiewicz E., Adamiec R., Szopa J.

Acta Biochimica Polonica

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1995

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tom 42

|

nr 1

We have isolated the nuclear matrices from Pisum sativum cell nuclei using three methods: i. standard procedure involving extraction of cell nuclei with 2 M NaCl and 1% Triton X-100; ii. the same with pretreatment of cell nuclei with 0.5 mM CuS04 (stabilisation step); and iii. method including lithium diiodosalicylate extraction. We compared the polypeptide pattern and residual DNA content of the nuclear matrices isolated. The nuclear matrices displayed a specific endonuclease activity which was due to the presence of a 32 kDa protein. The isolated nuclear matrices bound specifically the scaffold-attached (SAR) DNA derived from human p interferon gene, in the exogenous SAR binding assay. Using the DNA-protein binding blot assay we demonstrated the presence of two nuclear matrix proteins of 66 kDa and 62 kDa which bound specifically SAR DNA.

20

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

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.

Ograniczanie wyników

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

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

DNA-binding properties and cytotoxicity of biscationic extended diphenylfurans derivatives: effects of the terminal basic side chains

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

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

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

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

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

A new division of bacterial UvrA homologues

Identification of the DNA binding element of the human ZNF300 protein

The role of WRKY transcription factors in plants

Plant heat shock transcription factors: positive and negative aspects of regulation

Interference between DNA binding activities of AP-1 and GR transcription factors in rats thymocytes undergoing dexamethasone-induced apoptosis

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

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

Actinomycin D specifically inhibits the interaction between transcription factor Sp1 and its binding site

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

Physiological state-dependent changes in transcription factor DNA-binding activities of the rabbit mammary gland

Interaction of the Pisum sativum nuclear matrix proteins with SAR DNA

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