Rna duplexes rna double stranded. Medical search. Frequent questions

RNA polymerase II mainly transcribes microRNA genes as primary miRNA transcripts (pri-miRNAs) that contain 5′cap and 3′poly(A) tails ( 28 ). (frontiersin.org)
They are usually generated from either exons or introns of both protein-coding and non-coding transcripts that are processed by RNA polymerase II (Pol II) [ 12 - 14 ]. (ijbs.com)
Instead of heat, these methods typically employ a strand-displacing DNA polymerase, like Bst DNA Polymerase, Large Fragment , to separate duplex DNA. (neb.com)
The sequence profiles and Terminator digests suggest that CymRSV siRNAs are produced from the structured positive strand rather than from perfect double stranded RNA or by RNA dependent RNA polymerase. (uea.ac.uk)
A remarkable feature of RNAi is that, once started, it initiates a positive feedback loop, whereby the sliced RNA fragments are converted to more dsRNA by host RNA-dependent RNA polymerase, which give rise to more siRNAs. (unibas.ch)
Specific functional analogies are drawn between several components of CASS and proteins involved in eukaryotic RNAi, including the double-stranded RNA-specific helicase-nuclease (dicer), the endonuclease cleaving target mRNAs (slicer), and the RNA-dependent RNA polymerase. (biomedcentral.com)
In the process of transcription, DNA duplex unwinding inside the RNA polymerase, the RNA synthesis, RNA polymerase moves forward along the DNA duplex, RNA polymerase removed recombine into double stranded DNA structure, the entire process of transcription in, DNA double-stranded structure is still intact, but it will not break because there are gaps in the transcription process. (yantuo.com.cn)
This enzyme, called RNA polymerase, makes messenger RNA by moving along the right-handed DNA duplex. (mit.edu)
Only the genes that are being expressed have it, as only they have the RNA polymerase molecule moving along the DNA," Professor Rich said. (mit.edu)

RNAi can be performed in mammalian cells using short RNAs, which generally do not induce IFN responses. (idtdna.com)
Dicer-substrate RNAi methods take advantage of the link between Dicer and RISC loading that occurs when RNAs are processed by Dicer. (idtdna.com)
These 27mer duplexes have increased potency in RNAi compared to traditional 21mer siRNAs. (idtdna.com)
In particular, the RNA interference (RNAi) pathways are of notable significance for the control of viral infections. (mdpi.com)
Asn1 , Ppo5 , PhL , R1 , and VInv ), which results in the reduced level of mRNA transcripts (and subsequently expressed proteins) for those same genes using the RNA interference (RNAi) pathway. (canada.ca)
From RNA interference (RNAi) to CRISPR, there are several methods that researchers can use to manipulate gene function, each with its own strengths and weaknesses. (technologynetworks.com)
RNA interference (RNAi) was the primary tool for disrupting gene expression (along with zinc finger nucleases (ZFNs) and transcription activator-like effector nuclease (TALENs)) but newer CRISPR-based technologies, including CRISPR knockout (CRISPRko) and CRISPR interference (CRISPRi) are viable options. (technologynetworks.com)
RNAi involves transferring a double-stranded RNA (dsRNA) into a cell where it is cleaved and processed into smaller RNA fragments (21 nucleotides). (technologynetworks.com)
Importantly, RNAi-based knockdown is temporary, and effect duration is contingent upon RNA turnover (both for endogenous mRNA and exogenous RNAi modulators). (technologynetworks.com)
RNAi using dsRNA has been found to evoke a double-stranded RNA immune response in mammalian cells which can affect cell viability. (technologynetworks.com)
In contrast to RNAi, CRISPR-based gene manipulation requires a guide RNA and a programmable Cas endonuclease protein. (technologynetworks.com)
In antiviral RNA interference (RNAi) the DICER enzyme processes virus-derived double-stranded RNA (dsRNA) into small interfering RNAs (siRNAs) that guide ARGONAUTE proteins to silence complementary viral RNA. (biobender.com)
Although mammalian infections are vunerable to experimental RNA disturbance (RNAi) via artificial little interfering RNAs (siRNAs) VX-680 (1) the life of an all natural antiviral RNAi response in mammals is normally debated (2). (biobender.com)
First in lots of contaminated somatic cells viral double-stranded RNA (dsRNA) sets off the powerful and non-sequence-specific interferon (IFN) response (3) that may possess generally supplanted antiviral RNAi features (4). (biobender.com)
Since then, he has been working as a postodoc in Dr. Wassenegger's lab (RLP AgroScience GmbH, AlPlanta) and his main field of interest is RNA-interference (RNAi) and RNA-directed DNA methylation (RdDM) in plants. (degruyter.com)
Since then, she has been working as a postodoc in Dr. Wassenegger's lab (RLP AgroScience GmbH, AlPlanta) and her main field of interest is RNA-interference (RNAi) and viroid biology in plants. (degruyter.com)
Comparative-genomic analysis of CRISPR and cas genes leads to the hypothesis that the CRISPR-Cas system (CASS) is a mechanism of defense against invading phages and plasmids that functions analogously to the eukaryotic RNA interference (RNAi) systems. (biomedcentral.com)
RNA interference (RNAi) is a biological process conserved in most eukaryotes and characterized by the sequence-specific degradation of target RNA by complementary small RNAs (sRNAs) [ 1 ] . (encyclopedia.pub)
RNAi pathways are triggered by double-stranded RNA (dsRNA) processed into sRNA duplexes by Dicer ribonucleases [ 1 ] [ 2 ] . (encyclopedia.pub)
Comparative analyses of the genome indicated that CRISPR and cas proteins work together, and prokaryotic cells have an acquired immune system similar to that of the RNA-interference (RNAi) seen in eukaryotic cells (7). (idcmjournal.org)

