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G quadruplex

Yevgen P Yurenko, Jan Novotný, Radek Marek
The topology and energetics of guanine (G) quadruplexes is governed by supramolecular interactions within their strands. In this work, we performed an extensive QM study of supramolecular interactions shaping the stems of (4+0) parallel (P) and (2+2) antiparallel (AP) systems. The large-scale (~ 400 atoms) models of P and AP were constructed from high-quality experimental structures. The results evidence that each of the P and AP structures is shaped by a distinct network of supramolecular interactions. The analysis of electron topological characteristics of H-bonds in P and AP systems indicates that the P model benefits from the stronger intra-tetrad H-bonding...
February 22, 2017: Chemistry: a European Journal
Robert Hänsel-Hertsch, Marco Di Antonio, Shankar Balasubramanian
Single-stranded guanine-rich DNA sequences can fold into four-stranded DNA structures called G-quadruplexes (G4s) that arise from the self-stacking of two or more guanine quartets. There has been considerable recent progress in the detection and mapping of G4 structures in the human genome and in biologically relevant contexts. These advancements, many of which align with predictions made previously in computational studies, provide important new insights into the functions of G4 structures in, for example, the regulation of transcription and genome stability, and uncover their potential relevance for cancer therapy...
February 22, 2017: Nature Reviews. Molecular Cell Biology
Marko Ivancich, Zachary Schrank, Luke Wojdyla, Brandon Leviskas, Adijan Kuckovic, Ankita Sanjali, Neelu Puri
Telomerase is expressed in more than 85% of cancer cells. Tumor cells with metastatic potential may have a high telomerase activity, allowing cells to escape from the inhibition of cell proliferation due to shortened telomeres. Human telomerase primarily consists of two main components: hTERT, a catalytic subunit, and hTR, an RNA template whose sequence is complimentary to the telomeric 5'-dTTAGGG-3' repeat. In humans, telomerase activity is typically restricted to renewing tissues, such as germ cells and stem cells, and is generally absent in normal cells...
February 19, 2017: Antioxidants (Basel, Switzerland)
Hong Xu, Marco Di Antonio, Steven McKinney, Veena Mathew, Brandon Ho, Nigel J O'Neil, Nancy Dos Santos, Jennifer Silvester, Vivien Wei, Jessica Garcia, Farhia Kabeer, Daniel Lai, Priscilla Soriano, Judit Banáth, Derek S Chiu, Damian Yap, Daniel D Le, Frank B Ye, Anni Zhang, Kelsie Thu, John Soong, Shu-Chuan Lin, Angela Hsin Chin Tsai, Tomo Osako, Teresa Algara, Darren N Saunders, Jason Wong, Jian Xian, Marcel B Bally, James D Brenton, Grant W Brown, Sohrab P Shah, David Cescon, Tak W Mak, Carlos Caldas, Peter C Stirling, Phil Hieter, Shankar Balasubramanian, Samuel Aparicio
G-quadruplex DNAs form four-stranded helical structures and are proposed to play key roles in different cellular processes. Targeting G-quadruplex DNAs for cancer treatment is a very promising prospect. Here, we show that CX-5461 is a G-quadruplex stabilizer, with specific toxicity against BRCA deficiencies in cancer cells and polyclonal patient-derived xenograft models, including tumours resistant to PARP inhibition. Exposure to CX-5461, and its related drug CX-3543, blocks replication forks and induces ssDNA gaps or breaks...
February 17, 2017: Nature Communications
Zhuoliang Liu, Xingyu Luo, Zhu Li, Yan Huang, Zhou Nie, Hong-Hui Wang, Shouzhuo Yao
Fluorogenic probes targeting G-quadruplex structures have emerged as the promising toolkit for functional research of G-quadruplex and biosensor development. However, their biosensing applications are still largely limited in in-tube detection. Herein, we proposed a fluorescent bioimaging method based on enzyme-generated G-quadruplexes for detecting apoptotic cells at the cell and tissue level, namely, terminal deoxynucleotidyl transferase (TdT)-activated de novo G-quadruplex synthesis (TAGS) assay. The detection target is genomic DNA fragmentation, a biochemical hallmark of apoptosis...
February 7, 2017: Analytical Chemistry
Ramon Vilar, Chun-Qiong Zhou, Ting-Cong Liao, Zi-Qi Li, Jorge Gonzalez-Garcia, Matthew Reynolds, Min Zou
Three new polyether-tethered di-nickel-salphen complexes (2a-c) have been synthesized and fully characterized by NMR spectroscopy, mass spectrometry and elemental analyses. The binding affinity and selectivity of these complexes and of the parent mono-nickel complex (1) towards dimeric quadruplex DNA have been determined by UV-Vis titrations, fluorescence spectroscopy, CD spectroscopy and electrophoresis. These studies have shown that the di-nickel-salphen complex with the longest polyether linker (2c) has higher binding affinity and selectivity towards dimeric quadruplexes (over monomeric quadruplexes) than the di-nickel-salphen complexes with the shorter polyether linkers (2a and 2b)...
