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James P Vaughn - One of the best experts on this subject based on the ideXlab platform.
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g4 resolvase 1 binds both dna and rna tetramolecular quadruplex with high affinity and is the major source of tetramolecular quadruplex g4 dna and g4 rna resolving activity in hela cell lysates
Journal of Biological Chemistry, 2008Co-Authors: Steven D Creacy, Eric D Routh, Yoshikuni Nagamine, Steven A Akman, Fumiko Iwamoto, James P VaughnAbstract:Quadruplex structures that result from stacking of guanine quartets in nucleic acids possess such thermodynamic stability that their resolution in vivo is likely to require specific recognition by specialized enzymes. We previously identified the major tetramolecular quadruplex DNA resolving activity in HeLa cell lysates as the gene product of DHX36 (Vaughn, J. P., Creacy, S. D., Routh, E. D., Joyner-Butt, C., Jenkins, G. S., Pauli, S., Nagamine, Y., and Akman, S. A. (2005) J. Biol Chem. 280, 38117–38120), naming the enzyme G4 Resolvase 1 (G4R1). G4R1 is also known as RHAU, an RNA helicase associated with the AU-rich sequence of mRNAs. We now show that G4R1/RHAU binds to and resolves tetramolecular RNA quadruplex as well as tetramolecular DNA quadruplex structures. The apparent Kd values of G4R1/RHAU for tetramolecular RNA quadruplex and tetramolecular DNA quadruplex were exceptionally low: 39 ± 6 and 77 ± 6pm, respectively, as measured by gel mobility shift assay. In competition studies tetramolecular RNA quadruplex structures inhibited tetramolecular DNA quadruplex structure resolution by G4R1/RHAU more efficiently than tetramolecular DNA quadruplex structures inhibited tetramolecular RNA quadruplex structure resolution. Down-regulation of G4R1/RHAU in HeLa T-REx cells by doxycycline-inducible short hairpin RNA caused an 8-fold loss of RNA and DNA tetramolecular quadruplex resolution, consistent with G4R1/RHAU representing the major tetramolecular quadruplex helicase activity for both RNA and DNA structures in HeLa cells. This study demonstrates for the first time the RNA quadruplex resolving enzymatic activity associated with G4R1/RHAU and its exceptional binding affinity, suggesting a potential novel role for G4R1/RHAU in targeting in vivo RNA quadruplex structures.
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g4 resolvase 1 binds both dna and rna tetramolecular quadruplex with high affinity and is the major source of tetramolecular quadruplex g4 dna and g4 rna resolving activity in hela cell lysates
Journal of Biological Chemistry, 2008Co-Authors: Steven D Creacy, Eric D Routh, Yoshikuni Nagamine, Steven A Akman, Fumiko Iwamoto, James P VaughnAbstract:Quadruplex structures that result from stacking of guanine quartets in nucleic acids possess such thermodynamic stability that their resolution in vivo is likely to require specific recognition by specialized enzymes. We previously identified the major tetramolecular quadruplex DNA resolving activity in HeLa cell lysates as the gene product of DHX36 (Vaughn, J. P., Creacy, S. D., Routh, E. D., Joyner-Butt, C., Jenkins, G. S., Pauli, S., Nagamine, Y., and Akman, S. A. (2005) J. Biol Chem. 280, 38117–38120), naming the enzyme G4 Resolvase 1 (G4R1). G4R1 is also known as RHAU, an RNA helicase associated with the AU-rich sequence of mRNAs. We now show that G4R1/RHAU binds to and resolves tetramolecular RNA quadruplex as well as tetramolecular DNA quadruplex structures. The apparent Kd values of G4R1/RHAU for tetramolecular RNA quadruplex and tetramolecular DNA quadruplex were exceptionally low: 39 ± 6 and 77 ± 6pm, respectively, as measured by gel mobility shift assay. In competition studies tetramolecular RNA quadruplex structures inhibited tetramolecular DNA quadruplex structure resolution by G4R1/RHAU more efficiently than tetramolecular DNA quadruplex structures inhibited tetramolecular RNA quadruplex structure resolution. Down-regulation of G4R1/RHAU in HeLa T-REx cells by doxycycline-inducible short hairpin RNA caused an 8-fold loss of RNA and DNA tetramolecular quadruplex resolution, consistent with G4R1/RHAU representing the major tetramolecular quadruplex helicase activity for both RNA and DNA structures in HeLa cells. This study demonstrates for the first time the RNA quadruplex resolving enzymatic activity associated with G4R1/RHAU and its exceptional binding affinity, suggesting a potential novel role for G4R1/RHAU in targeting in vivo RNA quadruplex structures.
