Author: Giacomo Padroni
Publisher:
ISBN:
Category :
Languages : en
Pages : 0
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Pyrrole-Imidazole (Py-Im) hairpin polyamides are a programmable class of compounds that bind in the minor groove of double-stranded DNA (dsDNA). The hairpin conformationenables sufficient flexibility to form a side-by-side arrangement within the minor groove of target dsDNA sequences. An Im-Py pair discriminates G over C, A and T, whereas a Py-Pypair binds A and T over C and G. The possibility to target specific dsDNA sequences enables polyamides to modulate gene expression by the disruption of transcription factors such as the androgen receptor, over expressed in prostate cancer. A current limitation of the biological applications of Py-Im polyamides is their variable cell permeability profile. Im-richpolyamides tend to have reduced cellular and nuclear uptake in eukaryotic cells. Although modifications to the periphery of the polyamide scaffold have been explored at length, there has been limited studies on tuning the physicochemical properties of the G-recognising Imunit. This thesis describes the preparation and the evaluation of the binding mode of hairpin polyamides with Im units replaced by a series of 5-substituted 2-amino-4-carboxylic thiazole(Nt) building blocks. Chapter 1 introduces the endogenous and exogenous DNA recognition by protein and small molecules, the modulation of gene expression using Py-Im polyamides and the limitations of this approach. Chapter 2 describes the preparation of the building blocks and the optimisation of the solid phase synthesis of hairpin polyamides containing Nt units. These optimised conditions were used for the preparation of a suite of 8-ring polyamides incorporating Nt in different positions of the polyamide scaffold. Expanding the DNA binding repertoire of Pyrrole-Imidazole polyamides Chapter 3 describes the evaluation of the binding mode of Nt-containing polyamides using a combination of biophysical and biochemical methods. The 5-isopropyl substituted Nt (iPrNt) building block was identified as an alternative to Im for targeting G when incorporated at theN-terminus of the polyamide scaffold. Chapter 4 describes the structural characterisation of three selected polyamides binding to their dsDNA target sequence using NMR spectroscopy and molecular dynamics. This study reveals that the polyamide containing iPrNt at the N-terminus induces a greater compression of the major groove compared to the Im-containing analogue. Finally, Chapter 5 reflects on the work of this thesis and offers some perspective of the future development of Py-Im polyamides as gene expression modulators.
Author: David Church Montgomery
Publisher:
ISBN:
Category : DNA-protein interactions
Languages : en
Pages : 0
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DNA is nature's blueprint, holding within it the genetic code that defines the structure and function of an organism. A complex network of DNA-binding proteins called transcription factors can largely control the flow of information from DNA, so modulating the function of transcription factors is a promising approach for treating many diseases. Pyrrole-imidazole (Py-Im) polyamides are a class of DNA-binding oligomers, which can be synthetically programmed to bind a target sequence of DNA. Due to their unique shape complementarity and a series of favorable hydrogen bonding interactions that occur upon DNA-binding, Py-Im polyamides can bind to the minor groove of DNA with affinities comparable to transcription factors. Previous studies have demonstrated that these cell-permeable small molecules can enter cell nuclei and disrupt the transcription factor-DNA interface, thereby repressing transcription. As the use of Py-Im polyamides has significant potential as a type of modular therapeutic platform, the need for polyamides with extremely favorable biological properties and high potency will be essential. Described herein, a variety of studies have been performed aimed at improving the biological activity of Py-Im polyamides. To improve the biological potency and cellular uptake of these compounds, we have developed a next-generation class of polyamides bearing aryl-turn moieties, a simple structural modification that allows significant improvements in cellular uptake. This strategy was also applied to a panel of high-affinity cyclic Py-Im polyamides, again demonstrating the remarkable effect minor structural changes can have on biological activity. The solubility properties of Py-Im polyamides and use of formulating reagents with their treatment have also been examined. Finally, we describe the study of Py-Im polyamides as a potential artificial transcription factor.
