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Articles de revues sur le sujet « DNA-ligand interactions »

Auteur : Grafiati

Publié le 4 juin 2021

Mis à jour le 20 février 2023

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1

Piosik, Jacek, Kacper Wasielewski, Anna Woziwodzka, Wojciech Śledź, and Anna Gwizdek-Wiśniewska. "De-intercalation of ethidium bromide and propidium iodine from DNA in the presence of caffeine." Open Life Sciences 5, no. 1 (February 1, 2010): 59–66. http://dx.doi.org/10.2478/s11535-009-0077-2.

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AbstractCaffeine (CAF) is capable of interacting directly with several genotoxic aromatic ligands by stacking aggregation. Formation of such hetero-complexes may diminish pharmacological activity of these ligands, which is often related to its direct interaction with DNA. To check these interactions we performed three independent series of spectroscopic titrations for each ligand (ethidium bromide, EB, and propidium iodine, PI) according to the following setup: DNA with ligand, ligand with CAF and DNA-ligand mixture with CAF. We analyzed DNA-ligand and ligand-CAF mixtures numerically using wel

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Hopfinger, A. J., Mario G. Cardozo, and Y. Kawakami. "Molecular modelling of ligand–DNA intercalation interactions." J. Chem. Soc., Faraday Trans. 91, no. 16 (1995): 2515–24. http://dx.doi.org/10.1039/ft9959102515.

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Piehler, Jacob, Andreas Brecht, Günter Gauglitz, Marion Zerlin, Corinna Maul, Ralf Thiericke, and Susanne Grabley. "Label-Free Monitoring of DNA–Ligand Interactions." Analytical Biochemistry 249, no. 1 (June 1997): 94–102. http://dx.doi.org/10.1006/abio.1997.2160.

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van Royen, Martin E., Sónia M. Cunha, Maartje C. Brink, Karin A. Mattern, Alex L. Nigg, Hendrikus J. Dubbink, Pernette J. Verschure, Jan Trapman, and Adriaan B. Houtsmuller. "Compartmentalization of androgen receptor protein–protein interactions in living cells." Journal of Cell Biology 177, no. 1 (April 9, 2007): 63–72. http://dx.doi.org/10.1083/jcb.200609178.

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Steroid receptors regulate gene expression in a ligand-dependent manner by binding specific DNA sequences. Ligand binding also changes the conformation of the ligand binding domain (LBD), allowing interaction with coregulators via LxxLL motifs. Androgen receptors (ARs) preferentially interact with coregulators containing LxxLL-related FxxLF motifs. The AR is regulated at an extra level by interaction of an FQNLF motif in the N-terminal domain with the C-terminal LBD (N/C interaction). Although it is generally recognized that AR coregulator and N/C interactions are essential for transcription r

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Adasme, Melissa F., Katja L. Linnemann, Sarah Naomi Bolz, Florian Kaiser, Sebastian Salentin, V. Joachim Haupt, and Michael Schroeder. "PLIP 2021: expanding the scope of the protein–ligand interaction profiler to DNA and RNA." Nucleic Acids Research 49, W1 (May 5, 2021): W530—W534. http://dx.doi.org/10.1093/nar/gkab294.

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Abstract With the growth of protein structure data, the analysis of molecular interactions between ligands and their target molecules is gaining importance. PLIP, the protein–ligand interaction profiler, detects and visualises these interactions and provides data in formats suitable for further processing. PLIP has proven very successful in applications ranging from the characterisation of docking experiments to the assessment of novel ligand–protein complexes. Besides ligand–protein interactions, interactions with DNA and RNA play a vital role in many applications, such as drugs targeting DNA

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Murade, Chandrashekhar U., and George T. Shubeita. "A fluorescent reporter on electrostatic DNA-ligand interactions." Biomedical Optics Express 13, no. 1 (December 7, 2021): 159. http://dx.doi.org/10.1364/boe.439791.

