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Relevant bibliographies by topics / Sequence-specific DNA intercalators

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Academic literature on the topic 'Sequence-specific DNA intercalators'

Author: Grafiati

Published: 4 June 2021

Last updated: 6 February 2022

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Journal articles on the topic "Sequence-specific DNA intercalators"

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Beauchemin, Chantal, Nathan J. Moerke, Patrick Faloon, and Kenneth M. Kaye. "Assay Development and High-Throughput Screening for Inhibitors of Kaposi’s Sarcoma–Associated Herpesvirus N-Terminal Latency-Associated Nuclear Antigen Binding to Nucleosomes." Journal of Biomolecular Screening 19, no. 6 (2014): 947–58. http://dx.doi.org/10.1177/1087057114520973.

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Kaposi’s sarcoma–associated herpesvirus (KSHV) has a causative role in several human malignancies, especially in immunocompromised hosts. KSHV latently infects tumor cells and persists as an extrachromosomal episome (plasmid). KSHV latency-associated nuclear antigen (LANA) mediates KSHV episome persistence. LANA binds specific KSHV sequence to replicate viral DNA. In addition, LANA tethers KSHV genomes to mitotic chromosomes to efficiently segregate episomes to daughter nuclei after mitosis. N-terminal LANA (N-LANA) binds histones H2A and H2B to attach to chromosomes. Currently, there are no specific inhibitors of KSHV latent infection. To enable high-throughput screening (HTS) of inhibitors of N-LANA binding to nucleosomes, here we develop, miniaturize, and validate a fluorescence polarization (FP) assay that detects fluorophore-labeled N-LANA peptide binding to nucleosomes. We also miniaturize a counterscreen to identify DNA intercalators that nonspecifically inhibit N-LANA binding to nucleosomes, and also develop an enzyme-linked immunosorbent assay to assess N-LANA binding to nucleosomes in the absence of fluorescence. HTS of libraries containing more than 350,000 compounds identified multiple compounds that inhibited N-LANA binding to nucleosomes. No compounds survived all counterscreens, however. More complex small-molecule libraries will likely be necessary to identify specific inhibitors of N-LANA binding to histones H2A and H2B; these assays should prove useful for future screens.

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Liu, Shenghui, Jiannong Ye, Pingang He, and Yuzhi Fang. "Voltammetric determination of sequence-specific DNA by electroactive intercalator on graphite electrode." Analytica Chimica Acta 335, no. 3 (1996): 239–43. http://dx.doi.org/10.1016/s0003-2670(96)00331-5.

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Kirschstein, Omar, Miroslav Sip, and Leonhard Kittler. "Quantitative and sequence-specific analysis of DNA-ligand interaction by means of fluorescent intercalator probes." Journal of Molecular Recognition 13, no. 3 (2000): 157–63. http://dx.doi.org/10.1002/1099-1352(200005/06)13:3<157::aid-jmr498>3.0.co;2-y.

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Guelev, Vladimir, Jeeyeon Lee, Jonathan Ward, Steven Sorey, David W. Hoffman, and Brent L. Iverson. "Peptide bis-intercalator binds DNA via threading mode with sequence specific contacts in the major groove." Chemistry & Biology 8, no. 5 (2001): 415–25. http://dx.doi.org/10.1016/s1074-5521(01)00013-8.

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Moriguchi, Tomohisa, Tomoyuki Ohike, and Kazuo Shinozuka. "Development of DNA-intercalator-polyamine multi-conjugate bearing the ability of the sequence-specific RNA hydrolysis." Nucleic Acids Symposium Series 50, no. 1 (2006): 187–88. http://dx.doi.org/10.1093/nass/nrl093.

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Orson, Frank M., W. Michael McShan, and Berma M. Kinsey. "Sequence-specific binding and cleavage of duplex DNA by a radioiodinated, intercalator-linked, triplex-forming oligonucleotide." Nuclear Medicine and Biology 23, no. 4 (1996): 519–24. http://dx.doi.org/10.1016/0969-8051(96)00034-0.

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Sun, J. S., J. C. Francois, T. Montenay-Garestier, et al. "Sequence-specific intercalating agents: intercalation at specific sequences on duplex DNA via major groove recognition by oligonucleotide-intercalator conjugates." Proceedings of the National Academy of Sciences 86, no. 23 (1989): 9198–202. http://dx.doi.org/10.1073/pnas.86.23.9198.

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Cortes-Guzman, Fernando, Juan García-Ramos, Rodrigo Galindo-Murrillo, Rafael Moreno-Esparza, Lena Ruiz-Azuara, and Rosa Gómez. "Intercalation process of anticancer copper (II) complexes in DNA." Acta Crystallographica Section A Foundations and Advances 70, a1 (2014): C963. http://dx.doi.org/10.1107/s2053273314090366.

