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Journal articles on the topic 'DNA selectivity'

Author: Grafiati

Published: 4 June 2021

Last updated: 7 February 2022

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1

Reiss, Carol Shoshkes. "Selectivity and Quality." DNA and Cell Biology 32, no. 3 (2013): 89. http://dx.doi.org/10.1089/dna.2013.2526.

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2

Oberemok, V., and P. Nyadar. "The selectivity of DNA insecticides." Archives of Biological Sciences 66, no. 4 (2014): 1479–83. http://dx.doi.org/10.2298/abs1404479o.

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3

Langenegger, Simon M., and Robert Häner. "Selectivity in DNA interstrand-stacking." Bioorganic & Medicinal Chemistry Letters 16, no. 19 (2006): 5062–65. http://dx.doi.org/10.1016/j.bmcl.2006.07.039.

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4

Warpehoski, Martha A., and Laurence H. Hurley. "Sequence selectivity of DNA covalent modification." Chemical Research in Toxicology 1, no. 6 (1988): 315–33. http://dx.doi.org/10.1021/tx00006a001.

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5

Iqbal, Samir M., Demir Akin, and Rashid Bashir. "Solid-state nanopore channels with DNA selectivity." Nature Nanotechnology 2, no. 4 (2007): 243–48. http://dx.doi.org/10.1038/nnano.2007.78.

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6

Garg, A., and J. Bell. "Reexamining the DNA target selectivity of Scalloped." Genome 53, no. 8 (2010): 575–84. http://dx.doi.org/10.1139/g10-029.

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Selector proteins are transcription factors that coordinate the formation and identity of organs and appendages. The proper formation of these tissues requires the selector proteins to regulate the expression of a large set of genes. Many selector proteins are involved in regulating multiple developmental processes, yet it is not completely clear how they are able to activate different sets of genes in a tissue-specific manner. An association with cofactors is thought to be one method by which enhancer selectivity is achieved. During wing development the selector protein Scalloped (SD) interacts with the cofactor Vestigial (VG). This interaction leads to the activation of a specific set of downstream wing genes. Herein, data are presented indicating that the switch in binding selectivity is likely achieved by VG altering the general affinity that the SD protein has for DNA. The decreased affinity for DNA is compensated for by the fact that the VG protein forms a complex containing two SD proteins. These two properties ensure that the SD–VG complex is able to bind only to enhancers that have two consecutive binding sites. Furthermore, data are presented that indicate that the function of the two terminal domains of the VG protein is not restricted to activating transcription and promoting the recruitment of two SD proteins.

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7

Thomas, Thresia, and T. J. Thomas. "Selectivity of polyamines in triplex DNA stabilization." Biochemistry 32, no. 50 (1993): 14068–74. http://dx.doi.org/10.1021/bi00213a041.

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8

Huang, Haidong, and Peter C. Tlatelpa. "Tuning the selectivity of triplex DNA receptors." Chemical Communications 51, no. 25 (2015): 5337–39. http://dx.doi.org/10.1039/c4cc07805e.

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9

Leichnitz, S., J. Heinrich, and N. Kulak. "A fluorescence assay for the detection of hydrogen peroxide and hydroxyl radicals generated by metallonucleases." Chemical Communications 54, no. 95 (2018): 13411–14. http://dx.doi.org/10.1039/c8cc06996d.

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ROS quench assays for metal-based DNA cleavage show low selectivity and reliability – a fluorogenic assay was thus developed to reliably, selectively and sensitively detect H<sub>2</sub>O<sub>2</sub> and HO˙.

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10

Park, Ki Soo, Chang Yeol Lee, and Hyun Gyu Park. "Target DNA induced switches of DNA polymerase activity." Chemical Communications 51, no. 49 (2015): 9942–45. http://dx.doi.org/10.1039/c5cc02060c.

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A novel concept that target DNA can induce switching of DNA polymerase activity is devised. The method relies on the finding that a DNA aptamer can undergo conformational change upon hybridization with a complementary target DNA, which leads to activation or inactivation of DNA polymerase. This strategy is utilized to identify the presence of target DNA with high levels of sensitivity and selectivity.

