scholarly journals DNA binding specificity of two homeodomain proteins in vitro and in Drosophila embryos.

1996 ◽  
Vol 93 (7) ◽  
pp. 2680-2685 ◽  
Author(s):  
J. Walter ◽  
M. D. Biggin
Keyword(s):  
Dna Binding ◽  
Binding Specificity ◽  
Homeodomain Proteins ◽  
Dna Binding Specificity ◽  
Drosophila Embryos

scholarly journals Structural determinants of DNA recognition by plant MADS-domain transcription factors

2013 ◽  
Vol 42 (4) ◽  
pp. 2138-2146 ◽  
Author(s):  
Jose M. Muiño ◽  
Cezary Smaczniak ◽  
Gerco C. Angenent ◽  
Kerstin Kaufmann ◽  
Aalt D.J. van Dijk
Keyword(s):  
Transcription Factors ◽  
Dna Binding ◽  
Binding Site ◽  
Structural Characteristics ◽  
Binding Specificity ◽  
Structural Motif ◽  
Dna Binding Specificity ◽  
Dna Binding Site ◽  
Carg Box

Abstract Plant MADS-domain transcription factors act as key regulators of many developmental processes. Despite the wealth of information that exists about these factors, the mechanisms by which they recognize their cognate DNA-binding site, called CArG-box (consensus CCW6GG), and how different MADS-domain proteins achieve DNA-binding specificity, are still largely unknown. We used information from in vivo ChIP-seq experiments, in vitro DNA-binding data and evolutionary conservation to address these important questions. We found that structural characteristics of the DNA play an important role in the DNA binding of plant MADS-domain proteins. The central region of the CArG-box largely resembles a structural motif called ‘A-tract’, which is characterized by a narrow minor groove and may assist bending of the DNA by MADS-domain proteins. Periodically spaced A-tracts outside the CArG-box suggest additional roles for this structure in the process of DNA binding of these transcription factors. Structural characteristics of the CArG-box not only play an important role in DNA-binding site recognition of MADS-domain proteins, but also partly explain differences in DNA-binding specificity of different members of this transcription factor family and their heteromeric complexes.

In vitro selection of zinc fingers with altered DNA-binding specificity

Biochemistry ◽  
1994 ◽  
Vol 33 (19) ◽  
pp. 5689-5695 ◽  
Author(s):  
Andrew C. Jamieson ◽  
Sung-Hou Kim ◽  
James A. Wells
Keyword(s):  
Dna Binding ◽  
In Vitro Selection ◽  
Zinc Fingers ◽  
Binding Specificity ◽  
Dna Binding Specificity ◽  
Selection Of

Nucleotides flanking a conserved TAAT core dictate the DNA binding specificity of three murine homeodomain proteins

1993 ◽  
Vol 13 (4) ◽  
pp. 2354-2365
Author(s):  
K M Catron ◽  
N Iler ◽  
C Abate
Keyword(s):  
Dna Binding ◽  
Binding Sites ◽  
Target Genes ◽  
Equilibrium Constants ◽  
Binding Specificity ◽  
Binding Activity ◽  
Selection Strategy ◽  
Homeodomain Proteins ◽  
Control Regions

Murine homeobox genes play a fundamental role in directing embryogenesis by controlling gene expression during development. The homeobox encodes a DNA binding domain (the homeodomain) which presumably mediates interactions of homeodomain proteins with specific DNA sites in the control regions of target genes. However, the bases for these selective DNA-protein interactions are not well defined. In this report, we have characterized the DNA binding specificities of three murine homeodomain proteins, Hox 7.1, Hox 1.5, and En-1. We have identified optimal DNA binding sites for each of these proteins by using a random oligonucleotide selection strategy. Comparison of the sequences of the selected binding sites predicted a common consensus site that contained the motif (C/G)TAATTG. The TAAT core was essential for DNA binding activity, and the nucleotides flanking this core directed binding specificity. Whereas variations in the nucleotides flanking the 5' side of the TAAT core produced modest alterations in binding activity for all three proteins, perturbations of the nucleotides directly 3' of the core distinguished the binding specificity of Hox 1.5 from those of Hox 7.1 and En-1. These differences in binding activity reflected differences in the dissociation rates rather than the equilibrium constants of the protein-DNA complexes. Differences in DNA binding specificities observed in vitro may contribute to selective interactions of homeodomain proteins with potential binding sites in the control regions of target genes.

A single amino acid can determine the DNA binding specificity of homeodomain proteins

Cell ◽  
1989 ◽  
Vol 59 (3) ◽  
pp. 553-562 ◽  
Author(s):  
Jessica Trelsman ◽  
Pierre Gönczy ◽  
Malini Vashishtha ◽  
Esther Harris ◽  
Claude Desplan
Keyword(s):  
Amino Acid ◽  
Dna Binding ◽  
Binding Specificity ◽  
Single Amino Acid ◽  
Homeodomain Proteins ◽  
Dna Binding Specificity

scholarly journals In vitro DNA-binding profile of transcription factors: methods and new insights

2011 ◽  
Vol 210 (1) ◽  
pp. 15-27 ◽  
Author(s):  
Jinke Wang ◽  
Jie Lu ◽  
Guangming Gu ◽  
Yingxun Liu
Keyword(s):  
Transcription Factors ◽  
Dna Binding ◽  
Dna Sequences ◽  
Binding Sites ◽  
Target Genes ◽  
Binding Specificity ◽  
Cell Physiology ◽  
Binding Profile ◽  
Dna Binding Specificity

The DNA-binding specificity of transcription factors (TFs) has broad impacts on cell physiology, cell development and in evolution. However, the DNA-binding specificity of most known TFs still remains unknown. The specificity of a TF protein is determined by its relative affinity to all possible binding sites. In recent years, the development of several in vitro techniques permits high-throughput determination of relative binding affinity of a TF to all possible k bp-long DNA sequences, thus greatly promoting the characterization of DNA-binding specificity of many known TFs. All DNA sequences that can be bound by a TF with various binding affinities form their DNA-binding profile (DBP). The DBP is important to generate an accurate DNA-binding model, identify all DNA-binding sites and target genes of TFs in the whole genome, and build transcription regulatory network. This study reviewed these techniques, especially two master techniques: double-stranded DNA microarray and systematic evolution of ligands by exponential enrichment in combination with parallel DNA sequencing techniques (SELEX-seq).

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