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Journal articles on the topic 'I-motif DNA'

Author: Grafiati

Published: 6 September 2023

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1

Wright, Elisé P., Mahmoud A. S. Abdelhamid, Michelle O. Ehiabor, Melanie C. Grigg, Kelly Irving, Nicole M. Smith, and Zoë A. E. Waller. "Epigenetic modification of cytosines fine tunes the stability of i-motif DNA." Nucleic Acids Research 48, no. 1 (November 28, 2019): 55–62. http://dx.doi.org/10.1093/nar/gkz1082.

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Abstract i-Motifs are widely used in nanotechnology, play a part in gene regulation and have been detected in human nuclei. As these structures are composed of cytosine, they are potential sites for epigenetic modification. In addition to 5-methyl- and 5-hydroxymethylcytosine modifications, recent evidence has suggested biological roles for 5-formylcytosine and 5-carboxylcytosine. Herein the human telomeric i-motif sequence was used to examine how these four epigenetic modifications alter the thermal and pH stability of i-motifs. Changes in melting temperature and transitional pH depended on both the type of modification and its position within the i-motif forming sequence. The cytosines most sensitive to modification were next to the first and third loops within the structure. Using previously described i-motif forming sequences, we screened the MCF-7 and MCF-10A methylomes to map 5-methylcytosine and found the majority of sequences were differentially methylated in MCF7 (cancerous) and MCF10A (non-cancerous) cell lines. Furthermore, i-motif forming sequences stable at neutral pH were significantly more likely to be epigenetically modified than traditional acidic i-motif forming sequences. This work has implications not only in the epigenetic regulation of DNA, but also allows discreet tunability of i-motif stability for nanotechnological applications.

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2

Saha, Puja, Deepanjan Panda, Diana Müller, Arunabha Maity, Harald Schwalbe, and Jyotirmayee Dash. "In situ formation of transcriptional modulators using non-canonical DNA i-motifs." Chemical Science 11, no. 8 (2020): 2058–67. http://dx.doi.org/10.1039/d0sc00514b.

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3

Li, Tao, and Michael Famulok. "I-Motif-Programmed Functionalization of DNA Nanocircles." Journal of the American Chemical Society 135, no. 4 (January 22, 2013): 1593–99. http://dx.doi.org/10.1021/ja3118224.

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4

Dong, Yuanchen, Zhongqiang Yang, and Dongsheng Liu. "DNA Nanotechnology Based on i-Motif Structures." Accounts of Chemical Research 47, no. 6 (May 20, 2014): 1853–60. http://dx.doi.org/10.1021/ar500073a.

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5

Phan, Anh Tuân, and Jean-Louis Leroy. "Intramolecular i-Motif Structures of Telomeric DNA." Journal of Biomolecular Structure and Dynamics 17, sup1 (January 2000): 245–51. http://dx.doi.org/10.1080/07391102.2000.10506628.

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6

Butcher, David, and Jaroslava Miksovska. "DNA i-MOTIF Probed by Photoacoustic Calorimetry." Biophysical Journal 106, no. 2 (January 2014): 64a. http://dx.doi.org/10.1016/j.bpj.2013.11.434.

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7

Gade, Chandrasekhar Reddy, and Nagendra K. Sharma. "Hybrid DNA i-motif: Aminoethylprolyl-PNA (pC 5 ) enhance the stability of DNA (dC 5 ) i-motif structure." Bioorganic & Medicinal Chemistry Letters 27, no. 24 (December 2017): 5424–28. http://dx.doi.org/10.1016/j.bmcl.2017.11.004.

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8

Zeng, Huang, Shuangshuang Kang, Yu Zhang, Ke Liu, Qian Yu, Ding Li, and Lin-Kun An. "Synthesis and Biological Evaluation of Oleanolic Acid Derivatives as Selective Vascular Endothelial Growth Factor Promoter i-Motif Ligands." International Journal of Molecular Sciences 22, no. 4 (February 8, 2021): 1711. http://dx.doi.org/10.3390/ijms22041711.

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Vascular endothelial growth factor (VEGF) is an angiogenic growth factor and plays a key role in tumor progression. The C-rich DNA sequence of VEGF promoter can form i-motif structure, which is a potential target for the development of novel anticancer agents. However, there is a limited number of chemotypes as the selective ligands of VEGF promoter i-motif, which leaves much room for development. Herein, we report the discovery of the natural oleanolic acid scaffold as a novel chemotype for the development of selective ligands of VEGF i-motif. A series of oleanolic acid derivatives as VEGF promoter i-motif ligands were synthesized. Subsequent evaluations showed that 3c could selectively bind to and stabilize VEGF promoter i-motif without significant binding to G-quadruplex, duplex DNA, and other oncogene i-motifs. Cell-based assays indicated that 3c could effectively downregulate VEGF gene transcription and expression in MCF-7 cells, inhibit tumor cells proliferation and migration, and induce cancer cells apoptosis. This work provides evidence of VEGF promoter i-motif as an anticancer target and will facilitate future efforts for the discovery of oleanolic acid-based selective ligands of VEGF promoter i-motif.

