scholarly journals SSB–DNA Binding Monitored by Fluorescence Intensity and Anisotropy

2012 ◽  
pp. 55-83 ◽  
Author(s):  
Alexander G. Kozlov ◽  
Roberto Galletto ◽  
Timothy M. Lohman
Keyword(s):  
Dna Binding ◽  
Fluorescence Intensity

scholarly journals Competitive Binding of Novel Cyanine Dye AK3-5 and Europium Coordination Complexes to DNA

2019 ◽  
Keyword(s):  
Dna Binding ◽  
Fluorescence Intensity ◽  
Binding Sites ◽  
Association Constant ◽  
Antitumor Agents ◽  
Coordination Complexes ◽  
Cyanine Dye ◽  
Europium Complexes ◽  
Intensity Decrease ◽  
Dna Binding Sites

The present study was undertaken to assess the applicability of the novel trimethine cyanine dye AK3-5 as a competitive ligand for the antitumor agents, Eu(III) coordination complexes (EC), in the DNA-containing systems, using the displacement assay as an analytical instrument. The analysis of fluorescence spectra revealed a strong association of AK3-5 with nucleic acids, with the strength of interaction being higher for the double stranded DNA, compared to the single-stranded RNA. The binding parameters of the cyanine dye have been determined in terms of the McGhee & von Hippel neighbouring site-exclusion model and a classical Langmuir model. The AK3-5 association constant in the presence of DNA was found to be equal to 5.1×104 M-1, which is consistent to those of the well-known DNA intercalators. In turn, the binding of the cyanine to the RNA was characterized by a significantly lower association constant ( ~ 3.4×103 M-1) indicating either the external or “partially intercalated” binding mode. The addition of the europium complexes to the AK3-5-DNA system was followed by the fluorescence intensity decrease, with a magnitude of this effect being dependent on the EC structure. The observed fluorescence decrease of AK3-5 in the presence of europium complexes V7 and V9 points to the competition between the cyanine dye and antitumor drugs for the DNA binding sites. The dependencies of the AK3-5-DNA fluorescence intensity decrease vs. europium complex concentration were analyzed in terms of the Langmuir adsorption model, giving the values of the drug association constant equal to 5.4×104 M-1and 3.9×105 M-1 for the europium complexes V7 and V9, respectively. A more pronounced decrease of the AK3-5 fluorescence in the presence of V5 and V10 was interpreted in terms of the drug-induced quenching of the dye fluorescence, accompanying the competition between AK3-5 and Eu(III) complexes for the DNA binding sites. Cumulatively, the results presented here strongly suggest that AK3-5 can be effectively used in the nucleic acid studies and in the dye-drug displacement assays.

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.

scholarly journals Common Kinetic Mechanism of Abasic Site Recognition by Structurally Different Apurinic/Apyrimidinic Endonucleases

2021 ◽  
Vol 22 (16) ◽  
pp. 8874
Author(s):  
Alexandra A. Kuznetsova ◽  
Svetlana I. Senchurova ◽  
Alexander A. Ishchenko ◽  
Murat Saparbaev ◽  
Olga S. Fedorova ◽  
...  
Keyword(s):  
Dna Binding ◽  
Conformational Changes ◽  
Fluorescence Intensity ◽  
Dna Cleavage ◽  
Excision Repair ◽  
Kinetic Mechanism ◽  
Abasic Site ◽  
Catalytic Rate Constant ◽  
Base Excision ◽  
Ap Site

Apurinic/apyrimidinic (AP) endonucleases Nfo (Escherichia coli) and APE1 (human) represent two conserved structural families of enzymes that cleave AP-site–containing DNA in base excision repair. Nfo and APE1 have completely different structures of the DNA-binding site, catalytically active amino acid residues and catalytic metal ions. Nonetheless, both enzymes induce DNA bending, AP-site backbone eversion into the active-site pocket and extrusion of the nucleotide located opposite the damage. All these stages may depend on local stability of the DNA duplex near the lesion. Here, we analysed effects of natural nucleotides located opposite a lesion on catalytic-complex formation stages and DNA cleavage efficacy. Several model DNA substrates that contain an AP-site analogue [F-site, i.e., (2R,3S)-2-(hydroxymethyl)-3-hydroxytetrahydrofuran] opposite G, A, T or C were used to monitor real-time conformational changes of the tested enzymes during interaction with DNA using changes in the enzymes’ intrinsic fluorescence intensity mainly caused by Trp fluorescence. The extrusion of the nucleotide located opposite F-site was recorded via fluorescence intensity changes of two base analogues. The catalytic rate constant slightly depended on the opposite-nucleotide nature. Thus, structurally different AP endonucleases Nfo and APE1 utilise a common strategy of damage recognition controlled by enzyme conformational transitions after initial DNA binding.

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.

DNA-binding lipids protect bacteria

2017 ◽  
Author(s):  
Nadia El-Awady
Keyword(s):  
Dna Binding
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