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1.
Strand Invasion of DNA Quadruplexes by PNA: Comparison of Homologous and Complementary Hybridization
Dr. Anisha Gupta Ling‐Ling Lee Dr. Subhadeep Roy Farial A. Tanious Dr. W. David Wilson Dr. Danith H. Ly Dr. Bruce A. Armitage 《Chembiochem : a European journal of chemical biology》2013,14(12):1476-1484
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Responsive Fluorescent PNA Analogue as a Tool for Detecting G‐quadruplex Motifs of Oncogenes and Activity of Toxic Ribosome‐Inactivating Proteins
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Pramod M. Sabale Dr. Seergazhi G. Srivatsan 《Chembiochem : a European journal of chemical biology》2016,17(17):1665-1673
Fluorescent oligomers that are resistant to enzymatic degradation and report their binding to target oligonucleotides (ONs) by changes in fluorescence properties are highly useful in developing nucleic‐acid‐based diagnostic tools and therapeutic strategies. Here, we describe the synthesis and photophysical characterization of fluorescent peptide nucleic acid (PNA) building blocks made of microenvironment‐sensitive 5‐(benzofuran‐2‐yl)‐ and 5‐(benzothiophen‐2‐yl)‐uracil cores. The emissive monomers, when incorporated into PNA oligomers and hybridized to complementary ONs, are minimally perturbing and are highly sensitive to their neighboring base environment. In particular, benzothiophene‐modified PNA reports the hybridization process with significant enhancement in fluorescence intensity, even when placed in the vicinity of guanine residues, which often quench fluorescence. This feature was used in the turn‐on detection of G‐quadruplex‐forming promoter DNA sequences of human proto‐oncogenes (c‐myc and c‐kit). Furthermore, the ability of benzothiophene‐modified PNA oligomer to report the presence of an abasic site in RNA enabled us to develop a simple fluorescence hybridization assay to detect and estimate the depurination activity of ribosome‐inactivating protein toxins. Our results demonstrate that this approach with responsive PNA probes will provide new opportunities to develop robust tools to study nucleic acids. 相似文献
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Dr. Sebastian Müller Dr. Katta Laxmi‐Reddy Dr. Prakrit V. Jena Dr. Benoit Baptiste Dr. Zeyuan Dong Dr. Frédéric Godde Prof. Taekjip Ha Dr. Raphaël Rodriguez Prof. Shankar Balasubramanian Dr. Ivan Huc 《Chembiochem : a European journal of chemical biology》2014,15(17):2563-2570
We previously identified quinoline‐based oligoamide helical foldamers and a trimeric macrocycle as selective ligands of DNA quadruplexes. Their helical structures might permit targeting of the backbone loops and grooves of G‐quadruplexes instead of the G‐tetrads. Given the vast array of morphologies G‐quadruplex structures can adopt, this might be a way to achieve sequence selective binding. Here, we describe the design and synthesis of molecules based on macrocyclic and helically folded oligoamides. We tested their ability to interact with the human telomeric G‐quadruplex and an array of promoter G‐quadruplexes by using FRET melting assay and single‐molecule FRET. Our results show that they constitute very potent ligands—comparable to the best so far reported. Their modes of interaction differ from those of traditional tetrad binders, thus opening avenues for the development of molecules specific for certain G‐quadruplex conformations. 相似文献
5.
Ligand‐Mediated G‐Quadruplex Induction in a Double‐Stranded DNA Context by Cyclic Imidazole/Lysine Polyamide
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Sefan Asamitsu Yue Li Dr. Toshikazu Bando Prof. Hiroshi Sugiyama 《Chembiochem : a European journal of chemical biology》2016,17(14):1317-1322
G‐quadruplex (G4) DNA is often observed as a DNA secondary structure in guanine‐rich sequences, and is thought to be relevant to pharmacological and biological events. Therefore, G4 ligands have attracted great attention as potential anticancer therapies or in molecular probe applications. Here, we designed cyclic imidazole/lysine polyamide (cIKP) as a new class of G4 ligand. It was readily synthesized without time‐consuming column chromatography. cIKP selectively recognized particular G4 structures with low nanomolar affinity. Moreover, cIKP exhibited the ability to induce G4 formation of the promoter of G4‐containing DNA in the context of stable double‐stranded DNA (dsDNA) under molecular crowding conditions. This cIKP might be applicable as a molecular probe for the detection of potential G4‐forming sequences in dsDNA. 相似文献
6.
