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https://www.readbyqxmd.com/read/29161777/structure-based-design-and-evaluation-of-synthetic-porphyrin-derivatives-as-g-quadruplex-stabilizing-anticancer-agents
#1
R N Bhadane, D B Meshram, R M Gilhotra
G-quadruplex structures formed in telomeres and proto-oncogene represent a potentially useful target for anticancer drugs. Stabilization of this arrangement may inhibit the further action of different enzymes involved in cancer cell immortalization. In present work structure based drug design and synthesis was carried out on series of meso-substituted porphyrin analogues. The interaction of porphyrin derivatives with G-quadruplex DNA has been explored by virtual screening procedure. Some of the potential binding agents were then synthesized and evaluated in-vitro by MTT and PCR stop assay...
November 2017: Journal of Experimental Therapeutics & Oncology
https://www.readbyqxmd.com/read/29158004/probing-the-interaction-of-copper-cofactor-and-azachalcone-substrate-with-g-quadruplex-of-dna-based-diels-alderase-by-site-specific-fluorescence-quenching-titration
#2
Mingpan Cheng, Jingya Hao, Yinghao Li, Yu Cheng, Guoqing Jia, Jun Zhou, Can Li
DNAzymes have been widely used in biosensors, asymmetric synthesis and pharmaceuticals. Typically, metal cofactor and substrate interact with DNA by supramolecular interactions in DNAzyme based asymmetric catalysis. However, binding positions of cofactor and substrate with DNA scaffold are not well understood, which is an obstacle to reveal the assembly and catalysis mechanisms of DNAzyme. Herein, we report a method of site-specific fluorescence quenching titration to elucidate the assembly and catalysis processes of a G-quadruplex based Diels-Alderase DNAzyme...
November 17, 2017: Biochimie
https://www.readbyqxmd.com/read/29156002/specific-g-quadruplex-ligands-modulate-the-alternative-splicing-of-bcl-x
#3
Carika Weldon, Justine G Dacanay, Vijay Gokhale, Peda Venkat L Boddupally, Isabelle Behm-Ansmant, Glenn A Burley, Christiane Branlant, Laurence H Hurley, Cyril Dominguez, Ian C Eperon
Sequences with the potential to form RNA G-quadruplexes (G4s) are common in mammalian introns, especially in the proximity of the 5' splice site (5'SS). However, the difficulty of demonstrating that G4s form in pre-mRNA in functional conditions has meant that little is known about their effects or mechanisms of action. We have shown previously that two G4s form in Bcl-X pre-mRNA, one close to each of the two alternative 5'SS. If these G4s affect splicing but are in competition with other RNA structures or RNA binding proteins, then ligands that stabilize them would increase the proportion of Bcl-X pre-mRNA molecules in which either or both G4s had formed, shifting Bcl-X splicing...
November 16, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/29151259/exat-excitonic-analysis-tool
#4
Sandro Jurinovich, Lorenzo Cupellini, Ciro A Guido, Benedetta Mennucci
We introduce EXcitonic Analysis Tool (EXAT), a program able to compute optical spectra of large excitonic systems directly from the output of quantum mechanical calculations performed with the popular Gaussian 16 package. The software is able to combine in an excitonic scheme the single-chromophore properties and exciton couplings to simulate energies, coefficients, and excitonic spectra (UV-vis, CD, and LD). The effect of the environment can also be included using a Polarizable Continuum Model. EXAT also presents a simple graphical user interface, which shows on-screen both site and exciton properties...
November 19, 2017: Journal of Computational Chemistry
https://www.readbyqxmd.com/read/29149989/low-background-and-visual-detection-of-antibiotic-based-on-target-activated-colorimetric-split-peroxidase-dnazyme-coupled-with-dual-nicking-enzyme-signal-amplification
#5
REVIEW
Xuejun Cui, Rongguo Li, Xiaofei Liu, Jingfeng Wang, Xueqi Leng, Xiaolei Song, Qianqian Pei, Yu Wang, Su Liu, Jiadong Huang
Herein, we have reported the development of a simple, rapid, and low cost colorimetric method for the detection of antibiotic based on target-activated split peroxidase DNAzyme coupled with dual nicking enzyme signal amplification (NESA). To lower background signal in G-quadruplex DNAzyme-based detection, the two split G-rich parts are caged into two different hairpin probes, respectively, preventing the two parts from assembling into the G-quadruplex structure. By the combination of restriction endonuclease-assisted cleavage reaction with the spilt G-quadruplex probes, target-modulated release of the two split G-rich parts is achieved, affording high specificity of antibiotic detection...