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Cremers, Glenn A. O., Bas J. H. M. Rosier, Ab Meijs, Nicholas B. Tito, Sander M. J. van Duijnhoven, Hans van Eenennaam, Lorenzo Albertazzi, and Tom F. A. de Greef. "Determinants of Ligand-Functionalized DNA Nanostructure–Cell Interactions." Journal of the American Chemical Society 143, no. 27 (June 28, 2021): 10131–42. http://dx.doi.org/10.1021/jacs.1c02298.

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Peterman, Erwin J. G., and Peter Gross. "Biophysics of DNA–ligand interactions resolved by force." Physics of Life Reviews 7, no. 3 (September 2010): 344–45. http://dx.doi.org/10.1016/j.plrev.2010.06.005.

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Murat, Pierre, Yashveer Singh, and Eric Defrancq. "Methods for investigating G-quadruplex DNA/ligand interactions." Chemical Society Reviews 40, no. 11 (2011): 5293. http://dx.doi.org/10.1039/c1cs15117g.

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Shi, Xuesong, and Robert B. Macgregor. "Volume and hydration changes of DNA–ligand interactions." Biophysical Chemistry 125, no. 2-3 (February 2007): 471–82. http://dx.doi.org/10.1016/j.bpc.2006.10.011.

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Pullman, Bernard. "Molecular mechanisms of specificity in DNA-ligand interactions." Journal of Molecular Graphics 7, no. 3 (September 1989): 181. http://dx.doi.org/10.1016/0263-7855(89)80045-1.

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Scheepers, M. R. W., L. J. van IJzendoorn, and M. W. J. Prins. "Multivalent weak interactions enhance selectivity of interparticle binding." Proceedings of the National Academy of Sciences 117, no. 37 (August 28, 2020): 22690–97. http://dx.doi.org/10.1073/pnas.2003968117.

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Targeted drug delivery critically depends on the binding selectivity of cargo-transporting colloidal particles. Extensive theoretical work has shown that two factors are necessary to achieve high selectivity for a threshold receptor density: multivalency and weak interactions. Here, we study a model system of DNA-coated particles with multivalent and weak interactions that mimics ligand–receptor interactions between particles and cells. Using an optomagnetic cluster experiment, particle aggregation rates are measured as a function of ligand and receptor densities. The measured aggregation rate

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Rahman, Khondaker M., and David E. Thurston. "Effect of microwave irradiation on covalent ligand–DNA interactions." Chemical Communications, no. 20 (2009): 2875. http://dx.doi.org/10.1039/b902357g.

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Nelson, Stephanie M., Lynnette R. Ferguson, and William A. Denny. "Non-covalent ligand/DNA interactions: Minor groove binding agents." Mutation Research/Fundamental and Molecular Mechanisms of Mutagenesis 623, no. 1-2 (October 2007): 24–40. http://dx.doi.org/10.1016/j.mrfmmm.2007.03.012.

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Nguyen, Binh, and W. David Wilson. "The Effects of Hairpin Loops on Ligand−DNA Interactions." Journal of Physical Chemistry B 113, no. 43 (October 29, 2009): 14329–35. http://dx.doi.org/10.1021/jp904830m.

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Howerton, Shelley B., Akankasha Nagpal, and Loren Dean Williams. "Surprising roles of electrostatic interactions in DNA-ligand complexes." Biopolymers 69, no. 1 (April 21, 2003): 87–99. http://dx.doi.org/10.1002/bip.10319.

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Savory, Joanne G. A., Gratien G. Préfontaine, Claudia Lamprecht, Mingmin Liao, Rhian F. Walther, Yvonne A. Lefebvre, and Robert J. G. Haché. "Glucocorticoid Receptor Homodimers and Glucocorticoid-Mineralocorticoid Receptor Heterodimers Form in the Cytoplasm through Alternative Dimerization Interfaces." Molecular and Cellular Biology 21, no. 3 (February 1, 2001): 781–93. http://dx.doi.org/10.1128/mcb.21.3.781-793.2001.