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9

Dalyan, Ye B., L. G. Aslanyan, and I. V. Vardanyan. "THE INFLUENCE OF UREA ON G-QUADRUPLEX AND i-MOTIF STRUCTURES IN COMPLEMENTARY DNA SEQUENCES." Proceedings of the YSU A: Physical and Mathematical Sciences 54, no. 2 (252) (August 17, 2020): 115–22. http://dx.doi.org/10.46991/pysu:a/2020.54.2.115.

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In the present study, the methods of circular dichroism and UV/Vis spectrophotometry were used to study the influence of urea on the structural transitions i-motif $\leftrightarrows$ unfolded single strand in cytosine-rich ${\text{d[3}^{\prime}\text{-(CCCAAT)}_{3}\text{CCC-5)}^{\prime}]}$ region of telomeric DNA (Tel22C) and G-quadruplex $\leftrightarrows$ unfolded single strand in complementary guanine-rich strand ${\text{d[5}^{\prime}\text{-A(GGGTTA)}_{3}\text{GGG-3}^{\prime}]}$ (Tel22G) at pH 5.5 and 400 mM Na+. Under these conditions, Tel22C and Tel22G were found to form stable i-motif and G-quadruplex structures. It has been shown that urea (0-8 M) destabilizes the i-motif and G-quadruplex structures, but unlike thermal denaturation, it does not destroy the structures completely. The melting processes of G-quadruplex and i-motif are separated in the temperature scale (at any concentration of urea, the melting of the G-quadruplex starts at temperatures where the melting of the i-motifs has already been completed).

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10

Martins, Alexandra, Christian H. Gross, and Stewart Shuman. "Mutational Analysis of Vaccinia Virus Nucleoside Triphosphate Phosphohydrolase I, a DNA-Dependent ATPase of the DExH Box Family." Journal of Virology 73, no. 2 (February 1, 1999): 1302–8. http://dx.doi.org/10.1128/jvi.73.2.1302-1308.1999.

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ABSTRACT Vaccinia virus nucleoside triphosphate phosphohydrolase I (NPH-I) is a DNA-dependent ATPase that serves as a transcription termination factor during viral mRNA synthesis. NPH-I is a member of the DExH box family of nucleic acid-dependent nucleoside triphosphatases (NTPases), which is defined by the presence of several conserved sequence motifs. We have assessed the contributions of individual amino acids (underlined) in motifs I (GxGKT), II (DExHN), III (SAT), and VI (QxxGRxxR) to ATP hydrolysis by performing alanine scanning mutagenesis. Significant decrements in ATPase activity resulted from mutations at nine positions: Lys-61 and Thr-62 (motif I); Asp-141, Glu-142, His-144, and Asn-145 (motif II); and Gln-472, Arg-476, and Arg-479 (motif VI). Structure-function relationships at each of these positions were clarified by introducing conservative substitutions and by steady-state kinetic analysis of the mutant enzymes. Comparison of our findings for NPH-I with those of mutational studies of other DExH and DEAD box proteins underscores similarities as well as numerous disparities in structure-activity relationships. We conclude that the functions of the conserved amino acids of the NTPase motifs are context dependent.

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11

Day, Henry Albert, Elisé Patricia Wright, Colin John MacDonald, Andrew James Gates, and Zoë Ann Ella Waller. "Reversible DNA i-motif to hairpin switching induced by copper(ii) cations." Chemical Communications 51, no. 74 (2015): 14099–102. http://dx.doi.org/10.1039/c5cc05111h.

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i-Motif forming DNA sequences have previously been used for many different nanotechnological applications, but all have used changes in pH to fold the DNA. Here it is shown that Cu(ii) cations can be used to re-fold i-motifs into hairpin structures, without changing the pH.

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12

Brzeski, J., T. Grycuk, A. W. Lipkowski, W. Rudnicki, B. Lesyng, and A. Jerzmanowski. "Binding of SPXK- and APXK-peptide motifs to AT-rich DNA. Experimental and theoretical studies." Acta Biochimica Polonica 45, no. 1 (March 31, 1998): 221–31. http://dx.doi.org/10.18388/abp.1998_4304.

