Targeting the ARE with DNA-binding polyamides
Highly efficient synthesis of DNA-binding polyamides using a convergent fragment-based approach
... (Py-Im) polyamides (PAs) constitute a family of medium-sized molecules that bind in a sequence selective manner to double-stranded DNA (dsDNA) with nanomolar binding ...dsDNA binding profile ...
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Localization of DNA binding polyamides in living cells
... chromosomal DNA sequence-specifically and with high affinity would be important tools for gene ...Pyrrole-imidazole polyamides are small molecules that bind the minor groove of DNA in a ...
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Targeting DNA Repeat Sequences with Py Im Polyamides
... Figure 3.1 Py-Im polyamide recognition of DNA minor groove and corresponding ball-and-stick notation. showed that stimulation of CRT surface expression by anthracyclins or adsorbtion of the calreticulin protein on ...
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Synthesis and Biological Studies of DNA binding Cyclic Py Im Polyamides
... of DNA is composed of a phosphodiester deoxyribose sugar backbone that links together a sequence of four nucleotides - deoxythymine (T), deoxyadenine (A), deoxycytosine (C) and deoxyguanine (G) ...of DNA ...
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Structural Modifications to DNA Binding Polyamides for Improved Biological Activity in Cell Culture
... of DNA binding proteins capable of sequence- specific binding (1, ...interaction. Polyamides containing N-methylimidazole (Im) and N-methylpyrrole (Py) are a class of programmable ...
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Structural Variations on the Turn Unit of DNA Binding Hairpin Py Im Polyamides
... genome-wide binding of polyamides in the context of chromatin in vivo, we have synthesized polyamide-biotin conjugates to pull down DNA-polyamide complexes using magnetic streptavidin ...shearing ...
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Targeting Repeat Sequences with DNA Binding Small Molecules
... = 1.8x10 8 M- 1 • Quantitative fluorescence titrations with varying patterns of telomeric repeat suggest that the molecule can tolerate another polyamid e binding contiguously, but[r] ...
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Detection of DNA by sequence specific fluorescent polyamides
... groove binding distamycin derivatives that can recognize a large number of predetermined DNA sequences with affinities that rival natural transcription ...6,29,30 DNA binding polyamides ...
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Comparative Analysis of DNA-Binding Selectivity of Hairpin and Cyclic Pyrrole-Imidazole Polyamides Based on Next-Generation Sequencing
... protein– DNA interactions, and its concept does not fit to the cases of PI ...polyamide. Binding characteristics is considered to follow the pairing rules, which entail P/P cannot distinguish A/T from ...of ...
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Shape selective recognition of the DNA minor groove by hairpin polyamides
... Abstract Polyamides composed of N-methylpyrrole (Py), N-methylimidazole (Im), and 3-hydroxy-N-methylpyrrole (Hp) are crescent-shaped ligands that bind predetermined DNA sequences with affinities and ...
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Programming Protein Patterns on DNA Nanostructures with Pyrrole Imidazole Polyamides
... 73 polyamides, unlike the minor groove which would create a steric clash with larger linkers presumably leading to abrogated ...for targeting extended DNA ...linked polyamides can target ...
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One-to-one motif for DNA recognition by beta-alanine-linked polyamides
... Distance Constraints. Polyamide binding induces a high dispersion of NOESY crosspeaks. This enabled the identification of a large number of discrete NOEs, which allowed the use of 508 distance constraints for ...
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Structural basis of DNA duplex distortion induced by thiazole-containing hairpin polyamides
... promiscuous DNA binding profile was observed, characterized by footprints at 5’-ATTTACT, 5’- ATATACT and ...G-selective binding was observed for PA4, with PA4 exhibit- ing a clear preference for ...
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Prediction of DNA-Binding Proteins and their Binding Sites
... Abstract DNA-binding proteins play an important role in various essential biological processes such as DNA replication, recombination, repair, gene transcription, and ...of DNA-binding ...
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Thermodynamic analysis of DNA binding by a Bacillus single stranded DNA binding protein.
... 70 binding suggested that SSB BA forms a tetrameric assembly upon ssDNA ...for DNA binding through the formation of a transient tetrameric ...
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Targeting DNA damage in SCLC
... traditional DNA damaging therapies will expand our under- standing of how these agents are best positioned in the clinical setting and biomarker studies may provide insight into mechanisms of ac- quired and ...
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Novel Supramolecular Polyamides
... to Binding Methods and Theories The classical noncovalent forces that are involved in the formation of supramolecular bonds are those associated with van der Waals interactions, coulombic interactions, hydrogen ...
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Single-Nucleotide-Specific Targeting of the Tf1 Retrotransposon Promoted by the DNA-Binding Protein Sap1 of Schizosaccharomyces pombe
... http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM715390) (4). The integration values used for the above analysis were normalized by dividing the number of integration events at each position by the total number of ...
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Virus mediated delivery of antibody targeting TAR DNA binding protein 43 mitigates associated neuropathology
... JCI123931DS1). We then examined the ability of these 3 antibod- ies to disrupt the interaction between TDP-43 and p65 NF-κB. We performed an ELISA with human recombinant TDP-43 and human recombinant p65 protein ...
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Mammalian Argonaute-DNA binding?
... Reviewer ’ s report 2: Kira S. Makarova, National Center for Biotechnology Information Drs. Smalheiser and Gomes described a hypothesis sug- gesting that in pathological conditions specifically in cancer cells short DNAs ...
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