Nucleotides bearing aminophenyl- or aminonaphthyl-3-methoxychromone solvatochromic fluorophores for enzymatic construction of DNA probes for detection of protein-DNA binding

2021 ◽  
Author(s):  
Jan Matyasovsky ◽  
Laure Tack ◽  
Attila Palagyi ◽  
Miroslav Kuba ◽  
Radek Pohl ◽  
...  
Keyword(s):  
Dna Binding ◽  
Dna Probes ◽  
Nucleoside Triphosphates

We designed and synthesized nucleosides bearing aminophenyl- or aminonaphthyl-3-methoxychromone fluorophores attached at position 5 of cytosine or thymine and converted them to nucleoside triphosphates. The fluorophores exerted solvatochromic fluorescence with...

scholarly journals Dibenzopyridoimidazocinnolinium cations: a new family of light-up fluorescent DNA probes

2018 ◽  
Vol 5 (12) ◽  
pp. 1916-1927 ◽  
Author(s):  
Pedro Bosch ◽  
David Sucunza ◽  
Francisco Mendicuti ◽  
Alberto Domingo ◽  
Juan J. Vaquero
Keyword(s):  
Dna Binding ◽  
Fluorescence Intensity ◽  
Living Cells ◽  
Dna Probes ◽  
Live Cell ◽  
Binding Ability ◽  
Active Uptake ◽  
New Family ◽  
Cell Staining ◽  
New Compounds

A new family of weakly fluorescent azonia cations with DNA-binding ability by intercalation whose fluorescence intensity increases significantly upon DNA addition is reported. A live-cell staining cells analysis showed the capacity of these new compounds for active uptake and accumulation by living cells.

Tail-labelling of DNA probes using modified deoxynucleotide triphosphates and terminal deoxynucleotidyl tranferase. Application in electrochemical DNA hybridization and protein-DNA binding assays

2011 ◽  
Vol 9 (5) ◽  
pp. 1366 ◽  
Author(s):  
Petra Horáková ◽  
Hana Macíčková-Cahová ◽  
Hana Pivoňková ◽  
Jan Špaček ◽  
Luděk Havran ◽  
...  
Keyword(s):  
Dna Binding ◽  
Dna Hybridization ◽  
Dna Probes ◽  
Binding Assays

Single-Stranded DNA Binding Proteins (SSBPs) Interact with LDB1 Homodimers to Facilitate DNA Looping.

Blood ◽  
2009 ◽  
Vol 114 (22) ◽  
pp. 1469-1469
Author(s):  
Ying Cai ◽  
Lalitha Nagarajan ◽  
Stephen J. Brandt
Keyword(s):  
Dna Binding ◽  
Luciferase Activity ◽  
Conflicts Of Interest ◽  
Dna Probes ◽  
Dominant Negative ◽  
Cross Linking ◽  
Dimerization Domain ◽  
Interaction Domain

