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https://www.readbyqxmd.com/read/29773824/rnase-h-assisted-rna-primed-rolling-circle-amplification-for-targeted-rna-sequence-detection
#1
Hirokazu Takahashi, Masahiko Ohkawachi, Kyohei Horio, Toshiro Kobori, Tsunehiro Aki, Yukihiko Matsumura, Yutaka Nakashimada, Yoshiko Okamura
RNA-primed rolling circle amplification (RPRCA) is a useful laboratory method for RNA detection; however, the detection of RNA is limited by the lack of information on 3'-terminal sequences. We uncovered that conventional RPRCA using pre-circularized probes could potentially detect the internal sequence of target RNA molecules in combination with RNase H. However, the specificity for mRNA detection was low, presumably due to non-specific hybridization of non-target RNA with the circular probe. To overcome this technical problem, we developed a method for detecting a sequence of interest in target RNA molecules via RNase H-assisted RPRCA using padlocked probes...
May 17, 2018: Scientific Reports
https://www.readbyqxmd.com/read/29765512/dhx9-regulates-production-of-hepatitis-b-virus-derived-circular-rna-and-viral-protein-levels
#2
Kazuma Sekiba, Motoyuki Otsuka, Motoko Ohno, Takahiro Kishikawa, Mari Yamagami, Tatsunori Suzuki, Rei Ishibashi, Takahiro Seimiya, Eri Tanaka, Kazuhiko Koike
Hepatitis B virus (HBV) infection, which is a major health concern worldwide, can lead to liver cirrhosis and hepatocellular carcinoma. Although current nucleos(t)ide analogs efficiently inhibit viral reverse transcription and viral DNA load clinically, episomal viral covalently closed circular DNA (cccDNA) minichromosomes and transcripts from cccDNA continue to be expressed over the long term. We hypothesized that, under these conditions, viral transcripts may have biological functions involved in pathogenesis...
April 20, 2018: Oncotarget
https://www.readbyqxmd.com/read/29700819/circular-rna-expression-profile-and-potential-function-of-hsa_circ_0045272-in-systemic-lupus-erythematosus
#3
Lian-Ju Li, Zhi-Wei Zhu, Wei Zhao, Sha-Sha Tao, Bao-Zhu Li, Shu-Zhen Xu, Jie-Bing Wang, Ming-Yue Zhang, Jun Wu, Rui-Xue Leng, Yin-Guang Fan, Hai-Feng Pan, Dong-Qing Ye
Circular RNAs (circRNAs) represent as a class of non-coding RNAs which form covalently closed RNA circles, and their extensive expression and conservation in mammals are observed. CircRNAs regulate gene expression through acting as competitive endogenous RNAs (ceRNAs) and modulating gene transcription. Accumulating evidence supports the implication of circRNAs in a variety of human diseases. Yet, study exploring the role of circRNAs in systemic lupus erythematosus (SLE) is lacking. The present study measured the circRNAs expression profiles in T cells from SLE patients and healthy controls with human circRNA microarray and identified 127 differentially expressed circRNAs in SLE patients...
April 26, 2018: Immunology
https://www.readbyqxmd.com/read/29690513/research-progress-on-rolling-circle-amplification-rca-based-biomedical-sensing
#4
REVIEW
Lide Gu, Wanli Yan, Le Liu, Shujun Wang, Xu Zhang, Mingsheng Lyu
Enhancing the limit of detection (LOD) is significant for crucial diseases. Cancer development could take more than 10 years, from one mutant cell to a visible tumor. Early diagnosis facilitates more effective treatment and leads to higher survival rate for cancer patients. Rolling circle amplification (RCA) is a simple and efficient isothermal enzymatic process that utilizes nuclease to generate long single stranded DNA (ssDNA) or RNA. The functional nucleic acid unit (aptamer, DNAzyme) could be replicated hundreds of times in a short period, and a lower LOD could be achieved if those units are combined with an enzymatic reaction, Surface Plasmon Resonance, electrochemical, or fluorescence detection, and other different kinds of biosensor...
April 21, 2018: Pharmaceuticals
https://www.readbyqxmd.com/read/29675002/mutational-analysis-of-eggplant-latent-viroid-rna-circularization-by-the-eggplant-trna-ligase-in-escherichia-coli
#5
Teresa Cordero, Beltrán Ortolá, José-Antonio Daròs
Eggplant latent viroid (ELVd) is a relatively small non-coding circular RNA that induces asymptomatic infections in eggplants ( Solanum melongena L.). Like other viroid species that belong to the family Avsunviroidae , ELVd contains hammerhead ribozymes in the strands of both polarities that self-cleave RNAs producing terminal 5'-hydroxyl and 2',3'-cyclic phosphodiester groups. Available experimental data indicate that ELVd replicates in the chloroplasts of infected cells through a symmetric rolling-circle mechanism, in which RNA circularization is catalyzed by the chloroplastic isoform of the tRNA ligase...
