Copper(i) and nickel(ii) complexes with 1 : 1 vs. 1 : 2 coordination of ferrocenyl hydrazone ligands: Do the geometry and composition of complexes affect DNA binding/cleavage, protein binding, antioxidant and cytotoxic activities?

Abstract Main conclusion The present study showed that a rice (Oryza sativa)-specific protein-binding microarray (RPBM) can be applied to analyze DNA-binding motifs with a TF where binding is evaluated in extended natural promoter regions. The analysis may facilitate identifying TFs and their downstream genes and constructing gene networks through cis-elements. Abstract Transcription factors (TFs) regulate gene expression at the transcriptional level by binding a specific DNA sequence. Thus, predicting the DNA-binding motifs of TFs is one of the most important areas in the functional analysis of TFs in the postgenomic era. Although many methods have been developed to address this challenge, many TFs still have unknown DNA-binding motifs. In this study, we designed RPBM with 40-bp probes and 20-bp of overlap, yielding 49 probes spanning the 1-kb upstream region before the translation start site of each gene in the entire genome. To confirm the efficiency of RPBM technology, we selected two previously studied TFs, OsWOX13 and OsSMF1, and an uncharacterized TF, OsWRKY34. We identified the ATTGATTG and CCACGTCA DNA-binding sequences of OsWOX13 and OsSMF1, respectively. In total, 635 and 932 putative feature genes were identified for OsWOX13 and OsSMF1, respectively. We discovered the CGTTGACTTT DNA-binding sequence and 195 putative feature genes of OsWRKY34. RPBM could be applicable in the analysis of DNA-binding motifs for TFs where binding is evaluated in the promoter and 5′ upstream CDS regions. The analysis may facilitate identifying TFs and their downstream genes and constructing gene networks through cis-elements.

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NonO, a non-POU-domain-containing, octamer-binding protein, is the mammalian homolog of Drosophila nonAdiss

Molecular and Cellular Biology ◽

10.1128/mcb.13.9.5593-5603.1993 ◽

1993 ◽

Vol 13 (9) ◽

pp. 5593-5603

Author(s):

Y S Yang ◽

J H Hanke ◽

L Carayannopoulos ◽

C M Craft ◽

J D Capra ◽

...

Keyword(s):

Amino Acids ◽

Dna Binding ◽

Protein Binding ◽

Aromatic Amino Acids ◽

Courtship Song ◽

Dna Binding Domain ◽

Binding Motifs ◽

Dna And Rna ◽

Pou Domain ◽

A Site

We have cloned the ubiquitous form of an octamer-binding, 60-kDa protein (NonO) that appears to be the mammalian equivalent of the Drosophila visual and courtship song behavior protein, no-on-transient A/dissonance (nonAdiss). A region unprecedently rich in aromatic amino acids containing two ribonuclear protein binding motifs is highly conserved between the two proteins. A ubiquitous form of NonO is present in all adult tissues, whereas lymphocytes and retina express unique forms of NonO mRNA. The ubiquitous form contains a potential helix-turn-helix motif followed by a highly charged region but differs from prototypic octamer-binding factors by lacking the POU DNA-binding domain. In addition to its conventional octamer duplex-binding, NonO binds single-stranded DNA and RNA at a site independent of the duplex site.

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Ligatoxin B, a new cytotoxic protein with a novel helix–turn–helix DNA-binding domain from the mistletoe Phoradendron liga

Biochemical Journal ◽

10.1042/bj20020221 ◽

2002 ◽

Vol 366 (2) ◽

pp. 405-413 ◽

Cited By ~ 24

Author(s):

Shi-Sheng LI ◽

Joachim GULLBO ◽

Petra LINDHOLM ◽

Rolf LARSSON ◽

Eva THUNBERG ◽

...

Keyword(s):

Dna Binding ◽

Cell Line ◽

Binding Proteins ◽

Molecular Mechanisms ◽

Homology Modelling ◽

Dna Binding Proteins ◽

Dimensional Structure ◽

Cytotoxic Activities ◽

Cytotoxic Action ◽

Working Hypothesis

A new basic protein, designated ligatoxin B, containing 46 amino acid residues has been isolated from the mistletoe Phoradendron liga (Gill.) Eichl. (Viscaceae). The protein's primary structure, determined unambiguously using a combination of automated Edman degradation, trypsin enzymic digestion, and tandem MS analysis, was 1–KSCCPSTTAR–NIYNTCRLTG–ASRSVCASLS–GCKIISGSTC–DSGWNH–46. Ligatoxin B exhibited in vitro cytotoxic activities on the human lymphoma cell line U-937-GTB and the primary multidrug-resistant renal adenocarcinoma cell line ACHN, with IC50 values of 1.8μM and 3.2μM respectively. Sequence alignment with other thionins identified a new member of the class 3 thionins, ligatoxin B, which is similar to the earlier described ligatoxin A. As predicted by the method of homology modelling, ligatoxin B shares a three-dimensional structure with the viscotoxins and purothionins and so may have the same mode of cytotoxic action. The novel similarities observed by structural comparison of the helix–turn–helix (HTH) motifs of the thionins, including ligatoxin B, and the HTH DNA-binding proteins, led us to propose the working hypothesis that thionins represent a new group of DNA-binding proteins. This working hypothesis could be useful in further dissecting the molecular mechanisms of thionin cytotoxicity and of thionin opposition to multidrug resistance, and useful in clarifying the physiological function of thionins in plants.

