Stereochemical Control of the DNA Binding Affinity, Sequence Specificity, and Orientation Preference of Chiral Hairpin Polyamides in the Minor Groove

1998 ◽  
Vol 120 (7) ◽  
pp. 1382-1391 ◽  
Author(s):  
David M. Herman ◽  
Eldon E. Baird ◽  
Peter B. Dervan
Keyword(s):  
Dna Binding ◽  
Binding Affinity ◽  
Minor Groove ◽  
Sequence Specificity ◽  
Orientation Preference ◽  
Stereochemical Control ◽  
Dna Binding Affinity

scholarly journals Effect of single pyrrole replacement with β-alanine on DNA binding affinity and sequence specificity of hairpin pyrrole/imidazole polyamides targeting 5′-GCGC-3′

2013 ◽  
Vol 21 (17) ◽  
pp. 5436-5441 ◽  
Author(s):  
Yong-Woon Han ◽  
Gengo Kashiwazaki ◽  
Hironobu Morinaga ◽  
Tomoko Matsumoto ◽  
Kaori Hashiya ◽  
...  
Keyword(s):  
Dna Binding ◽  
Binding Affinity ◽  
Sequence Specificity ◽  
Dna Binding Affinity

Dithiocarbamate/piperazine bridged pyrrolobenzodiazepines as DNA-minor groove binders: Synthesis, DNA-binding affinity and cytotoxic activity

2015 ◽  
Vol 59 ◽  
pp. 23-30 ◽  
Author(s):  
Ahmed Kamal ◽  
Kokkonda Sreekanth ◽  
Nagula Shankaraiah ◽  
Manda Sathish ◽  
Shalini Nekkanti ◽  
...  
Keyword(s):  
Dna Binding ◽  
Cytotoxic Activity ◽  
Binding Affinity ◽  
Minor Groove ◽  
Dna Minor Groove ◽  
Minor Groove Binders ◽  
Dna Binding Affinity ◽  
Groove Binders

scholarly journals The Yeast a1 and α2 Homeodomain Proteins Do Not Contribute Equally to Heterodimeric DNA Binding

1999 ◽  
Vol 19 (1) ◽  
pp. 585-593 ◽  
Author(s):  
Yisheng Jin ◽  
Hualin Zhong ◽  
Andrew K. Vershon
Keyword(s):  
Dna Binding ◽  
Binding Affinity ◽  
Sequence Specificity ◽  
Wild Type ◽  
Homeodomain Proteins ◽  
Cell Type Specific ◽  
Dna Binding Affinity ◽  
Diploid Cells

ABSTRACT In diploid cells of the yeast Saccharomyces cerevisiae, the α2 and a1 homeodomain proteins bind cooperatively to sites in the promoters of haploid cell-type-specific genes (hsg) to repress their expression. Although both proteins bind to the DNA, in the α2 homeodomain substitutions of residues that are involved in contacting the DNA have little or no effect on repression in vivo or cooperative DNA binding with a1 protein in vitro. This result brings up the question of the contribution of each protein in the heterodimer complex to the DNA-binding affinity and specificity. To determine the requirements for the a1-α2 homeodomain DNA recognition, we systematically introduced single base-pair substitutions in an a1-α2 DNA-binding site and examined their effects on repression in vivo and DNA binding in vitro. Our results show that nearly all substitutions that significantly decrease repression and DNA-binding affinity are at positions which are specifically contacted by either the α2 or a1 protein. Interestingly, an α2 mutant lacking side chains that make base-specific contacts in the major groove is able to discriminate between the wild-type and mutant DNA sites with the same sequence specificity as the wild-type protein. These results suggest that the specificity of α2 DNA binding in complex with a1 does not rely solely on the residues that make base-specific contacts. We have also examined the contribution of the a1 homeodomain to the binding affinity and specificity of the complex. In contrast to the lack of a defective phenotype produced by mutations in the α2 homeodomain, many of the alanine substitutions of residues in the a1 homeodomain have large effects on a1-α2-mediated repression and DNA binding. This result shows that the two proteins do not make equal contributions to the DNA-binding affinity of the complex.

scholarly journals Lowering DNA binding affinity of SssI DNA methyltransferase does not enhance the specificity of targeted DNA methylation in E. coli

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Krystyna Ślaska-Kiss ◽  
Nikolett Zsibrita ◽  
Mihály Koncz ◽  
Pál Albert ◽  
Ákos Csábrádi ◽  
...  
Keyword(s):  
Dna Methylation ◽  
Dna Binding ◽  
Binding Affinity ◽  
Dna Methyltransferase ◽  
Restriction Enzymes ◽  
Dna Binding Protein ◽  
E Coli ◽  
Dna Binding Affinity ◽  
Higher Eukaryotes

AbstractTargeted DNA methylation is a technique that aims to methylate cytosines in selected genomic loci. In the most widely used approach a CG-specific DNA methyltransferase (MTase) is fused to a sequence specific DNA binding protein, which binds in the vicinity of the targeted CG site(s). Although the technique has high potential for studying the role of DNA methylation in higher eukaryotes, its usefulness is hampered by insufficient methylation specificity. One of the approaches proposed to suppress methylation at unwanted sites is to use MTase variants with reduced DNA binding affinity. In this work we investigated how methylation specificity of chimeric MTases containing variants of the CG-specific prokaryotic MTase M.SssI fused to zinc finger or dCas9 targeting domains is influenced by mutations affecting catalytic activity and/or DNA binding affinity of the MTase domain. Specificity of targeted DNA methylation was assayed in E. coli harboring a plasmid with the target site. Digestions of the isolated plasmids with methylation sensitive restriction enzymes revealed that specificity of targeted DNA methylation was dependent on the activity but not on the DNA binding affinity of the MTase. These results have implications for the design of strategies of targeted DNA methylation.

scholarly journals Quantification of transcription factor-DNA binding affinity in a living cell

2015 ◽  
Vol 44 (7) ◽  
pp. 3045-3058 ◽  
Author(s):  
Sergey Belikov ◽  
Otto G. Berg ◽  
Örjan Wrange
Keyword(s):  
Transcription Factor ◽  
Dna Binding ◽  
Binding Affinity ◽  
Living Cell ◽  
Dna Binding Affinity
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