DNA binding properties of the nuclear matrix and individual nuclear matrix proteins. Evidence for salt-resistant DNA binding sites

Mouse nuclear matrix proteins, examined by a filter assay, were found to bind to DNA. There was no preference for homologous mouse compared to heterologous E. coli DNA. Competition assays showed a preference for AT-rich DNA and of the 4 single-stranded homopolymers there was a preference for poly(dT). These observations are consistent with the possibility that the matrix may play a role in the formation of AT-rich chromomeres (G-bands).

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Composition and DNA-binding properties of the nuclear matrix proteins from mammalian cell nuclei

Biochimica et Biophysica Acta (BBA) - Gene Structure and Expression ◽

10.1016/0167-4781(82)90186-5 ◽

1982 ◽

Vol 698 (1) ◽

pp. 70-77 ◽

Cited By ~ 10

Author(s):

Leon H.F. Mullenders ◽

Jelle Eygensteyn ◽

André Broen ◽

Friedrich Wanka

Keyword(s):

Dna Binding ◽

Mammalian Cell ◽

Nuclear Matrix ◽

Matrix Proteins ◽

Cell Nuclei ◽

Binding Properties ◽

Nuclear Matrix Proteins ◽

Dna Binding Properties

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Sequence-specific DNA binding activities of nuclear matrix proteins of mammalian lens epithelial cells

Journal of Cellular Biochemistry ◽

10.1002/jcb.240580102 ◽

1995 ◽

Vol 58 (1) ◽

pp. 1-5 ◽

Cited By ~ 14

Author(s):

M. Bagchi ◽

A. Van Wijnen ◽

M. Katar ◽

H. Merriman ◽

J. Lian ◽

...

Keyword(s):

Dna Binding ◽

Epithelial Cells ◽

Nuclear Matrix ◽

Matrix Proteins ◽

Lens Epithelial Cells ◽

Nuclear Matrix Proteins

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The Arabidopsis class I TCP transcription factor AtTCP11 is a developmental regulator with distinct DNA-binding properties due to the presence of a threonine residue at position 15 of the TCP domain

Biochemical Journal ◽

10.1042/bj20101019 ◽

2011 ◽

Vol 435 (1) ◽

pp. 143-155 ◽

Cited By ~ 47

Author(s):

Ivana L. Viola ◽

Nora G. Uberti Manassero ◽

Rodrigo Ripoll ◽

Daniel H. Gonzalez

Keyword(s):

Dna Binding ◽

Binding Sites ◽

Class I ◽

Binding Properties ◽

Threonine Residue ◽

Dna Binding Specificity ◽

Systematic Evolution ◽

Enrichment Experiments ◽

Exponential Enrichment ◽

Dna Binding Properties

The TCP domain is a DNA-binding domain present in plant transcription factors that modulate different processes. In the present study, we show that Arabidopsis class I TCP proteins are able to interact with a dyad-symmetric sequence composed of two GTGGG half-sites. TCP20 establishes symmetric interactions with the 5′ half of each strand, whereas TCP11 interacts mainly with the 3′ half. SELEX (systematic evolution of ligands by exponential enrichment) experiments with TCP15 and TCP20 indicated that these proteins have similar, although not identical, DNA-binding preferences and are able to interact with non-palindromic binding sites of the type GTGGGNCCNN. TCP11 shows a different DNA-binding specificity, with a preference for the sequence GTGGGCCNNN. The distinct DNA-binding properties of TCP11 are due to the presence of a threonine residue at position 15 of the TCP domain, a position that is occupied by an arginine residue in most TCP proteins. TCP11 also forms heterodimers with TCP15 that have increased DNA-binding efficiency. The expression in plants of a repressor form of TCP11 demonstrated that this protein is a developmental regulator that influences the growth of leaves, stems and petioles, and pollen development. The results suggest that changes in DNA-binding preferences may be one of the mechanisms through which class I TCP proteins achieve functional specificity.

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DNA-binding activities of the Drosophila melanogaster even-skipped protein are mediated by its homeo domain and influenced by protein context.

Molecular and Cellular Biology ◽

10.1128/mcb.8.11.4598 ◽

1988 ◽

Vol 8 (11) ◽

pp. 4598-4607 ◽

Cited By ~ 51

Author(s):

T Hoey ◽

R Warrior ◽

J Manak ◽

M Levine

Keyword(s):