2018: Frontiers in Microbiology
https://www.readbyqxmd.com/read/29643011/the-effect-of-antiretroviral-intensification-with-dolutegravir-on-residual-virus-replication-in-hiv-infected-individuals-a-randomised-placebo-controlled-double-blind-trial
#6
Thomas A Rasmussen, James H McMahon, J Judy Chang, Jennifer Audsley, Ajantha Rhodes, Surekha Tennakoon, Ashanti Dantanarayana, Tim Spelman, Tina Schmidt, Stephen J Kent, Vincent Morcilla, Sarah Palmer, Julian H Elliott, Sharon R Lewin
BACKGROUND: Whether ongoing virus replication occurs in HIV-infected individuals on antiretroviral therapy (ART) is unclear; therefore, whether residual virus replication is a barrier to achieving a cure for HIV is also unknown. We aimed to establish whether ART intensification with dolutegravir would reveal or affect residual virus replication in HIV-infected individuals on suppressive treatment. METHODS: In this randomised, placebo-controlled, double-blind trial, we enrolled HIV-infected adults (aged 18 years and older) receiving combination ART (at least three agents) for at least 3 years from the Alfred Hospital and Melbourne Sexual Health Centre, Melbourne, VIC, Australia...
May 2018: Lancet HIV
https://www.readbyqxmd.com/read/29594533/determination-of-rnase-h-activity-via-real-time-monitoring-of-target-triggered-rolling-circle-amplification
#7
Chang Yeol Lee, Kyoung Suk Kang, Ki Soo Park, Hyun Gyu Park
The authors describe a method for real-time monitoring of the activity of ribonuclease H (RNase H). It is based on target-triggered rolling circle amplification (RCA). It utilizes a specially designed primer that contains a RNA sequence in the center and an amino group at the 3'-end. In the absence of RNase H, the primer when hybridized to a circular DNA template is not extended by DNA polymerase due to the amino group at the 3'-end. In contrast, the presence of RNase H specifically degrades the RNA sequence of the primer hybridized to the circular DNA template...
December 14, 2017: Mikrochimica Acta
https://www.readbyqxmd.com/read/29580320/ictv-virus-taxonomy-profile-avsunviroidae
#8
Francesco Di Serio, Shi-Fang Li, Jaroslav Matoušek, Robert A Owens, Vicente Pallás, John W Randles, Teruo Sano, Jacobus Th J Verhoeven, Georgios Vidalakis, Ricardo Flores, Ictv Report Consortium
Members of the family Avsunviroidae have a single-stranded circular RNA genome that adopts a rod-like or branched conformation and can form, in the strands of either polarity, hammerhead ribozymes involved in their replication in plastids through a symmetrical RNA-RNA rolling-circle mechanism. These viroids lack the central conserved region typical of members of the family Pospiviroidae. The family Avsunviroidae includes three genera, Avsunviroid, Pelamoviroid and Elaviroid, with a total of four species. This is a summary of the ICTV Report on the taxonomy of the family Avsunviroidae, which is available at http://www...
March 26, 2018: Journal of General Virology
https://www.readbyqxmd.com/read/29567323/circular-rna-circrna-was-an-important-bridge-in-the-switch-from-the-rna-world-to-the-dna-world
#9
Gerald Soslau
The concept that life on Earth began as an RNA world has been built upon extensive experimentation demonstrating that many of the building blocks required for living cells could be synthesized in the laboratory under conditions approximating our primordial world. Many of the building blocks for life have also been found in meteorites indicating that meteors may have been a source for these molecules, or more likely, that they represent the chemical library present in most/all bodies in the universe after the big bang...
March 19, 2018: Journal of Theoretical Biology
https://www.readbyqxmd.com/read/29554297/limited-reverse-transcriptase-activity-of-phi29-dna-polymerase
#10
Tomasz Krzywkowski, Malte Kühnemund, Di Wu, Mats Nilsson
Phi29 (Φ29) DNA polymerase is an enzyme commonly used in DNA amplification methods such as rolling circle amplification (RCA) and multiple strand displacement amplification (MDA), as well as in DNA sequencing methods such as single molecule real time (SMRT) sequencing. Here, we report the ability of phi29 DNA polymerase to amplify RNA-containing circular substrates during RCA. We found that circular substrates with single RNA substitutions are amplified at a similar amplification rate as non-chimeric DNA substrates, and that consecutive RNA pyrimidines were generally preferred over purines...