Abstract Abstract 1469 Poster Board I-492 The LIM domain binding protein LDB1 is an essential cofactor of LIM-homeodomain (LIM-HD) and LIM-only (LMO) proteins in hematopoiesis and other developmental programs. We have shown that LDB1 and its LIM-HD and LMO interaction partners are protected from ubiquitylation by a small family of SSBPs. Recently, we demonstrated that these SSBPs bind to LDB1 homodimers to promote formation of a ternary complex containing two molecules of LDB1 and SSBP. This was dependent on an intact LDB1 dimerization domain (DD) and produced a shift, directly or indirectly, in the equilibrium between LDB1 monomer and dimer. In the present study, we introduced a 24-glycine linker between two full-length LDB1 peptide-coding sequences and expressed this forced or tethered LDB1 dimer (TD-LDB1) in vitro and in vivo. First, both TD-LDB1, introduced into cells by transfection, and endogenous LDB1 were found to have the same turnover rate, indicating that protection from ubiquitylation was independent of dimerization status. Second, TD-LDB1 was fused to the DNA binding domain of GAL4 (GAL4DBD) and in a second construct to the activation domain of herpesvirus VP16 (VP16AD) and these constructs were expressed in cells with a GAL4 reporter plasmid. Co-expression of GAL4-LDB1 and VP16-LDB1 significantly increased reporter luciferase activity as a result of dimerization, while co-expression of GAL4-TD-LDB1 with VP16-LDB1 did not, ruling out formation of LDB1 trimers. Likewise, co-expression of GAL4-TD-LDB1 with VP16-TD-LDB1 did not significantly affect luciferase activity, indicating that LDB1 also cannot form protein tetramers. In contrast, TD-LDB1 was able to bind SSBP2 and SSBP3 in both chemical cross-linking and mammalian two-hybrid assays, consistent with the SSBP interacting with preformed LDB1 dimers. Finally, the complete 200-amino acid DD of LDB1, reported as necessary and sufficient for protein dimerization, was confirmed in cross-linking analysis to act as a dominant negative inhibitor of LDB1 dimerization. When the DD was introduced into Lhx2-, Ldb1-, and Ssbp3-expressing cells, application of a modified electrophoretic mobility assay that can detect linking of two DNA probes in solution revealed that the DD reduced formation of a ‘looped’ complex containing two DNA probes and led to the appearance of a new complex containing Lhx2, Ssbp3, and Ldb1, apparently in a monomeric form. In summary, this work elucidates a novel function of SSBPs in enhancing LDB1 dimerization and, ultimately, long-range communication between cis regulatory regions in genes. In addition, it suggests that SSBPs bind dimeric LDB1 and induce an allosteric change in the adjacent SSBP interaction domain rather than vice versa. Finally, these results lead to the prediction that an SSBP- and LDB1-containing complex could promote looping between promoter-proximal and promoter-distal LIM-HD binding elements. Disclosures: No relevant conflicts of interest to declare.

scholarly journals Nucleoside triphosphates promote the transformation of Ah receptor to its DNA-binding form

1991 ◽  
Vol 274 (2) ◽  
pp. 401-404 ◽  
Author(s):  
A J Cary ◽  
J J Dougherty
Keyword(s):  
Dna Binding ◽  
Aryl Hydrocarbon Receptor ◽  
Ah Receptor ◽  
Nucleotide Hydrolysis ◽  
Aryl Hydrocarbon ◽  
Low Concentrations ◽  
Nucleoside Triphosphates ◽  
Tetrachlorodibenzo P Dioxin ◽  
Specific Ligand

When it is bound to a specific ligand such as 2,3,7,8-tetrachlorodibenzo-p-dioxin, mild heating can convert the Ah (aryl hydrocarbon) receptor into a form capable of binding DNA. We found that physiological (1-3 mM) levels of ATP substantially increased the transformation of the receptor to its DNA-binding form. GTP, UTP and CTP had similar effects. ADP also promoted this transformation, but was less effective than ATP at low concentrations. Pyrophosphate too promoted transformation, but AMP had little effect. The process did not require nucleotide hydrolysis, since non-hydrolysable analogues of ATP such as adenosine 5′-[beta gamma-imido]triphosphate were nearly as effective as ATP itself. Inhibitors of ATP-stimulated proteases did not significantly affect the ability of ATP to promote receptor transformation, which suggests that the effect of ATP was not mediated by these proteases.

Water soluble palladium(ii) and platinum(ii) acyclic diaminocarbene complexes: solution behavior, DNA binding, and antiproliferative activity

2020 ◽  
Vol 44 (15) ◽  
pp. 5762-5773 ◽  
Author(s):  
Tatiyana V. Serebryanskaya ◽  
Mikhail A. Kinzhalov ◽  
Vladimir Bakulev ◽  
Georgii Alekseev ◽  
Anastasiya Andreeva ◽  
...  
Keyword(s):  
Dna Binding ◽  
Antiproliferative Activity ◽  
Water Soluble ◽  
Solution Behavior ◽  
Antitumor Potential ◽  
Acyclic Diaminocarbene

Water soluble Pd(ii) and Pt(ii)–ADC species synthesized via the metal-mediated coupling of isocyanides and 1,2-diaminobenzene have demonstrated antitumor potential.

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