This toxicity can be avoided by switching to short interfering RNAs (siRNAs), which are truncated RNA duplexes that bypass the aforementioned dsRNA cleavage step, retain targeted gene silencing abilities of dsRNA, and do not trigger the deleterious immune response in mammalian cells. (technologynetworks.com)
Fig. 1 EMCV-derived siRNAs in infected mESCs The symmetrical 5′ and 3′ EMCV reads mapped to the regions where dsRNA replication-intermediates (RIs) initiate during positive- and negative-strand synthesis. (biobender.com)
Phased perfect duplexes with 2-nt 3′ overhangs are signature products of sequential dicing of long dsRNA (19 20 The DCR-dependency of EMCV-derived vsRNAs was thus explored in knockout (mESCs and following differentiation The use of mESCs granted an investigation of viral siRNA accumulation in genetically identical cells but under distinct differentiation states. (biobender.com)
Over the past decade our double-stranded RNA (dsRNA)antibodies have been used extensively to detect and characterise plant and animal viruses with dsRNA genomes or intermediates. (nordicmubio.com)
in 2006, where J2 was used to show that all the positive strand RNA viruses tested produced copious amounts of dsRNA in infected cells, this antibody has been used extensively in a wide range of systems, as documented in over 200 scientific publications. (nordicmubio.com)
Mouse monoclonal antibody J2 recognises double-stranded RNA (dsRNA) provided that the length of the helix is greater than or equal to 40 bp. (nordicmubio.com)
Long dsRNA is chopped by dicer enzymes into small interfering (si)RNAs, 21 to 24 base pair duplexes, consisting of a guide and a passenger-strand. (unibas.ch)
From these sequences a series of constructs will be derived that express hairpins, i.e. dsRNA with a loop between the RNA arms. (unibas.ch)
Dicer cleaves long dsRNA molecules into short, 21-22 nucleotide duplexes which are subsequently unwound by the RISC to yield mature siRNAs. (biomedcentral.com)
The RNA editing enzyme ADAR1 has recently emerged as a key regulator that prevents innate immune pathway activation, principally the cytosolic dsRNA sensor MDA5, from inducing interferon in response to double-stranded RNA structures within endogenous RNAs. (edu.au)
Multiple complexes were formed between the intact domain and dsRNA, saturating at a density of about one p20 molecule/11.25 base-pairs (or one turn) of duplex, whereas p10 achieved only about half of this packing density. (cshl.edu)

The proteins involved in homologous recombination have to work around other processes that go on inside the nucleus, such as the transcription of DNA in genes into RNA molecules. (elifesciences.org)
These results reveal how Cas9 uses PAM recognition to quickly identify potential target sites while scanning large DNA molecules, and to regulate scission of double-stranded DNA. (nature.com)
Long dsRNAs are degraded by the endoribonuclease Dicer into small effector molecules called siRNAs (small interfering RNAs). (idtdna.com)
Garrett performed in vitro and in vivo genetic selections to understand prospects for use of SELEX methods in finding novel RNA molecules with novel inhibitory functions. (mayo.edu)
The team "RNA Molecular Machines and human pathlogies " specialises in structural biology of proteins and RNA, and of their complexes with small molecules. (cnrs.fr)
Ribonucleoproteins (RNPs) are complexes composed of proteins and RNA molecules that play crucial roles in the cell. (cnrs.fr)
Small non-protein-coding RNA molecules, composed of around 22 nucleotides, are commonly named as miRNAs ( 1 - 3 ). (frontiersin.org)
At least in plants, DNA regions that become de novo methylated can be defined by homologous RNA molecules in a process termed RNA-directed DNA methylation (RdDM). (degruyter.com)
Viroids are pathogenic circular, non-coding, single-stranded RNA molecules. (degruyter.com)
Viroids are non-encapsidated, single-stranded (ss), 250-400 nucleotide (nt)-long circular RNA molecules that do not encode proteins (1, 2). (degruyter.com)
Upon inoculation, mature Pospiviroidae RNA molecules enter the plant cell nucleus. (degruyter.com)
RNA molecules can also be detected and manipulated through amplification via the use of reverse transcriptases (RT), which are RNA-dependent DNA Polymerases. (neb.com)
A critical component of this defence is the capacity to discriminate foreign RNA molecules, which are distinct from most cellular RNAs in structure and/or modifications. (edu.au)
Both p20 and p10 bound preferentially to structured RNA molecules. (cshl.edu)
Lund University, P.O. Box 124 results from the free duplex with those from its complex with netropsin, S-22100, Lund, Sweden water molecules in the ``spine of hydration'' in the AATT region of the minor groove could be distinguished from hydration water elsewhere in the duplex. (lu.se)
The NMRD data show that all water molecules associated with the duplex, except the ®ve molecules in the spine, have residence times signi®cantly shorter than 1 ns at 4C. (lu.se)