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ABSTRACT Steroid hormone receptors act to regulate specific gene transcription primarily as steroid-specific dimers bound to palindromic DNA response elements. DNA-dependent dimerization contacts mediated between the receptor DNA binding domains stabilize DNA binding. Additionally, some steroid receptors dimerize prior to their arrival on DNA through interactions mediated through the receptor ligand binding domain. In this report, we describe the steroid-induced homomeric interaction of the rat glucocorticoid receptor (GR) in solution in vivo. Our results demonstrate that GR interacts in solut

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Mikheikin, A. L., A. L. Zhuze, and A. S. Zasedatelev. "Molecular Modelling of Ligand—DNA Minor Groove Binding: Role of Ligand—Water Interactions." Journal of Biomolecular Structure and Dynamics 19, no. 1 (August 2001): 175–78. http://dx.doi.org/10.1080/07391102.2001.10506729.

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Rocha, M. S. "Extracting physical chemistry from mechanics: a new approach to investigate DNA interactions with drugs and proteins in single molecule experiments." Integrative Biology 7, no. 9 (2015): 967–86. http://dx.doi.org/10.1039/c5ib00127g.

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Berdnikova, Daria V., Tseimur M. Aliyeu, Thomas Paululat, Yuri V. Fedorov, Olga A. Fedorova, and Heiko Ihmels. "DNA–ligand interactions gained and lost: light-induced ligand redistribution in a supramolecular cascade." Chemical Communications 51, no. 23 (2015): 4906–9. http://dx.doi.org/10.1039/c5cc01025j.

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Fong, Pedro, and Hong-Kong Wong. "Evaluation of Scoring Function Performance on DNA-ligand Complexes." Open Medicinal Chemistry Journal 13, no. 1 (July 31, 2019): 40–49. http://dx.doi.org/10.2174/1874104501913010040.

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Background: DNA has been a pharmacological target for different types of treatment, such as antibiotics and chemotherapy agents, and is still a potential target in many drug discovery processes. However, most docking and scoring approaches were parameterised for protein-ligand interactions; their suitability for modelling DNA-ligand interactions is uncertain. Objective: This study investigated the performance of four scoring functions on DNA-ligand complexes. Material & Methods: Here, we explored the ability of four docking protocols and scoring functions to discriminate the native pose of

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Shahabadi, Nahid, Soheila Kashanian, Maryam Mahdavi, and Noorkaram Sourinejad. "DNA Interaction and DNA Cleavage Studies of a New Platinum(II) Complex Containing Aliphatic and Aromatic Dinitrogen Ligands." Bioinorganic Chemistry and Applications 2011 (2011): 1–10. http://dx.doi.org/10.1155/2011/525794.

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A new Pt(II) complex, [Pt(DIP)(LL)](NO3)2(in which DIP is 4,7-diphenyl-1,10-phenanthroline and LL is the aliphatic dinitrogen ligand,N,N-dimethyl-trimethylenediamine), was synthesized and characterized using different physico-chemical methods. The interaction of this complex with calf thymus DNA (CT-DNA) was investigated by absorption, emission, circular dichroism (CD), and viscosity measurements. The complex binds to CT-DNA in an intercalative mode. The calculated binding constant,Kb, was M−1. The enthalpy and entropy changes of the reaction between the complex and CT-DNA showed that the van

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Brodbelt, Jennifer S. "Evaluation of DNA/Ligand Interactions by Electrospray Ionization Mass Spectrometry." Annual Review of Analytical Chemistry 3, no. 1 (June 2010): 67–87. http://dx.doi.org/10.1146/annurev.anchem.111808.073627.

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Rentzeperis, Dionisios, Luis A. Marky, and Donald W. Kupke. "Entropy-volume correlation with hydration changes in DNA-ligand interactions." Journal of Physical Chemistry 96, no. 24 (November 1992): 9612–13. http://dx.doi.org/10.1021/j100203a011.

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Cabeza de Vaca, Israel, Maria Fátima Lucas, and Victor Guallar. "New Monte Carlo Based Technique To Study DNA–Ligand Interactions." Journal of Chemical Theory and Computation 11, no. 12 (November 11, 2015): 5598–605. http://dx.doi.org/10.1021/acs.jctc.5b00838.