March 15, 2018: Nucleic Acids Research
https://www.readbyqxmd.com/read/29504183/a-paper-sensor-printed-with-multifunctional-bio-nano-materials
#11
Christy Y Hui, Meng Liu, Yingfu Li, John D Brennan
We report a paper-based aptasensor platform that uses two reaction zones and a connecting bridge along with printed multifunctional bio/nano materials to achieve molecular recognition and signal amplification. Upon addition of analyte to the first zone, a fluorescently labelled DNA or RNA aptamer is desorbed from printed graphene oxide, rapidly producing an initial fluorescence signal. The released aptamer then flows to the second zone where it reacts with printed reagents to initiate rolling circle amplification, generating DNA amplicons containing a peroxidase-mimicking DNAzyme, which produces a colorimetric readout that can be read in an equipment-free manner or with a smartphone...
April 16, 2018: Angewandte Chemie
https://www.readbyqxmd.com/read/29388767/kinetic-parameters-of-trans-scission-by-extended-hdv-like-ribozymes-and-the-prospect-for-the-discovery-of-genomic-trans-cleaving-rnas
#12
Chiu-Ho T Webb, Andrej Lupták
Hepatitis delta virus (HDV)-like ribozymes are self-cleaving catalytic RNAs with a widespread distribution in nature and biological roles ranging from self-scission during rolling-circle replication in viroids to co-transcriptional processing of eukaryotic retrotransposons, among others. The ribozymes fold into a double pseudoknot with a common catalytic core motif and highly variable peripheral domains. Like other self-cleaving ribozymes, HDV-like ribozymes can be converted into trans-acting catalytic RNAs by bisecting the self-cleaving variants at non-essential loops...
March 6, 2018: Biochemistry
https://www.readbyqxmd.com/read/29378611/episomal-hiv-1-dna-and-its-relationship-to-other-markers-of-hiv-1-persistence
#13
REVIEW
Javier Martinez-Picado, Ryan Zurakowski, María José Buzón, Mario Stevenson
Reverse transcription of HIV-1 results in the generation of a linear cDNA that serves as the precursor to the integrated provirus. Other classes of extrachromosomal viral cDNA molecules can be found in acutely infected cells including the 1-LTR and 2-LTR circles of viral DNA, also referred as episomal HIV-1 DNA. Circulating CD4+ T-cells of treatment-naïve individuals contain significant levels of unintegrated forms of HIV-1 DNA. However, the importance of episomal HIV-1 DNA in the study of viral persistence during antiviral therapy (ART) is debatable...
January 30, 2018: Retrovirology
https://www.readbyqxmd.com/read/29343298/circular-rnas-biogenesis-expression-and-their-potential-roles-in-reproduction
#14
REVIEW
Guobo Quan, Julang Li
Unlike other non-coding RNAs (ncRNAs), circular RNA (circRNA) is generally presented as a covalently linked circle lacking both a 5' cap and a 3' tail. circRNAs were thought to be spliced intermediates, byproducts, or products of abnormal RNA splicing events. However, the high-throughput sequencing technology coupled with bioinformatics has recently uncovered thousands of endogenous circRNAs in cells of many different species. These circRNAs show various features, such as abundant expression, evolutionary conservation, cell- or tissue-specific expression, and a higher resistance to degradation caused by exonuclease or ribonuclease (RNase), suggesting their potentially biological significance...
January 17, 2018: Journal of Ovarian Research
https://www.readbyqxmd.com/read/29333658/in-situ-shrna-synthesis-on-dna-polylactide-nanoparticles-to-treat-multidrug-resistant-breast-cancer
#15
Qianqian Ni, Fuwu Zhang, Yunlei Zhang, Guizhi Zhu, Zhe Wang, Zhaogang Teng, Chunyan Wang, Bryant C Yung, Gang Niu, Guangming Lu, Longjiang Zhang, Xiaoyuan Chen
Nanomedicine has shown unprecedented potential for cancer theranostics. Nucleic acid (e.g., DNA and RNA) nanomedicines are of particular interest for combination therapy with chemotherapeutics. However, current nanotechnologies to construct such nucleic acid nanomedicines, which rely on chemical conjugation or physical complexation of nucleic acids with chemotherapeutics, have restrained their clinical translation due to limitations such as low drug loading efficiency and poor biostability. Herein, in situ rolling circle transcription (RCT) is applied to synthesize short hairpin RNA (shRNA) on amphiphilic DNA-polylactide (PLA) micelles...