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Synthesis, crystal structure, DNA binding, molecular docking, cytotoxic activities and apoptosis of two copper (II) complexes constructed by 1,10-phen and semirigid bridge ligands

Inorganica Chimica Acta ◽

10.1016/j.ica.2018.06.025 ◽

2018 ◽

Vol 482 ◽

pp. 221-228 ◽

Cited By ~ 5

Author(s):

Ke-Hua Wang ◽

En-Jun Gao

Keyword(s):

Crystal Structure ◽

Molecular Docking ◽

Dna Binding ◽

Cytotoxic Activities

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Transcriptional control of the factor IX gene: analysis of five cis- acting elements and the deleterious effects of naturally occurring hemophilia B Leyden mutations

Blood ◽

10.1182/blood.v84.9.2992.2992 ◽

1994 ◽

Vol 84 (9) ◽

pp. 2992-3000 ◽

Cited By ~ 22

Author(s):

DJ Picketts ◽

CR Mueller ◽

D Lillicrap

Keyword(s):

Dna Binding ◽

Protein Binding ◽

Transcriptional Activation ◽

In Vitro Transcription ◽

Factor Ix ◽

Hemophilia B ◽

Transcription Assay ◽

Cis Acting ◽

Nuclear Extracts

Abstract Hemophilia B Leyden is a rare form of inherited factor IX deficiency in which patients experience spontaneous postpubertal recovery of factor IX levels. The mutations resulting in this disorder are localized in a 40-nucleotide region encompassing the major transcriptional start site for factor IX. Here we report the further characterization of five cis- acting elements in the factor IX promoter and the effects on protein binding and transcriptional activation of five Leyden mutations (at nucleotides +13, -5, -6, -20, and -26) that occur within the proximal three elements (sites 1 through 3). Bandshift studies using nuclear extracts from four different rat tissues have shown that at least some of the proteins binding to each of the five sites are ubiquitous in nature. The pattern of DNA binding at site 1 suggests that this element plays an important role in mediating the liver-specific expression of factor IX. Additional studies with liver nuclear extracts obtained at several different points in development have shown an increase in DNA binding at sites 1, 4, and 5 between 1 day and 1 week. Using DNase I footprint analysis and competition bandshift studies, we have shown that the binding of nuclear proteins to each of the mutant sites is disrupted to a variable extent. There appears to be some, although reduced, protein binding to all of the mutant oligonucleotides apart from the -26 mutant. In vitro transcription assays have shown that each of the mutations reduces the global proximal promoter activity by approximately 40%. Two double mutant promoters did not show any additional downregulation in the in vitro transcription assay. In experiments designed to assess the relative transcriptional activity mediated from each of the five sites independently, we have tested artificial homopolymer promoters of each site in the in vitro transcription assay. These studies show that sites 4 and 5 are the strongest activators and that transactivation from site 5 is further enhanced by the albumin D site-binding protein. In summary, these investigations show deleterious effects of each of the Leyden mutations tested on the binding of trans-acting factors and also show disruption of transcriptional activation in a functional in vitro transcription assay. Our results also show that cis-acting elements 4 and 5 are the principal activators of this locus.

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New binuclear Ni(ii) metallates containing ONS chelators: synthesis, characterisation, DNA binding, DNA cleavage, protein binding, antioxidant activity, antimicrobial and in vitro cytotoxicity

New Journal of Chemistry ◽

10.1039/c6nj03516g ◽

2017 ◽

Vol 41 (7) ◽

pp. 2543-2560 ◽

Cited By ~ 27

Author(s):

G. Kalaiarasi ◽

Ruchi Jain ◽

H. Puschman ◽

S. Poorna Chandrika ◽

K. Preethi ◽

...

Keyword(s):

Antioxidant Activity ◽

Dna Binding ◽

Protein Binding ◽

Hela Cell ◽

Antiproliferative Activity ◽

Dna Cleavage ◽

In Vitro Cytotoxicity ◽

Hela Cell Lines ◽

Mcf 7

Four new binuclear nickel(ii) metallates showed promising antiproliferative activity against MCF-7 and HeLa cell lines and were much less toxic against HaCaT.

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