DsiRNAs are 27mer duplex RNAs that demonstrate increased potency in RNA interference compared to traditional, 21mer siRNAs. (idtdna.com)
What is RNA interference? (idtdna.com)
RNA interference is a conserved pathway common to plants and mammals, where double-stranded RNAs (dsRNAs) suppress expression of genes with complementary sequences [ 1-2 ]. (idtdna.com)
A consortium of Swiss and Indian scientists T Hohn and K Veluthambi, experts in begomo-virology, transgenesis and RNA-interference was formed to gain knowledge of the genetic diversity of I/SL/ACMV and their satellites in Southern India, as well as of the host plants affected and about their interaction. (unibas.ch)

During the life cycle of HBV, RT utilizes a single-stranded viral genomic RNA as a template to synthesize a hybrid RNA-DNA duplex, and then converts it to double-stranded DNA (ds-DNA). (biomedcentral.com)
For example, murine gammaherpesvirus 68 (MHV-68)-encoded miRNAs are located downstream of viral tRNAs and transcribed by RNA Pol III [ 2 ]. (ijbs.com)
Third varied virus-infected mammalian cell types accumulate virus-derived small RNAs (vsRNAs) but these have unspecified functions (5) and lack the biochemical features size and distribution patterns of flower and invertebrate viral siRNAs (6-9). (biobender.com)
Is viral single-stranded RNA in the absence of reverse transcriptase infectious? (stackexchange.com)
A protein phosphatase 1 inhibitor, 1E7-03, and siRNA-mediated suppression of viral antigens were used to demonstrate de novo synthesis of viral RNAs and antigens in CD4 + T cells, respectively. (prolekarniky.cz)
Both deep sequencing techniques revealed a strong bias in vsiRNAs for the positive strand of the virus and identified regions on the viral genome that produced vsiRNA in much higher abundance than other regions. (uea.ac.uk)
The plant recognizes viral RNA in the form of double-strand (ds)RNA, a by-product of virus replication. (unibas.ch)
The guide-strand forms together with the Slicer protein AGO a "RISC"-complex which recognizes and cleaves cognate, i.e. in our case viral RNA. (unibas.ch)
The amiRNA transgene expresses a monocistronic MIRNA precursor sequentially processed into an amiRNA targeting a single site in a single viral RNA. (encyclopedia.pub)
The syn-tasiRNA transgene expresses a polycistronic TAS precursor sequentially processed into four different syn-tasiRNAs targeting multiple sites in multiple viral RNAs. (encyclopedia.pub)
Both amiRNA and syn-tasiRNA guide strands associated with AGO1 to silence viral RNAs through endonucleolytic cleavage or translational inhibition. (encyclopedia.pub)
Sequential processing by DCL1 produces the pre-amiRNA followed by the amiRNA duplex, and the amiRNA guide strand is incorporated into AGO1 to target complementary viral RNA, typically in a single site (Figure 1a). (encyclopedia.pub)

By controlling for end nucleotide identities and thermodynamics, the UC Berkeley team could "really start to pick apart the thermodynamic and structural parameters involved in strand selection," he said. (genomeweb.com)
Overall, the findings "indicate the presence of a hierarchy of parameters that dictate the necessity of human Dicer and its associated dsRBPs for strand-selection enhancement that considers thermodynamic, 5' nucleotide, and other structural contributions," the study's authors wrote. (genomeweb.com)
Artificial small RNAs (art-sRNAs) are 21-nucleotide small RNAs designed to recognize and silence complementary target RNAs with high specificity. (encyclopedia.pub)
They consist in 21-nucleotide sRNAs expressed in planta from endogenous sRNA precursors and computationally designed to silence target RNAs with high specificity [ 5 ] . (encyclopedia.pub)
Similarly, downregulation of Cdk9 was also observed following transfection of 22 nucleotide mature double stranded miR-1. (ac.ir)
Interestingly, transfection of synthetic 22 nucleotide mature single stranded miR-1 (miR-1-3p) induced Cdk9 expression in the fibroblast cells. (ac.ir)
Conclusion: Unlike miR-expressing vector or synthetic RNA duplexes designed to mimic the miRNA of interest that can downregulate gene expression, synthetic 22 nucleotide mature single stranded microRNA probably induces gene expression in a locus-specific manner. (ac.ir)
sgRNAs with +67 or +85 nucleotide (nt) tracrRNA tails mediated DNA cleavage at all target sites tested, with up to fivefold higher levels of indels than the corresponding crRNA-tracrRNA duplexes ( Fig. 1b and Supplementary Fig. 1a ). (cdc.gov)
Moreover, speci®c hy- found in narrow minor groove regions in a variety dration patterns seem to play a role in nucleotide sequence recognition by proteins (Otwinowski of oligonucleotide duplexes (PriveÂ et al. (lu.se)