Souvik Maiti - One of the best experts on this subject based on the ideXlab platform.
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inhibition of translation in living eukaryotic cells by an rna g quadruplex motif
RNA, 2008Co-Authors: Amit Arora, Mariola Dutkiewicz, Vinod Scaria, Manoj Hariharan, Souvik Maiti, Jens KurreckAbstract:Guanine-rich sequences can adopt intramolecular four-stranded structures, called G-Quadruplexes. These motifs have been intensively investigated on the DNA level, but their overall biological relevance remains elusive. Only recently has research concerning the function of G-Quadruplexes in RNAs commenced. Here, we demonstrate for the first time, that an RNA Gquadruplex structure inhibits translation in vivo in eukaryotic cells. We investigated the function of a highly conserved, thermodynamically stable RNA G-Quadruplex in the 59-UTR of the mRNA of the human Zic-1 zinc-finger protein. Using dual luciferase reporter assay, we demonstrate that the Zic-1 RNA G-Quadruplex represses protein synthesis inside eukaryotic cells. Quantitative RT-PCR assays confirmed that the reduction of protein synthesis is due to regulation of the translation process and not a consequence of reduced transcription. Western blot analysis revealed that expression of Zic-1 is strongly reduced by a 73 nucleotides-long fragment of the UTR containing the G-Quadruplex motif. These structures might add to the more recently discovered elements in untranslated regions of mRNAs that regulate their translation.
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energetics of the human tel 22 quadruplex telomestatin interaction a molecular dynamics study
Journal of Physical Chemistry B, 2008Co-Authors: Saurabh Agrawal, Rajendra Prasad Ojha, Souvik MaitiAbstract:The formation and stabilization of telomeric quadruplexes has been shown to inhibit the activity of telomerase, thus establishing telomeric DNA quadruplex as an attractive target for cancer therapeutic intervention. In this context, telomestatin, a G-Quadruplex-specific ligand known to bind and stabilize G-Quadruplex, is of great interest. Knowledge of the three-dimensional structure of telomeric quadruplex and its complex with telomestatin in solution is a prerequisite for structure-based rational drug design. Here, we report the relative stabilities of human telomeric quadruplex (AG3[T2AG3]3) structures under K+ ion conditions and their binding interaction with telomestatin, as determined by molecular dynamics simulations followed by energy calculations. The energetics study shows that, in the presence of K+ ions, mixed hybrid-type Tel-22 quadruplex conformations are more stable than other conformations. The binding free energy for quadruplex−telomestatin interactions suggests that 1:2 binding is favore...
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furan based cyclic oligopeptides selectively target g quadruplex
Journal of Medicinal Chemistry, 2007Co-Authors: Tushar Kanti Chakraborty, Amit Arora, Saumya Roy, Niti Kumar, Souvik MaitiAbstract:We report the binding properties of 18- and 24-membered cyclic oligopeptides developed from a novel furan amino acid, 5-(aminomethyl)-2-furancarboxylic acid, to G-Quadruplex. Comparative analysis of the binding data of these ligands with G-Quadruplex and double-strand DNA shows that 24-membered cyclic peptides are highly selective for telomeric G-Quadruplex structures and thus can be used as a scaffold to target quadruplex structures at the genomic level.
Steven D Creacy - One of the best experts on this subject based on the ideXlab platform.