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11

Capranico, Giovanni, and Monica Binaschi. "DNA sequence selectivity of topoisomerases and topoisomerase poisons." Biochimica et Biophysica Acta (BBA) - Gene Structure and Expression 1400, no. 1-3 (1998): 185–94. http://dx.doi.org/10.1016/s0167-4781(98)00135-3.

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12

ANTONY, THOMAS, THRESIA THOMAS, AKIRA SHIRAHATA, LEONARD H. SIGAL, and T. J. THOMAS. "Selectivity of Spermine Homologs on Triplex DNA Stabilization." Antisense and Nucleic Acid Drug Development 9, no. 2 (1999): 221–31. http://dx.doi.org/10.1089/oli.1.1999.9.221.

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13

Hase, Katsunori, Yuuki Fujiwara, Hisae Kikuchi, et al. "RNautophagy/DNautophagy possesses selectivity for RNA/DNA substrates." Nucleic Acids Research 43, no. 13 (2015): 6439–49. http://dx.doi.org/10.1093/nar/gkv579.

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14

Chen, Xiaoying, Steven E. Rokita, and Cynthia J. Burrows. "DNA modification: intrinsic selectivity of nickel(II) complexes." Journal of the American Chemical Society 113, no. 15 (1991): 5884–86. http://dx.doi.org/10.1021/ja00015a065.

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15

Brandis, J. W. "Dye structure affects Taq DNA polymerase terminator selectivity." Nucleic Acids Research 27, no. 8 (1999): 1912–18. http://dx.doi.org/10.1093/nar/27.8.1912.

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16

Sachdeva, Amit, and Scott K. Silverman. "DNA-catalyzed serine side chain reactivity and selectivity." Chemical Communications 46, no. 13 (2010): 2215. http://dx.doi.org/10.1039/b927317d.

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17

Rodrigues-Correia, Alexandre, Diana Knapp-Bühle, Joachim W. Engels, and Alexander Heckel. "Selective Uncaging of DNA through Reaction Rate Selectivity." Organic Letters 16, no. 19 (2014): 5128–31. http://dx.doi.org/10.1021/ol502478g.

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18

Ponti, M., RL Souhami, BW Fox, and JA Hartley. "DNA interstrand crosslinking and sequence selectivity of dimethanesulphonates." British Journal of Cancer 63, no. 5 (1991): 743–47. http://dx.doi.org/10.1038/bjc.1991.166.

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19

Farkas, Michelle E., Benjamin C. Li, Christian Dose, and Peter B. Dervan. "DNA sequence selectivity of hairpin polyamide turn units." Bioorganic & Medicinal Chemistry Letters 19, no. 14 (2009): 3919–23. http://dx.doi.org/10.1016/j.bmcl.2009.03.072.

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20

Bulock, Chelsea R., Xuanxuan Xing та Polina V. Shcherbakova. "DNA polymerase δ proofreads errors made by DNA polymerase ε". Proceedings of the National Academy of Sciences 117, № 11 (2020): 6035–41. http://dx.doi.org/10.1073/pnas.1917624117.

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During eukaryotic replication, DNA polymerases ε (Polε) and δ (Polδ) synthesize the leading and lagging strands, respectively. In a long-known contradiction to this model, defects in the fidelity of Polε have a much weaker impact on mutagenesis than analogous Polδ defects. It has been previously proposed that Polδ contributes more to mutation avoidance because it proofreads mismatches created by Polε in addition to its own errors. However, direct evidence for this model was missing. We show that, in yeast, the mutation rate increases synergistically when a Polε nucleotide selectivity defect is combined with a Polδ proofreading defect, demonstrating extrinsic proofreading of Polε errors by Polδ. In contrast, combining Polδ nucleotide selectivity and Polε proofreading defects produces no synergy, indicating that Polε cannot correct errors made by Polδ. We further show that Polδ can remove errors made by exonuclease-deficient Polε in vitro. These findings illustrate the complexity of the one-strand–one-polymerase model where synthesis appears to be largely divided, but Polδ proofreading operates on both strands.