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Murat, Pierre, Yashveer Singh, and Eric Defrancq. "ChemInform Abstract: Methods for Investigating G-Quadruplex DNA/Ligand Interactions." ChemInform 43, no. 3 (December 22, 2011): no. http://dx.doi.org/10.1002/chin.201203280.

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Chirivino, Emanuele, Cesare Giordano, Sara Faini, Luciano Cellai, and Marco Fragai. "Tuning Sensitivity in Paramagnetic NMR Detection of Ligand–DNA Interactions." ChemMedChem 2, no. 8 (August 13, 2007): 1153–56. http://dx.doi.org/10.1002/cmdc.200600311.

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Khan, Sabab Hasan, and C. Denise Okafor. "Interactions governing transcriptional activity of nuclear receptors." Biochemical Society Transactions 50, no. 6 (December 16, 2022): 1941–52. http://dx.doi.org/10.1042/bst20220338.

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The key players in transcriptional regulation are transcription factors (TFs), proteins that bind specific DNA sequences. Several mechanisms exist to turn TFs ‘on’ and ‘off’, including ligand binding which induces conformational changes within TFs, subsequently influencing multiple inter- and intramolecular interactions to drive transcriptional responses. Nuclear receptors are a specific family of ligand-regulated TFs whose activity relies on interactions with DNA, coregulator proteins and other receptors. These multidomain proteins also undergo interdomain interactions on multiple levels, fur

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Yusof, Enis Nadia Md, Mohammad Azam, Siti Syaida Sirat, Thahira B. S. A. Ravoof, Alister J. Page, Abhi Veerakumarasivam, Thiruventhan Karunakaran, and Mohd Rizal Razali. "Dithiocarbazate Ligand-Based Cu(II), Ni(II), and Zn(II) Complexes: Synthesis, Structural Investigations, Cytotoxicity, DNA Binding, and Molecular Docking Studies." Bioinorganic Chemistry and Applications 2022 (July 31, 2022): 1–13. http://dx.doi.org/10.1155/2022/2004052.

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S-4-methylbenzyl-β-N-(2-methoxybenzylmethylene)dithiocarbazate ligand, 1, prepared from S-(4-methylbenzyl)dithiocarbazate, was used to produce a novel series of transition metal complexes of the type, [M (L)2] [M = Cu(II) (2), Ni(II) (3), and Zn(II) (4), L = 1]. The ligand and its complexes were investigated by elemental analysis, FTIR, 1H and 13C-NMR, MS spectrometry, and molar conductivity. In addition, single X-ray crystallography was also performed for ligand, 1, and complex 3. The Hirshfeld surface analyses were also performed to know about various bonding interactions in the ligand, 1, a

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Linne, Christine, Daniele Visco, Stefano Angioletti-Uberti, Liedewij Laan, and Daniela J. Kraft. "Direct visualization of superselective colloid-surface binding mediated by multivalent interactions." Proceedings of the National Academy of Sciences 118, no. 36 (August 31, 2021): e2106036118. http://dx.doi.org/10.1073/pnas.2106036118.

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Reliably distinguishing between cells based on minute differences in receptor density is crucial for cell–cell or virus–cell recognition, the initiation of signal transduction, and selective targeting in directed drug delivery. Such sharp differentiation between different surfaces based on their receptor density can only be achieved by multivalent interactions. Several theoretical and experimental works have contributed to our understanding of this “superselectivity.” However, a versatile, controlled experimental model system that allows quantitative measurements on the ligand–receptor level i

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Chernikova, Ekaterina Y., Anna Y. Ruleva, Vladimir B. Tsvetkov, Yuri V. Fedorov, Valentin V. Novikov, Tseimur M. Aliyeu, Alexander A. Pavlov, Nikolay E. Shepel, and Olga A. Fedorova. "Cucurbit[7]uril-driven modulation of ligand–DNA interactions by ternary assembly." Organic & Biomolecular Chemistry 18, no. 4 (2020): 755–66. http://dx.doi.org/10.1039/c9ob02543j.