Author: Khalid Aman
Publisher:
ISBN:
Category :
Languages : en
Pages : 0
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Book Description
Chapter 1 introduces the regulation of gene expression using MGB small molecules.Chapter 2 describes the synthesis of hairpin polyamides, starting with the building blocks and then the solid phase synthetic protocol for constructing 8-ring hairpin polyamides.Chapter 3 showcases the thermal UV melt data, and examines the polyamide binding kinetics with DNA duplexes. Further insight into the binding was obtained with switchSENSE® technology, which allowed the generation of kinetic rate maps. The data outlined in this chapter enabled the profiling of the kinetic parameters that govern PA-dsDNA binding.Chapter 4 provides a structural view of a novel iPr-Im-containing polyamide-DNA complex, highlighting the closer proximity of the N-terminal iPr-Im N2 to the exocyclic amine of G5 compared with the N-terminal iPr-Nt analogue. Furthermore, the 3D NMR-restrained molecular dynamics (MD) structure indicated the major groove compression was greater for polyamide with the terminal iPr-Im monomer compared with the Me-Im analogue, highlighting the importance of a seemingly subtle change in steric bulk facing away from the minor groove for augmenting structural distortion of the DNA duplex.Chapter 5 takes the key findings of this thesis and uses them as a lens for looking to the future direction that this research may take. Namely, the potential of this novel iPr-Im monomer unit to replace imidazole as a G-selective residue that can induce greater structural distortion of the DNA duplex by polyamides.
Author: James J. Kelly (Attorney)
Publisher:
ISBN:
Category : DNA-binding proteins
Languages : en
Pages : 366
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Author: Yusuke Kawamoto
Publisher: Springer
ISBN: 9811369127
Category : Science
Languages : en
Pages : 130
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This book presents a novel method of synthesizing sequence-specific DNA binding pyrrole–imidazole (Py–Im) polyamides and demonstrates polyamides targeting longer base pairs than those previously reported and their cellular application. It discusses the development of the facile synthetic method of tandem hairpin Py–Im polyamides and the method of visualizing telomeres under mild conditions without harsh denaturation, as well as research resulting in the synthesis not only of previously reported tandem dimer polyamides but also longer tandem trimer and tetramer polyamides. Using fluorescently labeled tandem hairpin Py–Im polyamides targeting a human telomere repetitive sequence, the author successfully stained telomeres in fixed cells without denaturation. These fluorescently labeled tandem tetramer polyamides are able to visualize human telomeres with lower background signals than previous polyamide probes, suggesting that they have higher specificity for telomeres. As such, this book provides insights into recent advance in Py–Im polyamides, particularly the extension of the target sites c
Author: Bruce A. Armitage
Publisher: Springer Science & Business Media
ISBN: 9783540228356
Category : Science
Languages : en
Pages : 232
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Book Description
with contributions by numerous experts
Author: Michael J Waring
Publisher: Royal Society of Chemistry
ISBN: 1788014286
Category : Science
Languages : en
Pages : 432
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Book Description
There have been remarkable advances towards discovering agents that exhibit selectivity and sequence-specificity for DNA, as well as understanding the interactions that underlie its propensity to bind molecules. This progress has important applications in many areas of biotechnology and medicine, notably in cancer treatment as well as in future gene targeting therapies. The editor and contributing authors are leaders in their fields and provide useful perspectives from diverse and interdisciplinary backgrounds on the current status of this broad area. The role played by chemistry is a unifying theme. Early chapters cover methodologies to evaluate DNA-interactive agents and then the book provides examples of DNA-interactive molecules and technologies in development as therapeutic agents. DNA-binding metal complexes, peptide and polyamide–DNA interactions, and gene targeting tools are some of the most compelling topics treated in depth. This book will be a valuable resource for postgraduate students and researchers in chemical biology, biochemistry, structural biology and medicinal fields. It will also be of interest to supramolecular chemists and biophysicists.
Author:
Publisher:
ISBN:
Category : Dissertations, Academic
Languages : en
Pages : 782
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Author:
Publisher:
ISBN:
Category : Nucleic acids
Languages : en
Pages : 918
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Author: National Academy of Sciences (U.S.)
Publisher:
ISBN:
Category : Electronic journals
Languages : en
Pages : 1352
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