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21

Amjadi Oskouie, Akbar, and Ardavan Abiri. "Refining our methodologies for assessing quadruplex DNA ligands; selectivity or an illusion of selectivity?" Analytical Biochemistry 613 (January 2021): 113744. http://dx.doi.org/10.1016/j.ab.2020.113744.

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22

Wowor, Andy J., Kausiki Datta, Greg Thompson, and Vince J. LiCata. "DNA Structure Selectivity of Escherichia coli versus Thermus aquaticus DNA Polymerase I." Biophysical Journal 96, no. 3 (2009): 418a. http://dx.doi.org/10.1016/j.bpj.2008.12.2137.

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23

Punchihewa, Chandanamali, Megan Carver, and Danzhou Yang. "DNA sequence selectivity of human topoisomerase I-mediated DNA cleavage induced by camptothecin." Protein Science 18, no. 6 (2009): 1326–31. http://dx.doi.org/10.1002/pro.138.

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24

Rusmintratip, V. "Examination of the DNA substrate selectivity of DNA cytosine methyltransferases using mass tagging." Nucleic Acids Research 28, no. 18 (2000): 3594–99. http://dx.doi.org/10.1093/nar/28.18.3594.

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25

Halder, Georg, and Sean B. Carroll. "Binding of the Vestigial co-factor switches the DNA-target selectivity of the Scalloped selector protein." Development 128, no. 17 (2001): 3295–305. http://dx.doi.org/10.1242/dev.128.17.3295.

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The formation and identity of organs and appendages are regulated by specific selector genes that encode transcription factors that regulate potentially large sets of target genes. The DNA-binding domains of selector proteins often exhibit relatively low DNA-binding specificity in vitro. It is not understood how the target selectivity of most selector proteins is determined in vivo. The Scalloped selector protein controls wing development in Drosophila by regulating the expression of numerous target genes and forming a complex with the Vestigial protein. We show that binding of Vestigial to Scalloped switches the DNA-binding selectivity of Scalloped. Two conserved domains of the Vestigial protein that are not required for Scalloped binding in solution are required for the formation of the heterotetrameric Vestigial-Scalloped complex on DNA. We suggest that Vestigial affects the conformation of Scalloped to create a wing cell-specific DNA-binding selectivity. The modification of selector protein DNA-binding specificity by co-factors appears to be a general mechanism for regulating their target selectivity in vivo.

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26

Sharma, Sanjeev Kumar, and William Fraser. "Selectivity of a bromoacridine-containing fluorophore for triplex DNA." Monatshefte für Chemie - Chemical Monthly 152, no. 8 (2021): 1013–16. http://dx.doi.org/10.1007/s00706-021-02816-5.

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AbstractFluorophore 1,8-naphthilamide was linked to 2-bromoacridine through an ethylenediamine spacer using a succinct synthetic route to give a bromoacridine-linked, bifunctional fluorophore conjugate for the detection of triplex DNA. Acridine is well known to intercalate into duplex DNA whereas introduction of a bulky bromine atom at position C2 redirects specificity for triplex over duplex DNA. In this work, photoelectron transfer assay was used to demonstrate that the synthesised 2-bromoacridine-linked fluorophore conjugate had good selectivity for the representative triplex DNA target sequence d(T*A.T)20 compared with double-stranded d(T.A)20, single-stranded dT20 or d(G/A)19 DNA sequences. Graphic abstract

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27

Kupis-Rozmysłowicz, Justyna, Alessandra Antonucci, and Ardemis A. Boghossian. "Review—Engineering the Selectivity of the DNA-SWCNT Sensor." ECS Journal of Solid State Science and Technology 5, no. 8 (2016): M3067—M3074. http://dx.doi.org/10.1149/2.0111608jss.

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28

Poon, Gregory M. K., and Hye Mi Kim. "Signatures of DNA target selectivity by ETS transcription factors." Transcription 8, no. 3 (2017): 193–203. http://dx.doi.org/10.1080/21541264.2017.1302901.