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Ternary Copper (II) Complexes (TCC) have shown cytotoxic, genotoxic, and antineoplastic activity in vitro and in vivo. There are evidences that these compounds interact directly with DNA but it is not clear how deep TCC penetrates into the DNA double helix and their specific interactions have not been established. Recently, our group found that the deoxyribose-phosphate group is the specific recognition site of TCC in DNA. Here we report a crystallographic and theoretical study to determine each step of intercalation process of TCC in DNA with the recognition site as starting point. On the basis of crystal structures, Molecular Dynamics, DFT calculations and Electron Density Analysis we found that the family of analyzed TCC prefers the sequence Thymine-Adenine-Thymine to start the insertion. The intercalation process consists of an opening of a base pair as the complex intercalates within a succession of axial ligand exchange. The copper center migrates from phosphate to ribose then to thymine and finally to adenine. It is possible that the biological activity of TCC is related to its capability to evert base pairs and perform the necessary migrations from the recognition site to the complete intercalation

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Stavros, Kallie M., Edward K. Hawkins, Carmelo J. Rizzo, and Michael P. Stone. "Base-displaced intercalation of the 2-amino-3-methylimidazo[4,5-f]quinolone N2-dG adduct in the NarI DNA recognition sequence." Nucleic Acids Research 42, no. 5 (2013): 3450–63. http://dx.doi.org/10.1093/nar/gkt1109.

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Abstract 2-Amino-3-methylimidazo[4,5-f]quinolone (IQ), a heterocyclic amine found in cooked meats, undergoes bioactivation to a nitrenium ion, which alkylates guanines at both the C8-dG and N2-dG positions. The conformation of a site-specific N2-dG-IQ adduct in an oligodeoxynucleotide duplex containing the iterated CG repeat restriction site of the NarI endonuclease has been determined. The IQ moiety intercalates, with the IQ H4a and CH3 protons facing the minor groove, and the IQ H7a, H8a and H9a protons facing the major groove. The adducted dG maintains the anti-conformation about the glycosyl bond. The complementary dC is extruded into the major groove. The duplex maintains its thermal stability, which is attributed to stacking between the IQ moiety and the 5′- and 3′-neighboring base pairs. This conformation is compared to that of the C8-dG-IQ adduct in the same sequence, which also formed a ‘base-displaced intercalated’ conformation. However, the C8-dG-IQ adopted the syn conformation placing the Watson−Crick edge of the modified dG into the major groove. In addition, the C8-dG-IQ adduct was oriented with the IQ CH3 group and H4a and H5a facing the major groove. These differences may lead to differential processing during DNA repair and replication.

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Hansen, Mark, Sang Yun, and Laurence Hurley. "Hedamycin intercalates the DNA helix and, through carbohydrate-mediated recognition in the minor groove, directs N7-alkylation of guanine in the major groove in a sequence-specific manner." Chemistry & Biology 2, no. 4 (1995): 229–40. http://dx.doi.org/10.1016/1074-5521(95)90273-2.

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Dissertations / Theses on the topic "Sequence-specific DNA intercalators"

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Fechter, Eric James. "Design of Sequence-Specific DNA Intercalators." Thesis, 2005. https://thesis.library.caltech.edu/2456/2/02Intro.pdf.

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Small molecules that bind specific DNA sequences may have powerful therapeutic applications by influencing the mechanisms of abnormal gene expression. Polyamides containing N-methylimidazole (Im) and N-methylpyrrole (Py) specifically bind the minor groove of DNA and have been shown to inhibit many protein-DNA complexes. However, some major groove-binding proteins can co-occupy the same DNA sequences as polyamides. Presented here are polyamide-intercalator conjugates that specifically bind target regions of DNA and deliver a non-specific intercalator to an adjacent site. The studies detail intercalative unwinding of specific DNA sequences to allosterically inhibit any protein:DNA complex. The evolution of sequence-specific polyamides to bisintercalate DNA and cause larger distortion of the helix is described. The success of hybrid molecules containing mixed DNA binding modes led to the development of a bis-polyamide-intercalator motif, modeled after the natural product actinomycin D, which is capable of specifically binding extended sequences of DNA. Also described is a polyamide-intercalator series which shows large fluorescence enhancement upon specific DNA binding and may be useful in detecting specific DNA sequences within living cells.

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Elmuccio, Michael L. "Progress towards visualizing the controlled assembly of gold nanoparticles on DNA." Thesis, 2011. http://hdl.handle.net/2152/ETD-UT-2011-05-2925.