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Kobren, Shilpa Nadimpalli, and Mona Singh. "Systematic domain-based aggregation of protein structures highlights DNA-, RNA- and other ligand-binding positions." Nucleic Acids Research 47, no. 2 (December 7, 2018): 582–93. http://dx.doi.org/10.1093/nar/gky1224.

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Abstract Domains are fundamental subunits of proteins, and while they play major roles in facilitating protein–DNA, protein–RNA and other protein–ligand interactions, a systematic assessment of their various interaction modes is still lacking. A comprehensive resource identifying positions within domains that tend to interact with nucleic acids, small molecules and other ligands would expand our knowledge of domain functionality as well as aid in detecting ligand-binding sites within structurally uncharacterized proteins. Here, we introduce an approach to identify per-domain-position interacti

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Cheskis, B., and L. P. Freedman. "Ligand modulates the conversion of DNA-bound vitamin D3 receptor (VDR) homodimers into VDR-retinoid X receptor heterodimers." Molecular and Cellular Biology 14, no. 5 (May 1994): 3329–38. http://dx.doi.org/10.1128/mcb.14.5.3329-3338.1994.

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Protein dimerization facilitates cooperative, high-affinity interactions with DNA. Nuclear hormone receptors, for example, bind either as homodimers or as heterodimers with retinoid X receptors (RXR) to half-site repeats that are stabilized by protein-protein interactions mediated by residues within both the DNA- and ligand-binding domains. In vivo, ligand binding among the subfamily of steroid receptors unmasks the nuclear localization and DNA-binding domains from a complex with auxiliary factors such as the heat shock proteins. However, the role of ligand is less clear among nuclear receptor

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Cheskis, B., and L. P. Freedman. "Ligand modulates the conversion of DNA-bound vitamin D3 receptor (VDR) homodimers into VDR-retinoid X receptor heterodimers." Molecular and Cellular Biology 14, no. 5 (May 1994): 3329–38. http://dx.doi.org/10.1128/mcb.14.5.3329.

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Protein dimerization facilitates cooperative, high-affinity interactions with DNA. Nuclear hormone receptors, for example, bind either as homodimers or as heterodimers with retinoid X receptors (RXR) to half-site repeats that are stabilized by protein-protein interactions mediated by residues within both the DNA- and ligand-binding domains. In vivo, ligand binding among the subfamily of steroid receptors unmasks the nuclear localization and DNA-binding domains from a complex with auxiliary factors such as the heat shock proteins. However, the role of ligand is less clear among nuclear receptor

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Pohle, W., and H. Fritzsche. "Infrared spectroscopy as a tool for investigations of DNA structure and DNA - ligand interactions." Journal of Molecular Structure 219 (March 1990): 341–46. http://dx.doi.org/10.1016/0022-2860(90)80079-y.

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Issa, Naiem T., Stephen W. Byers, and Sivanesan Dakshanamurthy. "ES-Screen: A Novel Electrostatics-Driven Method for Drug Discovery Virtual Screening." International Journal of Molecular Sciences 23, no. 23 (November 27, 2022): 14830. http://dx.doi.org/10.3390/ijms232314830.

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Electrostatic interactions drive biomolecular interactions and associations. Computational modeling of electrostatics in biomolecular systems, such as protein-ligand, protein–protein, and protein-DNA, has provided atomistic insights into the binding process. In drug discovery, finding biologically plausible ligand-protein target interactions is challenging as current virtual screening and adjuvant techniques such as docking methods do not provide optimal treatment of electrostatic interactions. This study describes a novel electrostatics-driven virtual screening method called ‘ES-Screen’ that

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Rodrigues, Tatiane P., Jorddy N. Cruz, Tiago S. Arouche, Tais S. S. Pereira, Wanessa A. Costa, Sebastião G. Silva, Raul N. C. Junior, Mozaniel S. Oliveira, and Antonio M. J. C. Neto. "Molecular Modeling Approach to Investigate the Intercalation of Phthalates and Their Metabolites in DNA Macromolecules." Journal of Computational and Theoretical Nanoscience 16, no. 2 (February 1, 2019): 373–80. http://dx.doi.org/10.1166/jctn.2019.8110.