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29

Triantafillidi, Katelitsa, Konstantina Karidi, Olga Novakova, Jaroslav Malina, and Achilleas Garoufis. "DNA binding selectivity of oligopyridine-ruthenium(ii)-lysine conjugate." Dalton Trans. 40, no. 2 (2011): 472–83. http://dx.doi.org/10.1039/c0dt00554a.

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30

Peterson, Amberlyn M., Frank M. Jahnke, and Jennifer M. Heemstra. "Modulating the Substrate Selectivity of DNA Aptamers Using Surfactants." Langmuir 31, no. 43 (2015): 11769–73. http://dx.doi.org/10.1021/acs.langmuir.5b02818.

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31

Haber, Charbel, Jonathan Skupsky, Ann Lee, and Russ Lander. "Membrane chromatography of DNA: Conformation-induced capacity and selectivity." Biotechnology and Bioengineering 88, no. 1 (2004): 26–34. http://dx.doi.org/10.1002/bit.20201.

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32

Granzhan, Anton, Eric Largy, Nicolas Saettel, and Marie-Paule Teulade-Fichou. "Macrocyclic DNA-Mismatch-Binding Ligands: Structural Determinants of Selectivity." Chemistry - A European Journal 16, no. 3 (2009): 878–89. http://dx.doi.org/10.1002/chem.200901989.

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33

Kohli, P. "DNA-Functionalized Nanotube Membranes with Single-Base Mismatch Selectivity." Science 305, no. 5686 (2004): 984–86. http://dx.doi.org/10.1126/science.1100024.

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34

Bunkin, A. F., S. M. Pershin, R. S. Khusainova, and S. A. Potekhin. "Spin isomeric selectivity of water molecules upon DNA hydration." Biophysics 54, no. 3 (2009): 275–79. http://dx.doi.org/10.1134/s0006350909030026.

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35

Liu, XiangDong, Tetsuro Kubo, WenXing Chen, Jonganurakkun Benjamas, Tomomi Yonemichi, and Norio Nishi. "Adsorptive Selectivity of DNA/Polyvinyl Alcohol Interpenetrating Polymer Networks." Separation Science and Technology 46, no. 4 (2011): 641–47. http://dx.doi.org/10.1080/01496395.2010.517592.

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36

Yoon, Hanwool. "On the Origin of Sugar Selectivity by DNA Polymerases." Biophysical Journal 110, no. 3 (2016): 63a. http://dx.doi.org/10.1016/j.bpj.2015.11.405.

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37

Valente, J. F. A., J. A. Queiroz, and F. Sousa. "Dilemma on plasmid DNA purification: binding capacity vs selectivity." Journal of Chromatography A 1637 (January 2021): 461848. http://dx.doi.org/10.1016/j.chroma.2020.461848.

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38

Yoon, Jung-Hoon, and Chong-Soon Lee. "Sequence selectivity of DNA alkylation by adozelesin and carzelesin." Archives of Pharmacal Research 21, no. 4 (1998): 385–90. http://dx.doi.org/10.1007/bf02974631.

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39

Acar, Elif Turker, Steven F. Buchsbaum, Cody Combs, Francesco Fornasiero, and Zuzanna S. Siwy. "Biomimetic potassium-selective nanopores." Science Advances 5, no. 2 (2019): eaav2568. http://dx.doi.org/10.1126/sciadv.aav2568.

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Reproducing the exquisite ion selectivity displayed by biological ion channels in artificial nanopore systems has proven to be one of the most challenging tasks undertaken by the nanopore community, yet a successful achievement of this goal offers immense technological potential. Here, we show a strategy to design solid-state nanopores that selectively transport potassium ions and show negligible conductance for sodium ions. The nanopores contain walls decorated with 4′-aminobenzo-18-crown-6 ether and single-stranded DNA (ssDNA) molecules located at one pore entrance. The ionic selectivity stems from facilitated transport of potassium ions in the pore region containing crown ether, while the highly charged ssDNA plays the role of a cation filter. Achieving potassium selectivity in solid-state nanopores opens new avenues toward advanced separation processes, more efficient biosensing technologies, and novel biomimetic nanopore systems.

