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https://www.readbyqxmd.com/read/28276503/ultrasensitive-colorimetric-detection-of-circulating-tumor-dna-using-hybridization-chain-reaction-and-the-pivot-of-triplex-dna
#1
Ruimin Li, Li Zou, Yanwei Luo, Manjun Zhang, Liansheng Ling
This work presents an amplified colorimetric biosensor for circulating tumor DNA (ctDNA), which associates the hybridization chain reaction (HCR) amplification with G-Quadruplex DNAzymes activity through triplex DNA formation. In the presence of ctDNA, HCR occurs. The resulting HCR products are specially recognized by one sequence to include one GGG repeat and the other containing three GGG repeats, through the synergetic effect of triplex DNA and asymmetrically split G-Quadruplex forming. Such design takes advantage of the amplification property of HCR and the high peroxidase-like catalytic activity of asymmetrically split G-Quadruplex DNAzymes by means of triplex DNA formation, which produces color signals in the presence of ctDNA...
March 9, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28270074/molecular-and-thermodynamic-studies-on-dna-triplex-formed-in-the-promoter-region-of-hmgb1-gene-as-a-selective-target-for-anticancer-drugs
#2
Neelam Lohani, Rajeswari Raja Moganty
HMGB1 (High Mobility Group Box-1) is a very versatile highly abundant architectural protein that plays multiple roles in human health and diseases. Under physiological condition it serves an amazing assortment of roles in different compartments of cell. The reported high expression of HMGB1 in almost all types of human cancers and inflammatory diseases make it a critical molecular therapeutic target. In the present study we have mobilized a proximal twenty one bp nucleotide (21RY) which is in the promoter region (-55 to-75) of hmgb1 gene and targeted it with triplex forming oligonucleotide (TFO) in combination with two widely used chemotherapeutic drugs actinomycin (ACT) and adriamycin (ADM)...
February 13, 2017: Anti-cancer Agents in Medicinal Chemistry
https://www.readbyqxmd.com/read/28266759/bioinspired-helical-microfibers-from-microfluidics
#3
Yunru Yu, Fanfan Fu, Luoran Shang, Yao Cheng, Zhongze Gu, Yuanjin Zhao
Helical objects are among the most important and landmark structures in nature, and represent an emerging group of materials with unique spiral geometry; because of their enriched physical and chemical properties, they can have multiple functionalities. However, the fabrication of such complex helical materials at the micro- or nanoscale level remains a challenge. Here, a coaxial capillary microfluidic system, with the functions of consecutive spinning and spiraling, is presented for scalable generation of helical microfibers...
March 7, 2017: Advanced Materials
https://www.readbyqxmd.com/read/28248966/a-magnesium-induced-triplex-pre-organizes-the-sam-ii-riboswitch
#4
Susmita Roy, Heiko Lammert, Ryan L Hayes, Bin Chen, Regan LeBlanc, T Kwaku Dayie, José N Onuchic, Karissa Y Sanbonmatsu
Our 13C- and 1H-chemical exchange saturation transfer (CEST) experiments previously revealed a dynamic exchange between partially closed and open conformations of the SAM-II riboswitch in the absence of ligand. Here, all-atom structure-based molecular simulations, with the electrostatic effects of Manning counter-ion condensation and explicit magnesium ions are employed to calculate the folding free energy landscape of the SAM-II riboswitch. We use this analysis to predict that magnesium ions remodel the landscape, shifting the equilibrium away from the extended, partially unfolded state towards a compact, pre-organized conformation that resembles the ligand-bound state...
March 2017: PLoS Computational Biology
https://www.readbyqxmd.com/read/28248486/stimuli-responsive-dna-based-hydrogels-from-basic-principles-to-applications
#5
Jason S Kahn, Yuwei Hu, Itamar Willner
The base sequence of nucleic acids encodes structural and functional information into the DNA biopolymer. External stimuli such as metal ions, pH, light, or added nucleic acid fuel strands provide triggers to reversibly switch nucleic acid structures such as metal-ion-bridged duplexes, i-motifs, triplex nucleic acids, G-quadruplexes, or programmed double-stranded hybrids of oligonucleotides (DNA). The signal-triggered oligonucleotide structures have been broadly applied to develop switchable DNA nanostructures and DNA machines, and these stimuli-responsive assemblies provide functional scaffolds for the rapidly developing area of DNA nanotechnology...