G‐Quadruplexes with Tetra(ethylene glycol)‐Modified Deoxythymidines are Resistant to Nucleases and Inhibit HIV‐1 Reverse Transcriptase
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Dr. Hisae Tateishi‐Karimata Dr. Takahiro Muraoka Prof. Kazushi Kinbara Prof. Dr. Naoki Sugimoto 《Chembiochem : a European journal of chemical biology》2016,17(15):1399-1402
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Osman Doluca Prof. Dr. Alexandre S. Boutorine Dr. Vyacheslav V. Filichev 《Chembiochem : a European journal of chemical biology》2011,12(15):2365-2374
The majority of studies on DNA triple helices have been focused on pH‐sensitive parallel triplexes with Hoogsteen CT‐containing third strands that require protonation of cytosines. Reverse Hoogsteen GT/GA‐containing antiparallel triplex‐forming oligonucleotides (TFOs) do not require an acidic pH but their applicability in triplex technology is limited because of their tendency to form undesired highly stable aggregates such as G‐quadruplexes. In this study, G‐rich oligonucleotides containing 2–4 insertions of twisted intercalating nucleic acid (TINA) monomers are demonstrated to disrupt the formation of G‐quadruplexes and form stable antiparallel triplexes with target DNA duplexes. The structure of TINA‐incorporated oligonucleotides was optimized, the rules of their design were established and the optimal triplex‐forming oligonucleotides were selected. These oligonucleotides show high affinity towards a 16 bp homopurine model sequence from the HIV‐1 genome; dissociation constants as low as 160 nM are observed whereas the unmodified TFO does not show any triplex formation and instead forms an intermolecular G‐quadruplex with Tm exceeding 90 °C in the presence of 50 mM NaCl. Here we present a set of rules that help to reach the full potential of TINA‐TFOs and demonstrate the effect of TINA on the formation and stability of triple helical DNA. 相似文献
8.
Peptide Nucleic Acid Conjugated with Ruthenium‐Complex Stabilizing Double‐Duplex Invasion Complex Even under Physiological Conditions
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Masaki Hibino Dr. Yuichiro Aiba Prof. Dr. Yoshihito Watanabe Dr. Osami Shoji 《Chembiochem : a European journal of chemical biology》2018,19(15):1601-1604
Peptide nucleic acid (PNA) can form a stable duplex with DNA, and, accordingly, directly recognize double‐stranded DNA through the formation of a double‐duplex invasion complex, wherein a pair of complementary PNA strands form two PNA/DNA duplexes. Because invasion does not require prior denaturation of DNA, PNA holds great potential for in cellulo or in vivo applications. To broaden the applicability of PNA invasion, we developed a new conjugate of PNA with a ruthenium complex. This Ru–PNA conjugate exhibits higher DNA‐binding affinity, which results in enhanced invasion efficiency, even under physiological conditions. 相似文献
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Balayeshwanth R. Vummidi Dr. Jawad Alzeer Prof. Dr. Nathan W. Luedtke 《Chembiochem : a European journal of chemical biology》2013,14(5):540-558
Mounting evidence supports the presence of biologically relevant G‐quadruplexes in single‐cell organisms, but the existence of endogenous G‐quadruplex structures in mammalian cells remains highly controversial. This is due, in part, to the common misconception that DNA and RNA molecules are passive information carriers with relatively little structural or functional complexity. For those working in the field, however, the lack of available tools for characterizing DNA structures in vivo remains a major limitation to addressing fundamental questions about structure–function relationships of nucleic acids. In this review, we present progress towards the direct detection of G‐quadruplex structures by using small molecules and modified oligonucleotides as fluorescent probes. While most development has focused on cell‐permeable probes that selectively bind to G‐quadruplex structures with high affinity, these same probes can induce G‐quadruplex folding, thereby making the native conformation of the DNA or RNA molecule (i.e., in the absence of probe) uncertain. For this reason, modified oligonucleotides and fluorescent base analogues that serve as “internal” fluorescent probes are presented as an orthogonal means for detecting conformational changes, without necessarily perturbing the equilibria between G‐quadruplex, single‐stranded, and duplex DNA. The major challenges and motivation for the development of fluorescent probes for G‐quadruplex structures are presented, along with a summary of the key photophysical, biophysical, and biological properties of reported examples. 相似文献
11.
Looking for Efficient G‐Quadruplex Ligands: Evidence for Selective Stabilizing Properties and Telomere Damage by Drug‐Like Molecules
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Dr. Bruno Pagano Dr. Jussara Amato Nunzia Iaccarino Dr. Chiara Cingolani Dr. Pasquale Zizza Dr. Annamaria Biroccio Prof. Ettore Novellino Prof. Antonio Randazzo 《ChemMedChem》2015,10(4):640-649
There is currently significant interest in the development of G‐quadruplex‐interactive compounds, given the relationship between the ability to stabilize these non‐canonical DNA structures and anticancer activity. In this study, a set of biophysical assays was applied to evaluate the binding of six drug‐like ligands to DNA G‐quadruplexes with different folding topologies. Interestingly, two of the investigated ligands showed selective G‐quadruplex‐stabilizing properties and biological activity. These compounds may represent useful leads for the development of more potent and selective ligands. 相似文献
12.
