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Robert A Hom, Deborah Sharon Wuttke
The human CST (CTC1-STN1-TEN1) heterotrimeric complex plays roles in both telomere maintenance and DNA replication through its ability to interact with ssDNA of a variety of sequences. The precise sequence specificity required to execute these functions is unknown. Telomere-binding proteins have been shown to specifically recognize key telomeric sequence motifs within ssDNA while accommodating non-specifically recognized sequences through conformationally plastic interfaces. To better understand the role CST plays in these processes, we have produced highly purified heterotrimer and elucidated the sequence requirements for CST recognition of ssDNA in vitro...
July 20, 2017: Biochemistry
Lihua Lu, Huijuan Su, Feng Li
The assay and monitoring of transcription factors (TFs) has attracted extensive attention, due to their important roles in regulation of gene expressions. Herein, a simple, low cost, rapid, and highly sensitive homogeneous electrochemical method utilizing the coupled isothermal cleavage reaction and cycling amplification based on exonuclease III (Exo III) was explored for the analysis of transcription factor NF-κB p50 in aqueous solution. In the assay, a 3-methylene blue (MB)-labeled hairpin probe is designed, which can be opened up by the single stranded DNA (ssDNA) protected by NF-κB p50 from the Exo III cleavage, to trigger the subsequent Exo III-assisted digestion, thus a large amount of MB-labeled mononucleotides are liberated to result in the greatly amplified electrochemical signal...
July 20, 2017: Analytical Chemistry
Elina Laanto, Sari Mäntynen, Luigi De Colibus, Jenni Marjakangas, Ashley Gillum, David I Stuart, Janne J Ravantti, Juha T Huiskonen, Lotta-Riina Sundberg
Viruses have impacted the biosphere in numerous ways since the dawn of life. However, the evolution, genetic, structural, and taxonomic diversity of viruses remain poorly understood, in part because sparse sampling of the virosphere has concentrated mostly on exploring the abundance and diversity of dsDNA viruses. Furthermore, viral genomes are highly diverse, and using only the current sequence-based methods for classifying viruses and studying their phylogeny is complicated. Here we describe a virus, FLiP (Flavobacterium-infecting, lipid-containing phage), with a circular ssDNA genome and an internal lipid membrane enclosed in the icosahedral capsid...
July 17, 2017: Proceedings of the National Academy of Sciences of the United States of America
Zhen Xu, Xiaoling Lei, Yusong Tu, Zhi-Jie Tan, Bo Song, Haiping Fang
Functional nanoscale structures consisting of a DNA molecule coupled to graphene or graphene oxide (GO) have great potential for applications in biosensors, biomedicine, nanotechnology, and materials science. Extensive studies using the most sophisticated experimental techniques and theoretical methods have still not clarified the dynamic process of single-stranded DNA (ssDNA) adsorbed on a GO surface. Based on a molecular dynamics simulation, this work shows that an ssDNA segment could be stably adsorbed on a GO surface through hydrogen bonding and a π-π stacking interaction, with preferential binding to an oxidized region rather than to an unoxidized region of the GO surface...
July 16, 2017: Chemistry: a European Journal
Edyta Đermić, Davor Zahradka, Dušica Vujaklija, Siniša Ivanković, Damir Đermić
Double-strand breaks (DSBs) are lethal DNA lesions, which are repaired by homologous recombination in Escherichia coli To study DSB processing in vivo, we induced DSBs into the E. coli chromosome by gamma irradiation and measured chromosomal degradation. We show that the DNA degradation is regulated by RecA protein concentration and its rate of association with ssDNA. RecA decreased DNA degradation in wild-type, recB and recD strains, indicating that it is a general phenomenon in E. coli On the other hand, DNA degradation was greatly reduced and unaffected by RecA in the recB1080 mutant (which produces long overhangs) and in a strain devoid of four exonucleases that degrade a 3' tail (ssExos)...
July 14, 2017: G3: Genes—Genomes—Genetics
Lunbiao Cui, Binyao Wu, Xiaojuan Zhu, Xiling Guo, Yiyue Ge, Kangchen Zhao, Xian Qi, Zhiyang Shi, Fengcai Zhu, Lixin Sun, Minghao Zhou
Metagenomic analysis through high-throughput sequencing is a tool for detecting both known and novel viruses. Using this technique, a novel circular single-stranded DNA (ssDNA) virus genome was discovered in respiratory secretions from a febrile traveler. The virus, named human respiratory-associated PSCV-5-like virus (HRAPLV), has a genome comprising 3,018 bases, with two major putative ORFs inversely encoding capsid (Cap) and replicase (Rep) protein and separated by two intergenic regions. One stem-loop structure was predicted in the larger intergenic region (LIR)...