When the RNA fragments complex with a complementary (target) mRNA sequence and an endogenous silencing complex, mRNA is fragmented, preventing its translation. (technologynetworks.com)
However, a series of rare autoimmune/autoinflammatory diseases in humans highlight the propensity for the innate immune sensing system to be activated by endogenous cellular double-stranded RNAs (dsRNAs), underscoring the fine line between distinguishing self from non-self. (edu.au)
Background: MicroRNAs (miRNAs) are endogenous, non-coding short RNAs (~22 nt) that can downregulate gene expression by translational repression, mRNA degradation, or transcriptional repression. (ac.ir)

As a result, more siRNAs are produced, more virus RNA is destroyed and more systemic silencing signal reaches the growing tissue. (unibas.ch)
siRNAs are produced from double-stranded RNAs of viruses and transposable elements, which are processed by the dicer nuclease, one of the essential components of the RNA-Induced Silencing Complexes (RISCs) [ 7 - 9 ]. (biomedcentral.com)

DNA-templated assembly was shown to enable the patterning of proteins and create conductive nanowires ( 2 ), and the complexity of these systems increased with landmark demonstration of structures like the DNA octahedron folded from 1.7-kb single-stranded (ss)DNA ( 3 ). (allenpress.com)
Single-stranded DNAs (ssDNA) with lengths ranging from 10-120mer were compared to double stranded DNA (dsDNA) with lengths of 10-300mer as well as to proteins of different sizes. (chromatographytoday.com)
His fields of research comprise RNA-mediated gene silencing processes with a focus on epigenetic phenomena, including studies on RNA-directed DNA methylation, the characterization of virus silencing suppressor proteins, the development of plant bioreactor platforms and viroid research. (degruyter.com)
The double-stranded (ds) RNA-activated protein kinase, DAI (also known as PKR), contains an RNA-binding domain comprising two tandem repeats of a motif, the dsRBM, which is shared with a number of other proteins that interact with structured RNAs. (cshl.edu)
We have expressed the entire domain and the first copy of the motif in Escherichia coli and purified the two proteins, p20 and p10, to apparent homogeneity in order to study their interactions with RNA and with the intact kinase enzyme. (cshl.edu)
Firstly, the spacer sequences in the CRISPR system, which arise from the phage genome, were transcribed with small RNAs, known as crRNA that were responsible for guiding the cas proteins to the target DNA (9). (idcmjournal.org)

In animals, the degree of base pairing between a miRNA and its target messenger RNA seems to determine whether the regulation occurs through cleavage or translation inhibition 1 . (nature.com)
After pre-miRNAs are transported to the cytoplasm, RNase III Dicer and TRBP (transactivation-response RNA-binding protein) cleave them into double-stranded miRNA duplexes of ~22 nt ( 30 , 31 ). (frontiersin.org)
Subsequently, the duplex unwinds and miRNA loads into RNA-induced silencing complex (RISC) to execute gene-silencing either through cleavage of the complementary mRNA or by suppression of mRNA translation [ 3 ]. (biomedcentral.com)
RIIIa and RIIIb process the 3p and 5p arms of hairpin respectively and liberate the duplex of miRNA:miRNA* with two nucleotides (nt) 3' overhang [ 9 ]. (biomedcentral.com)
In order to investigate microRNA functions in gene regulation and/or to modulate their expression in pathogenic conditions, microRNAs are overexpressed by using plasmid or synthetic RNA duplexes designed to mimic the miRNA of interest. (ac.ir)
This study aims to reveal the mechanisms of miRNA-RNA interactions in nucleus and cytoplasm. (biomedcentral.com)
Then, the Dicer protein can act on the pre-miRNA and cleave the end loop of the pre-miRNA to generate a double-stranded RNA with a length of approximately 22 base pairs (bp) [ 1 , 2 ]. (biomedcentral.com)