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The binding properties of the SPXK- and APXK-type peptides to the AT-rich DNA fragments of different length were studied by measuring the competition of peptides with Hoechst 33258 dye for DNA binding and by the gel shift assay analysis. In parallel to the experimental studies, molecular modeling techniques were used to analyze possible binding modes of the SPXZ and APXK motifs to the AT-rich DNA. The results of the competition measurements and gel shift assays suggest that serine at the i-1 position (i is proline) can be replaced by alanine without affecting the binding properties of the motif. Thus, the presence of the conserved serine in this motif in many DNA-binding proteins is probably not dictated by structural requirements. Based on the results of molecular modeling studies we propose that the binding mode of the SPXK-type motifs to the AT-rich DNA resembles closely that between the N-terminal arm of the homeodomain and DNA. This model confirms that serine in the SPXK motifs is not essential for the DNA binding. The model also indicates that if X in the motif is glutamic acid, this residue is probably protonated in the complex with DNA.

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13

Modi, Souvik, Ajazul Hamid Wani, and Yamuna Krishnan. "The PNA–DNA hybrid I-motif: implications for sugar–sugar contacts in i-motif tetramerization." Nucleic Acids Research 34, no. 16 (August 26, 2006): 4354–63. http://dx.doi.org/10.1093/nar/gkl443.

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14

Shi, Lili, Pai Peng, Jiao Zheng, Qiwei Wang, Zhijin Tian, Huihui Wang, and Tao Li. "I-Motif/miniduplex hybrid structures bind benzothiazole dyes with unprecedented efficiencies: a generic light-up system for label-free DNA nanoassemblies and bioimaging." Nucleic Acids Research 48, no. 4 (January 17, 2020): 1681–90. http://dx.doi.org/10.1093/nar/gkaa020.

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Abstract I-motif DNAs have been widely employed as robust modulating components to construct reconfigurable DNA nanodevices that function well in acidic cellular environments. However, they generally display poor interactivity with fluorescent ligands under these complex conditions, illustrating a major difficulty in utilizing i-motifs as the light-up system for label-free DNA nanoassemblies and bioimaging. Towards addressing this challenge, here we devise new types of i-motif/miniduplex hybrid structures that display an unprecedentedly high interactivity with commonly-used benzothiazole dyes (e.g. thioflavin T). A well-chosen tetranucleotide, whose optimal sequence depends on the used ligand, is appended to the 5′-terminals of diverse i-motifs and forms a minimal parallel duplex thereby creating a preferential site for binding ligands, verified by molecular dynamics simulation. In this way, the fluorescence of ligands can be dramatically enhanced by the i-motif/miniduplex hybrids under complex physiological conditions. This provides a generic light-up system with a high signal-to-background ratio for programmable DNA nanoassemblies, illustrated through utilizing it for a pH-driven framework nucleic acid nanodevice manipulated in acidic cellular membrane microenvironments. It enables label-free fluorescence bioimaging in response to extracellular pH change.

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15

Chakraborty, Saikat, and Yamuna Krishnan. "Kinetic hybrid i-motifs: Intercepting DNA with RNA to form a DNA2–RNA2 i-motif." Biochimie 90, no. 7 (July 2008): 1088–95. http://dx.doi.org/10.1016/j.biochi.2008.02.022.

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16

Brown, Susie L., and Samantha Kendrick. "The i-Motif as a Molecular Target: More Than a Complementary DNA Secondary Structure." Pharmaceuticals 14, no. 2 (January 27, 2021): 96. http://dx.doi.org/10.3390/ph14020096.

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Stretches of cytosine-rich DNA are capable of adopting a dynamic secondary structure, the i-motif. When within promoter regions, the i-motif has the potential to act as a molecular switch for controlling gene expression. However, i-motif structures in genomic areas of repetitive nucleotide sequences may play a role in facilitating or hindering expansion of these DNA elements. Despite research on the i-motif trailing behind the complementary G-quadruplex structure, recent discoveries including the identification of a specific i-motif antibody are pushing this field forward. This perspective reviews initial and current work characterizing the i-motif and providing insight into the biological function of this DNA structure, with a focus on how the i-motif can serve as a molecular target for developing new therapeutic approaches to modulate gene expression and extension of repetitive DNA.

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17

Gao, Ning, Yanbo Wang, and Chunying Wei. "Interactions of phenanthroline compounds with i-motif DNA." Chemical Research in Chinese Universities 30, no. 3 (March 7, 2014): 495–99. http://dx.doi.org/10.1007/s40242-014-3391-9.

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18

Liu, Huajie, Yun Xu, Fengyu Li, Yang Yang, Wenxing Wang, Yanlin Song, and Dongsheng Liu. "Light-Driven Conformational Switch of i-Motif DNA." Angewandte Chemie 119, no. 14 (March 26, 2007): 2567–69. http://dx.doi.org/10.1002/ange.200604589.

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19

Liu, Huajie, Yun Xu, Fengyu Li, Yang Yang, Wenxing Wang, Yanlin Song, and Dongsheng Liu. "Light-Driven Conformational Switch of i-Motif DNA." Angewandte Chemie International Edition 46, no. 14 (March 26, 2007): 2515–17. http://dx.doi.org/10.1002/anie.200604589.

