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Ankur Bikash Pradhan, Sutanwi Bhuiya, Lucy Haque, Suman Das
We have reported the interaction of two flavonoids namely quercetin (Q) and morin (M) with double stranded poly(A).poly(U) (herein after A.U) and triple stranded poly(U).poly(A)*poly(U) (herein after U.A*U, dot represents the Watson-Crick and asterisk represents Hoogsteen base pairing respectively) in this article. It has been observed that relative positions of hydroxyl groups on the B-ring of the flavonoids affect the stabilization of RNA. The double strand as well as the triple strand of RNA-polymers become more stabilized in presence of Q, however both the duplex and triplex remain unaffected in presence of M...
November 18, 2017: Archives of Biochemistry and Biophysics
Sutanwi Bhuiya, Lucy Haque, Rapti Goswami, Suman Das
The interactions of RNA triplex (U.A*U) and duplex (A.U) with the naturally occurring flavonoid fisetin (FTN) have been examined at pH 7.0 using various spectroscopic, viscometric and theoretical studies. Experimental observations showed that the ligand binds with both double and triple helical forms of RNA, although the binding affinity is greater for the triplex structure (5.94106 M-1) compared to the duplex counterpart (1.0105 M-1). Thermal melting experiments revealed that the Hoogsteen base paired third strand of triplex was stabilized to a greater extent (~14 C) compared to the Watson-Crick base paired second strand (~4 C) in presence of FTN...
November 16, 2017: Journal of Physical Chemistry. B
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
P K V Koerich, B B Fonseca, E Balestrin, V Tagliari, P G Hoepers, C Ueira-Vieira, I Oldoni, R H Rauber, L Ruschel, V P Do Nascimento
1. The aim of the present study was to determine if the 9R-strain of the Salmonella gallinarum live vaccine was responsible for having fowl typhoid outbreaks in chicken flocks from both chicken and turkey breeders as well as to verify the antimicrobial resistance of the isolates from the outbreaks. 2. The triplex polymerase chain reaction (PCR), standard antimicrobial test, beta-lactamase genes identification and Ion Torrent PMG whole genome sequence were used in the field isolates and in the vaccine strain of S...
November 15, 2017: British Poultry Science
X Niu, H Wang, L Wei, M Zhang, J Yang, H Chen, Y Tang, Y Diao
To deepen the knowledge about epidemic prevalence in the goose breeding field, a triplex PCR assay was established, and 478 samples were collected from scaled goose farms in 11 provinces in China. The results of this epidemiological investigation showed that incidence rates of H9 avian influenza and goose circovirus were the highest among five infectious diseases that were evaluated. In addition, the triplex PCR assay established remarkable sensitivity, rapidity and versatility compared to other diagnostic methods...
November 13, 2017: Transboundary and Emerging Diseases
Tao Bing, Wei Zheng, Xin Zhang, Luyao Shen, Xiangjun Liu, Fuyi Wang, Jie Cui, Zehui Cao, Dihua Shangguan
Apart from the canonical Watson-Crick duplex, nucleic acids can often form other structures, e.g. G-quadruplex and triplex. These structures give nucleic acid additional functions besides coding for genetic information. Aptamers are one type of functional nucleic acids that bind to specific targets with high selectivity and affinity by folding into special tertiary structures. Despite the fact that numerous aptamers have been reported, only a few different types of aptamer structures are identified. Here we report a novel triplex-quadruplex hybrid scaffold formed by a codeine binding aptamer (CBA)...
November 13, 2017: Scientific Reports
Junli Liu, Lu Yao, Feifei Zhai, Yuqing Chen, Jing Lei, Zhenwei Bi, Jianhua Hu, Qian Xiao, Suquan Song, Liping Yan, Jiyong Zhou
Avian influenza virus (AIV), especially subtypes H5, H7 and H9, has contributed to enormous economic losses and poses a potential pandemic threat to global human public health. Early screening of suspected cases is key to controlling the spread of AIVs. In this study, an accurate, rapid, and triplex real-time polymerase chain reaction (PCR) assay was developed for the simultaneous detection of AIV subtypes H5, H7 and H9. The sensitivity of the real-time PCR was at least 100 times higher than that of the conventional PCR, with a detection limit of 50 copies and an EID50 of 1 (50% egg infections dose) for the H5, H7, and H9 subtypes...