A guide RNA (gRNA) is a piece of RNA that functions as a guide for RNA- or DNA-targeting enzymes, with which it forms complexes. (wikipedia.org)
Cas9-guide RNA complexes are also effective genome engineering agents in animals and plants. (nature.com)
We utilized a hybrid computational approach to model the atomistic structures of HBV-RT/DNA-RNA/dATP and HBV-RT/DNA-RNA/TFV-DP (tenofovir diphosphate) complexes with the native hybrid DNA-RNA substrate in place. (biomedcentral.com)
Solvated interaction energy (SIE) calculated in MD simulations of HBV-RT/DNA-RNA/TFV-DP complexes indicate no differential binding affinity between TFV-DP and HBV-RT variants identified in patients with slow or rapid response to TDF treatment. (biomedcentral.com)
Where possible, we have also tackled protein/RNA complexes, when the RNA binding site is known. (cnrs.fr)
The guide RNA complexes with the Cas endonuclease, is transported to the nucleus, and creates a DNA double-strand break (DSB) at a site pre-programmed in the targeting sequence of the guide RNA. (technologynetworks.com)
More commonly, RNA is single stranded and can form complexes and unusual shapes. (nakb.org)
The apparent Kd for the p20-VA RNA interaction was estimated as 3.5 x 10(-7) M and at least three complexes were detected, but no distinct complexes were visualized for the interaction between p10 and VA RNA. (cshl.edu)

The nascent siRNA associates with Dicer, TRBP, and Argonaut (Ago2) to form the RNA-induced silencing complex (RISC), which mediates gene silencing (Figure 1) [ 3 ]. (idtdna.com)
Once in RISC, one strand of the siRNA (the passenger strand) is degraded or discarded, while the other strand (the guide strand) remains to direct sequence selection of the silencing complex. (idtdna.com)
The Ago2 component of RISC is a ribonuclease that cleaves a target RNA under direction of the guide strand. (idtdna.com)
The RNA-induced silencing complex (RISC) pathway in mammalian cells. (idtdna.com)
It was previously concluded that Dicer is dispensable for asymmetric RISC loading, but our expanded set of duplex RNAs has demonstrated that this conclusion is true only for certain types of duplex RNAs such as those with unfavorable 5' nucleotides on the passenger strand or with terminal mismatches," they wrote in RNA . (genomeweb.com)
4. Incorporate 2'-F bases, 5-me dC or 2-amino dA preferentially at the 5' end of the sense strand to block incorporation of the sense strand in to the RISC. (genelink.com)
One of the strands of the duplex is preferentially loaded into an ARGONAUTE (AGO) protein, and the resulting complex termed RNA-induced silencing complex (RISC) recognizes and silences complementary target RNA through diverse mechanisms [ 3 ] [ 4 ] . (encyclopedia.pub)
The double-stranded RNA duplex leads RNA-induced silencing complex (RISC), containing a member of the conserved Argonaute (Ago) protein family, to target sites of mRNAs, resulting in the destabilization of the mRNAs and/or inhibition of translation [ 4 , 5 ]. (biomedcentral.com)

Basically, we showed that Dicer is the physical sensor of thermodynamic asymmetry of siRNA duplexes in humans," he said. (genomeweb.com)
1. Alternating 2'-F bases and 2'OMe bases in siRNA enhances duplex stability and are more resistant to RNase degradation. (genelink.com)
Some oligonucleotides, such as antisense oligonucleotides, act as single-strands, but also double stranded oligonucleotides exist, such as the case of small interfering RNA (siRNA) duplexes. (chromatographytoday.com)

The University of Tokyo team, however, only looked at a "very limited set" of duplex RNAs with "very particular parameters in terms of the end nucleotides and terminal mismatches" - all of which could have affected their findings. (genomeweb.com)
microRNAs (miRNAs) are a large class of small non-coding RNAs with a length of 21-23 nucleotides (nt) [ 11 ]. (ijbs.com)

The protein, double-stranded RNA adenosine deaminase, has long been recognized as an "editor" of the genetic message. (mit.edu)

Since the DSB ends undergo nucleolytic degradation (resection) of their 5′-ending strands, we investigated the contribution of resection in this DSB-induced transcriptional inhibition. (elifesciences.org)
The recruitment of this machinery results in the production of viroid-derived small RNAs (vd-sRNAs) that mediate RNA degradation and DNA methylation of cognate sequences. (degruyter.com)
The TREX1 double-stranded DNA degradation activity is defective in dominant mutations associated with autoimmune disease. (wakehealth.edu)

Small CRISPR RNAs guide antiviral defense in prokaryotes. (nature.com)
Art-sRNAi tools have been broadly used in plants to confer antiviral resistance against multiple RNA and DNA viruses, and to viroids as well, however there are still important limitations to overcome. (encyclopedia.pub)

Building on previous research, representative nucleic acid duplexes were split into logical monomer segments, and atomic coordinates were used to create solid models for 3D printing. (allenpress.com)
RNase H recognizes A-form nucleic acid duplexes, which strongly suggests the domain IV core interacts with double-stranded RNA in the context of the spliceosome. (ualberta.ca)