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20

Lee, Il Joon, Sachin P. Patil, Karim Fhayli, Shahad Alsaiari, and Niveen M. Khashab. "Probing structural changes of self assembled i-motif DNA." Chemical Communications 51, no. 18 (2015): 3747–49. http://dx.doi.org/10.1039/c4cc06824f.

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21

Wei, Zuzhuang, Bobo Liu, Xiaomin Lin, Jing Wang, Zhi-Shu Huang, and Ding Li. "Development of a Smart Fluorescent Probe Specifically Interacting with C-Myc I-Motif." International Journal of Molecular Sciences 23, no. 7 (March 31, 2022): 3872. http://dx.doi.org/10.3390/ijms23073872.

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I-motifs play key regulatory roles in biological processes, holding great potential as attractive therapeutic targets. In the present study, we developed a novel fluorescent probe G59 with strong and selective binding to the c-myc gene promoter i-motif. G59 had an i-motif-binding carbazole moiety conjugated with naphthalimide fluorescent groups. G59 could differentiate the c-myc i-motif from other DNA structures through selective activation of its fluorescence, with its apparent visualization in solution. The smart probe G59 showed excellent sensitivity, with a low fluorescent detection limit of 154 nM and effective stabilization to the c-myc i-motif. G59 could serve as a rapid and sensitive probe for label-free screening of selective c-myc i-motif binding ligands under neutral crowding conditions. To the best of our knowledge, G59 is the first fluorescent probe with high sensitivity for recognizing the i-motif structure and screening for selective binding ligands.

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22

Takahashi, Shuntaro, John A. Brazier, and Naoki Sugimoto. "Topological impact of noncanonical DNA structures on Klenow fragment of DNA polymerase." Proceedings of the National Academy of Sciences 114, no. 36 (August 21, 2017): 9605–10. http://dx.doi.org/10.1073/pnas.1704258114.

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Noncanonical DNA structures that stall DNA replication can cause errors in genomic DNA. Here, we investigated how the noncanonical structures formed by sequences in genes associated with a number of diseases impacted DNA polymerization by the Klenow fragment of DNA polymerase. Replication of a DNA sequence forming an i-motif from a telomere, hypoxia-induced transcription factor, and an insulin-linked polymorphic region was effectively inhibited. On the other hand, replication of a mixed-type G-quadruplex (G4) from a telomere was less inhibited than that of the antiparallel type or parallel type. Interestingly, the i-motif was a better inhibitor of replication than were mixed-type G4s or hairpin structures, even though all had similar thermodynamic stabilities. These results indicate that both the stability and topology of structures formed in DNA templates impact the processivity of a DNA polymerase. This suggests that i-motif formation may trigger genomic instability by stalling the replication of DNA, causing intractable diseases.

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23

Messier, Nancy, and Paul H. Roy. "Integron Integrases Possess a Unique Additional Domain Necessary for Activity." Journal of Bacteriology 183, no. 22 (November 15, 2001): 6699–706. http://dx.doi.org/10.1128/jb.183.22.6699-6706.2001.

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ABSTRACT Integrons are genetic elements capable of integrating genes by a site-specific recombination system catalyzed by an integrase. Integron integrases are members of the tyrosine recombinase family and possess the four invariant residues (RHRY) and conserved motifs (boxes I and II and patches I, II, and III). An alignment of integron integrases compared to other tyrosine recombinases shows an additional group of residues around the patch III motif. We have analyzed the DNA binding and recombination properties of class I integron integrase (IntI1) variants carrying mutations at residues that are well conserved among all tyrosine recombinases and at some residues from the additional motif that are conserved among the integron integrases. The well-conserved residues studied were H277 from the conserved tetrad RHRY (about 90% conserved), E121 found in the patch I motif (about 80% conserved in prokaryotic recombinases), K171 from the patch II motif (near 100% conserved), W229 and F233 from the patch III motif, and G302 of box II (about 80% conserved in prokaryotic recombinases). Additional IntI1 mutated residues were K219 and a deletion of the sequence ALER215. We observed that E121, K171, and G302 play a role in the recombination activity but can be mutated without disturbing binding to DNA. W229, F233, and the conserved histidine (H277) may be implicated in protein folding or DNA binding. Some of the extra residues of IntI1 seem to play a role in DNA binding (K219) while others are implicated in the recombination activity (ALER215 deletion).

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24

Megalathan, Anoja, Bobby D. Cox, Peter D. Wilkerson, Anisa Kaur, Kumar Sapkota, Joseph E. Reiner, and Soma Dhakal. "Single-molecule analysis of i-motif within self-assembled DNA duplexes and nanocircles." Nucleic Acids Research 47, no. 14 (July 9, 2019): 7199–212. http://dx.doi.org/10.1093/nar/gkz565.

