Assessment of DNA-binding affinity of cholinesterase reactivators and electrophoretic determination of their effect on topoisomerase I and II activity

2016 ◽  
Vol 12 (9) ◽  
pp. 2910-2920 ◽  
Author(s):  
J. Janockova ◽  
E. Zilecka ◽  
J. Kasparkova ◽  
V. Brabec ◽  
O. Soukup ◽  
...  
Keyword(s):  
Biological Activity ◽  
Dna Binding ◽  
Binding Affinity ◽  
Topoisomerase I ◽  
Biochemical Properties ◽  
Cholinesterase Reactivators ◽  
Dna Binding Affinity

In this paper, we describe the biochemical properties and biological activity of a series of cholinesterase reactivators (symmetrical bisquaternary xylene-linked compounds,K106–K114) with ctDNA.

scholarly journals Consensus and Variant cAMP-regulated Enhancers Have Distinct CREB-binding Properties

2000 ◽  
Vol 276 (15) ◽  
pp. 11719-11728 ◽  
Author(s):  
Johanna C. Craig ◽  
Maria A. Schumacher ◽  
Steven E. Mansoor ◽  
David L. Farrens ◽  
Richard G. Brennan ◽  
...  
Keyword(s):  
Dna Binding ◽  
Binding Affinity ◽  
Leucine Zipper ◽  
Camp Response Element Binding ◽  
Camp Response Element ◽  
Basic Leucine Zipper ◽  
Binding Characteristics ◽  
Element Binding Protein ◽  
Dna Binding Affinity

Recent determination of the cAMP response element-binding protein (CREB) basic leucine zipper (bZIP) consensus CRE crystal structure revealed key dimerization and DNA binding features that are conserved among members of the CREB/CREM/ATF-1 family of transcription factors. Dimerization appeared to be mediated by a Tyr307–Glu312interhelical hydrogen bond and a Glu319–Arg314electrostatic interaction. An unexpected hexahydrated Mg2+ion was centered above the CRE in the dimer cavity. In the present study, we related these features to CREB dimerization and DNA binding. A Y307F substitution reduced dimer stability and DNA binding affinity, whereas a Y307R mutation produced a stabilizing effect. Mutation of Glu319to Ala or Lys attenuated dimerization and DNA binding. Mg2+ions enhanced the binding affinity of wild-type CREB to the palindromic CRE by ∼20-fold but did not do so for divergent CREs. Similarly, mutation of Lys304, which mediates the CREB interaction with the hydrated Mg2+, blocked CREB binding to the palindromic but not the variant CRE sequences. The distinct binding characteristics of the K304A mutants to the consensus and variant CRE sequences indicate that CREB binding to these elements is differentially regulated by Mg2+ions. We suggest that CREB binds the consensus and variant CRE sequences through fundamentally distinct mechanisms.

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

scholarly journals Sequence-dependent contribution of distal binding domains to CAP protein-DNA binding affinity

1991 ◽  
Vol 19 (3) ◽  
pp. 611-616 ◽  
Author(s):  
Dennise D. Dalma-Weiszhausz ◽  
Marc R. Gartenberg ◽  
Donald M. Crothers
Keyword(s):  
Dna Binding ◽  
Binding Affinity ◽  
Binding Domains ◽  
Sequence Dependent ◽  
Dna Binding Affinity

Synthesis of C8–C8/C2–C8-linked triazolo pyrrolobenzodiazepine dimers by employing ‘click’ chemistry and their DNA-binding affinity

2008 ◽  
Vol 49 (22) ◽  
pp. 3620-3624 ◽  
Author(s):  
Ahmed Kamal ◽  
S. Prabhakar ◽  
N. Shankaraiah ◽  
Ch. Ratna Reddy ◽  
P. Venkat Reddy
Keyword(s):  
Dna Binding ◽  
Click Chemistry ◽  
Binding Affinity ◽  
Dna Binding Affinity
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