The clustered regularly interspaced short palindromic repeats (CRISPR)-associated enzyme Cas9 is an RNA-guided endonuclease that uses RNA-DNA base-pairing to target foreign DNA in bacteria. (nature.com)
This enzyme, usually isolated from bacteriophage T4 and called T4 DNA ligase, forms a covalent bond between the 5′- phosphate at the end of one strand and the 3′-hydroxyl of the adjacent strand. (biologydiscussion.com)
We used the Terminator 5′-Phosphate-Dependent Exonuclease to study the 5′ end of vsiRNAs and showed that a perfect control duplex was not digested by the enzyme without denaturation and that the efficiency of the Terminator was strongly affected by the concentration of the substrate. (uea.ac.uk)
The enzyme acts only on double-stranded RNA. (mit.edu)
Hence, the Z-DNA binding domain on this enzyme may facilitate its finding genes that are actively transcribing and producing messenger RNA. (mit.edu)

Breaks that form across both strands in a DNA double helix are considered the most dangerous type of DNA damage, and can cause a cell to die or become cancerous if they are not repaired accurately. (elifesciences.org)
Garrett's work included in vitro selections to optimize DNA recognition by RNA using triple helix formation in libraries that maximized display if the interacting macromolecules, and in techniques for reversible immobilization of duplex DNA on solid supports. (mayo.edu)
B-DNA is a right-handed double helix with a wide and narrow groove. (nakb.org)
A-DNA is also a right-handed double helix. (nakb.org)
Characterizing the binding preferences of the domain IV revealed the highest affinity is for a 4-helix junction structure adopted by the very RNAs at the spliceosome active site. (ualberta.ca)
Higher-order structure of DNA is also called DNA topology, means on the basis of the DNA double helix, further distort the specific spatial structure formation. (yantuo.com.cn)
Wherein, topoisomerase I and may be connected to the catalytic instantaneous breaking the DNA double helix structure of single strand DNA, and no energy is required cofactors such as ATP or NAD. (yantuo.com.cn)
This finding suggests that the plasmid DNA double helix gap little effect on its transcription. (yantuo.com.cn)

The initial editing event occurs when a gRNA forms an RNA duplex with a complementary mRNA sequence just downstream of the editing site. (wikipedia.org)
In the case of "pan-edited" mRNAs, the duplex unwinds and another gRNA then forms a duplex with the edited mRNA sequence and initiates another round of editing. (wikipedia.org)
These single-stranded DNA 'tails' are then free to interact with an intact copy of the same DNA sequence from elsewhere in the cell's nucleus, which is used as a guide when repairing the damage. (elifesciences.org)
Competition assays provide evidence that DNA strand separation and RNA-DNA heteroduplex formation initiate at the PAM and proceed directionally towards the distal end of the target sequence. (nature.com)
Manipulation of the oligo sequence to increase the duplex stability or in some cases to decrease the duplex stability in certain loop structure will lead to oligos with increased affinity for the target molecule. (genelink.com)
The stability of a particular double stranded sequence is related to the number of hydrogen bonds formed. (dnastar.com)
Binds the conventional octamer sequence in double-stranded DNA. (nih.gov)
Different high-throughput sequencing techniques have different reproducible sequence bias and generate different profiles of short RNAs. (uea.ac.uk)
In solution, the studied sequence is forming a symmetric double-stranded structure with four central consecutive T·T wobble pairs flanked by G·C Watson-Crick base pairs. (ox.ac.uk)
We find that SpCas9 tolerates mismatches between guide RNA and target DNA at different positions in a sequence-dependent manner, sensitive to the number, position and distribution of mismatches. (cdc.gov)
Because the major difference between this sgRNA design and the native crRNA-tracrRNA duplex is the length of the tracrRNA sequence, we tested whether extension of the tracrRNA tail would improve SpCas9 activity. (cdc.gov)

Emerging evidence indicate that the mammalian checkpoint kinase ATM induces transcriptional silencing in cis to DNA double-strand breaks (DSBs) through a poorly understood mechanism. (elifesciences.org)
In mammalian cells, inhibiting the transcription of genes around a double-strand DNA break depends on a signaling pathway that is activated whenever DNA damage is detected. (elifesciences.org)
The structure of the mammalian RNase H2 complex provides insight into RNA.NA hybrid processing to prevent immune dysfunction. (wakehealth.edu)

RNA-guided human genome engineering via Cas9. (nature.com)
RNA-programmed genome editing in human cells. (nature.com)
Genome engineering of Drosophila with the CRISPR RNA-guided Cas9 nuclease. (nature.com)
The Streptococcus pyogenes Cas9 (SpCas9) nuclease can be efficiently targeted to genomic loci by means of singleguide RNAs (sgRNAs) to enable genome editing 1 - 10 . (cdc.gov)
Both crRNA-tracrRNA duplexes and sgRNAs can be used to target SpCas9 for multiplexed genome editing in eukaryotic cells 1 , 3 . (cdc.gov)

