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Dyes for Labeling Organelles and Compartments
Published in Guy Cox, Fundamentals of Fluorescence Imaging, 2019
Because there is a practical benefit to reserving emission channels in 500–650 nm wavelength region for detection of lower abundance protein targets by FPs and labeled antibodies, the main alternatives to Hoechst 33258, Hoechst 33342, and DAPI are the anthraquinone derivative DRAQ5 [8] for live cells and the cationic cyanine dye TO-PRO-3 for fixed cells. Both dyes have excitation/emission spectral characteristics similar to Cy5. DRAQ5 has an extremely low fluorescence quantum yield (0.004), but its strong binding affinity for DNA coupled with the high cellular abundance of its target result in good signal-to-background characteristics in fluorescence microscopy applications. DRAQ5 does not bind appreciably to RNA [9]. The primary DNA binding site of DRAQ5 overlaps that of Hoechst 33342, indicated by displacement of the latter in competition experiments [8]. Both DRAQ5 and Hoechst 33342 induce cellular DNA damage responses at typical working concentrations [10]. TO-PRO-3 is a cyanine dye that has largely superseded the phenanthridine derivative propidium iodide (PI) for nuclear staining applications, although PI remains in widespread use for cell viability analysis (see Chapter 8). Both TO-PRO-3 and PI form fluorescent complexes with RNA as well as DNA, resulting in additional utility for Nissl staining (Section 7.7).
Plants Signaling toward Drought Stress
Published in Hasanuzzaman Mirza, Nahar Kamrun, Fujita Masayuki, Oku Hirosuke, Tofazzal M. Islam, Approaches for Enhancing Abiotic Stress Tolerance in Plants, 2019
Muhammad Jamil, Aamir Ali, Alvina Gul, Khalid Farooq Akbar, Abdul Aziz Napa, A. Mujeeb-Kazi
Rushton et al. (2010) reviewed that WRKY TFs are responsible for defense signaling and regulation of growth, developmental processes, senescence, biotic and abiotic stresses. These are equipped with DNA-binding domain with signature sequence (WRKYGQK) at the N-terminus along with 60 amino acids. Moreover, zinc finger motif is there at C-terminus. At the major groove of DNA, WRKY signature sequence binds with the appropriate DNA-binding site (TTGACC/T) also called W box (Yamasaki et al., 2013). It is now made well clear by Yamasaki et al. (2013) that a four-stranded beta sheet inserts the major groove of DNA, forming beta-wedge. Tao et al. (2011) reported the role of OsWRKY 45 in the drought and cold tolerance in rice. Transcription factors such as WRKY46, WRKY54 and WRKY70 are reportedly (Chen et al., 2017) involved in drought stress. Using RT-qPCR, the expression of SlyWRKY75 has also been reported (López-Galiano et al., 2018) under drought stress.
Toward Understanding the Intelligent Properties of Biological Macromolecules
Published in George K. Knopf, Amarjeet S. Bassi, Smart Biosensor Technology, 2018
One of the insights that has resulted from analysis of these high-resolution structure databases has been a general recognition of how proteins in sequence-specific DNA–protein complexes distort their DNA recognition sites. An example of this type of DNA distortion is shown in Figure 2.42 where an x-ray structure of the bacteriophage cro protein is presented on the right in the form of a ribbon diagram of its secondary structure. It is depicted binding to its 14-bp DNA recognition sequence (164). Note that at either end of the DNA region contacted by the protein dimer, the DNA helix axis bends to the right. Distortion of DNA binding sites by sequence-specific recognition proteins is a commonly observed phenomenon (165,166). It has led to the calculation of a DNA physical property parameter called the protein deformability (PD). The magnitude of any local PD region in a DNA binding site has been shown to be very much a local property that is dependent upon the dinucleotide neighbor pair sequence. That is, on average, sequence-specific proteins deform DNA not based upon which base j occurs at a specific position for the protein to interact with, but based upon the two dinucleotides ij and jk at that specific position j. The PD values for all 16 possible dinucleotide pairs in DNA have been determined. They are based upon averaged representations of how each protein specifically deformed its DNA recognition sequence in a dataset of nearly 100 high-resolution DNA–protein structures (167).
Investigation of spectral and structural properties of a coordination compound with phthalic acid: DFT and molecular docking studies
Published in Journal of Coordination Chemistry, 2020
Molecular docking calculation is an important computational technique to predict interaction mode and ideal DNA binding site in molecular pharmaceutics. To explain DNA-interaction mode of complex, docking of Cu(II) complex with B-DNA DODECAMER (1BNA) was performed. The results showed that the copper complex is the most basic residue found in the active sites of DA5, DG4, DC3, DG2 and DG24 in the interaction with DNA. It has shown that it makes more hydrogen bonds with complex DNA. The possible interaction models including interactions and the types of interactions of the basic residues are shown in Table S2. Interactions between the target DNA and the complex are shown in Figure 8. The interaction energies for the complex and the ligand docked to DNA are examined and it is seen that the free ligand has Gibbs energy higher than the complex. Inhibition constants for the complex and free ligand were calculated as 8.344 μM and 16.433 μM, respectively. The inhibition constant provides information that predicts how a ligand will inhibit an enzyme and may interact with a substrate for the enzyme. The inhibition constant is also a measure of the binding affinity of the ligand to the protein. In general, high affinity ligand binding results in greater intermolecular force between the ligand and its receptor, while low affinity ligand binding contains less intermolecular force. As the Ki concentration decreases, the probability of a chemical reaction between the ion and the recipient antigen increases. Low affinity binding (high Ki level) means that a relatively high ligand concentration is required before the binding site is occupied most and the maximum physiological response to the bond is achieved. That is, the smaller the inhibition constant, the less drugs are needed to inhibit enzyme activity [67].