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40

Ogawa, Shuji, Shun-ichi Wada, and Hidehito Urata. "Base recognition by l-nucleotides in heterochiral DNA." RSC Advances 2, no. 6 (2012): 2274–75. http://dx.doi.org/10.1039/c2ra01013e.

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41

Hudson, Nicholas O., and Bethany A. Buck-Koehntop. "Zinc Finger Readers of Methylated DNA." Molecules 23, no. 10 (2018): 2555. http://dx.doi.org/10.3390/molecules23102555.

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DNA methylation is a prevalent epigenetic modification involved in regulating a number of essential cellular processes, including genomic accessibility and transcriptional outcomes. As such, aberrant alterations in global DNA methylation patterns have been associated with a growing number of disease conditions. Nevertheless, the full mechanisms by which DNA methylation information is interpreted and translated into genomic responses is not yet fully understood. Methyl-CpG binding proteins (MBPs) function as important mediators of this essential process by selectively reading DNA methylation signals and translating this information into down-stream cellular outcomes. The Cys2His2 zinc finger scaffold is one of the most abundant DNA binding motifs found within human transcription factors, yet only a few zinc finger containing proteins capable of conferring selectivity for mCpG over CpG sites have been characterized. This review summarizes our current structural understanding for the mechanisms by which the zinc finger MBPs evaluated to date read this essential epigenetic mark. Further, some of the biological implications for mCpG readout elicited by this family of MBPs are discussed.

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42

Boger, Dale L., Stephen A. Munk, and Hamideh Zarrinmayeh. "(+)-CC-1065 DNA alkylation: key studies demonstrating a noncovalent binding selectivity contribution to the alkylation selectivity." Journal of the American Chemical Society 113, no. 10 (1991): 3980–83. http://dx.doi.org/10.1021/ja00010a046.

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43

Zinchenko, Anatoly A., Ning Chen, Shizuaki Murata, and Kenichi Yoshikawa. "How Does DNA Compaction Favor Chiral Selectivity with Cationic Species? Higher Selectivity with Lower Cationic Charge." ChemBioChem 6, no. 8 (2005): 1419–22. http://dx.doi.org/10.1002/cbic.200500032.

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44

Maschera, B., E. Ferrazzi, M. Rassu, M. Toni, and G. Palù. "Evaluation of Topoisomerase Inhibitors as Potential Antiviral Agents." Antiviral Chemistry and Chemotherapy 4, no. 2 (1993): 85–91. http://dx.doi.org/10.1177/095632029300400202.

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Anti-eukaryotic topoisomerase drugs, Camptothecin and Etoposide, were tested for their ability of selectively interfering with the replication of simian virus 40 (SV40) DNA. Nalidixic acid was also assayed for a comparison, since the compound has been previously reported to affect papoyavirus growth. Our results indicate that anti-eukaryotic topoisomerase drugs significantly inhibit viral DNA replication but at concentrations that are also toxic for uninfected cells. Etoposide treatment produced a relatively higher number of DNA-protein cross-links in virus-infected cells as compared to uninfected control cells. Nalidixic acid displayed some degree of selectivity for inhibiting SV40 DNA synthesis more effectively than synthesis of cellular DNA without appreciable reduction of cell growth. This activity does not appear to depend on DNA damage or interference with topoisomerase II and deserves further evaluation.

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45

Li, Jin, Lilin Wang, Pasi A. Jänne, and G. Mike Makrigiorgos. "Coamplification at Lower Denaturation Temperature-PCR Increases Mutation-Detection Selectivity of TaqMan-Based Real-Time PCR." Clinical Chemistry 55, no. 4 (2009): 748–56. http://dx.doi.org/10.1373/clinchem.2008.113381.

