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exonuclease HIV

Daoqing Fan, Xiaoqing Zhu, Qingfeng Zhai, Erkang Wang, Shaojun Dong
In this work, the effective fluorescence quenching ability of polydopamine nanotubes (PDANTs) toward various fluorescent dyes was studied and further applied to fluorescent biosensing for the first time. The PDANTs could quench the fluorophores with different emission frequencies, aminomethylcoumarin acetate (AMCA), 6-carboxyfluorescein (FAM), 6-carboxytetramethylrhodamine (TAMRA), and Cy5. All the quenching efficiencies reached to more than 97%. Taking advantage of PDANTs' different affinities toward ssDNA and dsDNA and utilizing the complex of FAM-labeled ssDNA and PDANTs as a sensing platform, we achieved highly sensitive and selective detection of human immunodeficiency virus (HIV) DNA and adenosine triphosphate (ATP) assisted with Exonuclease III amplification...
September 20, 2016: Analytical Chemistry
Siarhei Kharytonchyk, Steven R King, Clement B Ndongmo, Krista L Stilger, Wenfeng An, Alice Telesnitsky
A key contributor to HIV-1 genetic variation is reverse transcriptase errors. Some mutations result because reverse transcriptase (RT) lacks 3' to 5' proofreading exonuclease and can extend mismatches. However, RT also excises terminal nucleotides to a limited extent, and this activity contributes to AZT resistance. Because HIV-1 mismatch resolution has been studied in vitro but only indirectly during replication, we developed a novel system to study mismatched base pair resolution during HIV-1 replication in cultured cells using vectors that force template switching at defined locations...
June 5, 2016: Journal of Molecular Biology
Wen Yang, Jianniao Tian, Lijun Wang, Shui Fu, Hongyun Huang, Yanchun Zhao, Shulin Zhao
A label-free and sensitive fluorescence biosensing platform for human immunodeficiency virus gene (HIV-DNA) detection has been fabricated based on luminescent DNA-scaffolded silver nanoclusters (DNA/AgNCs) and autonomous exonuclease III (Exo III)-assisted recycling signal amplification. One long-chain DNA (X-DNA) molecule can hybridize with two assistant DNA (F-DNA) molecules and one HIV-DNA molecule; after Exo III digests X-DNA to liberate F-DNA and HIV-DNA. F-DNA combines with P-DNA (template of DNA/AgNCs), accordingly, P-DNA is cut and the fluorescence of the system is quenched...
May 10, 2016: Analyst
Yijia Wang, Xiaoning Bai, Wei Wen, Xiuhua Zhang, Shengfu Wang
Because human immunodeficiency virus (HIV) has been one of the most terrible viruses in recent decades, early diagnosis of the HIV gene is of great importance for all scientists around the world. In our work, we developed a novel electrochemical biosensor based on one-step ultrasonic synthesized graphene stabilized gold nanocluster (GR/AuNC) modified glassy carbon electrode (GCE) with an exonuclease III (Exo III)-assisted target recycling amplification strategy for the detection of HIV DNA. It is the first time that GR/AuNCs have been used as biosensor platform and aptamer with cytosine-rich base set as capture probe to construct the biosensor...
August 26, 2015: ACS Applied Materials & Interfaces
Ai-Li Sun, Kun Deng, Wei-Ling Fu
A new homogeneous electrochemical sensing strategy based on exonuclease III-assisted target recycling amplification was utilized for simple, rapid and highly sensitive detection of human immunodeficiency virus (HIV) DNA on an immobilization-free Ag(I)-assisted hairpin DNA through the cytosine-Ag(+)-cytosine coordination chemistry. The assay involved target-induced strand-displacement reaction accompanying dissociation of the chelated Ag(+) in the hairpins and exonuclease III-triggered target recycling. Initially, the added target DNA hybridized with hairpin DNA to disrupt the Ag(I)-coordinated hairpin probe and releases the coordinated Ag(+) ion...
December 15, 2015: Biosensors & Bioelectronics
Kyle J Seamon, Zhiqiang Sun, Luda S Shlyakhtenko, Yuri L Lyubchenko, James T Stivers
The HIV-1 restriction factor SAMHD1 is a tetrameric enzyme activated by guanine nucleotides with dNTP triphosphate hydrolase activity (dNTPase). In addition to this established activity, there have been a series of conflicting reports as to whether the enzyme also possesses single-stranded DNA and/or RNA 3'-5' exonuclease activity. SAMHD1 was purified using three chromatography steps, over which the DNase activity was largely separated from the dNTPase activity, but the RNase activity persisted. Surprisingly, we found that catalytic and nucleotide activator site mutants of SAMHD1 with no dNTPase activity retained the exonuclease activities...
July 27, 2015: Nucleic Acids Research
Haiyan Zhao, Lei Wang, Jing Zhu, Haiping Wei, Wei Jiang
Based on DNA templated Ag NCs (DNA/Ag NCs) fluorescent probe, a label-free fluorescent method was developed for the detection of clinical significant DNA fragments from human immunodeficiency virus type 1 (HIV-1) DNA. Firstly, a hairpin probe, containing target DNA recognition sequence and guanine-rich sequence, was designed to hybridize with the target DNA and form a blunt 3'-terminus DNA duplex. Then, exonuclease III (Exo III) was employed to stepwise hydrolyze the mononucleotides from formed blunt 3'-terminus DNA duplex, releasing the target DNA and guanine-rich sequence...
