Relevant bibliographies by topics / Intercalated Motif

Academic literature on the topic 'Intercalated Motif'

Author: Grafiati
Published: 10 December 2022
Last updated: 29 January 2023

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Journal articles on the topic "Intercalated Motif"

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Ruggiero, Emanuela, Sara Lago, Primož Šket, Matteo Nadai, Ilaria Frasson, Janez Plavec, and Sara N. Richter. "A dynamic i-motif with a duplex stem-loop in the long terminal repeat promoter of the HIV-1 proviral genome modulates viral transcription." Nucleic Acids Research 47, no. 21 (October 29, 2019): 11057–68. http://dx.doi.org/10.1093/nar/gkz937.

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Abstract I-motifs are non-canonical nucleic acids structures characterized by intercalated H-bonds between hemi-protonated cytosines. Evidence on the involvement of i-motif structures in the regulation of cellular processes in human cells has been consistently growing in the recent years. However, i-motifs within non-human genomes have never been investigated. Here, we report the characterization of i-motifs within the long terminal repeat (LTR) promoter of the HIV-1 proviral genome. Biophysical and biochemical analysis revealed formation of a predominant i-motif with an unprecedented loop composition. One-dimensional nuclear magnetic resonance investigation demonstrated formation of three G-C H-bonds in the long loop, which likely improve the structure overall stability. Pull-down experiments combined with mass spectrometry and protein crosslinking analysis showed that the LTR i-motif is recognized by the cellular protein hnRNP K, which induced folding at physiological conditions. In addition, hnRNP K silencing resulted in an increased LTR promoter activity, confirming the ability of the protein to stabilize the i-motif-forming sequence, which in turn regulates the LTR-mediated HIV-1 transcription. These findings provide new insights into the complexity of the HIV-1 virus and lay the basis for innovative antiviral drug design, based on the possibility to selectively recognize and target the HIV-1 LTR i-motif.
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Canalia, Muriel, and Jean-Louis Leroy. "[5mCCTCTCTCC]4: An i-Motif Tetramer with Intercalated T•T Pairs." Journal of the American Chemical Society 131, no. 36 (September 16, 2009): 12870–71. http://dx.doi.org/10.1021/ja903210t.

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Schumacher, Maria A., and Wenjie Zeng. "Structures of the activator ofK. pneumoniabiofilm formation, MrkH, indicates PilZ domains involved in c-di-GMP and DNA binding." Proceedings of the National Academy of Sciences 113, no. 36 (August 22, 2016): 10067–72. http://dx.doi.org/10.1073/pnas.1607503113.

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The pathogenesis ofKlebsiella pneumoniais linked to the bacteria’s ability to form biofilms. Mannose-resistantKlebsiella-like (Mrk) hemagglutinins are critical forK.pneumoniabiofilm development, and the expression of the genes encoding these proteins is activated by a 3′,5′-cyclic diguanylic acid (c-di-GMP)–regulated transcription factor, MrkH. To gain insight into MrkH function, we performed structural and biochemical analyses. Data revealed MrkH to be a monomer with a two-domain architecture consisting of a PilZ C-domain connected to an N domain that unexpectedly also harbors a PilZ-like fold. Comparison of apo- and c-di-GMP–bound MrkH structures reveals a large 138° interdomain rotation that is induced by binding an intercalated c-di-GMP dimer. c-di-GMP interacts with PilZ C-domain motifs 1 and 2 (RxxxR and D/NxSxxG) and a newly described c-di-GMP–binding motif in the MrkH N domain. Strikingly, these c-di-GMP–binding motifs also stabilize an open state conformation in apo MrkH via contacts from the PilZ motif 1 to residues in the C-domain motif 2 and the c-di-GMP–binding N-domain motif. Use of the same regions in apo structure stabilization and c-di-GMP interaction allows distinction between the states. Indeed, domain reorientation by c-di-GMP complexation with MrkH, which leads to a highly compacted structure, suggests a mechanism by which the protein is activated to bind DNA. To our knowledge, MrkH represents the first instance of specific DNA binding mediated by PilZ domains. The MrkH structures also pave the way for the rational design of inhibitors that targetK.pneumoniabiofilm formation.
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Lee, Gyeong Jin, and Tae-il Kim. "pH-Responsive i-motif Conjugated Hyaluronic Acid/Polyethylenimine Complexes for Drug Delivery Systems." Pharmaceutics 11, no. 5 (May 27, 2019): 247. http://dx.doi.org/10.3390/pharmaceutics11050247.

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i-motif is cytosine (C)-rich oligonucleotide (ODN) which shows pH-responsive structure change in acidic condition. Therefore, it has been utilized for the trigger of intercalated drug release, responding to environmental pH change. In this study, 2.76 molecules of i-motif binding ODNs (IBOs) were conjugated to each hyaluronic acid (HA) via amide bond linkages. Synthesis of HA-IBO conjugate (HB) was confirmed by FT-IR and agarose gel electrophoresis with Stains-All staining. After hybridization of HB with i-motif ODN (IMO), it was confirmed that doxorubicin (DOX) could be loaded in HB-IMO hybrid structure (HBIM) with 65.6% of drug loading efficiency (DLE) and 25.0% of drug loading content (DLC). At pH 5.5, prompt and significant DOX release from HBIM was observed due to the disruption of HBIM hybrid structure via i-motif formation of IMO, contrary to pH 7.4 condition. Then, HBIM was complexed with low molecular weight polyethylenimine (PEI1.8k), forming positively charged nanostructures (Z-average size: 126.0 ± 0.4 nm, zeta-potential: 16.1 ± 0.3 mV). DOX-loaded HBIM/PEI complexes displayed higher anticancer efficacy than free DOX in A549 cells, showing the potential for pH-responsive anticancer drug delivery systems.
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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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6

Cai, L., L. Chen, S. Raghavan, A. Rich, R. Ratliff, and R. Moyzis. "Intercalated cytosine motif and novel adenine clusters in the crystal structure of the Tetrahymena telomere." Nucleic Acids Research 26, no. 20 (October 1, 1998): 4696–705. http://dx.doi.org/10.1093/nar/26.20.4696.