November 10, 2017: Journal of Virological Methods
Ru Ying Puah, Huan Jia, Manikantha Maraswami, Desiree-Faye Kaixin Toh, Rya Ero, Lixia Yang, Kiran M Patil, Alan Ann Lerk Ong, Manchugondanahalli S Krishna, Ruimin Sun, Cailing Tong, Mei Huang, Xin Chen, Teck-Peng Loh, Yonggui Gao, Ding Xiang Liu, Gang Chen
Minus-one programmed ribosomal frameshifting (-1 PRF) allows the precise maintenance of the ratio between viral proteins, and is involved in the regulation of the half-lives of cellular mRNAs. Minus-one ribosomal frameshifting (-1 RF) is activated by several stimulatory elements such as a heptameric slippery sequence (X XXY YYZ) and an mRNA secondary structure (hairpin or pseudoknot) that is positioned 2-8 nucleotides downstream from the slippery site. Upon -1 RF, the ribosomal reading frame is shifted from the normal zero frame to the -1 frame with the heptameric slippery sequence decoded as XXX YYY Z instead of X XXY YYZ...
November 8, 2017: Biochemistry
Changwon Yang, Mandar Kulkarni, Manho Lim, Youngshang Pak
The reversible folding of the thrombin-binding DNA aptamer G-quadruplexes (GQs) (TBA-15) starting from fully unfolded states was demonstrated using a prolonged time scale (10-12 μs) parallel tempering metadynamics (PTMetaD) simulation method in conjunction with a modified version of the AMBER bsc1 force field. For unbiased descriptions of the folding free energy landscape of TBA-15, this force field was minimally modified. From this direct folding simulation using the modified bsc1 force field, reasonably converged free energy landscapes were obtained in K+-rich aqueous solution (150 mM), providing detailed atomistic pictures of GQ folding mechanisms for TBA-15...
November 3, 2017: Nucleic Acids Research
Shinjiro Sawada, Toshifumi Takao, Nobuo Kato, Kunihiro Kaihatsu
DNA carries genetic information in its sequence of bases. Synthetic oligonucleotides that can sequence-specifically recognize a target gene sequence are a useful tool for regulating gene expression or detecting target genes. Among the many synthetic oligonucleotides, tail-clamp peptide nucleic acid (TC-PNA) offers advantages since it has two homopyrimidine PNA strands connected via a flexible ethylene glycol-type linker that can recognize complementary homopurine sequences via Watson-Crick and Hoogsteen base pairings and form thermally-stable PNA/PNA/DNA triplex structures...
October 27, 2017: Molecules: a Journal of Synthetic Chemistry and Natural Product Chemistry
Shuangna Liu, Pai Peng, Huihui Wang, Lili Shi, Tao Li
A molecular rotor thioflavin T (ThT) is usually used as a fluorescent ligand specific for G-quadruplexes. Here, we demonstrate that ThT can tightly bind non-G-quadruplex DNAs with several GA motifs and dimerize them in a parallel double-stranded mode, accompanied by over 100-fold enhancement in the fluorescence emission of ThT. The introduction of reverse Watson-Crick T-A base pairs into these dimeric parallel-stranded DNA systems remarkably favors the binding of ThT into the pocket between G•G and A•A base pairs, where ThT is encapsulated thereby restricting its two rotary aromatic rings in the excited state...
October 20, 2017: Nucleic Acids Research
Jeong Hwan Song, Tangla D Kongnyuy, Naser Hosseini, Pieter Neutens, Federico Buja, Roelof Jansen, Xavier Rottenberg
Compact wavelength splitters based on angled multimode interferometers (AMMIs) on silicon nitride platforms working in visible lights are reported for fluorescence sensing applications. A diplexer and triplexer with different footprints are designed and experimentally demonstrated. The diplexer and triplexer have the insertion loss of ∼1.7 and ∼2.7  dB/channel with cross talks of less than -22  dB and -17  dB on target wavelengths, respectively. These splitters are used to distinguish the signals collected from two fluorescent dyes that give different emission spectra when excited with an excitation source, due to their different Stokes shifts...
October 10, 2017: Applied Optics
Desiree-Faye Kaixin Toh, Kiran M Patil, Gang Chen
RNAs are emerging as important biomarkers and therapeutic targets. Thus, there is great potential in developing chemical probes and therapeutic ligands for the recognition of RNA sequence and structure. Chemically modified Peptide Nucleic Acid (PNA) oligomers have been recently developed that can recognize RNA duplexes in a sequence-specific manner. PNAs are chemically stable with a neutral peptide-like backbone. PNAs can be synthesized relatively easily by the manual Boc-chemistry solid-phase peptide synthesis method...