MicroRNAs (miRNAs) are short non-coding RNAs that posttranscriptionally regulate gene expression inside the cell. (frontiersin.org)
Recombinant human Argonaute2 alone is capable of acquiring a guide RNA strand by associating with siRNAs or microRNAs, triggering targeted cleavage of transcripts in vitro , according to a paper published last month. (genomeweb.com)
The two main classes of plant art-sRNAs are artificial microRNAs (amiRNAs) and artificial/synthetic trans-acting small interfering RNAs (atasiRNAs/syn-tasiRNAs, hereafter syn-tasiRNAs) [ 5 ] . (encyclopedia.pub)

RNA-editing Guide RNA was discovered in 1990 by B. Blum, N. Bakalara, and L. Simpson in maxicircle DNA and contains sequences matching those within the edited regions of the mRNA. (wikipedia.org)
The guide RNA are mainly transcribed from the intergenic region of DNA maxicircle and these are complementary to mature mRNA. (wikipedia.org)
A single gRNA usually encodes the information for several editing sites (an editing "block"), the editing of which produces a complete gRNA/mRNA duplex. (wikipedia.org)
Ribonucleic acid (RNA) is present in several forms - messenger RNA (mRNA), transfer RNA (tRNA), and ribosomal RNA (rRNA). (nakb.org)
The ribosomes pick the appropriate t-RNA which has brought the corresponding aminoacid to the three letter code found on the mRNA to make the protein. (nakb.org)

The insertions and deletions are mediated by short guide RNA (gRNAs) which encode the editing information in the form of complementary sequences (allowing GU as well as GC base pairs). (wikipedia.org)
A second major difference between A- and B-forms is the placement of the base-pairs within the duplex. (nakb.org)

CRISPR RNA maturation by trans-encoded small RNA and host factor RNase III. (nature.com)
the CRISPR-associated nuclease Cas9 (SpCas9), a specificity-determining CRISPR RNA (crRNA), and an auxiliary trans-activating crRNA (tracrRNA) 11 . (cdc.gov)

strands were offset by VX-680 2 nt (Fig. 1D and fig. S1 C to E). Northern analyses using oligonucleotide probes confirmed accumulation of the predicted 5′-end 22-nt siRNAs in EMCV-infected cells (Fig. 1E). (biobender.com)
I am interested in the structural differences caused by benzopurines and benzopyrimidines at the oligonucleotide level between RNA and xRNA, both in single-stranded and double-stranded form. (stackexchange.com)

In mammals, Dicer processing occurs as a complex with the RNA-binding protein TRBP. (idtdna.com)
However, this is true only in certain cases, and Dicer and trans-activation response RNA-binding protein - TRBP - or protein activator of PKR - PACT - are often "essential" for achieving maximal levels of strand selection, the report, appearing in RNA , notes. (genomeweb.com)
In a 2011 paper , he and his colleagues in the lab of UC Berkeley researcher Jennifer Doudna examined Dicer and TRBP and PACT, its double-stranded RNA-binding protein partners, to see if they sense the thermodynamics of duplex RNAs in human cells the same way they do in flies. (genomeweb.com)
Furthermore, even when Ago2 alone is capable of robust strand selection, Dicer and TRBP or PACT, in some cases, enhance that selection, as is the case with the miRNAs tested here," they added. (genomeweb.com)

This process is called 'resection' and it exposes single strands of DNA. (elifesciences.org)

SmartBase TM modifications go beyond the traditional use of RNA bases for constructing synthetic siRNAs to specifically increase duplex stability, nuclease resistance and cell permeation. (genelink.com)
Using the SURVEYOR nuclease assay 13 , we assessed the ability of each Cas9-sgRNA complex to generate indels in human embryonic kidney (HEK) 293FT cells through the induction of DNA doublestranded breaks (DSBs) and subsequent nonhomologous end joining (NHEJ) DNA damage repair (Online Methods). (cdc.gov)

A large amount of short interfering RNA (vsiRNA) is generated from plant viruses during infection, but the function, structure and biogenesis of these is not understood. (uea.ac.uk)
We will construct variants that target all these viruses, including those that mimic natural micro (mi)RNAs or transacting (ta)siRNAs down-regulating host genes, and those provided with constitutive or virus-inducible promoters. (unibas.ch)
In particular, numerous studies have reported the successful application of art-sRNAi tools to induce resistance against a large number of RNA and DNA viruses in model and crop species. (encyclopedia.pub)

This unnatural nucleic acid was developed as a mimic for A-RNA. (ox.ac.uk)

The Terminator experiments also showed that vsiRNAs were not perfect duplexes. (uea.ac.uk)

DsiRNAs are chemically synthesized, 27 nt RNA duplexes that are optimized for Dicer processing and are ideal for small-scale in vitro applications. (idtdna.com)
There are two major, distinct forms of regulatory small RNAs involved in eukaryotic gene silencing: small interfering (si) RNAs and micro (mi) RNAs. (biomedcentral.com)
From the studies on the CRISPR-Cas9 system, in addition to the crRNA, a second small trans-activating CRISP RNA (tracrRNA) was discovered in 2011. (idcmjournal.org)
As reported, miR-25 and miR-92a show clear nuclear enrichment in rat primary cortical neurons by using a combination of microarray analysis and small RNA deep sequencing [ 10 ]. (biomedcentral.com)