July 13, 2017: Archives of Virology
Eirik Hovland, Getachew Tesfaye Beyene, Stephan A Frye, Håvard Homberset, Seetha V Balasingham, Marta Gómez-Muñoz, Jeremy P Derrick, Tone Tønjum, Ole H Ambur
DNA processing chain A (DprA) is a DNA-binding protein that is ubiquitous in bacteria and expressed in some archaea. DprA is active in many bacterial species that are competent for transformation of DNA, but its role in Neisseriameningitidis (Nm) is not well characterized. An Nm mutant lacking DprA was constructed, and the phenotypes of the wild-type and ΔdprA mutant were compared. The salient feature of the phenotype of dprA null cells is the total lack of competence for genetic transformation shown by all of the donor DNA substrates tested in this study...
July 12, 2017: Microbiology
Chao Hu, Xiang Juan Kong, Ru Qin Yu, Ting Ting Chen, Xia Chu
A novel fluorescence sensing platform for ultrasensitive detection of S1 nuclease activity has been constructed based on MnO2 nanosheets and FAM labeled single-stranded DNA (FAM-ssDNA). In this system, MnO2 nanosheets were found to have different adsorbent ability toward ssDNA and mono- or oligonucleotide fragments. FAM-ssDNA could adsorb on MnO2 nanosheets and resulted in significant fluorescence quenching through fluorescence resonance energy transfer (FRET), while mono- or oligonucleotide fragments could not adsorb on MnO2 nanosheets and still retained strong fluorescence emission...
2017: Analytical Sciences: the International Journal of the Japan Society for Analytical Chemistry
XiaoQing Zhang, Ye Feng, QiongQiong Yao, Fengjiao He
A rapid and accurate detection method for Mycobacterium tuberculosis (M. tuberculosis) is essential for effectively treating tuberculosis. However, current detection methods cannot meet these clinical requirements because the methods are slow or of low specificity. Consequently, a new highly specific ssDNA aptamer against M. tuberculosis reference strain H37Rv was selected by using the whole-cell systematic evolution of ligands by exponential enrichment technique. The selected aptamer was used to construct a fast and highly specific H37Rv sensor...
June 20, 2017: Biosensors & Bioelectronics
M H Korayem, M Estaji, A Homayooni
Nanocarriers are useful tools in biological and medical research fields. In nanomanipulation, a nondestructive and successful process can be achieved by using nanocarriers. In this paper, a nonclassical multiscale approach has been presented for modeling a single strand DNA (ssDNA) manipulation based on AFM. To achieve a nondestructive nanomanipulation process, carbon nanotube (CNT) has been used as a nanocarrier. AFM setup has been separated into a Micro field (MF) and a Nano field (NF). The governing equations of the MF have been derived based on Kirchhoff plate model and a modified couple stress theory...
June 24, 2017: Colloids and Surfaces. B, Biointerfaces
Chang Yeol Lee, Ki Soo Park, Hyun Gyu Park
We develop a novel approach to determine formamidopyrimidine DNA glycosylase (Fpg) activity by taking advantage of the unique fluorescence property of pyrrolo-dC (PdC) positioned opposite to 8-oxoguanine (8-oxoG) in duplex DNA. In its initial state, PdC in duplex DNA undergoes the efficient stacking and collisional quenching interactions, showing the low fluorescence signal. In contrast, the presence of Fpg, which specifically removes 8-oxoG and incises resulting apurinic (AP) site, transforms duplex DNA into single-stranded (ss) DNAs...
June 27, 2017: Biosensors & Bioelectronics
Zhenqiang Wang, Jixi Zhang, Feng Chen, Kaiyong Cai
The combination of fluorophore-labelled single-strand DNA probes and nanomaterial quenchers has shown great potential in miRNA detection. The development of advanced detection systems by understanding and controlling the fluorescence quenching/recovery via nanoquenchers' microstructures and local morphologies is an attractive area warranting further investigations. Inspired by nanopore sequencing, we present a novel miRNA sensing strategy using fluorophore-labeled DNA as probes and a type of large-pore-sized mesoporous polydopamine nanoparticles (MPDA-L, 70 nm in diameter) as fluorescence quenchers...
July 6, 2017: Analyst
P Kumar, V Arun, T S Lokeswari
Banana bunchy top virus (BBTV) affects all varieties of banana plants and causes heavy economic loss in most of the banana cultivating areas. The BBTV genome comprises of six DNA components; in this study, we have cloned the six BBTV-DNA components from one of the BBTV-infected plants (Tri-8) and were submitted to GenBank. Analysis of the BBTV DNA-R component showed that it belonged to south Pacific group. Resistance against BBTV has not been observed so far in banana plants and removal and killing of the infected plants has been routinely practiced...
July 2017: 3 Biotech
Dong-Mei Wang, Qi-Qi Gai, Rong-Fu Huang, Xingwang Zheng
Development of ultrasensitive method for Hg(2+) analysis is important for human health protection and environment monitoring. In this work, we present a highly sensitive and selective electrochemiluminescence (ECL) assay in a "turn-on" mode for the detection of Hg(2+) through selective assembly of gold nanoparticles (AuNPs) on the surface of indium tin oxide (ITO) electrode. In the absence of Hg(2+), the nonthiolated ssDNA could protected AuNPs against its assembly on ITO surface, producing rather low ECL emission for Ru(bpy)3(2+)/TPA system...