Fluorescent Dansyl‐Guanosine Conjugates that Bind c‐MYC Promoter G‐Quadruplex and Downregulate c‐MYC Expression
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Y. Pavan Kumar Puja Saha Dhurjhoti Saha Irene Bessi Prof. Dr. Harald Schwalbe Dr. Shantanu Chowdhury Prof. Dr. Jyotirmayee Dash 《Chembiochem : a European journal of chemical biology》2016,17(5):388-393
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Samwel K. Cheruiyot Dr. Eriks Rozners 《Chembiochem : a European journal of chemical biology》2016,17(16):1558-1562
Development of new fluorescent peptide nucleic acids (PNAs) is important for fundamental research and practical applications. The goal of this study was the design of fluorogenic nucleobases for incorporation in triplex‐forming PNAs. The underlying design principle was the use of a protonation event that accompanied binding of a 2‐aminopyridine (M) nucleobase to a G‐C base pair as an on switch for a fluorescence signal. Two fluorogenic nucleobases, 3‐(1‐phenylethynyl)‐M and phenylpyrrolo‐M, were designed, synthesized and studied. The new M derivatives provided modest enhancement of fluorescence upon protonation but showed reduced RNA binding affinity and quenching of fluorescence signal upon triple‐helix formation with cognate double‐stranded RNA. Our study illustrates the principal challenges of design and provides guidelines for future improvement of fluorogenic PNA nucleobases. The 3‐(1‐phenylethynyl)‐M may be used as a fluorescent nucleobase to study PNA–RNA triple‐helix formation. 相似文献
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Andrea Funke Beatrice Karg Dr. Jonathan Dickerhoff Dr. Darko Balke Prof. Dr. Sabine Müller Prof. Dr. Klaus Weisz 《Chembiochem : a European journal of chemical biology》2018,19(5):505-512
Binding of an indoloquinoline derivative with an aminoalkyl side chain to a truncated sequence from the MYC promoter region was studied through isothermal titration calorimetry (ITC). The targeted MYC3 sequence lacks 3′‐flanking nucleotides and forms a monomeric parallel quadruplex (G4) with a blunt‐ended 3′‐outer tetrad under the solution conditions employed. Analysis of ITC isotherms reveals multiple binding equilibria with the initial formation of a 1:2 ligand/quadruplex complex. Evaluation of electrophoretic mobilities as well as NMR spectral data confirm ligand‐induced dimerization of MYC3 quadruplexes with the ligand sandwiched between the two 3′‐outer tetrads. Additional ligand molecules in excess bind to the 5′‐outer tetrads of the sandwich complex. Such a ligand‐promoted G4 dimerization may be exploited for the controlled assembly or disassembly of G4 aggregates to expand on present quadruplex‐based technologies. 相似文献
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Dr. Jonathan Dickerhoff Prof. Dr. Klaus Weisz 《Chembiochem : a European journal of chemical biology》2018,19(9):927-930
A (3+1)‐hybrid‐type G‐quadruplex was substituted within its central tetrad by a single 2′‐fluoro‐modified guanosine. Driven by the anti‐favoring nucleoside analogue, a novel quadruplex fold with inversion of a single G‐tract and conversion of a propeller loop into a lateral loop emerges. In addition, scalar couplings across hydrogen bonds demonstrate the formation of intra‐ and inter‐residual F ??? H8?C8 pseudo‐hydrogen bonds within the modified quadruplexes. Alternative folding can be rationalized by the impact of fluorine on intermediate species on the basis of a kinetic partitioning mechanism. Apparently, chemical or other environmental perturbations are able to redirect folding of a quadruplex, possibly modulating its regulatory role in physiological processes. 相似文献
16.