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g4 resolvase 1 binds both dna and rna tetramolecular quadruplex with high affinity and is the major source of tetramolecular quadruplex g4 dna and g4 rna resolving activity in hela cell lysates
Journal of Biological Chemistry, 2008Co-Authors: Steven D Creacy, Eric D Routh, Yoshikuni Nagamine, Steven A Akman, Fumiko Iwamoto, James P VaughnAbstract:Quadruplex structures that result from stacking of guanine quartets in nucleic acids possess such thermodynamic stability that their resolution in vivo is likely to require specific recognition by specialized enzymes. We previously identified the major tetramolecular quadruplex DNA resolving activity in HeLa cell lysates as the gene product of DHX36 (Vaughn, J. P., Creacy, S. D., Routh, E. D., Joyner-Butt, C., Jenkins, G. S., Pauli, S., Nagamine, Y., and Akman, S. A. (2005) J. Biol Chem. 280, 38117–38120), naming the enzyme G4 Resolvase 1 (G4R1). G4R1 is also known as RHAU, an RNA helicase associated with the AU-rich sequence of mRNAs. We now show that G4R1/RHAU binds to and resolves tetramolecular RNA quadruplex as well as tetramolecular DNA quadruplex structures. The apparent Kd values of G4R1/RHAU for tetramolecular RNA quadruplex and tetramolecular DNA quadruplex were exceptionally low: 39 ± 6 and 77 ± 6pm, respectively, as measured by gel mobility shift assay. In competition studies tetramolecular RNA quadruplex structures inhibited tetramolecular DNA quadruplex structure resolution by G4R1/RHAU more efficiently than tetramolecular DNA quadruplex structures inhibited tetramolecular RNA quadruplex structure resolution. Down-regulation of G4R1/RHAU in HeLa T-REx cells by doxycycline-inducible short hairpin RNA caused an 8-fold loss of RNA and DNA tetramolecular quadruplex resolution, consistent with G4R1/RHAU representing the major tetramolecular quadruplex helicase activity for both RNA and DNA structures in HeLa cells. This study demonstrates for the first time the RNA quadruplex resolving enzymatic activity associated with G4R1/RHAU and its exceptional binding affinity, suggesting a potential novel role for G4R1/RHAU in targeting in vivo RNA quadruplex structures.
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g4 resolvase 1 binds both dna and rna tetramolecular quadruplex with high affinity and is the major source of tetramolecular quadruplex g4 dna and g4 rna resolving activity in hela cell lysates
Journal of Biological Chemistry, 2008Co-Authors: Steven D Creacy, Eric D Routh, Yoshikuni Nagamine, Steven A Akman, Fumiko Iwamoto, James P VaughnAbstract:Quadruplex structures that result from stacking of guanine quartets in nucleic acids possess such thermodynamic stability that their resolution in vivo is likely to require specific recognition by specialized enzymes. We previously identified the major tetramolecular quadruplex DNA resolving activity in HeLa cell lysates as the gene product of DHX36 (Vaughn, J. P., Creacy, S. D., Routh, E. D., Joyner-Butt, C., Jenkins, G. S., Pauli, S., Nagamine, Y., and Akman, S. A. (2005) J. Biol Chem. 280, 38117–38120), naming the enzyme G4 Resolvase 1 (G4R1). G4R1 is also known as RHAU, an RNA helicase associated with the AU-rich sequence of mRNAs. We now show that G4R1/RHAU binds to and resolves tetramolecular RNA quadruplex as well as tetramolecular DNA quadruplex structures. The apparent Kd values of G4R1/RHAU for tetramolecular RNA quadruplex and tetramolecular DNA quadruplex were exceptionally low: 39 ± 6 and 77 ± 6pm, respectively, as measured by gel mobility shift assay. In competition studies tetramolecular RNA quadruplex structures inhibited tetramolecular DNA quadruplex structure resolution by G4R1/RHAU more efficiently than tetramolecular DNA quadruplex structures inhibited tetramolecular RNA quadruplex structure resolution. Down-regulation of G4R1/RHAU in HeLa T-REx cells by doxycycline-inducible short hairpin RNA caused an 8-fold loss of RNA and DNA tetramolecular quadruplex resolution, consistent with G4R1/RHAU representing the major tetramolecular quadruplex helicase activity for both RNA and DNA structures in HeLa cells. This study demonstrates for the first time the RNA quadruplex resolving enzymatic activity associated with G4R1/RHAU and its exceptional binding affinity, suggesting a potential novel role for G4R1/RHAU in targeting in vivo RNA quadruplex structures.