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Abstract Background: DNA genotyping with mutation-specific TaqMan® probes (Applied Biosystems) is broadly used in detection of single-nucleotide polymorphisms but is less so for somatic mutations because of its limited selectivity for low-level mutations. We recently described coamplification at lower denaturation temperature-PCR (COLD-PCR), a method that amplifies minority alleles selectively from mixtures of wild-type and mutation-containing sequences during the PCR. We demonstrate that combining COLD-PCR with TaqMan technology provides TaqMan genotyping with the selectivity needed to detect low-level somatic mutations. Methods: Minor-groove binder-based or common TaqMan probes were designed to contain a nucleotide that matches the desired mutation approximately in the middle of the probe. The critical denaturation temperature (Tc) of each amplicon was then experimentally determined. COLD-PCR/TaqMan genotyping was performed in 2 steps: denaturation at the Tc, followed by annealing and extension at a single temperature (fast COLD-PCR). The threshold cycle was used to identify mutations on the basis of serial dilutions of mutant DNA into wild-type DNA and to identify TP53 (tumor protein p53) and EGFR [epidermal growth factor receptor (erythroblastic leukemia viral (v-erb-b) oncogene homolog, avian)] mutations in tumors. Results: COLD-PCR/TaqMan genotyping identified G&gt;A mutations within TP53 exon 8 (codon 273 mutation hot spot) and C&gt;T mutations within the EGFR gene (drug-resistance mutation T790M) with a selectivity improvement of 15- to 30-fold over regular PCR/TaqMan genotyping. A second round of COLD-PCR/TaqMan genotyping improved the selectivity by another 15- to 30-fold and enabled detection of 1 mutant in 2000 wild-type alleles. Use of COLD-PCR/TaqMan genotyping allowed quantitative identification of low-level TP53 and T790 mutations in colon tumor samples and in non-small-cell lung cancer cell lines treated with kinase inhibitors. Conclusions: The major improvement in selectivity provided by COLD-PCR enables the popular TaqMan genotyping method to become a powerful tool for detecting low-level mutations in clinical samples.

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46

Lilley, David M. J. "The interaction of four-way DNA junctions with resolving enzymes." Biochemical Society Transactions 38, no. 2 (2010): 399–403. http://dx.doi.org/10.1042/bst0380399.

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Four-way DNA (Holliday) junctions are resolved into duplex species by the action of the junction-resolving enzymes, nucleases selective for the structure of helical branchpoints. These have been isolated from bacteria and their phages, archaea, yeasts and mammals, including humans. They are all dimeric proteins that bind with high selectivity to DNA junctions and generate bilateral cleavage within the lifetime of the DNA–protein complex. Recent success in obtaining X-ray crystal structures of resolving enzymes bound to DNA junctions has revealed how the structural selectivity of these enzymes is achieved.

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47

Yett, Ariana, Linda Yingqi Lin, Dana Beseiso, Joanne Miao, and Liliya A. Yatsunyk. "N-methyl mesoporphyrin IX as a highly selective light-up probe for G-quadruplex DNA." Journal of Porphyrins and Phthalocyanines 23, no. 11n12 (2019): 1195–215. http://dx.doi.org/10.1142/s1088424619300179.

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[Formula: see text]-methyl mesoporphyrin IX (NMM) is a water-soluble, non-symmetric porphyrin with excellent optical properties and unparalleled selectivity for G-quadruplex (GQ) DNA. G-quadruplexes are non-canonical DNA structures formed by guanine-rich sequences. They are implicated in genomic stability, longevity, and cancer. The ability of NMM to selectively recognize GQ structures makes it a valuable scaffold for designing novel GQ binders. In this review, we survey the literature describing the GQ-binding properties of NMM as well as its wide utility in chemistry and biology. We start with the discovery of the GQ-binding properties of NMM and the development of NMM-binding aptamers. We then discuss the optical properties of NMM, focusing on the light-switch effect — high fluorescence of NMM induced upon its binding to GQ DNA. Additionally, we examine the affinity and selectivity of NMM for GQs, as well as its ability to stabilize GQ structures and favor parallel GQ conformations. Furthermore, a portion of the review is dedicated to the applications of NMM-GQ complexes as biosensors for heavy metals, small molecules ([Formula: see text] ATP and pesticides), DNA, and proteins. Finally and importantly, we discuss the utility of NMM as a probe to investigate the roles of GQs in biological processes.

