Trends in Biochemical Sciences
Protein motifs that recognize structural features of DNA
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The heparin-binding hemagglutinin protein of Mycobacterium tuberculosis is a nucleoid-associated protein
2023, Journal of Biological ChemistryEnergetics of twisted DNA topologies
2021, Biophysical JournalCitation Excerpt :With further negative twist, the torque remains constant as B-DNA transitions to L-DNA. Because L-DNA has a much higher twist persistence length (CL ϵ (10–20) nm) (48) than intertwined, melted DNA (Cmelt ≈ 1 nm, Eq. 1), L-DNA is believed to be composed of intertwined, melted DNA and other noncanonical structures like Z-DNA (49). Previous models have shown that less energy is required to denature an A:T basepair than a C:G basepair (ΔG ≈ 1.9 and 2.9 kBT, respectively (50)), so DNA melting occurs preferentially in AT-rich regions.
Identification and expression analysis of the AHL gene family in grape (Vitis vinifera)
2021, Plant GeneCitation Excerpt :It is a specific structure mainly composed of four residues of arginine (Arg) – glycine (Gly) – arginine (Arg) – proline (Pro) (RGRP) (Zhao et al., 2013; Zhang et al., 2014). It is widely found in DNA binding proteins of bacteria, fungi and animals (Goodwin et al., 1973; Eckner and Birnstiel, 1989; Churchill and Travers, 1991; Aravind and Landsman, 1998; Do et al., 2006; Zhao et al., 2013). PPC domain is located at the carboxyl terminus of AT-hook motif and has about 120 amino acids, which are responsible for the nuclear localization of AHL protein (Fujimoto et al., 2004).
Development of a Targeted anti-HER2 scFv Chimeric Peptide for Gene Delivery into HER2-Positive Breast Cancer Cells
2016, International Journal of PharmaceuticsRegulation of the bacteriophage T4 Dda helicase by Gp32 single-stranded DNA-binding protein
2015, DNA RepairCitation Excerpt :As shown in Fig. 1A, Gp32 alone (Fig. 1A, lane 1) migrates as a diffuse band with relatively low apparent molecular weight. The smearing of this band is likely due to the formation of small mixed oligomers of Gp32 under native conditions [43]. The mobility of the Gp32 band appears to be shifted upon addition of Dda (Fig. 1A, lane 2), while Dda alone migrates as a diffuse band at relatively high apparent molecular weight (Fig. 1A, lane 9).
Prediction of replication origins by calculating DNA structural properties
2012, FEBS LettersCitation Excerpt :The parameters of tetranucleotides were derived by Greenbaum et al. from experiments in which DNA sequences were exposed to hydroxyl radicals [17]. However, this type of hydroxyl radical cleavage pattern considers properties of a single DNA strand of the double helix, and therefore could not measure the minor groove width, which depends on both DNA strands and is an important recognition element for protein binding [20–22]. Recently, Bishop et al. [23] developed the ORChID2 algorithm (http://dna.bu.edu/orchid/) to predict cleavage intensity by incorporating hydroxyl radical cleavage information from both strands of the DNA duplex.