January 2, 2018: Analytica Chimica Acta
https://www.readbyqxmd.com/read/29149833/g4-interacting-dna-helicases-and-polymerases-potential-therapeutic-targets
#6
Katrina Estep, Thomas J Butler, Jun Ding, Robert M Brosh
Guanine-rich DNA can fold into highly stable non-canonical four-stranded DNA structures called G-quadruplexes. These structures present obstacles for the DNA replication machinery, and it has been hypothesized that both eukaryotic DNA helicases and polymerases have evolved to resolve G4 DNA in vivo. Since the discovery of G-quadruplex DNA in the early 1960's, a number of studies have emerged reporting G-quadruplex DNA unfolding by helicase enzymes and DNA synthesis past G4 by specialized translesion polymerase enzymes...
November 16, 2017: Current Medicinal Chemistry
https://www.readbyqxmd.com/read/29149495/a-redox-activated-g-quadruplex-dna-binder-based-on-a-platinum-iv-salphen-complex
#7
Ramon Vilar, Stephane Bandeira, Jorge Gonzalez Garcia, Evangelina Pensa, Tim Albrecht
There has been increasing interest in the development of small molecules that can selectively bind to G-quadruplex DNA structures. The latter have been associated to a number of key biological processes and therefore are proposed to be potential targets for drug development. In this paper we report the first example of a reduction-activated G-quadruplex DNA binder. We show that a new octahedral platinum(IV)-salphen complex does not interact with DNA in aqueous media at pH 7.4; however, upon addition of bio-reductants such as ascorbic acid or glutathione, the compound readily reduces to the corresponding square planar platinum(II) complex...
November 17, 2017: Angewandte Chemie
https://www.readbyqxmd.com/read/29149299/twj-screen-an-isothermal-screening-assay-to-assess-ligand-dna-junction-interactions-in-vitro
#8
Ludivine Guyon, Marc Pirrotta, Katerina Duskova, Anton Granzhan, Marie-Paule Teulade-Fichou, David Monchaud
The quest for chemicals able to operate at selected genomic loci in a spatiotemporally controlled manner is desirable to create manageable DNA damages. Mounting evidence now shows that alternative DNA structures, including G-quadruplexes and branched DNA (or DNA junctions), might hamper proper progression of replication fork, thus triggering DNA damages and genomic instability. Therefore, small molecules that stabilize these DNA structures are currently scrutinized as a promising way to create genomic defects that cannot be dealt with properly by cancer cells...
November 15, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/29148817/specific-recognition-of-g-quadruplexes-over-duplex-dna-by-a-macromolecular-nir-two-photon-fluorescent-probe
#9
Marco Deiana, Bastien Mettra, Lara Martinez-Fernandez, Leszek Mateusz Mazur, Krzysztof Pawlik, Chantal Andraud, Marek Samoc, Roberto Improta, Cyrille Monnereau, Katarzyna Matczyszyn
The implication of guanine-rich DNA sequences in biologically important roles such as telomerase dysfunction and the regulation of gene expression has prompted the search for structure-specific G-quadruplex agents for targeted diagnostic and therapeutic applications. To date, the number of two-photon absorbing fluorogenic dyes with intrinsically large two-photon absorption (TPA) cross-section (σ2) and quantum yield (φf), capable of specific detection of G-motifs over duplex DNAs is still limited. Herein, we report on a NIR two-photon poly(cationic) anthracene-based macromolecule able to selectively target G-quadruplexes (G4s) over genomic double-stranded DNA...
November 17, 2017: Journal of Physical Chemistry Letters
https://www.readbyqxmd.com/read/29148767/role-of-the-benzodioxole-group-in-the-interactions-between-the-natural-alkaloids-chelerythrine-and-coptisine-and-the-human-telomeric-g-quadruplex-dna-a-multiapproach-investigation
#10
F Papi, M Ferraroni, R Rigo, S Da Ros, C Bazzicalupi, C Sissi, P Gratteri
The binding properties toward the human telomeric G-quadruplex of the two natural alkaloids coptisine and chelerythrine were studied using spectroscopic techniques, molecular modeling, and X-ray diffraction analysis. The results were compared with reported data for the parent compounds berberine and sanguinarine. Spectroscopic studies showed modest, but different rearrangements of the DNA-ligand complexes, which can be explained considering particular stereochemical features for these alkaloids, in spite of the similarity of their skeletons...