September 21, 2017: Journal of Visualized Experiments: JoVE
Chunan Zhong, Jijun Liu, Yuzhe Zhang, Jianping Luo, Jia Zheng
AIMS: Osteosarcoma (OS) is the most common primary bone malignancy that affects adolescents. Although great attention has been paid to the diagnosis of and therapy for OS, the 5-year survival rate of patients with this disease remains poor. MicroRNAs are small non-coding RNAs involved in pathogenesis and progression of human malignancies. MiR-139 has been implicated in several human cancers. However, the role played by miR-139 in pathogenesis of human OS has remained largely unknown. MAIN METHODS: Realtime PCR was used to detect the expression of miR-139...
October 6, 2017: Life Sciences
Volker Dahmen, Sabine Schmitz, Ralf Kriehuber
Triplex-Forming oligonucleotides (TFO) bind sequence-specific to the DNA double helix in-vitro and in-vivo and are a promising tool to manipulate genes or gene regulatory elements. TFO as a carrier molecule for short-range particle emitter such as Auger-Electron-Emitters (AEE) bear the potential to introduce radiation-induced site-specific complex DNA lesions, which are known to induce chromosomal translocations. We studied gene expression, translocation frequency and protein expression in SCL-II cells after transfection with the AEE Iodine-125 (I-125) labeled TFO-BCL2 targeting the human BCL2 gene...
November 2017: Mutation Research
Hayleigh Kearns, Royston Goodacre, Lauren E Jamieson, Duncan Graham, Karen Faulds
Successful pathogen detection is crucial for public health as the threat of infectious disease is dramatically increasing globally due to bacteria developing resistance to many antimicrobial drugs. The increase in bacterial infections has led to urgent demands for simpler, faster, and more reliable detection methods to be developed allowing the most appropriate therapy to be provided. Surface enhanced Raman scattering (SERS) is an analytical technique which has gained a great deal of interest for biosensing due to its sensitivity, selectivity, and multiplexing capabilities...
October 20, 2017: Analytical Chemistry
Xi-Miao Hou, Yi-Ben Fu, Wen-Qiang Wu, Lei Wang, Fang-Yuan Teng, Ping Xie, Peng-Ye Wang, Xu-Guang Xi
G-quadruplex (G4) can be formed by G-rich DNA sequences that are widely distributed throughout the human genome. Although G-triplex and G-hairpin have been proposed as G4 folding intermediates, their formation still requires further investigation by experiments. Here, we employed single-molecule FRET to characterize the folding dynamics of G4 from human telomeric sequence. First, we observed four states during G4 folding initially assigned to be anti-parallel G4, G-triplex, G-hairpin and unfolded ssDNA. Then we constructed putative intra-strand G-triplex, G-hairpin structures and confirmed their existences in both NaCl and KCl...
August 29, 2017: Nucleic Acids Research
Jin Chen, Qingnan Tang, Shiwen Guo, Chen Lu, Shimin Le, Jie Yan
The interaction between the single-stranded DNA and the homologous duplex DNA is essential for DNA homologous repair. Here, we report that parallel triplex structure can form spontaneously between a mechanically extended ssDNA and a homologous dsDNA in protein-free condition. The triplex has a contour length close to that of a B-form DNA duplex and remains stable after force is released. The binding energy between the ssDNA and the homologous dsDNA in the triplex is estimated to be comparable to the basepairing energy in a B-form dsDNA...
September 29, 2017: Nucleic Acids Research
Benjamin Y Owusu, Shantasia Thomas, Phanindra Venukadasula, Zhenfu Han, James W Janetka, Robert A Galemmo, Lidija Klampfer
Targeted therapeutic agents, such as inhibitors of epithelial growth factor receptor (EGFR), have transformed the management of non-small cell lung cancer (NSCLC) patients. MET-amplified NSCLC cells display resistance to EGFR-targeting agents, but are addicted to MET signaling for survival and proliferation and are sensitive to MET inhibition. However, responsive cancer cells invariably develop resistance to MET-targeted treatment. The tumor microenvironment plays a major role in resistance to anticancer therapy...
September 8, 2017: Oncotarget
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