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Our laboratory has used the 1,4,5,8 Naphthalenetetracarboxylic diimine (NDI) unit to develop threading polyintercalators that bind DNA with the NDI units intercalated in between GpG steps and two different peptide linkers, which connect the NDI units, situated in either the major or minor grooves. The first generation bisintercalators, G₃K and [beta]Ala₃K, were shown to bind two different sequences of DNA, where the peptide linkers reside in the major and minor grooves respectively. These binding modules were then combined to generate threading polyintercalators that bound different DNA sequences with simultaneous occupation of both grooves. In particular, a cyclic bisintercalator was designed and DNAse I footprinting revealed a strong preference for the sequence 5'-GGTACC-3'. NMR structural studies of the complex with d(CGGTACCG)₂ verified a pseudocatenane structure in which the NDI units reside four base pairs apart, with one linker located in the minor groove and the other in the major groove. This was the first structurally well-characterized pseudocatenane complex between a sequence-specific cyclic bisintercalator and its preferred binding sequence. The ability to simultaneously occupy both groves of the same sequence is interesting for several reasons. Most significantly, it raises questions about a complex DNA intercalator's ability to locate its preferred sequence within a long strand of DNA. In order to directly assess this, the intercalator was modified (CBI-Cys) to incorporate a gold nanoparticle probe to allow for the direct visualization of the intercalator locating its preferred sequence within a long DNA strand. The appropriate protocols to visualize DNA using electron and atomic force microscopy were unsuccessful; however, the foundation has been set for future work to develop the appropriate method to determine the mechanism by which the cyclic bisintercalator locates its preferred sequence. Additionally, the bisintercalators developed in our laboratory offered a unique opportunity to exploit their sequence specificity for controlled nanoparticle assembly. Over the past decade, nanoparticles and DNA have been used to develop novel nanoparticle assembly systems with the goal of developing electronic devices and nanomaterials. The G₃K bisintercalator was synthetically modified to incorporate a gold nanoparticle probe. This intercalator-nanoparticle conjugate, BisKC·Au, maintained its binding specificity (5'-GGTACC-3') to a modified DNA fragment containing multiple G₃K binding sites. The atomic force microscope has become the most promising tool in visualizing individual DNA molecules. A modified procedure utilized APS to allow for the direct visualizing of plasmid DNA. The framework is now in place to confirm the controlled assembly of the gold nanoparticles. This protocol can then be used for the [beta]Ala₃K bisintercalator to lead to the development of a nanoparticle assembly system that can precisely control the organization of multiple types of nanoparticles.<br>text

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Holman, Garen Gilman. "Binding studies of a sequence specific threading NDI intercalator." Thesis, 2011. http://hdl.handle.net/2152/ETD-UT-2011-08-3863.

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A series of studies from our lab have investigated the threading polyintercalator approach to sequence specific DNA binding using a 1,4,5,8-naphthalene tetracarboxylic diimide (NDI) intercalating unit connected by flexible peptide linkers. Herein is a report of the sequence specificity, as well as a detailed kinetic analysis, of a threading NDI tetraintercalator. DNase I footprinting using two ~500 base pair DNA fragments containing one designed binding site for the tetraintercalator confirmed highly sequence specific binding. Kinetic analyses include 1H NMR, gel mobility-shift assays, and stopped-flow UV measurements to reveal a polyintercalation binding mode that demonstrates significant similarities between association rate profiles and rate constants for the tetraintercalator binding to its preferred versus a random oligonucleotide sequence. Sequence specificity was found to derive almost entirely from large differences in dissociation rates from the preferred versus random oligonucleotide sequences. Interestingly, the dissociation rate constant of the tetraintercalator complex dissociating from its preferred binding site was extremely slow, corresponding to a 16 day half-life at a benchmark 100 mM [Na+]. This dissociation result for the tetraintercalator is one of the longest bound half-lives yet measured, and to the best of our knowledge, the longest for a DNA binding small molecule. Such a long-lived complex raises the possibility of using threading polyintercalators to disrupt biological processes for extended periods. Current focus is given to deciphering a mechanism for the molecular recognition of the tetraintercalator preferred binding site within a long sequence of DNA. Initial DNase I footprinting results on an approximate 500mer DNA sequence containing three sequential preferred binding sites reveal that the tetraintercalator likely locates its designed binding site by a macro- or microscopic dissociation/re-association type of mechanism. Cooperativity is a possible ally to binding, leaving future studies to distinguish the mechanism for molecular recognition in a manner that is capable of circumventing cooperative binding. Taken together, the threading polyintercalation binding mode presents an interesting topology to sequence specific DNA binding. Extraordinarily long dissociation rates from preferred binding sites offers many future possibilities to disrupt biological processes in vivo.<br>text

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Book chapters on the topic "Sequence-specific DNA intercalators"

1

Hélène, C., C. Giovannangeli, J. S. Sun, and T. Garestier. "Sequence-Specific Recognition of DNA and Control of Gene Expression by Oligonucleotide-Intercalator Conjugates." In Recent Trends in Molecular Recognition. Springer Berlin Heidelberg, 1998. http://dx.doi.org/10.1007/978-3-662-03574-0_6.

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