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Abstract The cytosine (C)-rich sequences that can fold into tetraplex structures known as i-motif are prevalent in genomic DNA. Recent studies of i-motif–forming sequences have shown increasing evidence of their roles in gene regulation. However, most of these studies have been performed in short single-stranded oligonucleotides, far from the intracellular environment. In cells, i-motif–forming sequences are flanked by DNA duplexes and packed in the genome. Therefore, exploring the conformational dynamics and kinetics of i-motif under such topologically constrained environments is highly relevant in predicting their biological roles. Using single-molecule fluorescence analysis of self-assembled DNA duplexes and nanocircles, we show that the topological environments play a key role on i-motif stability and dynamics. While the human telomere sequence (C3TAA)3C3 assumes i-motif structure at pH 5.5 regardless of topological constraint, it undergoes conformational dynamics among unfolded, partially folded and fully folded states at pH 6.5. The lifetimes of i-motif and the partially folded state at pH 6.5 were determined to be 6 ± 2 and 31 ± 11 s, respectively. Consistent with the partially folded state observed in fluorescence analysis, interrogation of current versus time traces obtained from nanopore analysis at pH 6.5 shows long-lived shallow blockades with a mean lifetime of 25 ± 6 s. Such lifetimes are sufficient for the i-motif and partially folded states to interact with proteins to modulate cellular processes.

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25

Tikhomirov, Alexander S., Mahmoud A. S. Abdelhamid, Georgy Y. Nadysev, George V. Zatonsky, Eugene E. Bykov, Pin Ju Chueh, Zoë A. E. Waller, and Andrey E. Shchekotikhin. "Water-Soluble Heliomycin Derivatives to Target i-Motif DNA." Journal of Natural Products 84, no. 5 (May 11, 2021): 1617–25. http://dx.doi.org/10.1021/acs.jnatprod.1c00162.

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26

Ren, Jiangtao, Tianshu Wang, Erkang Wang, and Jin Wang. "I-motif-stapled and spacer-dependent multiple DNA nanostructures." RSC Advances 6, no. 90 (2016): 87021–25. http://dx.doi.org/10.1039/c6ra15201e.

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The DNA spacers between duplexes and i-motif structures are critical for the morphology of assembled pH-responsive DNA nanostructures, which is very instructive for fabrication of distinct-scale molecular devices in the future.

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27

Garabedian, Alyssa, David Butcher, Jennifer L. Lippens, Jaroslava Miksovska, Prem P. Chapagain, Daniele Fabris, Mark E. Ridgeway, Melvin A. Park, and Francisco Fernandez-Lima. "Structures of the kinetically trapped i-motif DNA intermediates." Physical Chemistry Chemical Physics 18, no. 38 (2016): 26691–702. http://dx.doi.org/10.1039/c6cp04418b.

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28

Smiatek, Jens, and Andreas Heuer. "Deprotonation mechanism of a single-stranded DNA i-motif." RSC Adv. 4, no. 33 (2014): 17110–13. http://dx.doi.org/10.1039/c4ra01420k.

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29

Choi, Jungkweon, Sooyeon Kim, Takashi Tachikawa, Mamoru Fujitsuka, and Tetsuro Majima. "pH-Induced Intramolecular Folding Dynamics of i-Motif DNA." Journal of the American Chemical Society 133, no. 40 (October 12, 2011): 16146–53. http://dx.doi.org/10.1021/ja2061984.

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30

Day, Henry A., Pavlos Pavlou, and Zoë A. E. Waller. "i-Motif DNA: Structure, stability and targeting with ligands." Bioorganic & Medicinal Chemistry 22, no. 16 (August 2014): 4407–18. http://dx.doi.org/10.1016/j.bmc.2014.05.047.

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31

Lannes, Laurie, Saheli Halder, Yamuna Krishnan, and Harald Schwalbe. "Tuning the pH Response of i-Motif DNA Oligonucleotides." ChemBioChem 16, no. 11 (June 30, 2015): 1647–56. http://dx.doi.org/10.1002/cbic.201500182.

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32

Berthiol, Florian, Joseph Boissieras, Hugues Bonnet, Marie Pierrot, Christian Philouze, Jean-François Poisson, Anton Granzhan, Jérôme Dejeu, and Eric Defrancq. "Novel Synthesis of IMC-48 and Affinity Evaluation with Different i-Motif DNA Sequences." Molecules 28, no. 2 (January 10, 2023): 682. http://dx.doi.org/10.3390/molecules28020682.

