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Christy Hui, Meng Liu, Yingfu Li, John David 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...
March 5, 2018: Angewandte Chemie
Judy Chiu-Ho Webb, Andrej Lupták
Hepatitis delta virus (HDV)-like ribozymes are self-cleaving catalytic RNAs with 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...
February 1, 2018: Biochemistry
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
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
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...
January 15, 2018: Advanced Materials
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...
January 4, 2018: Stroke; a Journal of Cerebral Circulation
Meng Liu, Qingxin Yin, Erin McConnell, Yangyang Chang, John 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
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
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...
October 31, 2017: British Journal of Ophthalmology
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
Lin Li, Yong-Chang Zheng, Masood Ur Rehman Kayani, Wen Xu, Guan-Qun Wang, Pei Sun, Ning Ao, Li-Na Zhang, Zhao-Qi Gu, Liang-Cai Wu, Hai-Tao Zhao
Circular RNAs (circRNAs) are pervasively expressed circles of non‑coding RNAs. Even though many circRNAs have been reported in humans, their expression patterns and functions remain poorly understood. In this study, we employed a pipeline named RAISE to detect circRNAs in RNA‑seq data. RAISE can fully characterize circRNA structure and abundance. We evaluated inter-individual variations in circRNA expression in humans by applying this pipeline to numerous non‑poly(A)-selected RNA‑seq data. We identified 59,128 circRNA candidates in 61 human liver samples, with almost no overlap in the circRNA of the recruited samples...
December 2017: International Journal of Oncology
Masami Shiimori, Sandra C Garrett, Dwain P Chambers, Claiborne V C Glover, Brenton R Graveley, Michael P Terns
To acquire CRISPR-Cas immunity against invasive mobile genetic elements, prokaryotes must first integrate fragments of foreign DNA into their genomic CRISPR arrays for use in future invader silencing. Here, we found that the hyperthermophilic archaeaon, Pyrococcus furiosus, actively incorporates DNA fragments (spacers) from both plasmid (foreign) and host genome (self) sequences into its seven CRISPR loci. The majority of new spacers were derived from DNA immediately downstream from a 5'-CCN-3' protospacer adjacent motif (PAM) that is critical for invader targeting...
November 2, 2017: Nucleic Acids Research
Dillon Friday, Priyadarshini Mukkara, Robert A Owens, Tilman Baumstark, Michael F Bruist
Potato spindle tuber viroid (PSTVd) is a circular, single-stranded, noncoding RNA plant pathogen that is a useful model for studying the processing of noncoding RNA in eukaryotes. Infective PSTVd circles are replicated via an asymmetric rolling circle mechanism to form linear multimeric RNAs. An endonuclease cleaves these into monomers, and a ligase seals these into mature circles. All eukaryotes may have such enzymes for processing noncoding RNA. As a test, we investigated the processing of three PSTVd RNA constructs in the yeast Saccharomyces cerevisiae Of these, only one form, a construct that adopts a previously described tetraloop-containing conformation (TL), produces circles...
December 15, 2017: Journal of Virology
He Yan, Youchun Xu, Ying Lu, Wanli Xing
MicroRNAs (miRNAs) are endogenous molecules with regulatory functions. The purification and enrichment of miRNA are essential for its precise and sensitive detection. miRNA isolated using commercial kits contains abundant interfering RNAs, and the concentration of miRNA may not be adequate for detection. Herein, we prepared a reduced graphene oxide (rGO)-based magnetic solid-phase extraction material for the enrichment and ultrasensitive detection of miRNA from intricate nucleic acid solutions. In situ reverse transcription (RT) was developed as the most efficient approach to desorb miRNA from rGO among the methods that are compatible for the subsequent amplification reported thus far...
September 22, 2017: Analytical Chemistry
Darran Yates
No abstract text is available yet for this article.
September 19, 2017: Nature Reviews. Neuroscience
A R Sakhabutdinova, M A Maksimova, R R Garafutdinov
Currently, isothermal methods of nucleic acid amplification have been well established; in particular, rolling circle amplification is of great interest. In this approach, circular ssDNA molecules have been used as a target that can be obtained by the intramolecular template-dependent ligation of an oligonucleotide C-probe. Here, a new method of synthesizing small circular DNA molecules via the cyclization of ssDNA based on T4 RNA ligase has been proposed. Circular ssDNA is further used as the template for the rolling circle amplification...
July 2017: Molekuliarnaia Biologiia
Mary C M Weiser-Evans
No abstract text is available yet for this article.
September 1, 2017: Circulation Research
Sangwoo Han, Hyejin Kim, Jong Bum Lee
Since the discovery of RNA interference (RNAi), small interfering RNA (siRNA) has been powerful tools for gene downregulation in biomedical applications. Despite the outstanding efficacy of siRNA, the development of a therapeutic delivery system remains a challenge owing to the instability of RNA. In this study, we describe a new method for the design of siRNA-generating nanosponges by using complementary rolling circle transcription (cRCT), a technique that requires two complementary circular DNA. The sequences of one of the circular DNA are designed to have complete complementarity to the target mRNA resulting in double stranded RNA (dsRNA) that can be digested to siRNA by cellular Dicer activity...
August 30, 2017: Scientific Reports
Meng Liu, Dingran Chang, Yingfu Li
DNA-based enzymes, or DNAzymes, are not known to exist in Nature but can be isolated from random-sequence DNA pools using test tube selection techniques. Since the report of the first DNAzyme in 1994, many catalytic DNA molecules for catalyzing wide-ranging chemical transformations have been isolated and studied. Our laboratory has a keen interest in searching for diverse DNAzymes capable of cleaving RNA-containing substrates, determining their sequence requirements and structural properties, and examining their potential as biosensors...
September 19, 2017: Accounts of Chemical Research
Deirdre C Tatomer, Dongming Liang, Jeremy E Wilusz
Thousands of eukaryotic protein-coding genes are noncanonically spliced to generate circular RNAs. Because they have covalently linked ends, circular RNAs are resistant to degradation by exonucleases and some accumulate to higher levels than their associated linear mRNAs. The functions of most circular RNAs are still unknown, but recent work has revealed key insights into how the pre-mRNA splicing machinery catalyzes backsplicing. Exons that circularize are often flanked by intronic repeat sequences that are complementary to one another, and backsplicing is triggered when these repeats base pair and bring the intervening splice sites into close proximity...
2017: Methods in Molecular Biology
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