February 16, 2017: Chemistry: a European Journal
Alyssa B Chinen, Chenxia M Guan, Caroline H Ko, Chad A Mirkin
The effect of serum protein adsorption on the biological fate of Spherical Nucleic Acids (SNAs) is investigated. Through a proteomic analysis, it is shown that G-quadruplexes templated on the surface of a gold nanoparticle in the form of SNAs mediate the formation of a protein corona that is rich in complement proteins relative to SNAs composed of poly-thymine (poly-T) DNA. Cellular uptake studies show that complement receptors on macrophage cells recognize the SNA protein corona, facilitating their internalization, and causing G-rich SNAs to accumulate in the liver and spleen more than poly-T SNAs in vivo...
February 14, 2017: Small
George Koutsoudakis, Alexia Paris de León, Carolina Herrera, Marcus Dorner, Gemma Pérez-Vilaró, Sébastien Lyonnais, Santiago Grijalvo, Ramon Eritja, Andreas Meyerhans, Gilles Mirambeau, Juana Díez
An HCV epidemic affecting HIV-infected men who have sex with men (MSM) is expanding worldwide. Albeit the improved cure rates obtained with the new direct-acting antiviral drug (DAA) combinations, the high rate of reinfection within this population calls urgently for novel preventive interventions. Here we show in cell culture and ex vivo experiments with human colorectal tissue that lipoquads, G-quadruplex DNA structures fused to cholesterol, are efficient HCV pangenotypic entry and cell-to-cell transmission inhibitors...
February 13, 2017: Antimicrobial Agents and Chemotherapy
Xingping Zhang, Baomiao Ding, Huawei Wu, Jiujun Wang, Hualin Yang
In the present work, a simple design of "turn-on" fluorescence method for mercury ion was developed and explored based on specific T-Hg-T mismatches as a recognizer and N-methyl mesoporphyrin IX (NMM)/G-quadruplex DNA system as a reporter. The titration experiment showed that the mercury-ion concentration and the fluorescence intensity signal change exhibited a consistent linear correlation within the 50 to 500 nM range with a detection limit down to 12.9 nM. In a selectivity experiment, our method showed obvious selectivity against other metal ions, being consistent with other reported detection methods of mercury ion based on the specific reactivity of T-Hg-T mismatches...
2017: Analytical Sciences: the International Journal of the Japan Society for Analytical Chemistry
Hualin Yang, Qinghua Wu, Dongxiao Su, Yun Wang, Li Li, Xingping Zhang
In the present work, a simple design of a "label-free" fluorescence method for kanamycin was developed and explored based on a specific DNA aptamer as a recognizer and a NMM/G-quadruplex DNA system as a reporter. The titration experiment showed a linear detection range of 0.5 to 100 nM with a low detection limit of 0.5 nM. It also showed excellent selectivity in a selectivity experiment. It was then successfully employed to detect kanamycin in milk with a excellent reliability.
2017: Analytical Sciences: the International Journal of the Japan Society for Analytical Chemistry
Shuntaro Takahashi, Naoki Sugimoto
DNA guanine-quadruplexes (G-quadruplexes) are unique DNA structures formed by guanine-rich sequences. The loop regions of G-quadruplexes play key roles in stability and topology of G-quadruplexes. Here, we investigated volumetric changes induced by pressure in the folding of the G-quadruplex formed by the thrombin binding aptamer (TBA) with mutations within the loop regions. The change of partial molar volume in the transition from coil to G-quadruplex, ∆Vtr, of TBA with a mutation from T to A in the 5' most loop (TBA T3A) was 75...
February 6, 2017: Biophysical Chemistry
Paul E Reyes-Gutiérrez, Tomáš Kapal, Blanka Klepetářová, David Šaman, Radek Pohl, Zbigniew Zawada, Erika Kužmová, Miroslav Hájek, Filip Teplý
No abstract text is available yet for this article.
February 9, 2017: Scientific Reports
Hong-Liang Bao, Takumi Ishizuka, Takashi Sakamoto, Kenzo Fujimoto, Tamayo Uechi, Naoya Kenmochi, Yan Xu
No abstract text is available yet for this article.
February 9, 2017: Nucleic Acids Research
Chao-Da Xiao, Takumi Ishizuka, Xiao-Qing Zhu, Yue Li, Hiroshi Sugiyama, Yan Xu
Human telomeric RNA performs various cellular functions such as telomere length regulation, heterochromatin formation, and chromosome end protection. Using a combination of nuclear magnetic reso-nance (NMR), circular dichroism (CD), and gel electro-phoresis, we observed an unusual topological structure formed by human telomere RNA r(GUUAGGGU). Our results showed that every set of four strands formed a parallel G-quadruplex as symmetry-related units con-taining four G-tetrads, two U-tetrads, and one A-tetrad...