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During the last decade, the evidence for the biological relevance of i-motif DNA (i-DNA) has been accumulated. However, relatively few molecules were reported to interact with i-DNA, and a controversy concerning their binding mode, affinity, and selectivity persists in the literature. In this context, the cholestane derivative IMC-48 has been reported to modulate bcl-2 gene expression by stabilizing an i-motif structure in its promoter. In the present contribution, we report on a novel, more straightforward, synthesis of IMC-48 requiring fewer steps compared to the previous approach. Furthermore, the interaction of IMC-48 with four different i-motif DNA sequences was thoroughly investigated by bio-layer interferometry (BLI) and circular dichroism (CD) spectroscopy. Surprisingly, our results show that IMC-48 is a very weak ligand of i-DNA as no quantifiable interaction or significant stabilization of i-motif structures could be observed, stimulating a quest for an alternative mechanism of its biological activity.

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33

Wildeman, A. G., M. Zenke, C. Schatz, M. Wintzerith, T. Grundström, H. Matthes, K. Takahashi, and P. Chambon. "Specific protein binding to the simian virus 40 enhancer in vitro." Molecular and Cellular Biology 6, no. 6 (June 1986): 2098–105. http://dx.doi.org/10.1128/mcb.6.6.2098-2105.1986.

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HeLa cell nuclear extracts and wild-type or mutated simian virus 40 enhancer DNA were used in DNase I footprinting experiments to study the interaction of putative trans-acting factors with the multiple enhancer motifs. We show that these nuclear extracts contain proteins that bind to these motifs. Because point mutations which are detrimental to the activity of a particular enhancer motif in vivo specifically prevent protection of that motif against DNase I digestion in vivo, we suggest that the bound proteins correspond to trans-acting factors involved in enhancement of transcription. Using mutants in which the two domains A and B of the simian virus 40 enhancer are either separated by insertion of DNA fragments or inverted with respect to their natural orientation, we also demonstrate that the trans-acting factors bind independently to the two domains.

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34

Wildeman, A. G., M. Zenke, C. Schatz, M. Wintzerith, T. Grundström, H. Matthes, K. Takahashi, and P. Chambon. "Specific protein binding to the simian virus 40 enhancer in vitro." Molecular and Cellular Biology 6, no. 6 (June 1986): 2098–105. http://dx.doi.org/10.1128/mcb.6.6.2098.

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HeLa cell nuclear extracts and wild-type or mutated simian virus 40 enhancer DNA were used in DNase I footprinting experiments to study the interaction of putative trans-acting factors with the multiple enhancer motifs. We show that these nuclear extracts contain proteins that bind to these motifs. Because point mutations which are detrimental to the activity of a particular enhancer motif in vivo specifically prevent protection of that motif against DNase I digestion in vivo, we suggest that the bound proteins correspond to trans-acting factors involved in enhancement of transcription. Using mutants in which the two domains A and B of the simian virus 40 enhancer are either separated by insertion of DNA fragments or inverted with respect to their natural orientation, we also demonstrate that the trans-acting factors bind independently to the two domains.

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35

Shamim, Amen, Maria Razzaq, and Kyeong Kyu Kim. "MD-TSPC4: Computational Method for Predicting the Thermal Stability of I-Motif." International Journal of Molecular Sciences 22, no. 1 (December 23, 2020): 61. http://dx.doi.org/10.3390/ijms22010061.

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I-Motif is a tetrameric cytosine-rich DNA structure with hemi-protonated cytosine: cytosine base pairs. Recent evidence showed that i-motif structures in human cells play regulatory roles in the genome. Therefore, characterization of novel i-motifs and investigation of their functional implication are urgently needed for comprehensive understanding of their roles in gene regulation. However, considering the complications of experimental investigation of i-motifs and the large number of putative i-motifs in the genome, development of an in silico tool for the characterization of i-motifs in the high throughput scale is necessary. We developed a novel computation method, MD-TSPC4, to predict the thermal stability of i-motifs based on molecular modeling and molecular dynamic simulation. By assuming that the flexibility of loops in i-motifs correlated with thermal stability within certain temperature ranges, we evaluated the correlation between the root mean square deviations (RMSDs) of model structures and the thermal stability as the experimentally obtained melting temperature (Tm). Based on this correlation, we propose an equation for Tm prediction from RMSD. We expect this method can be useful for estimating the overall structure and stability of putative i-motifs in the genome, which can be a starting point of further structural and functional studies of i-motifs.

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36

Satpathi, Sagar, Subrahmanyam Sappati, Konoya Das, and Partha Hazra. "Structural characteristics requisite for the ligand-based selective detection of i-motif DNA." Organic & Biomolecular Chemistry 17, no. 21 (2019): 5392–99. http://dx.doi.org/10.1039/c9ob01020c.