Development of Fluorescent Protein Probes Specific for Parallel DNA and RNA G‐Quadruplexes
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Dr. Dung Thanh Dang Prof. Dr. Anh Tuân Phan 《Chembiochem : a European journal of chemical biology》2016,17(1):42-45
We have developed fluorescent protein probes specific for parallel G‐quadruplexes by attaching cyan fluorescent protein to the G‐quadruplex‐binding motif of the RNA helicase RHAU. Fluorescent probes containing RHAU peptide fragments of different lengths were constructed, and their binding to G‐quadruplexes was characterized. The selective recognition and discrimination of G‐quadruplex topologies by the fluorescent protein probes was easily detected by the naked eye or by conventional gel imaging. 相似文献
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Effect of ATRX and G‐Quadruplex Formation by the VNTR Sequence on α‐Globin Gene Expression
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Yue Li Dr. Junetha Syed Dr. Yuki Suzuki Sefan Asamitsu Dr. Norifumi Shioda Dr. Takahito Wada Prof. Hiroshi Sugiyama 《Chembiochem : a European journal of chemical biology》2016,17(10):928-935
ATR‐X (α‐thalassemia/mental retardation X‐linked) syndrome is caused by mutations in chromatin remodeler ATRX. ATRX can bind the variable number of tandem repeats (VNTR) sequence in the promoter region of the α‐globin gene cluster. The VNTR sequence, which contains the potential G‐quadruplex‐forming sequence CGC(GGGGCGGGG)n, is involved in the downregulation of α‐globin expression. We investigated G‐quadruplex and i‐motif formation in single‐stranded DNA and long double‐stranded DNA. The promoter region without the VNTR sequence showed approximately twofold higher luciferase activity than the promoter region harboring the VNTR sequence. G‐quadruplex stabilizers hemin and TMPyP4 reduced the luciferase activity, whereas expression of ATRX led to a recovery in reporter activity. Our results demonstrate that stable G‐quadruplex formation by the VNTR sequence downregulates the expression of α‐globin genes and that ATRX might bind to and resolve the G‐quadruplex. 相似文献
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We have fabricated a DNA-based nanofiber created by self-assembly of guanine quadruplex (Hoogsteen base pairing) and double-stranded DNA (Watson-Crick base pairing). When duplexes containing a long stretch of contiguous guanines and single-stranded overhangs are incubated in potassium-containing buffer, the preformed duplexes create high molecular weight species that contain quadruplexes. In addition to observation of these larger species by gel electrophoresis, solutions were analyzed by atomic force microscopy to reveal nanofibers. Analysis of the atomic force microscopy images indicates that fibers form with lengths ranging from 250 to 2,000 nm and heights from 0.45 to 4.0 nm. This work is a first step toward the creation of new structurally heterogeneous (quadruplex/duplex), yet controllable, DNA-based materials exhibiting novel properties suitable for a diverse array of nanotechnology applications. 相似文献
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Molecular Recognition of Parallel DNA Quadruplex d(TTAGGGT)4 by Mitoxantrone: Binding with 1:2 Stoichiometry Leading to Thermal Stabilization and Telomerase Inhibition
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Sweta Tripathi Tarikere Palakshan Pradeep Dr. Ritu Barthwal 《Chembiochem : a European journal of chemical biology》2016,17(7):554-560
The interaction of the anthraquinone derivative mitoxantrone, a semisynthetic anti‐cancer drug with two non‐planar side chains, with heptamer G‐quadruplex d(TTAGGGT)4, which contains the human telomere DNA sequence, was evaluated by differential scanning calorimetry, fluorescence Job plotting, absorption, and NMR and CD spectroscopy. Binding led to thermal stabilization of DNA (ΔTm=13–20 °C). The spectra revealed that two mitoxantrone molecules bind externally at two sites of the DNA quadruplex as monomers, by partial insertion of the chromophore and side‐chain interaction at the grooves. The inhibition of telomerase (IC50=2 μm), as determined by a TRAP assay, can be attributed to thermal stabilization of the DNA quadruplex because of the interactions with mitoxantrone. The studies revealed highly specific molecular recognition between a ligand and a parallel‐stranded G‐quadruplex; this might serve as a platform for the rational design of new drugs. 相似文献
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Nina Hüsken Magdalena Gębala Wolfgang Schuhmann Prof. Dr. Nils Metzler‐Nolte Prof. Dr. 《Chembiochem : a European journal of chemical biology》2010,11(12):1754-1761
A Fc–PNA biosensor (Fc: ferrocenyl, C10H9Fe) was designed by using two electrochemically distinguishable recognition elements with different molecular information at a single electrode. Two Fc–PNA capture probes were therefore synthesized by N‐terminal labeling different dodecamer PNA sequences with different ferrocene derivatives by click chemistry. Each of the two strands was thereby tethered with one specific ferrocene derivative. The two capture probes revealed quasi‐reversible redox processes of the Fc0/+ redox couple with a significant difference in their electrochemical half‐wave potentials of ΔE1/2=160 mV. A carefully designed biosensor interface, consisting of a ternary self‐assembled monolayer (SAM) of the two C‐terminal cysteine‐tethered Fc–PNA capture probes and 6‐mercaptohexanol, was electrochemically investigated by square wave (SWV) and cyclic voltammetry (CV). The biosensor properties of this interface were analyzed by studying the interaction with DNA sequences that were complementary to either of the two capture probes by SWV. Based on distinct changes in both peak current and potential, a parallel identification of these two DNA sequences was successful with one interface design. Moreover, the primary electrochemical response could be converted by a simple mathematical analysis into a clear‐cut electrochemical signal about the hybridization event. The discrimination of single‐nucleotide polymorphism (SNP) was proven with a chosen single‐mismatch DNA sequence. Furthermore, experiments with crude bacterial RNA confirm the principal suitability of this dual‐potential sensor under real‐life conditions. 相似文献