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Recent studies have reported that phthalates are capable of causing mutations and other changes in the genetic material. This study aimed to investigate the molecular interactions between phthalate di(2-ethylhexyl) phthalate (DEHP) and its metabolites monobutyl phthalate (MBP) and monoethyl phthalate (MEP), interacting with DNA. The research was conducted using molecular modeling techniques such as molecular docking and molecular dynamics simulations. Molecular docking revealed that the DEHP, MBP, and MEP are able to establish hydrogen interactions with various nucleotide bases. Molecular dyna

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Mie, Masayasu, Rie Sugita, Tamaki Endoh, and Eiry Kobatake. "Evaluation of small ligand–protein interactions by using T7 RNA polymerase with DNA-modified ligand." Analytical Biochemistry 405, no. 1 (October 2010): 109–13. http://dx.doi.org/10.1016/j.ab.2010.06.011.

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Przibilla, S., W. W. Hitchcock, M. Szécsi, M. Grebe, J. Beatty, V. C. Henrich, and M. Spindler-Barth. "Functional studies on the ligand-binding domain of Ultraspiracle from Drosophila melanogaster." Biological Chemistry 385, no. 1 (January 5, 2004): 21–30. http://dx.doi.org/10.1515/bc.2004.004.

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AbstractThe functional insect ecdysteroid receptor is comprised of the ecdysone receptor (EcR) and Ultraspiracle (USP). The ligand-binding domain (LBD) of USP was fused to the GAL4 DNA-binding domain (GAL4-DBD) and characterized by analyzing the effect of site-directed mutations in the LBD. Normal and mutant proteins were tested for ligand and DNA binding, dimerization, and their ability to induce gene expression. The presence of helix 12 proved to be essential for DNA binding and was necessary to confer efficient ecdysteroid binding to the heterodimer with the EcR (LBD), but did not influence

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Joachimiak, Andrzej, Grazyna Joachimiak, Lance Bigelow, Garrett Cobb, and Youngchang Kim. "HcaR Ligand and DNA Interactions in the Regulation of Catabolic Gene Expression." Acta Crystallographica Section A Foundations and Advances 70, a1 (August 5, 2014): C203. http://dx.doi.org/10.1107/s2053273314097964.

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Precise tuning of gene expression by transcriptional regulators determines the response to internal and external chemical signals and adjusts the metabolic machinery for many cellular processes. As a part of ongoing efforts by the Midwest Center for Structural Genomics, a number of transcription factors were selected to study protein-ligand and protein-DNA interactions. HcaR, a new member of the MarR/SlyA family of transcription regulators from soil bacteria Acinetobacter sp. ADP1, is an evolutionarily atypical regulator and represses hydroxycinnamate (hca) catabolic genes. Hydroxycinnamates c

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Li, Min, Hongming Ding, Meihua Lin, Fangfei Yin, Lu Song, Xiuhai Mao, Fan Li, et al. "DNA Framework-Programmed Cell Capture via Topology-Engineered Receptor–Ligand Interactions." Journal of the American Chemical Society 141, no. 47 (November 6, 2019): 18910–15. http://dx.doi.org/10.1021/jacs.9b11015.

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Hamdan, I. I., G. G. Skellern, and R. D. Waigh. "Use of capillary electrophoresis in the study of ligand-DNA interactions." Nucleic Acids Research 26, no. 12 (June 1, 1998): 3053–58. http://dx.doi.org/10.1093/nar/26.12.3053.

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Misra, V. K., and B. Honig. "On the magnitude of the electrostatic contribution to ligand-DNA interactions." Proceedings of the National Academy of Sciences 92, no. 10 (May 9, 1995): 4691–95. http://dx.doi.org/10.1073/pnas.92.10.4691.

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Kupferschmitt, G., J. Schmidt, Th Schmidt, B. Fera, F. Buck, and H. Riiterjans. "15N labeling of oligodeoxynucleotides for NMR studies of DNA-ligand interactions." Nucleic Acids Research 15, no. 15 (1987): 6225–41. http://dx.doi.org/10.1093/nar/15.15.6225.

