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  • Buffer
  • This "gel" shows the cleavage pattern that would be expected if the "test" RNA were 5' radiolabeled, digested with nucleases in the included Structure Buffer, and then separated by denaturing polyacrylamide gel electrophroresis. (thermofisher.com)
  • sequences
  • The rooted universal 3-domains tree of Life ( Fig. 1 A ) based on small subunit (SSU) ribosomal (r)RNA sequences, shows eukaryotes and archaebacteria as monophyletic groups that share a common ancestor to the exclusion of eubacteria ( 1 ). (pnas.org)
  • To choose our hypothetical sample RNA, we analyzed several random RNA sequences with the mfold program developed by Dr. Michael Zuker (5). (thermofisher.com)
  • Comparing the sequences within these regions (Figure 2, Panel A), two double-stranded regions within the RNA become apparent (Figure 3): regions 1 and 4 form Stem I (8 bp), and regions 2 and 3 form Stem II (6 bp). (thermofisher.com)
  • RNA-seq produces millions of sequences from complex RNA samples. (uoregon.edu)
  • In all cases an RNA-seq experiment involves making a collection of cDNA fragments which are flanked by specific constant sequences (known as adapters) that are necessary for sequencing (see Figure 0.1 ). (uoregon.edu)
  • The present invention is directed to methods and materials for RNA-mediated gene assembly from oligonucleotide sequences. (justia.com)
  • The present invention is based on the inventor's recent discovery of an RNA-mediated assembly method using oligonucleotide sequences on a DNA array. (justia.com)
  • microRNAs
  • The discovery of new classes of ncRNAs including endogenous small interfering RNAs, microRNAs, and PIWI-interacting RNAs is a hallmark in the understanding of RNA-dependent gene regulation. (hindawi.com)
  • Several types of sRNA including plant microRNAs (miRNA), piwi-interacting RNAs (piRNA) in insects, nematodes and mammals, and small interfering RNAs (siRNA) in insects and plants contain a 2'-O-methyl (2'-OMe) modification at their 3′ terminal nucleotide. (biomedcentral.com)
  • Eukaryotic regulatory sRNAs typically range in size from ~ 20 to 30 nt and the three major classes are microRNAs (miRNA), small interfering RNAs (siRNA) and piwi-interacting RNAs (piRNA). (biomedcentral.com)
  • MicroRNAs (miRNAs) are small RNAs important to transcriptional and post-transcriptional regulation in animals, plants, and viruses. (biomedcentral.com)
  • molecule
  • 24870230 ). Component of a multi-helicase-TICAM1 complex that acts as a cytoplasmic sensor of viral double-stranded RNA (dsRNA) and plays a role in the activation of a cascade of antiviral responses including the induction of proinflammatory cytokines via the adapter molecule TICAM1. (uniprot.org)
  • This problem can be eliminated by first using the ligase to attach a 5'-App-modified adaptor to the 3'-OH end of the miRNA in the absence of ATP , and then attaching a second adaptor to the 5'-phosphate end of the resulting miRNA-3'-adaptor molecule using the ligase in the presence of ATP. (genelink.com)
  • structural analysis is integral to understanding the biochemical role of an RNA molecule. (thermofisher.com)
  • This article serves as a brief introduction, and includes a hypothetical example, on using nuclease digestion data to deduce the secondary structure of an RNA molecule. (thermofisher.com)
  • The RNA molecule is readily copied by RT-PCR to yield the corresponding gene or target double strand DNA fragment. (justia.com)
  • Accordingly, in a first aspect described herein is a method for RNA-mediated assembly method for providing a target RNA molecule. (justia.com)
  • miRNAs
  • Hence, the discovery of miRNAs represents a hallmark in RNA science for understanding RNA-dependent regulation of many complex biological processes such as development, function of metabolic pathways, cell fate and death [ 16 ]. (hindawi.com)
  • In addition, the universe of small RNAs has expanded to include not only miRNAs but new classes including endogenous small interfering RNAs (siRNAs), 21U RNAs, and Piwi-interacting RNAs (piRNAs) [ 17 ]. (hindawi.com)
  • Of these small RNA classes, only miRNAs form a characteristic thermodynamically stable hairpin structure. (hindawi.com)
  • On the other hand, de novo finding of miRNAs in species whose genomes have yet to be sequenced and discovering new classes of small RNAs must still rely upon in vitro cloning from purified cellular RNAs. (hindawi.com)
  • miRNAs are small non-coding RNAs ∼22 nucleotides in length that regulate gene expression by altering mRNA stability and transcription. (frontiersin.org)