February 8, 2017: Journal of the American Chemical Society
Asfa Ali, Mohini Kamra, Soma Roy, K Muniyappa, Santanu Bhattacharya
Metal based salen complexes have been considered as an important scaffold toward targeting of DNA structures. In the present work, we have synthesized nickel(II) and palladium(II) salen and salphen complexes by using readily available fluorescein as the backbone to provide an extended aromatic surface. The metal complexes exhibit affinity toward the human telomeric G-quadruplex DNA with promising inhibition of telomerase activity. This has been ascertained by their efficiency in the long term cell proliferation assay which showed significant cancer cell toxicity in the presence of the metal complexes...
February 6, 2017: Bioconjugate Chemistry
Yang Yun Li, David N Dubins, Dianna My Nhi Thi Le, Karen Leung, Robert B Macgregor
In aqueous solutions containing sodium or potassium cations, oligodeoxyribonucleotides (ODNs) rich in guanine form four-stranded DNA structures called G-quadruplexes (G4s). These structures are destabilized by elevated hydrostatic pressure. Here, we use pressure to investigate the volumetric changes arising from the formation of G4 structures. G4s display a great deal of structural heterogeneity that depends on the stabilizing cation as well as the oligonucleotide sequence. Using UV thermal unfolding at different pressures, we have investigated the volume change of the helix-coil equilibrium of a series of ODNs whose sequences are related to the G-rich ODN HTel (d[A(GGGTTA)3GGG]), which contains four repeats of the human telomeric sequence...
January 6, 2017: Biophysical Chemistry
Andrea Milelli, Chiara Marchetti, Maria Laura Greco, Federica Moraca, Giosuè Costa, Eleonora Turrini, Elena Catanzaro, Nibal Betari, Cinzia Calcabrini, Claudia Sissi, Stefano Alcaro, Carmela Fimognari, Vincenzo Tumiatti, Anna Minarini
Naphthalene diimides (NDIs) have been widely used as scaffold to design DNA-directed agents able to target peculiar DNA secondary arrangements endowed with relevant biochemical roles. Recently, we have reported disubstituted linear- and macrocyclic-NDIs that bind telomeric and non-telomeric G-quadruplex with high degree of affinity and selectivity. Herein, the synthesis, biological evaluation and molecular modelling studies of a series of asymmetrically substituted NDIs are reported. Among these, compound 9 emerges as the most interesting of the series being able to bind telomeric G-quadruplex (ΔTm = 29 °C at 2...
January 22, 2017: European Journal of Medicinal Chemistry
Hengzhi Zhao, Qiang Liu, Mei Liu, Yan Jin, Baoxin Li
T4 polynucleotide kinase phosphatase (T4 PNKP) is a bifunctional tool enzyme with 5'-kinase and 3'-phosphatase activities. Considering its important roles in the repair of strand breaks, assay of T4 PNKP activity is of great importance. In this work, we proposed a novel label-free sensing strategy for T4 PNKP activity based on G-quadruplexe-thioflavin T fluorescent indicator. In the assay, we used a single stranded oligonucleotide with 3'-phosphoryl and 5'-phosphoryl ends as enzyme substrate. Upon the addition of T4 PNKP, the 3'-PO3 of the substrate was changed to 3'-OH which initiated the polymerization in the presence of terminal deoxynucleotidyl transferase and G-rich dNTP substrates...
April 1, 2017: Talanta
Tianyu Hu, Weidan Na, Xu Yan, Xingguang Su
We have developed a near-infrared (NIR) fluorescent aptamer-based sensor for sensitive detection of adenosine-5'-triphosphate (ATP) by using a ATP-binding aptamer and β-Cyclodextrin-CuInS2 quantum dots (β-CD-CuInS2 QDs). The fluorescence of β-CD-CuInS2 QDs has a slight enhancement with the addition of ATP-binding aptamer due to the host-guest recognition between aptamer and β-CD. When ATP is added, it will bind to aptamer to form G-quadruplexes. Aptamer-ATP complexes can enter into the hydrophobic cavities of β-CD and result in great enhancement of the fluorescence intensity...
April 1, 2017: Talanta
Rakesh Naduvile Veedu, Lukas Aaldering, Vasanthanathan Poongavanam, Niels Langkjaer, Arul Murugan, Per Trolle Jørgensen, Jesper Wengel
Thrombin binding aptamer (TBA) that shows anticoagulant properties is one of the most studied G-quadruplex forming aptamers. In this study, we investigated the impact of different chemical modifications such as Spacer-C3, unlocked nucleic acid (UNA) and 3'-amine-modified UNA (amino-UNA) on the structural dynamics and stability of TBA. All three modifications were incorporated at three different loop positions (T3, T7 and T12) of the TBA G-quadruplex structure rendering a series of TBA variants and studied their stability by thermal denaturation studies, folding by circular dichroism spectroscopy and thrombin clotting time...
February 2, 2017: Chembiochem: a European Journal of Chemical Biology
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