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Krafcikova, Michaela, Simon Dzatko, Coralie Caron, Anton Granzhan, Radovan Fiala, Tomas Loja, Marie-Paule Teulade-Fichou, et al. "Monitoring DNA–Ligand Interactions in Living Human Cells Using NMR Spectroscopy." Journal of the American Chemical Society 141, no. 34 (August 9, 2019): 13281–85. http://dx.doi.org/10.1021/jacs.9b03031.

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Mahapatra, Tufan Singha, Susmitnarayan Chaudhury, Swagata Dasgupta, Valerio Bertolasi, and Debashis Ray. "Dinuclear nickel complexes of divergent Ni⋯Ni separation showing ancillary ligand addition and bio-macromolecular interaction." New Journal of Chemistry 40, no. 3 (2016): 2268–79. http://dx.doi.org/10.1039/c5nj02410b.

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Reactions of ligand HL with nickel(ii) salts produce a family of five [Ni<sub>2</sub>] complexes of varying co-ligand environments and intermetallic separations and show prominent interactions with HSA and CT-DNA.

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Banasiak, Anna, Nicolò Zuin Fantoni, Andrew Kellett, and John Colleran. "Mapping the DNA Damaging Effects of Polypyridyl Copper Complexes with DNA Electrochemical Biosensors." Molecules 27, no. 3 (January 19, 2022): 645. http://dx.doi.org/10.3390/molecules27030645.

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Several classes of copper complexes are known to induce oxidative DNA damage that mediates cell death. These compounds are potentially useful anticancer agents and detailed investigation can reveal the mode of DNA interaction, binding strength, and type of oxidative lesion formed. We recently reported the development of a DNA electrochemical biosensor employed to quantify the DNA cleavage activity of the well-studied [Cu(phen)2]2+ chemical nuclease. However, to validate the broader compatibility of this sensor for use with more diverse—and biologically compatible—copper complexes, and to probe

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Gautam, Pankaj, and Sudipta Kumar Sinha. "Anticipating response function in gene regulatory networks." Journal of The Royal Society Interface 18, no. 179 (June 2021): 20210206. http://dx.doi.org/10.1098/rsif.2021.0206.

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The origin of an ordered genetic response of a complex and noisy biological cell is intimately related to the detailed mechanism of protein–DNA interactions present in a wide variety of gene regulatory (GR) systems. However, the quantitative prediction of genetic response and the correlation between the mechanism and the response curve is poorly understood. Here, we report in silico binding studies of GR systems to show that the transcription factor (TF) binds to multiple DNA sites with high cooperativity spreads from specific binding sites into adjacent non-specific DNA and bends the DNA. Our

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Chao, Hui, and Liang-Nian Ji. "DNA Interactions with Ruthenium(II) Polypyridine Complexes Containing Asymmetric Ligands." Bioinorganic Chemistry and Applications 3, no. 1-2 (2005): 15–28. http://dx.doi.org/10.1155/bca.2005.15.

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In an attempt to probe nucleic acid structures, numerous Ru(II) complexes with different ligands have been synthesized and investigated. In this contribution we focus on the DNA-binding properties of ruthenium(II) complexes containing asymmetric ligands that have attracted little attention in the past decades. The influences of the shape and size of the ligand on the binding modes, affinity, enantioselectivities and photocleavage of the complexes to DNA are described.

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Ihmels, H., M. Karbasiyoun, K. Löhl, and C. Stremmel. "Structural flexibility versus rigidity of the aromatic unit of DNA ligands: binding of aza- and azoniastilbene derivatives to duplex and quadruplex DNA." Organic & Biomolecular Chemistry 17, no. 26 (2019): 6404–13. http://dx.doi.org/10.1039/c9ob00809h.

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The increased flexibility of a quadruplex-DNA ligand does not necessarily lead to stronger interactions with the quadruplex DNA as compared with rigid ligands that have essentially the same size and extent of π system.

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