November 17, 2017: Journal of Natural Products
https://www.readbyqxmd.com/read/29145502/hi-fidelity-discrimination-of-isomirs-using-g-quadruplex-gatekeepers
#11
Nianjia Seow, Renzo A Fenati, Ashley R Connolly, Amanda V Ellis
Core microRNA (miRNA) sequences exist as populations of variants called isomiRs made up of different lengths and nucleotide compositions. In particular, the short sequences of miRNA make single-base isomiR mismatches very difficult to be discriminated. Non-specific hybridizations often arise when DNA probe-miRNA target hybridization is the primary, or initial, mode of detection. These errors then become exacerbated through subsequent amplification steps. Here, we present the design of DNA probes modified with poly-guanine (PG) tracts that were induced to form G-quadruplexes (G4) for hi-fidelity discrimination of miRNA core target sequence from single-base mismatched isomiRs...
2017: PloS One
https://www.readbyqxmd.com/read/29144554/a-sensitive-colorimetric-dna-biosensor-for-specific-detection-of-the-hbv-gene-based-on-silver-coated-glass-slide-and-g-quadruplex-hemin-dnazyme
#12
Yubin Li, Sheng Liu, Qiujuan Deng, Liansheng Ling
A sensitive colorimetric DNA biosensor for specific detection of single stranded oligonucleotide (ssDNA) is proposed in this paper. The biosensor is based on silver-coated glass (SCGS) and G-quadruplex-hemin DNAzyme. Capture DNA is immobilized on the surface of SCGS by Ag-S bond. Signal DNA can be used to hybridize with the target DNA which is selected from the Hepatitis B virus(HBV) gene as target HBV DNA, and the HRP-mimicking G-quadruplex-hemin DNAzyme can be formed through the function of a guanine-rich fragment from signal DNA to catalyze the oxidation of 2,2-azinobis(3-ethylbenzothiozoline)-6-sulfonicacid (ABTS(2-) ) by H2 O2 ...
November 16, 2017: Journal of Medical Virology
https://www.readbyqxmd.com/read/29144399/dna-g-wire-formation-using-an-artificial-peptide-is-controlled-by-protease-activity
#13
Kenji Usui, Arisa Okada, Shungo Sakashita, Masayuki Shimooka, Takaaki Tsuruoka, Shu-Ichi Nakano, Daisuke Miyoshi, Tsukasa Mashima, Masato Katahira, Yoshio Hamada
The development of a switching system for guanine nanowire (G-wire) formation by external signals is important for nanobiotechnological applications. Here, we demonstrate a DNA nanostructural switch (G-wire <--> particles) using a designed peptide and a protease. The peptide consists of a PNA sequence for inducing DNA to form DNA-PNA hybrid G-quadruplex structures, and a protease substrate sequence acting as a switching module that is dependent on the activity of a particular protease. Micro-scale analyses via TEM and AFM showed that G-rich DNA alone forms G-wires in the presence of Ca(2+), and that the peptide disrupted this formation, resulting in the formation of particles...
November 16, 2017: Molecules: a Journal of Synthetic Chemistry and Natural Product Chemistry
https://www.readbyqxmd.com/read/29143069/hemin-g-quadruplex-horseradish-peroxidase-mimicking-dnazyme-principle-and-biosensing-application
#14
Negar Alizadeh, Abdollah Salimi, Rahman Hallaj
Enzymes are macromolecular biological catalysts that accelerate chemical reactions. Enzyme labels are commonly used to obtain signal amplification in sensors and biosensors on the basis of reactions of some enzymes such as horseradish peroxidase (HRP). However, use of natural enzymes can encounter some challenges. Lately, nucleic acids that exhibit catalytic properties have attracted growing interest because they have certain advantages in comparison with traditional protein enzymes. DNAzymes are DNA-based catalysts, representing an important class of functional DNA, which have been widely used because of their excellent activity, programmability, signal amplification through catalytic turnover, high chemical stability, simple synthesis, and easy modification...
November 16, 2017: Advances in Biochemical Engineering/biotechnology
https://www.readbyqxmd.com/read/29140695/rna-g-quadruplexes-in-kirsten-ras-kras-oncogene-as-targets-for-small-molecules-inhibiting-translation
#15
Giulia Miglietta, Susanna Cogoi, Jessica Marinello, Giovanni Capranico, Alexander S Tikhomirov, Andrey E Shchekotikhin, Luigi E Xodo
The human KRAS transcript contains a G-rich 5'-UTR sequence (77 % GC) harbouring several G4 motifs capable to form stable RNA G-quadruplex (RG4) structures that can serve as targets for small molecules. A biotin-streptavidin pull-down assay showed that 4,11-bis(2-aminoethylamino)anthra[2,3-b]furan-5,10-dione (2a) binds to RG4s in the KRAS transcript under low-abundance cellular conditions. Dual-luciferase assays demonstrated that 2a and its analogue 4,11-bis(2-aminoethylamino)anthra[2,3-b]thiophene-5,10-dione 2b) repress translation in a dose-dependent manner...