Naoki Sugimoto - One of the best experts on this subject based on the ideXlab platform.
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2020Co-Authors: Takeshi Fujimoto, Daisuke Miyoshi, Shuichi Nakano, Naoki SugimotoAbstract:Both cellular environmental factors and chemical modifications critically affect the properties of nucleic acids. However, the structure and stability of DNA containing abasic sites under cell-mimicking molecular crowding conditions remain unclear. Here, we investigated the molecular crowding effects on the structure and stability of the G-Quadruplexes including a single abasic site. Structural analysis by circular dichroism showed that molecular crowding by PEG200 did not affect the topology of the Gquadruplex structure with or without an abasic site. Thermodynamic analysis further demonstrated that the degree of stabilization of the G-Quadruplex by molecular crowding decreased with substitution of an abasic site for a single guanine. Notably, we found that the molecular crowding effects on the enthalpy change for G-Quadruplex formation had a linear relationship with the abasic site effects depending on its position. These results are useful for predicting the structure and stability of G-Quadruplexes with abasic sites in the cell-mimicking conditions
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destabilization of dna g quadruplexes by chemical environment changes during tumor progression facilitates transcription
Journal of the American Chemical Society, 2018Co-Authors: Hisae Tateishikarimata, Keiko Kawauchi, Naoki SugimotoAbstract:DNA G-Quadruplex formation is highly responsive to surrounding conditions, particularly K+ concentration. Malignant cancer cells have a much lower K+ concentration than normal cells because of overexpression of a K+ channel; thus, G-Quadruplexes may be unstable in cancer cells. Here, we physicochemically investigated how changes in intracellular chemical environments in vitro and in cells influence G-Quadruplex formation and transcription during tumor progression. In vitro, the stable G-Quadruplex formation inhibits transcription in a solution containing 150 mM KCl (normal condition). As K+ concentration decreases, which decreases G-Quadruplex stability, transcript production from templates with G-Quadruplex-forming potential increases. In normal cells, the trend in transcript productions was similar to that in in vitro experiments, with transcription efficiency inversely correlated with G-Quadruplex stability. Interestingly, higher transcript levels were produced from templates with G-Quadruplex-forming ...
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Destabilization of DNA G‑Quadruplexes by Chemical Environment Changes during Tumor Progression Facilitates Transcription
2017Co-Authors: Hisae Tateishi-karimata, Keiko Kawauchi, Naoki SugimotoAbstract:DNA G-Quadruplex formation is highly responsive to surrounding conditions, particularly K+ concentration. Malignant cancer cells have a much lower K+ concentration than normal cells because of overexpression of a K+ channel; thus, G-Quadruplexes may be unstable in cancer cells. Here, we physicochemically investigated how changes in intracellular chemical environments in vitro and in cells influence G-Quadruplex formation and transcription during tumor progression. In vitro, the stable G-Quadruplex formation inhibits transcription in a solution containing 150 mM KCl (normal condition). As K+ concentration decreases, which decreases G-Quadruplex stability, transcript production from templates with G-Quadruplex-forming potential increases. In normal cells, the trend in transcript productions was similar to that in in vitro experiments, with transcription efficiency inversely correlated with G-Quadruplex stability. Interestingly, higher transcript levels were produced from templates with G-Quadruplex-forming potential in Ras-transformed and highly metastatic breast cancer cells (MDA-MB-231) than in nontransformed and control MCF-7 cells. Moreover, the amount of transcript produced from G-Quadruplex-forming templates decreased upon addition of siRNA targeting KCNH1 mRNA, which encodes a potassium voltage-gated channel subfamily H member 1 (KV10.1). Importantly, G-Quadruplex dissociation during tumor progression was observed by immunofluorescence using a G-Quadruplex-binding antibody in cells. These results suggest that in normal cells, K+ ions attenuate the transcription of certain oncogenes by stabilizing G-Quadruplex structures. Our findings provide insight into the novel mechanism of overexpression of certain G-rich genes during tumor progression