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48

Sierra, Miguel A., David Sánchez, Rafael Gutierrez, Gianaurelio Cuniberti, Francisco Domínguez-Adame, and Elena Díaz. "Spin-Polarized Electron Transmission in DNA-Like Systems." Biomolecules 10, no. 1 (2019): 49. http://dx.doi.org/10.3390/biom10010049.

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The helical distribution of the electronic density in chiral molecules, such as DNA and bacteriorhodopsin, has been suggested to induce a spin–orbit coupling interaction that may lead to the so-called chirality-induced spin selectivity (CISS) effect. Key ingredients for the theoretical modelling are, in this context, the helically shaped potential of the molecule and, concomitantly, a Rashba-like spin–orbit coupling due to the appearance of a magnetic field in the electron reference frame. Symmetries of these models clearly play a crucial role in explaining the observed effect, but a thorough analysis has been largely ignored in the literature. In this work, we present a study of these symmetries and how they can be exploited to enhance chiral-induced spin selectivity in helical molecular systems.

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49

Wu, Guanhui, Desiree Tillo, Sreejana Ray, et al. "Custom G4 Microarrays Reveal Selective G-Quadruplex Recognition of Small Molecule BMVC: A Large-Scale Assessment of Ligand Binding Selectivity." Molecules 25, no. 15 (2020): 3465. http://dx.doi.org/10.3390/molecules25153465.

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G-quadruplexes (G4) are considered new drug targets for human diseases such as cancer. More than 10,000 G4s have been discovered in human chromatin, posing challenges for assessing the selectivity of a G4-interactive ligand. 3,6-bis(1-Methyl-4-vinylpyridinium) carbazole diiodide (BMVC) is the first fluorescent small molecule for G4 detection in vivo. Our previous structural study shows that BMVC binds to the MYC promoter G4 (MycG4) with high specificity. Here, we utilize high-throughput, large-scale custom DNA G4 microarrays to analyze the G4-binding selectivity of BMVC. BMVC preferentially binds to the parallel MycG4 and selectively recognizes flanking sequences of parallel G4s, especially the 3′-flanking thymine. Importantly, the microarray results are confirmed by orthogonal NMR and fluorescence binding analyses. Our study demonstrates the potential of custom G4 microarrays as a platform to broadly and unbiasedly assess the binding selectivity of G4-interactive ligands, and to help understand the properties that govern molecular recognition.

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50

Morel, Elodie, Claire Beauvineau, Delphine Naud-Martin, et al. "Selectivity of Terpyridine Platinum Anticancer Drugs for G-quadruplex DNA." Molecules 24, no. 3 (2019): 404. http://dx.doi.org/10.3390/molecules24030404.

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Abstract:

Guanine-rich DNA can form four-stranded structures called G-quadruplexes (G4s) that can regulate many biological processes. Metal complexes have shown high affinity and selectivity toward the quadruplex structure. Here, we report the comparison of a panel of platinum (II) complexes for quadruplex DNA selective recognition by exploring the aromatic core around terpyridine derivatives. Their affinity and selectivity towards G4 structures of various topologies have been evaluated by FRET-melting (Fluorescence Resonance Energy Transfert-melting) and Fluorescent Intercalator Displacement (FID) assays, the latter performed by using three different fluorescent probes (Thiazole Orange (TO), TO-PRO-3, and PhenDV). Their ability to bind covalently to the c-myc G4 structure in vitro and their cytotoxicity potential in two ovarian cancerous cell lines were established. Our results show that the aromatic surface of the metallic ligands governs, in vitro, their affinity, their selectivity for the G4 over the duplex structures, and platination efficiency. However, the structural modifications do not allow significant discrimination among the different G4 topologies. Moreover, all compounds were tested on ovarian cancer cell lines and normal cell lines and were all able to overcome cisplatin resistance highlighting their interest as new anticancer drugs.

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