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A new approach has been explored to detect i-motif DNA structures over its complementary GQ DNA based on the hemi-protonated cytosine–cytosine (C⁺–C) base pairing recognition. This approach also shows its versatility by detecting various i-motif DNA structures with different chain lengths, molecularity and sizes, etc.

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Tsvetkov, Vladimir B., Timofei S. Zatsepin, Evgeny S. Belyaev, Yury I. Kostyukevich, George V. Shpakovski, Victor V. Podgorsky, Galina E. Pozmogova, Anna M. Varizhuk, and Andrey V. Aralov. "i-Clamp phenoxazine for the fine tuning of DNA i-motif stability." Nucleic Acids Research 46, no. 6 (February 21, 2018): 2751–64. http://dx.doi.org/10.1093/nar/gky121.

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Wenzel, Jürgen J., Heidi Rossmann, Christian Fottner, Stefan Neuwirth, Carolin Neukirch, Peter Lohse, Julia K. Bickmann, et al. "Identification and Prevention of Genotyping Errors Caused by G-Quadruplex– and i-Motif–Like Sequences." Clinical Chemistry 55, no. 7 (July 1, 2009): 1361–71. http://dx.doi.org/10.1373/clinchem.2008.118661.

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Abstract Background: Reliable PCR amplification of DNA fragments is the prerequisite for most genetic assays. We investigated the impact of G-quadruplex– or i-motif–like sequences on the reliability of PCR-based genetic analyses. Methods: We found the sequence context of a common intronic polymorphism in the MEN1 gene (multiple endocrine neoplasia I) to be the cause of systematic genotyping errors by inducing preferential amplification of one allelic variant [allele dropout (ADO)]. Bioinformatic analyses and pyrosequencing-based allele quantification enabled the identification of the underlying DNA structures. Results: We showed that G-quadruplex– or i-motif–like sequences can reproducibly cause ADO. In these cases, amplification efficiency strongly depends on the PCR enzyme and buffer conditions, the magnesium concentration in particular. In a randomly chosen subset of candidate single-nucleotide polymorphisms (SNPs) defined by properties deduced from 2 originally identified ADO cases, we confirmed preferential PCR amplification in up to 50% of the SNPs. We subsequently identified G-quadruplex and i-motifs harboring a SNP that alters the typical motif as the cause of this phenomenon, and a genomewide search based on the respective motifs predicted 0.5% of all SNPs listed by dbSNP and Online Mendelian Inheritance in Man to be potentially affected. Conclusions: Undetected, the described phenomenon produces systematic errors in genetic analyses that may lead to misdiagnoses in clinical settings. PCR products should be checked for G-quadruplex and i-motifs to avoid the formation of ADO-causing secondary structures. Truly affected assays can then be identified by a simple experimental procedure, which simultaneously provides the solution to the problem. .

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Singh, Raghvendra P., Ralf Blossey, and Fabrizio Cleri. "DNA i-motif provides steel-like tough ends to chromosomes." MRS Proceedings 1621 (2014): 135–41. http://dx.doi.org/10.1557/opl.2014.282.

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ABSTRACTWe studied the structure and mechanical properties of DNA i-motif nanowires by means of molecular dynamics computer simulations. We built up to 230 nm-long nanowires, based on a repeated TC5 sequence from NMR crystallographic data, fully relaxed and equilibrated in water. The unusual C●C+ stacked structure, formed by four ssDNA strands arranged in an intercalated tetramer, is here fully characterized both statically and dynamically. By applying stretching, compression and bending deformations with the steered molecular dynamics and umbrella sampling methods, we extract the apparent Young’s and bending moduli of the nanowire, as well as estimates for the tensile strength and persistence length. According to our results, i-motif nanowires share similarities with structural proteins, as far as their tensile stiffness, but are closer to nucleic acids and flexible proteins, as far as their bending rigidity is concerned. Curiously enough, their tensile strength makes such DNA fragments tough as mild steel or a nickel alloy. Besides their yet to be clarified biological significance, i-motif nanowires may qualify as interesting candidates for nanotechnology templates, due to such outstanding mechanical properties.

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Panczyk, Tomasz, Krzysztof Nieszporek, and Pawel Wolski. "Stability and Existence of Noncanonical I-motif DNA Structures in Computer Simulations Based on Atomistic and Coarse-Grained Force Fields." Molecules 27, no. 15 (August 1, 2022): 4915. http://dx.doi.org/10.3390/molecules27154915.