March 2018: Advanced Materials
https://www.readbyqxmd.com/read/29301971/intracranial-aneurysm-associated-single-nucleotide-polymorphisms-alter-regulatory-dna-in-the-human-circle-of-willis
#16
Melanie D Laarman, Marit W Vermunt, Rachel Kleinloog, Jelkje J de Boer-Bergsma, Netherlands Brain Bank, Gabriël J E Rinkel, Menno P Creyghton, Michal Mokry, Jeroen Bakkers, Ynte M Ruigrok
BACKGROUND AND PURPOSE: Genome-wide association studies significantly link intracranial aneurysm (IA) to single-nucleotide polymorphisms (SNPs) in 6 genomic loci. To gain insight into the relevance of these IA-associated SNPs, we aimed to identify regulatory regions and analyze overall gene expression in the human circle of Willis (CoW), on which these aneurysms develop. METHODS: We performed chromatin immunoprecipitation and sequencing for histone modifications H3K4me1 and H3K27ac to identify regulatory regions, including distal enhancers and active promoters, in postmortem specimens of the human CoW...
February 2018: Stroke; a Journal of Cerebral Circulation
https://www.readbyqxmd.com/read/29240289/dnazyme-feedback-amplification-relaying-molecular-recognition-to-exponential-dna-amplification
#17
Meng Liu, Qingxin Yin, Erin M McConnell, Yangyang Chang, John D Brennan, Yingfu Li
Technologies capable of linking DNA amplification to molecular recognition are very desirable for ultrasensitive biosensing applications. We have developed a simple but powerful isothermal DNA amplification method, termed DNAzyme feedback amplification (DFA), that is capable of relaying molecular recognition to exponential DNA amplification. The method incorporates both an RNA-cleaving DNAzyme (RCD) and rolling circle amplification (RCA) carried out by a special DNA polymerase using a circular DNA template...
December 14, 2017: Chemistry: a European Journal
https://www.readbyqxmd.com/read/29133898/intertwining-dna-rna-nanocapsules-loaded-with-tumor-neoantigens-as-synergistic-nanovaccines-for-cancer-immunotherapy
#18
Guizhi Zhu, Lei Mei, Harshad D Vishwasrao, Orit Jacobson, Zhantong Wang, Yijing Liu, Bryant C Yung, Xiao Fu, Albert Jin, Gang Niu, Qin Wang, Fuwu Zhang, Hari Shroff, Xiaoyuan Chen
Nanomedicines that co-deliver DNA, RNA, and peptide therapeutics are highly desirable yet remain underdeveloped for cancer theranostics. Herein, we report self-assembled intertwining DNA-RNA nanocapsules (iDR-NCs) that efficiently delivered synergistic DNA CpG and short hairpin RNA (shRNA) adjuvants, as well as tumor-specific peptide neoantigens into antigen presenting cells (APCs) in lymph nodes for cancer immunotherapy. These nanovaccines were prepared by (1) producing tandem CpG and shRNA via concurrent rolling circle replication and rolling circle transcription, (2) self-assembling CpG and shRNA into DNA-RNA microflowers, (3) shrinking microflowers into iDR-NCs using PEG-grafted cationic polypeptides, and (4) physically loading neoantigen into iDR-NCs...
November 14, 2017: Nature Communications
https://www.readbyqxmd.com/read/29089355/assessment-of-retinoblastoma-rna-reflux-after-intravitreal-injection-of-melphalan
#19
Ursula Winter, Michael Nicolas, Mariana Sgroi, Claudia Sampor, Ana Torbidoni, Adriana Fandiño, Guillermo L Chantada, Francis L Munier, Paula Schaiquevich
BACKGROUND: Intravitreal injection of chemotherapy in retinoblastoma eyes with vitreous seeds may lead to a risk of extraocular tumour dissemination that has not been assessed so far. AIMS: To develop a sensitive and clinically feasible technique to assess for potential retinoblastoma cell reflux after intravitreal injection of melphalan. METHODS: Filter papers were cut in 6 mm diameter circles and sterilised before use. Eyes with retinoblastoma vitreous seeds (group D, International Classification) received weekly intravitreal melphalan injections (20 µg or 30 µg/dose) followed by cryotherapy as part of local treatment...
March 2018: British Journal of Ophthalmology
https://www.readbyqxmd.com/read/29055871/acute-telomerase-components-depletion-triggers-oxidative-stress-as-an-early-event-previous-to-telomeric-shortening
#20
José Santiago Ibáñez-Cabellos, Giselle Pérez-Machado, Marta Seco-Cervera, Ester Berenguer-Pascual, José Luis García-Giménez, Federico V Pallardó
Loss of function of dyskerin (DKC1), NOP10 and TIN2 are responsible for different inheritance patterns of Dyskeratosis congenita (DC; ORPHA1775). They are key components of telomerase (DKC1 and NOP10) and shelterin (TIN2), and play an important role in telomere homeostasis. They participate in several fundamental cellular processes by contributing to Dyskeratosis congenita through mechanisms that are not fully understood. Presence of oxidative stress was postulated to result from telomerase ablation. However, the resulting disturbed redox status can promote telomere attrition by generating a vicious circle, which promotes cellular senescence...
April 2018: Redox Biology
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