March 1, 2017: Accounts of Chemical Research
https://www.readbyqxmd.com/read/28248374/ultra-fast-analog-to-digital-converter-based-on-a-nonlinear-triplexer-and-an-optical-coder-with-a-photonic-crystal-structure
#6
Farhad Mehdizadeh, Mohammad Soroosh, Hamed Alipour-Banaei, Ebrahim Farshidi
In this paper, we propose what we believe is a novel all-optical analog-to-digital converter (ADC) based on photonic crystals. The proposed structure is composed of a nonlinear triplexer and an optical coder. The nonlinear triplexer is for creating discrete levels in the continuous optical input signal, and the optical coder is for generating a 2-bit standard binary code out of the discrete levels coming from the nonlinear triplexer. Controlling the resonant mode of the resonant rings through optical intensity is the main objective and working mechanism of the proposed structure...
March 1, 2017: Applied Optics
https://www.readbyqxmd.com/read/28240889/correction-to-triplex-forming-peptide-nucleic-acid-probe-having-thiazole-orange-as-a-base-surrogate-for-fluorescence-sensing-of-double-stranded-rna
#7
Takaya Sato, Yusuke Sato, Seiichi Nishizawa
No abstract text is available yet for this article.
February 27, 2017: Journal of the American Chemical Society
https://www.readbyqxmd.com/read/28237796/permanganate-s1-nuclease-footprinting-reveals-non-b-dna-structures-with-regulatory-potential-across-a-mammalian-genome
#8
Fedor Kouzine, Damian Wojtowicz, Laura Baranello, Arito Yamane, Steevenson Nelson, Wolfgang Resch, Kyong-Rim Kieffer-Kwon, Craig J Benham, Rafael Casellas, Teresa M Przytycka, David Levens
DNA in cells is predominantly B-form double helix. Though certain DNA sequences in vitro may fold into other structures, such as triplex, left-handed Z form, or quadruplex DNA, the stability and prevalence of these structures in vivo are not known. Here, using computational analysis of sequence motifs, RNA polymerase II binding data, and genome-wide potassium permanganate-dependent nuclease footprinting data, we map thousands of putative non-B DNA sites at high resolution in mouse B cells. Computational analysis associates these non-B DNAs with particular structures and indicates that they form at locations compatible with an involvement in gene regulation...
February 17, 2017: Cell Systems
https://www.readbyqxmd.com/read/28214743/tio2-nanowire-arrays-modified-with-a-simultaneous-etching-doping-and-deposition-technique-for-ultrasensitive-amperometric-immunosensing
#9
Xiaoqiang Liu, Xiaohe Huo, Peipei Liu, Yunfei Tang, Jun Xu, Huangxian Ju
In this work, an ultrasensitive immunosensing scaffold was structured with TiO2 nanowire (TiNW) arrays modified with molybdenum (Mo) and MoS2 flakes by a triplex "etching, doping and deposition" technique. The triply modification of TiNW arrays improved their electron transfer, and the decoration of MoS2 flakes on TiNW arrays increased both the conductivity and the specific surface area of TiNW. Accordingly, the triply modified TiNW arrays provided a biocompatible microenviroment for the biomolecules and high specific surface area to load big amount of biomolecules...
June 15, 2017: Biosensors & Bioelectronics
https://www.readbyqxmd.com/read/28210721/3-pyrene-modified-unlocked-nucleic-acids-synthesis-fluorescence-properties-and-a-surprising-stabilization-effect-on-duplexes-and-triplexes
#10
Maria Ejlersen, Niels Langkjær, Jesper Wengel
Efficient synthesis of a new 3'-O-amino-UNA monomer was developed as a scaffold for further functionalization and incorporation into oligonucleotides (ONs). Pyrene-functionalized 3'-O-amino-UNA was incorporated one, two or three times into 21-mer DNA and 2'-O-Me-RNA ONs. Duplex melting temperatures, circular dichroism (CD) spectra, steady-state fluorescence emission spectra, UV/Vis absorption spectra and triplex melting temperatures were measured for the modified duplexes. The presence of the pyrene-modified UNA monomer lead to a surprising and unprecedented thermal stabilization of especially DNA:DNA duplexes when compared to the corresponding unmodified DNA:DNA duplexes...