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Cytosine-rich DNA sequences are able to fold into noncanonical structures, in which semi-protonated cytosine pairs develop extra hydrogen bonds, and these bonds are responsible for the overall stability of a structure called the i-motif. The i-motif can be formed in many regions of the genome, but the most representative is the telomeric region in which the CCCTAA sequences are repeated thousands of times. The ability to reverse folding/unfolding in response to pH change makes the above sequence and i-motif very promising components of nanomachines, extended DNA structures, and drug carriers. Molecular dynamics analysis of such structures is highly beneficial due to direct insights into the microscopic structure of the considered systems. We show that Amber force fields for DNA predict the stability of the i-motif over a long timescale; however, these force fields are not able to predict folding of the cytosine-rich sequences into the i-motif. The reason is the kinetic partitioning of the folding process, which makes the transitions between various intermediates too time-consuming in atomistic force field representation. Application of coarse-grained force fields usually highly accelerates complex structural transitions. We, however, found that three of the most popular coarse-grained force fields for DNA (oxDNA, 3SPN, and Martini) were not able to predict the stability of the i-motif structure. Obviously, they were not able to accelerate the folding of unfolded states into an i-motif. This observation must be strongly highlighted, and the need to develop suitable extensions of coarse-grained force fields for DNA is pointed out. However, it will take a great deal of effort to successfully solve these problems.

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Gao, Xiang, Matthew Gethers, Si-ping Han, William A. Goddard, Ruojie Sha, Richard P. Cunningham, and Nadrian C. Seeman. "The PX Motif of DNA Binds Specifically to Escherichia coli DNA Polymerase I." Biochemistry 58, no. 6 (December 17, 2018): 575–81. http://dx.doi.org/10.1021/acs.biochem.8b01148.

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Sheng, Qiran, Joseph C. Neaverson, Tasnim Mahmoud, Clare E. M. Stevenson, Susan E. Matthews, and Zoë A. E. Waller. "Identification of new DNA i-motif binding ligands through a fluorescent intercalator displacement assay." Organic & Biomolecular Chemistry 15, no. 27 (2017): 5669–73. http://dx.doi.org/10.1039/c7ob00710h.

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Saha, Puja, Deepanjan Panda, Raj Paul, and Jyotirmayee Dash. "A DNA nanosensor for monitoring ligand-induced i-motif formation." Organic & Biomolecular Chemistry 19, no. 9 (2021): 1965–69. http://dx.doi.org/10.1039/d1ob00248a.

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Zhou, Xu, Chuang Li, Yu Shao, Chun Chen, Zhongqiang Yang, and Dongsheng Liu. "Reversibly tuning the mechanical properties of a DNA hydrogel by a DNA nanomotor." Chemical Communications 52, no. 70 (2016): 10668–71. http://dx.doi.org/10.1039/c6cc04724f.

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The microscopic conformational transition of an i-motif sequence integrated into a DNA hydrogel network leads to a reversible change in the macroscopic mechanical properties of the hydrogel without changing its initial topological structure.

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Smiatek, Jens, Chun Chen, Dongsheng Liu, and Andreas Heuer. "Stable Conformations of a Single Stranded Deprotonated DNA i-Motif." Journal of Physical Chemistry B 115, no. 46 (November 24, 2011): 13788–95. http://dx.doi.org/10.1021/jp208640a.

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Jin, Kyeong Sik, Su Ryon Shin, Byungcheol Ahn, Yecheol Rho, Seon Jeong Kim, and Moonhor Ree. "pH-Dependent Structures of an i-Motif DNA in Solution." Journal of Physical Chemistry B 113, no. 7 (February 19, 2009): 1852–56. http://dx.doi.org/10.1021/jp808186z.

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Mergny, Jean-Louis, Laurent Lacroix, Xiaogang Han, Jean-Louis Leroy, and Claude Helene. "Intramolecular Folding of Pyrimidine Oligodeoxynucleotides into an i-DNA Motif." Journal of the American Chemical Society 117, no. 35 (September 1995): 8887–98. http://dx.doi.org/10.1021/ja00140a001.

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Zhang, Jinli, Xian Wang, Yan Fu, You Han, Jingyao Cheng, Yanqing Zhang, and Wei Li. "Highly Active Subnano Palladium Clusters Embedded in i-Motif DNA." Langmuir 29, no. 47 (August 16, 2013): 14345–50. http://dx.doi.org/10.1021/la402153b.

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Sengupta, Bidisha, Kerianne Springer, Jenna G. Buckman, Sandra P. Story, Oluwamuyiwa Henry Abe, Zahiyah W. Hasan, Zachary D. Prudowsky, Sheldon E. Rudisill, Natalya N. Degtyareva, and Jeffrey T. Petty. "DNA Templates for Fluorescent Silver Clusters and I-Motif Folding." Journal of Physical Chemistry C 113, no. 45 (October 19, 2009): 19518–24. http://dx.doi.org/10.1021/jp906522u.

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Abou Assi, Hala, Miguel Garavís, Carlos González, and Masad J. Damha. "i-Motif DNA: structural features and significance to cell biology." Nucleic Acids Research 46, no. 16 (August 16, 2018): 8038–56. http://dx.doi.org/10.1093/nar/gky735.

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