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study on effects of molecular crowding on g quadruplex ligand binding and ligand mediated telomerase inhibition
Methods, 2013Co-Authors: Hidenobu Yaku, Shuichi Nakano, Daisuke Miyoshi, Hisae Tateishikarimata, Takashi Murashima, Naoki SugimotoAbstract:The telomere G-Quadruplex-binding and telomerase-inhibiting capacity of two cationic (TMPyP4 and PIPER) and two anionic (phthalocyanine and Hemin) G-Quadruplex-ligands were examined under conditions of molecular crowding (MC). Osmotic experiments showed that binding of the anionic ligands, which bind to G-Quadruplex DNA via π-π stacking interactions, caused some water molecules to be released from the G-Quadruplex/ligand complex; in contrast, a substantial number of water molecules were taken up upon electrostatic binding of the cationic ligands to G-Quadruplex DNA. These behaviors of water molecules maintained or reduced the binding affinity of the anionic and the cationic ligands, respectively, under MC conditions. Consequently, the anionic ligands (phthalocyanine and Hemin) robustly inhibited telomerase activity even with MC; in contrast, the inhibition of telomerase caused by cationic TMPyP4 was drastically reduced by MC. These results allow us to conclude that the binding of G-Quadruplex-ligands to G-Quadruplex via non-electrostatic interactions is preferable for telomerase inhibition under physiological conditions.
Anh Tuân Phan - One of the best experts on this subject based on the ideXlab platform.
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major g quadruplex form of hiv 1 ltr reveals a 3 1 folding topology containing a stem loop
Journal of the American Chemical Society, 2018Co-Authors: Elena Butovskaya, Brahim Heddi, Blaž Bakalar, Sara N Richter, Anh Tuân PhanAbstract:Nucleic acids can form noncanonical four-stranded structures called G-Quadruplexes. G-Quadruplex-forming sequences are found in several genomes including human and viruses. Previous studies showed that the G-rich sequence located in the U3 promoter region of the HIV-1 long terminal repeat (LTR) folds into a set of dynamically interchangeable G-Quadruplex structures. G-Quadruplexes formed in the LTR could act as silencer elements to regulate viral transcription. Stabilization of LTR G-Quadruplexes by G-Quadruplex-specific ligands resulted in decreased viral production, suggesting the possibility of targeting viral G-Quadruplex structures for antiviral purposes. Among all the G-Quadruplexes formed in the LTR sequence, LTR-III was shown to be the major G-Quadruplex conformation in vitro. Here we report the NMR structure of LTR-III in K+ solution, revealing the formation of a unique quadruplex–duplex hybrid consisting of a three-layer (3 + 1) G-Quadruplex scaffold, a 12-nt diagonal loop containing a conserved...
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structure of human telomeric dna in crowded solution
Journal of the American Chemical Society, 2011Co-Authors: Brahim Heddi, Anh Tuân PhanAbstract:G-Quadruplex structures formed by DNA at the human telomeres are attractive anticancer targets. Human telomeric sequences can adopt a diverse range of intramolecular G-Quadruplex conformations: a parallel-stranded conformation was observed in the crystalline state, while at least four other forms were seen in K+ solution, raising the question of which conformation is favored in crowded cellular environment. Here, we report the first NMR structure of a human telomeric G-Quadruplex in crowded solution. We show that four different G-Quadruplex conformations are converted to a propeller-type parallel-stranded G-Quadruplex in K+-containing crowded solution due to water depletion. This study also reveals the formation of a new higher-order G-Quadruplex structure under molecular crowding conditions. Our molecular dynamics simulations of solvent distribution provide insights at molecular level on the formation of parallel-stranded G-Quadruplex in environment depleted of water. These results regarding human telome...