February 17, 2017: Organic & Biomolecular Chemistry
https://www.readbyqxmd.com/read/28208646/recognition-of-local-dna-structures-by-p53-protein
#11
Václav Brázda, Jan Coufal
p53 plays critical roles in regulating cell cycle, apoptosis, senescence and metabolism and is commonly mutated in human cancer. These roles are achieved by interaction with other proteins, but particularly by interaction with DNA. As a transcription factor, p53 is well known to bind consensus target sequences in linear B-DNA. Recent findings indicate that p53 binds with higher affinity to target sequences that form cruciform DNA structure. Moreover, p53 binds very tightly to non-B DNA structures and local DNA structures are increasingly recognized to influence the activity of wild-type and mutant p53...
February 10, 2017: International Journal of Molecular Sciences
https://www.readbyqxmd.com/read/28194966/what-makes-telomeres-unique
#12
Adam K Sieradzan, Paweł Krupa, David J Wales
Telomeres are repetitive nucleotide sequences, which are essential for protecting the termini of chromosomes. Thousands of such repetitions are necessary to maintain the stability of the whole chromosome. Several similar repeated telomeric sequences have been found in different species, but why has nature chosen them? What features do telomeres have in common? In this article, we study the physical properties of human-like (TTAGGG), plant (TTTAGG), insect (TTAGG), and Candida guilermondi (GGTGTAC) telomeres in comparison with seven control, nontelomeric sequences...
March 1, 2017: Journal of Physical Chemistry. B
https://www.readbyqxmd.com/read/28169560/bovine-lactoferrin-and-lactoferricin-exert-antitumor-activities-on-human-colorectal-cancer-cells-ht-29-by-activating-various-signaling-pathways
#13
Rulan Jiang, Bo Lönnerdal
Lactoferrin (Lf) is an iron-binding glycoprotein that is present at high concentrations in milk. Bovine lactoferricin (LfcinB) is a peptide fragment generated by pepsin proteolysis of bovine lactoferrin (bLf). LfcinB consists of amino acid residues 17-41 proximal to the N-terminus of bLf and a disulfide bond between residues 19 and 36, forming a loop. Both bLf and LfcinB have been demonstrated to have antitumor activities. Colorectal cancer is the second most common cause of cancer death in developed countries...
February 2017: Biochemistry and Cell Biology, Biochimie et Biologie Cellulaire
https://www.readbyqxmd.com/read/28153952/qmc-pcrx-a-novel-method-for-rapid-mutation-detection
#14
Henry O Ebili, James Hassall, Abutaleb Asiri, Hersh Ham-Karim, Wakkas Fadhil, Ayodeji Johnson Agboola, Mohammad Ilyas
AIMS: We previously described the quick multiplex consensus PCR (QMC-PCR) as a method for rapid mutation screening in low-quality template. QMC-PCR has two-stages: a prediagnostic multiplex (PDM) reaction followed by a single specific diagnostic reaction with high-resolution melting (HRM) analysis. We aimed to develop QMC-PCRx in which second stage was multiplexed to allow testing of multiple targets. METHODS: The PDM reaction was retained without change. For the second stage, in silico design was used to identify targets amenable to a multiplex specific diagnostic reaction and multiplex HRM (mHRM) analysis...
February 2, 2017: Journal of Clinical Pathology
https://www.readbyqxmd.com/read/28138667/high-throughput-screening-of-triplex-dna-binders-from-complicated-samples-by-96-well-pate-format-in-conjunction-with-peak-area-fading-uhplc-orbitrap-ms
#15
Hongmei Yang, Wenbin Yao, Yihan Wang, Lei Shi, Rui Su, Debin Wan, Niusheng Xu, Wenhui Lian, Changbao Chen, Shuying Liu
Conventional strategies for the screening of DNA triplex binders cannot be used for complicated samples, such as ligand libraries created by combinatorial chemistry or from natural product extracts. In the current study, an ultra-high-performance liquid chromatography coupled with an Orbitrap mass spectrometry (UHPLC-Orbitrap-MS)-based approach, which we call peak area-fading (PAF) UHPLC-Orbitrap-MS and was designed for just such a purpose, is reported. The triplex DNA modified 96-well plate and the single stranded oligonucleotide modified 96-well plate (as control) were incubated with ligand libraries, and the unbound ligands were directly determined via UHPLC-ESI-MS...