Dna Binding ◽

Binding Sites ◽

Consensus Sequence ◽

Binding Properties ◽

Binding Behavior ◽

High Affinity ◽

Homeo Box ◽

Acid Protein ◽

Dna Binding Properties ◽

Amino Acid Protein

The homeo box gene even-skipped (eve) encodes a 376-amino-acid protein that binds with high affinity to sequences located near the 5' termini of the eve and en genes. The 5' en sites are A + T rich and contain copies of the 10-base-pair (bp) consensus sequence T-C-A-A-T-T-A-A-A-T. In contrast, the 5' eve sites are G + C rich and contain the 9-bp sequence T-C-A-G-C-A-C-C-G. Among the five different homeo box proteins that have been tested for binding, eve is unique in that it shows virtually equal preference for the A + T-rich 5' en binding sites and the G + C-rich 5' eve sites. Most of the other proteins bind with a relatively higher affinity to the en sites than to the eve sites. In an effort to identify the regions of the eve protein that are responsible for its efficient binding to both classes of recognition sequences, we analyzed the DNA-binding properties of various mutant eve proteins. These studies suggest that the homeo domain of the eve protein is responsible for both binding activities. However, mutations in distant regions of the protein influenced the binding behavior of the eve homeo domain and caused a reduction in binding to the G + C class of recognition sites. We propose that the protein context of the homeo domain can influence its DNA-binding properties.

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DNA-binding activities of the Drosophila melanogaster even-skipped protein are mediated by its homeo domain and influenced by protein context

Molecular and Cellular Biology ◽

10.1128/mcb.8.11.4598-4607.1988 ◽

1988 ◽

Vol 8 (11) ◽

pp. 4598-4607

Author(s):

T Hoey ◽

R Warrior ◽

J Manak ◽

M Levine

Keyword(s):

Dna Binding ◽

Binding Sites ◽

Consensus Sequence ◽

Binding Properties ◽

Binding Behavior ◽

High Affinity ◽

Homeo Box ◽

Acid Protein ◽

Dna Binding Properties ◽

Amino Acid Protein

The homeo box gene even-skipped (eve) encodes a 376-amino-acid protein that binds with high affinity to sequences located near the 5' termini of the eve and en genes. The 5' en sites are A + T rich and contain copies of the 10-base-pair (bp) consensus sequence T-C-A-A-T-T-A-A-A-T. In contrast, the 5' eve sites are G + C rich and contain the 9-bp sequence T-C-A-G-C-A-C-C-G. Among the five different homeo box proteins that have been tested for binding, eve is unique in that it shows virtually equal preference for the A + T-rich 5' en binding sites and the G + C-rich 5' eve sites. Most of the other proteins bind with a relatively higher affinity to the en sites than to the eve sites. In an effort to identify the regions of the eve protein that are responsible for its efficient binding to both classes of recognition sequences, we analyzed the DNA-binding properties of various mutant eve proteins. These studies suggest that the homeo domain of the eve protein is responsible for both binding activities. However, mutations in distant regions of the protein influenced the binding behavior of the eve homeo domain and caused a reduction in binding to the G + C class of recognition sites. We propose that the protein context of the homeo domain can influence its DNA-binding properties.

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Differential DNA Binding of Transcriptional Regulator PcaU from Acinetobacter sp. Strain ADP1

Journal of Bacteriology ◽

10.1128/jb.184.7.1988-1997.2002 ◽

2002 ◽

Vol 184 (7) ◽

pp. 1988-1997 ◽

Cited By ~ 28

Author(s):

Roland Popp ◽

Tobias Kohl ◽

Patricia Patz ◽

Gaby Trautwein ◽

Ulrike Gerischer

Keyword(s):

Dna Binding ◽

Binding Site ◽

Binding Sites ◽

Specific Binding ◽

Transcriptional Regulator ◽

Intrinsic Curvature ◽

Binding Properties ◽

Expression Of Genes ◽

Intergenic Dna ◽

Dna Binding Properties

ABSTRACT Transcriptional regulator PcaU from Acinetobacter sp. strain ADP1 governs expression of genes for protocatechuate degradation (pca genes) as a repressor or an activator depending on the levels of the inducer protocatechuate and of its own gene. PcaU is a member of the IclR protein family. Here the DNA binding properties of the purified protein are described in terms of the location of the binding sites and the affinity to these sites. Native PcaU was purified after overexpression of the pcaU gene in Escherichia coli. It is a dimer in solution. The binding site in the pcaU-pcaI intergenic region is located between the two divergent promoters covering 45 bp, which includes three perfect 10-bp repetitions. A PcaU binding site downstream of pcaU is covered by PcaU across two palindromic sequence repetitions. The affinity of PcaU for the intergenic binding sites is 50-fold higher (dissociation constant [Kd ], 0.16 nM) than the affinity for the site downstream of pcaU (Kd , 8 nM). The binding of PcaU was tested after modifications of the intergenic binding site. Removal of any external sequence repetition still allowed for specific binding of PcaU, but the affinity was significantly reduced, suggesting an important role for all three sequence repetitions in gene expression. The involvement of DNA bending in the regulatory process is suggested by the observed strong intrinsic curvature displayed by the pcaU-pcaI intergenic DNA.

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