June 28, 2017: Biosensors & Bioelectronics
Nelly Sapojnikova, Nino Asatiani, Tamar Kartvelishvili, Lali Asanishvili, Vitaly Zinkevich, Irina Bogdarina, Julian Mitchell, Abdulmohsen Al-Humam
The efficiency of hybridization signal detection in a biochip is affected by the method used for test DNA preparation, such as fragmentation, amplification and fluorescent labelling. DNA fragmentation is the commonest methods used and it is recognised as a critical step in biochip analysis. Currently methods used for DNA fragmentation are based either on sonication or on the enzymatic digestion. In this study, we compared the effect of different types of enzymatic DNA fragmentations, using DNase I to generate ssDNA breaks, NEBNext dsDNA fragmentase and SaqAI restrictase, on DNA labelling...
June 27, 2017: Journal of Biotechnology
Jean-Christophe Dubois, Maïlyn Yates, Antoine Gaudreau-Lapierre, Geneviève Clément, Laurent Cappadocia, Luc Gaudreau, Lee Zou, Alexandre Maréchal
RPA-coated single-stranded DNA (RPA-ssDNA), a nucleoprotein structure induced by DNA damage, promotes ATR activation and homologous recombination (HR). RPA is hyper-phosphorylated and ubiquitylated after DNA damage. The ubiquitylation of RPA by PRP19 and RFWD3 facilitates ATR activation and HR, but how it is stimulated by DNA damage is still unclear. Here, we show that RFWD3 binds RPA constitutively, whereas PRP19 recognizes RPA after DNA damage. The recruitment of PRP19 by RPA depends on PIKK-mediated RPA phosphorylation and a positively charged pocket in PRP19...
June 28, 2017: Nucleic Acids Research
Suganya Rangaswamy, Arvind Pandey, Sankar Mitra, Muralidhar L Hegde
Genomic fidelity in the humans is continuously challenged by genotoxic reactive oxygen species (ROS) generated both endogenously during metabolic processes, and by exogenous agents. Mispairing of most ROS-induced oxidized base lesions during DNA replication induces mutations. Although bulky base adducts induced by ultraviolet light and other environmental mutagens block replicative DNA polymerases, most oxidized base lesions do not block DNA synthesis. In 8-oxo-G:A mispairs generated by the incorporation of A opposite unrepaired 8-oxo-G, A is removed by MutYH (MYH) for post-replicative repair, and other oxidized base lesions must be repaired prior to replication in order to prevent mutation fixation...
June 30, 2017: Genes
Shu Tian, Oara Neumann, Michael J McClain, Xiao Yang, Linan Zhou, Chao Zhang, Peter Nordlander, Naomi J Halas
Since its discovery in the 1970's, surface-enhanced Raman scattering (SERS) has been primarily associated with substrates composed of nanostructured noble metals. Here we investigate chemically synthesized nanocrystal aggregates of Aluminum, an inexpensive, highly abundant, and sustainable metal, as SERS substrates. Al nanocrystal aggregates are capable of substantial near-infrared SERS enhancements, similar to Au nanoparticles. The intrinsic nanoscale surface oxide of Al nanocrystals supports molecule-substrate interactions that differ dramatically from noble metal substrates...
June 30, 2017: Nano Letters
Yufang Hu, Qingqing Zhang, Zhiyong Guo, Sui Wang, Chunnuan Du, Chunyang Zhai
A novel label-free electrochemical strategy was established based on the unique electro-catalytic activity of graphene oxide (GO)-supported terminal deoxynucleotidyl transferase (TdT)-generated C-rich DNA nanotail-templated silver nanoclusters (DNA-AgNCs). TdT can catalyze the deoxycytidine triphosphate (dCTP) to the 3'-OH terminus of single-stranded DNA (ssDNA) with no template; then, in the presence of Ag(I), TdT-generated C-rich DNA sequence was employed for the synthetic template of AgNCs because of the formed complexes of nitrogen atoms of cytosine based with silver atoms...
June 10, 2017: Biosensors & Bioelectronics
Vaibhav Bhatia, Emilia Herrera-Moyano, Andrés Aguilera, Belén Gómez-González
The nascent RNA can reinvade the DNA double helix to form a structure termed the R-loop, where a single-stranded DNA (ssDNA) is accompanied by a DNA-RNA hybrid. Unresolved R-loops can impede transcription and replication processes and lead to genomic instability by a mechanism still not fully understood. In this sense, a connection between R-loops and certain chromatin markers has been reported that might play a key role in R-loop homeostasis and genome instability. To counteract the potential harmful effect of R-loops, different conserved messenger ribonucleoprotein (mRNP) biogenesis and nuclear export factors prevent R-loop formation, while ubiquitously-expressed specific ribonucleases and DNA-RNA helicases resolve DNA-RNA hybrids...
June 27, 2017: Genes
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