November 15, 2017: Journal of Medicinal Chemistry
https://www.readbyqxmd.com/read/29140681/orthogonal-operation-of-constitutional-dynamic-networks-consisting-of-dna-tweezer-machines
#16
Liang Yue, Shan Wang, Alessandro Cecconello, Jean-Marie Lehn, Itamar Willner
Overexpression or down-regulation of cellular processes are often controlled by dynamic chemical networks. Bioinspired by nature, we introduce constitutional dynamic networks (CDNs) as systems that emulate principle of the nature processes. The CDNs comprise of dynamically exchangeable equilibrated constituents that respond to external triggers by adapting the composition of the dynamic mixture to the energetic stabilization of the constituents. We introduce a nucleic acid-based CDN that includes four exchangeable and mechanically-triggered tweezers AA', BB', AB' and BA' existing in close, close, open and open configurations, respectively...
November 15, 2017: ACS Nano
https://www.readbyqxmd.com/read/29139578/structure-property-relationships-in-cuii-binding-tetramolecular-g-quadruplex-dna
#17
David M Engelhard, Lukas M Stratmann, Guido H Clever
A series of artificial metal-base tetrads composed of a CuII cation coordinating to four pyridines, covalently attached to the ends of tetramolecular G-quadruplex DNA strands [LA-Dd(G4)]4 (LA-D = ligand derivatives), was systematically studied. Structurally, the square-planar [Cu(pyridine)4] complex behaves analogous to the canonical guanine quartet. Copper coordination to all studied ligand derivatives was found to increase G-quadruplex thermodynamic stability, tolerating a great variety of ligand linker lengths (1 - 5 atoms) and thus demonstrating the robustness of the chosen ligand design...
November 15, 2017: Chemistry: a European Journal
https://www.readbyqxmd.com/read/29138008/g-quadruplex-structure-at-intron-2-of-tfe3-and-its-role-in-xp11-2-translocation-and-splicing
#18
Shiv Prakash Verma, Parimal Das
Transcription Factor E3 (TFE3) translocation is found in a group of different type of cancers and most of the translocations are located in the 5' region of TFE3 which may be considered as Breakpoint Region (BR). In our In silico study by QGRS mapper and non BdB web servers we found a Potential G-quadruplex forming Sequence (PQS) in the intron 2 of TFE3 gene. In vitro G-quadruplex formation was shown by native PAGE in presence of Pyridostatin(PDS), which with inter molecular secondary structure caused reduced mobility to migrate slower...
November 11, 2017: Biochimica et Biophysica Acta
https://www.readbyqxmd.com/read/29136926/simple-g-quadruplex-based-2-aminopurine-fluorescence-probe-for-highly-sensitive-and-amplified-detection-of-microrna-21
#19
Shiyu Li, Chan Liu, Hang Gong, Chunyan Chen, Xiaoming Chen, Changqun Cai
Based on 2-aminopurine (2-AP) probe in conjunction with a G-quadruplex structure and signal amplification technique, a simple and highly sensitive fluorescence sensor for detecting microRNA (miRNA) is developed for high signal-to-background ratio and wide linear range. The proposed sensor contains two hairpins DNA: H1 and H2. H1 is labeled by 2-AP incorporated into a G-rich sequence. Upon the addition of a target miRNA, H1 is unfolded and forms DNA/RNA complexes that contain a G-quadruplex, thereby significantly enhancing 2-AP fluorescence due to the protection provided by the G-quadruplex...
February 1, 2018: Talanta
https://www.readbyqxmd.com/read/29136853/electrochemical-strategy-for-pyrophosphatase-detection-based-on-the-peroxidase-like-activity-of-g-quadruplex-cu-2-dnazyme
#20
Yonghong Wang, Yaohui Wu, Wen Liu, Lei Chu, Zhibin Liao, Wentao Guo, Gao-Qiang Liu, Xiaoxiao He, Kemin Wang
A new simple and highly sensitive electrochemical method for pyrophosphatase (PPase) activity detection was developed based on the peroxidase-like activity of G-quadruplex-Cu(2+) DNAzyme. In the absence of PPase, Cu(2+) could coordinate with pyrophosphate (PPi) to form Cu(2+)-PPi compound. While in the presence of PPase, it could destroy the coordinate compound because PPase catalyzed the hydrolysis of PPi into inorganic phosphate and produced free Cu(2+), which then could be coupled with G-rich DNA to form G-quadruplex-Cu(2+) DNAzyme...
February 1, 2018: Talanta
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