January 31, 2017: Analyst
https://www.readbyqxmd.com/read/28132873/detection-of-macrolide-resistance-genes-in-culture-negative-specimens-from-bangladeshi-children-with-invasive-pneumococcal-diseases
#16
Md Hasanuzzaman, Roly Malaker, Maksuda Islam, Abdullah H Baqui, Gary L Darmstadt, Cynthia G Whitney, Samir K Saha
OBJECTIVES: In recent years, an increasing prevalence of macrolide resistance among pneumococci in Bangladesh has been observed. However, the scenario remains incomplete, as few isolates (<1%) are available from pneumonia cases and most pneumococcal meningitis cases (>80%) are culture-negative. This study optimised a triplex PCR method to detect macrolide resistance genes (MRGs) (mefA and ermB) and cpsA from culture-negative pneumococcal cases to predict the prevalence and level of macrolide resistance...
January 26, 2017: Journal of Global Antimicrobial Resistance
https://www.readbyqxmd.com/read/28131897/long-noncoding-rnas-and-sulforaphane-a-target-for-chemoprevention-and-suppression-of-prostate-cancer
#17
Laura M Beaver, Rachael Kuintzle, Alex Buchanan, Michelle W Wiley, Sarah T Glasser, Carmen P Wong, Gavin S Johnson, Jeff H Chang, Christiane V Löhr, David E Williams, Roderick H Dashwood, David A Hendrix, Emily Ho
Long noncoding RNAs (lncRNAs) have emerged as important in cancer development and progression. The impact of diet on lncRNA expression is largely unknown. Sulforaphane (SFN), obtained from vegetables like broccoli, can prevent and suppress cancer formation. Here we tested the hypothesis that SFN attenuates the expression of cancer-associated lncRNAs. We analyzed whole-genome RNA-sequencing data of normal human prostate epithelial cells and prostate cancer cells treated with 15 μM SFN or dimethylsulfoxide. SFN significantly altered expression of ~100 lncRNAs in each cell type and normalized the expression of some lncRNAs that were differentially expressed in cancer cells...
April 2017: Journal of Nutritional Biochemistry
https://www.readbyqxmd.com/read/28113380/sampled-data-stabilization-for-fuzzy-genetic-regulatory-networks-with-leakage-delays
#18
M Syed Ali, N Gunasekaran, Choon Ki Ahn, Peng Shi
This paper deals with the sampled-data stabilization problem for Takagi-Sugeno (T-S) fuzzy genetic regulatory networks with leakage delays. A novel Lyapunov-Krasovskii functional (LKF) is established by the non-uniform division of the delay intervals with triplex and quadruplex integral terms. Using such LKFs for constant and time-varying delay cases, new stability conditions are obtained in the T-S fuzzy framework. Based on this, a new condition for the sampled-data controller design is proposed using a linear matrix inequality representation...
September 7, 2016: IEEE/ACM Transactions on Computational Biology and Bioinformatics
https://www.readbyqxmd.com/read/28108011/interference-between-triplex-and-protein-binding-to-distal-sites-on-supercoiled-dna
#19
Agnes Noy, Anthony Maxwell, Sarah A Harris
We have explored the interdependence of the binding of a DNA triplex and a repressor protein to distal recognition sites on supercoiled DNA minicircles using MD simulations. We observe that the interaction between the two ligands through their influence on their DNA template is determined by a subtle interplay of DNA mechanics and electrostatics, that the changes in flexibility induced by ligand binding play an important role and that supercoiling can instigate additional ligand-DNA contacts that would not be possible in simple linear DNA sequences...
February 7, 2017: Biophysical Journal
https://www.readbyqxmd.com/read/28106202/a-colorimetric-sensing-platform-based-upon-recognizing-hybridization-chain-reaction-products-with-oligonucleotide-modified-gold-nanoparticles-through-triplex-formation
#20
Li Zou, Ruimin Li, Manjun Zhang, Yanwei Luo, Nian Zhou, Jing Wang, Liansheng Ling
A novel colorimetric sensing strategy for biomolecule assay has been developed, which integrates the signal amplification of the hybridization chain reaction (HCR) with the assembly of gold nanoparticles (AuNPs) through triplex formation. In the presence of targets, the HCR process can be triggered, the HCR products are specifically recognized by triplex-forming oligonucleotide (TFO) functionalized AuNPs, accompanying the aggregation of AuNPs and a dramatic absorbance change at 522 nm. In addition, the DNA hairpin probes can form rigid triplex structures with TFO-functionalized AuNPs in the absence of targets, resulting in a negligible background signal...
January 20, 2017: Nanoscale
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