June 1, 2015: Talanta
Sarah Schmidt, Kristina Schenkova, Tarek Adam, Elina Erikson, Judith Lehmann-Koch, Serkan Sertel, Bruno Verhasselt, Oliver T Fackler, Felix Lasitschka, Oliver T Keppler
The deoxynucleoside triphosphate triphosphohydrolase and 3' → 5' exonuclease SAMHD1 restricts HIV-1 infection in noncycling hematopoietic cells in vitro, and SAMHD1 mutations are associated with AGS. Little is known about the in vivo expression and functional regulation of this cellular factor. Here, we first assessed the SAMHD1 protein expression profile on a microarray of 25 human tissues from >210 donors and in purified primary cell populations. In vivo, SAMHD1 was expressed in the majority of nucleated cells of hematopoietic origin, including tissue-resident macrophages, DCs, pDCs, all developmental stages of thymic T cells, monocytes, NK cells, as well as at lower levels in B cells...
July 2015: Journal of Leukocyte Biology
Gregory Berger, Madeleine Lawrence, Stephane Hué, Stuart J D Neil
UNLABELLED: The accessory gene vpr, common to all primate lentiviruses, induces potent G2/M arrest in cycling cells. A recent study showed that human immunodeficiency virus type 1 (HIV-1) viral protein R (Vpr) mediates this through activation of the SLX4/MUS81/EME1 exonuclease complex that forms part of the Fanconi anemia DNA repair pathway. To confirm these observations, we have examined the G2/M arrest phenotypes of a panel of simian immunodeficiency virus (SIV) Vpr proteins. We show that SIV Vpr proteins differ in their ability to promote cell cycle arrest in human cells...
January 2015: Journal of Virology
Thijs Booiman, Laurentia C Setiawan, Neeltje A Kootstra
OBJECTIVE: Three prime repair exonuclease 1 (TREX1) plays a pivotal role in HIV-1 infection. In-vitro studies have shown that TREX1 degrades excess HIV-1 DNA, thereby shielding HIV-1 from recognition by innate immune receptors and preventing a type 1 interferon response. To determine whether TREX1 plays a role in HIV-1 pathogenesis, we analyzed whether genetic variation in Trex1 is associated with the clinical course of HIV-1 infection. DESIGN/METHODS: Two tagging single nucleotide polymorphisms (SNPs) in Trex1 were genotyped in a cohort of 304 HIV-1-infected MSM and a cohort of 66 high-risk seronegative individuals...
November 13, 2014: AIDS
Maroof Hasan, Nan Yan
Innate immune recognition is crucial for host responses against viral infections, including infection by human immunodeficiency virus 1 (HIV-1). Human cells detect such invading pathogens with a collection of pattern recognition receptors that activate the production of antiviral proteins, such as the cytokine interferon-type I, to initiate antiviral responses immediately as well as the adaptive immune response for long-term protection. To establish infection in the host, many viruses have thus evolved strategies for subversion of these mechanisms of innate immunity...
2014: Frontiers in Microbiology
Christelle Brégnard, Monsef Benkirane, Nadine Laguette
Viruses have been long known to perturb cell cycle regulators and key players of the DNA damage response to benefit their life cycles. In the case of the human immunodeficiency virus (HIV), the viral auxiliary protein Vpr activates the structure-specific endonuclease SLX4 complex to promote escape from innate immune sensing and, as a side effect, induces replication stress in cycling cells and subsequent cell cycle arrest at the G2/M transition. This novel pathway subverted by HIV to prevent accumulation of viral reverse transcription by-products adds up to facilitating effects of major cellular exonucleases that degrade pathological DNA species...
2014: Frontiers in Microbiology
Antonios Katsounas, Joseph J Rasimas, Joerg F Schlaak, Richard A Lempicki, Donald L Rosenstein, Shyam Kottilil
Hepatitis C Virus (HCV) infection occurs frequently in patients with preexisting mental illness. Treatment for chronic hepatitis C using interferon formulations often increases risk for neuro-psychiatric symptoms. Pegylated-Interferon-α (PegIFN-α) remains crucial for attaining sustained virologic response (SVR); however, PegIFN-α based treatment is associated with psychiatric adverse effects, which require dose reduction and/or interruption. This study's main objective was to identify genes induced by PegIFN-α and expressed in the central nervous system and immune system, which could mediate the development of psychiatric toxicity in association with antiviral outcome...
August 2014: Journal of Medical Virology
Wenjiao Zhou, Xue Gong, Yun Xiang, Ruo Yuan, Yaqin Chai
Visual detections have attracted great research attentions recently due to their convenient monitoring of the target analytes without using any advanced instruments. However, achieving visual detection of trace amounts of biomolecules with PCR-like sensitivity remains a major challenge. In current work, we describe a new quadratic signal amplification strategy for sensitive visual detection of HIV DNA biomarkers based on exonuclease III (Exo III)-assisted DNA recycling amplification and DNAzymes. The presence of the target HIV DNA leads to two independent and simultaneous DNA recycling processes to achieve quadratic signal amplification with the assistance of Exo III...