  • Indirect sampling of miRNAs in blood and cerebrospinal fluid, because of their small amounts of total RNA, have not easily leant themselves for profiling by next generation sequencing (NGS). (frontiersin.org)
  • mRNA
  • RNA structure is thought to play a central role in many cellular processes, including transcription initiation, elongation and termination, mRNA splicing, and retroviral infection of eukaryotic cells. (thermofisher.com)
  • synthesis
  • FUNCTION: DNA ligase, which is expressed in the early stage of CC lytic development, has been implicated in T7 DNA synthesis and CC genetic recombination. (genome.jp)
  • We have developed an extensive portfolio of products for the synthesis and modification of RNA in order to further understand the role of RNA structure. (thermofisher.com)
  • ribosomal
  • 16S ribosomal RNA (rRNA) sequencing is a common amplicon sequencing method used to identify and compare bacteria present within a given sample. (mclab.com)
  • transcriptional
  • The approach is generalizable to other mi RNA s and post‐transcriptional regulators to improve the understanding of gene expression dynamics in individual cell types. (embopress.org)
  • The "RNA revolution" that started at the end of the 20th century with the discovery of post-transcriptional gene silencing and its mechanism via RNA interference (RNAi) placed tiny 21-24 nucleotide long noncoding RNAs (ncRNAs) in the forefront of biology as one of the most important regulatory elements in a host of physiologic processes. (hindawi.com)
  • RNAi
  • Like RNAi, this phenomenon, initially called short temporary RNA (stRNA), was at first regarded as a one-off curiosity but, again like RNAi, persistence paid off with the explosive validation of the microRNA (miRNA) [ 9 - 12 ]. (hindawi.com)
  • subunit
  • Catalytic subunit of the tRNA-splicing ligase complex that acts by directly joining spliced tRNA halves to mature-sized tRNAs by incorporating the precursor-derived splice junction phosphate into the mature tRNA as a canonical 3,5-phosphodiester. (genecards.org)
  • adapters
  • The use of a novel type of randomised adapters called MidRand-Like (MRL) adapters and PEG improved the detection of 2' OMe RNAs both in the TruSeq as well as in the NEXTflex protocol. (biomedcentral.com)
  • In a typical sRNA library preparation process, adapters are ligated to the RNAs followed by reverse transcription and PCR amplification. (biomedcentral.com)
  • phosphodiester
  • in the third step, the 5-OH from the opposite RNA strand attacks the activated 3-P to form a 3,5-phosphodiester bond and release GMP (PubMed:24870230). (genecards.org)
  • analyses
  • These analyses further reveal that at intermediate expression levels, where targets respond ultrasensitively to the mi RNA , the correlation in target expression increases 2-3 fold. (embopress.org)
  • biochemical
  • Stochastic variation in single‐cell gene expression can be used to infer biochemical parameters of mi RNA ‐target interaction. (embopress.org)
  • experimental
  • When designing an RNA-seq experiment researchers are faced with choosing between many experimental options, and decisions must be made at each step of the process. (uoregon.edu)
  • Before one even begins an RNA-seq experiment they should have an understanding of each step and should put together a carefully devised experimental plan. (uoregon.edu)
  • Table 1.1 Recommendations for RNA-seq options based upon experimental objectives. (uoregon.edu)
  • fragments
  • If the "test" RNA were 5' radiolabeled and digested individually with RNases A, T1 and V1, and the fragments were then analyzed by denaturing gel electrophoresis, the results would resemble the hypothetical data shown in Figure 1. (thermofisher.com)
  • function
  • May act as an RNA ligase with broad substrate specificity, and may function toward other RNAs. (genecards.org)
  • Performing detailed structure-function studies on long, catalytically-active, naturally-occurring RNA ( e.g. , group I and II introns, ribonuclease P) often requires incorporation of site-specific modifications. (genelink.com)
  • Moine H, Ehresmann B, Ehresmann C, and Romby P. (1998) Probing RNA structure and function in solution. (thermofisher.com)
  • RNA Structure and Function, Cold Spring Harbor Laboratory Press. (thermofisher.com)
  • proteins
  • Analysis of RNAs associated with the snoRNP proteins revealed remarkably high signal-to-noise ratios and identified specific binding sites for each of these proteins on the U3 RNA. (pnas.org)
  • RNA immunoprecipitation uses formaldehyde to cross-link RNA to proteins ( 1 , 2 ). (pnas.org)
  • This problem can be avoided by cross-linking proteins and RNA with UV light, and several techniques have been reported ( 3 ⇓ ⇓ ⇓ - 7 ). (pnas.org)