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7

Eigenthaler, Martin, Stefan Engelhardt, Birgitta Schinke, Anna Kobsar, Eva Schmitteckert, Stepan Gambaryan, Catherine M. Engelhardt, et al. "Disruption of cardiac Ena-VASP protein localization in intercalated disks causes dilated cardiomyopathy." American Journal of Physiology-Heart and Circulatory Physiology 285, no. 6 (December 2003): H2471—H2481. http://dx.doi.org/10.1152/ajpheart.00362.2003.

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Vasodilator-stimulated phosphoprotein (VASP) and mammalian enabled (Mena) are actin cytoskeleton and signaling modulators. Ena-VASP proteins share an identical domain organization with an NH2-terminal Ena VASP homology (EVH1) domain, which mediates the binding of these proteins to FPPPP-motif containing partners such as zyxin and vinculin. VASP and Mena are abundantly expressed in the heart. However, previous studies showed that disruption by gene targeting of VASP or Mena genes in mice did not reveal any cardiac phenotype, whereas mice lacking both VASP and Mena died during embryonic development. To determine the in vivo function of Ena-VASP proteins in the heart, we used a dominant negative strategy with cardiac-specific expression of the VASP-EVH1 domain. Transgenic mice with cardiac myocyte-restricted, α-myosin heavy chain promoter-directed expression of the VASP-EVH1 domain were generated. Overexpression of the EVH1 domain resulted in specific displacement of both VASP and Mena from cardiac intercalated disks. VASP-EVH1 transgenic mice developed dilated cardiomyopathy with myocyte hypertrophy and bradycardia, which resulted in early postnatal lethality in mice with high levels of transgene expression. The results demonstrate that Ena-VASP proteins may play an important role in intercalated disk function at the interface between cardiac myocytes.
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8

Chou, Shan-Ho, and Ko-Hsin Chin. "Quadruple intercalated G-6 stack: a possible motif in the fold-back structure of the Drosophila centromeric dodeca-satellite?" Journal of Molecular Biology 314, no. 1 (November 2001): 139–52. http://dx.doi.org/10.1006/jmbi.2001.5131.

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9

Berger, Imre, ChulHee Kang, April Fredian, Robert Ratliff, Robert Moyzis, and Alexander Rich. "Extension of the four-stranded intercalated cytosine motif by adenine•adenine base pairing in the crystal structure of d(CCCAAT)." Nature Structural & Molecular Biology 2, no. 5 (May 1995): 416–25. http://dx.doi.org/10.1038/nsb0595-416.

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10

Toye, Ashley M. "Defective kidney anion-exchanger 1 (AE1, Band 3) trafficking in dominant distal renal tubular acidosis (dRTA)." Biochemical Society Symposia 72 (January 1, 2005): 47–63. http://dx.doi.org/10.1042/bss0720047.

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dRTA (distal renal tubular acidosis) results from the failure of the a-intercalated cells in the distal tubule of the nephron to acidify the urine. A truncated form of AE1 (anion-exchanger 1; Band 3), kAE1 (kidney isoform of AE1), is located in the basolateral membrane of the intercalated cell. Mutations in the AE1 gene cause autosomal dominant and recessive forms of dRTA. All the dominant dRTA mutations investigated cause aberrant trafficking of kAE1, resulting in its intracellular retention or mistargeting to the apical plasma membrane. Therefore the intracellular retention of hetero-oligomers containing wild-type and dRTA mutants, or the mistargeted protein in the apical membrane neutralizing acid secretion, explains dominant dRTA. The kAE1 (Arg901→stop) mutant has been studied in more detail, since the mistargeting kAE1 (Arg901→stop) from the basolateral to the apical membrane is consistent with the removal of a basolateral localization signal. The C-terminal amino acids deleted by the Arg901→stop mutation, contain a tyrosine motif and a type II PDZ interaction domain. The tyrosine residue (Tyr904), but not the PDZ domain, is critical for basolateral localization. In the absence of the N-terminus of kAE1, the C-terminus was not sufficient to localize kAE1 to the basolateral membrane. This suggests that a determinant within the kAE1 N-terminus co-operates with the C-terminus for kAE1 basolateral localization. Interestingly, Tyr359, in the N-terminal domain, and Tyr904 in the C-terminus of AE1 are phosphorylated in red blood cells. A potential scheme is suggested where successive phosphorylation of these residues is necessary for correct localization and recycling of kAE1 to the basolateral membrane.
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Book chapters on the topic "Intercalated Motif"

1

Berger, Imre, ChulHee Kang, April Fredian, Robert Ratliff, Robert Moyzis, and Alexander Rich. "Extension of the four-stranded intercalated cytosine motif by adenine•adenine base pairing in the crystal structure of d(CCCAAT)." In The Excitement of Discovery: Selected Papers of Alexander Rich, 275–84. WORLD SCIENTIFIC, 2018. http://dx.doi.org/10.1142/9789813272682_0040.

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