May 15, 2014: Biosensors & Bioelectronics
Henning Hofmann, Thomas D Norton, Megan L Schultz, Sylvie B Polsky, Nicole Sunseri, Nathaniel R Landau
The deoxynucleoside triphosphohydrolase SAMHD1 restricts retroviral replication in myeloid cells. Human immunodeficiency virus type 2 (HIV-2) and a simian immunodeficiency virus from rhesus macaques (SIVmac) encode Vpx, a virion-packaged accessory protein that counteracts SAMHD1 by inducing its degradation. SAMHD1 is thought to work by depleting the pool of intracellular deoxynucleoside triphosphates but has also been reported to have exonuclease activity that could allow it to degrade the viral genomic RNA or viral reverse-transcribed DNA...
November 2013: Journal of Virology
Rayk Behrendt, Tina Schumann, Alexander Gerbaulet, Laura A Nguyen, Nadja Schubert, Dimitra Alexopoulou, Ursula Berka, Stefan Lienenklaus, Katrin Peschke, Kathrin Gibbert, Sabine Wittmann, Dirk Lindemann, Siegfried Weiss, Andreas Dahl, Ronald Naumann, Ulf Dittmer, Baek Kim, Werner Mueller, Thomas Gramberg, Axel Roers
Aicardi-Goutières syndrome (AGS), a hereditary autoimmune disease, clinically and biochemically overlaps with systemic lupus erythematosus (SLE) and, like SLE, is characterized by spontaneous type I interferon (IFN) production. The finding that defects of intracellular nucleases cause AGS led to the concept that intracellular accumulation of nucleic acids triggers inappropriate production of type I IFN and autoimmunity. AGS can also be caused by defects of SAMHD1, a 3' exonuclease and deoxynucleotide (dNTP) triphosphohydrolase...
August 29, 2013: Cell Reports
Aihua Zheng, Ming Luo, Dongshan Xiang, Xia Xiang, Xinghu Ji, Zhike He
We have developed a new fluorescence method for specific single-stranded DNA sequences with exonuclease III (Exo III) and nucleic acid dye SYBR Green I. It is demonstrated by a reverse transcription oligonucleotide sequence (target DNA, 27 bases) of RNA fragment of human immunodeficiency virus (HIV) as a model system. In the absence of the target DNA, the hairpin-probe is in the stem-closed structure, the fluorescence of SYBR Green I is very strong. In the presence of the target DNA, the hairpin-probe hybridizes with the target DNA to form double-stranded structure with a blunt 3'-terminus...
September 30, 2013: Talanta
Natalia Beloglazova, Robert Flick, Anatoli Tchigvintsev, Greg Brown, Ana Popovic, Boguslaw Nocek, Alexander F Yakunin
The human HD domain protein SAMHD1 is implicated in the Aicardi-Goutières autoimmune syndrome and in the restriction of HIV-1 replication in myeloid cells. Recently, this protein has been shown to possess dNTP triphosphatase activity, which is proposed to inhibit HIV-1 replication and the autoimmune response by hydrolyzing cellular dNTPs. Here, we show that the purified full-length human SAMHD1 protein also possesses metal-dependent 3'→5' exonuclease activity against single-stranded DNAs and RNAs in vitro...
March 22, 2013: Journal of Biological Chemistry
Margaret J Lange, Tarun K Sharma, Angela S Whatley, Linda A Landon, Michael A Tempesta, Marc C Johnson, Donald H Burke
RNA aptamers that bind human immunodeficiency virus 1 (HIV-1) reverse transcriptase (RT) also inhibit viral replication, making them attractive as therapeutic candidates and potential tools for dissecting viral pathogenesis. However, it is not well understood how aptamer-expression context and cellular RNA pathways govern aptamer accumulation and net antiviral bioactivity. Using a previously-described expression cassette in which aptamers were flanked by two "minimal core" hammerhead ribozymes, we observed only weak suppression of pseudotyped HIV...
December 2012: Molecular Therapy: the Journal of the American Society of Gene Therapy
Manuela Sironi, Mara Biasin, Diego Forni, Rachele Cagliani, Mariacristina De Luca, Irma Saulle, Sergio Lo Caputo, Francesco Mazzotta, Juan Macias, Juan A Pineda, Antonio Caruz, Mario Clerici
Three prime repair exonuclease 1 (TREX1) degrades excess HIV-1 DNA, thereby preventing recognition by innate immunity receptors and type I interferon responses. Analyses performed in two HIV-exposed seronegative (HESN) cohorts did not show any differences in TREX1 sequence, single nucleotide polymorphisms frequency, or expression in HESN compared to controls, suggesting that, despite its central role in the HIV-1 infection process, genetic diversity at TREX1 is not a major determinant of susceptibility to infection in humans...
July 17, 2012: AIDS
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