Despite differing in their biogenesis pathway (see below), both classes of art-sRNAs function similarly by associating with AGO1 to specifically silence target RNAs through endonucleolytic cleavage or translation repression (Figure 1). (encyclopedia.pub)

3. Guide strand 5' end (Antisense) has a seed region of 2-8 bases that should be A-U rich. (genelink.com)

A programmable dual-RNA-guided DNA endonuclease in adaptive bacterial immunity. (nature.com)

Here we use single-molecule and bulk biochemical experiments to determine how Cas9-RNA interrogates DNA to find specific cleavage sites. (nature.com)
We show that both binding and cleavage of DNA by Cas9-RNA require recognition of a short trinucleotide protospacer adjacent motif (PAM). (nature.com)
Non-target DNA binding affinity scales with PAM density, and sequences fully complementary to the guide RNA but lacking a nearby PAM are ignored by Cas9-RNA. (nature.com)
Figure 1: DNA curtains assay for target binding by Cas9-RNA. (nature.com)
Figure 2: Cas9-RNA remains bound to cleaved products and localizes to PAM-rich regions during the target search. (nature.com)
Figure 3: Cas9-RNA searches for PAMs and unwinds dsDNA in a directional manner. (nature.com)
Both RNAs formed a duplex which directed the Cas9 to its target (10). (idcmjournal.org)

Our characterization of the protein/RNA binding interface by complementary footprinting techniques currently provides the best model of how RNA interacts with an essential protein component at the heart of the spliceosome. (ualberta.ca)

Bolandi Z, Ghanbarian H. Increasing the specific expression of Cdk9 gene by single-stranded adult microRNA-1 in fibroblast cells. (ac.ir)
2 µg RNA samples were reverse transcribed to cDNA using microRNA-1 specific stem loop and random hexamer primers and MLV reverse transcriptase.q-PCR was performed with the 'SYBR Green I Master Mix' kit. (ac.ir)

Previous research has reported that forming a double-strand break in the DNA reduces the levels of transcription for the genes that surround the break, but it was not clear how this occurred. (elifesciences.org)
One of the next challenges will be to see if the resection process makes any contribution to changes in the transcription of genes that surround a double-strand break in mammals as well. (elifesciences.org)
More than 90% of human genes undergo a processing step called splicing, whereby non-coding introns are removed from initial transcripts and coding exons are ligated together to yield mature messenger RNA. (ualberta.ca)
Its affinity for Z-DNA may help it find genes that are producing the messenger RNA which it "edits. (mit.edu)

In the end, the investigators found that Ago2 could properly select a guide strand on its own in some cases. (genomeweb.com)
2. Use a few 2'OMe bases in the seed region of the guide strand to decrease the Tm below 21.5 of this region. (genelink.com)

Drosha, RNase III, and DGCR8, the RNA-binding protein, further process pri-miRNAs into stem-loop structured precursor miRNAs (pre-miRNAs) of ~70 nt ( 29 ). (frontiersin.org)

The Fap7 ribosome assembly factor is involved in regulates ribosomal RNA processing and is essential for embryogenesis and tumour growth, most probably through the ribosomal protein-hDM2-p53 pathway. (cnrs.fr)

Members of the Pospiviroidae family replicate in the nucleus through double-stranded RNA intermediates, attracting the host RNA silencing machinery. (degruyter.com)
This changes the information carried by the RNA from the nucleus of the cell to the cellular machinery. (mit.edu)
In this study, the miRNAs and their target mRNAs in the Argonaute2 (Ago2) complex of nucleus and cytoplasm of gastric cancer cells were characterized using high-throughput sequencing of RNAs isolated by crosslinking immunoprecipitation (HITS-CLIP). (biomedcentral.com)

These RNPs are involved in a wide range of cellular and biochemical functions, from maturation of different classes of RNAs to protein synthesis, and represent some of the most complicated molecular machines. (cnrs.fr)
Each of these RNA forms is involved in different steps of protein synthesis. (nakb.org)

Uridylyltransferase inserts 'U' at 3' terminal and RNA ligase is responsible for joining two cut ends. (wikipedia.org)
The ssRNA(+), likely transferred into the nucleolus, is finally processed by a type III RNase and a DNA LIGASE into unit-length circular RNAs (8) ( Figure 1 ). (degruyter.com)

crRNA and tracrRNA duplexes can also be fused to generate a chimeric sgRNA 12 that mimics the natural crRNA-tracrRNA hybrid. (cdc.gov)

Although an sgRNA design consisting of a truncated crRNA and tracrRNA had been previously shown to mediate efficient cleavage in vitro 12 , it failed to achieve detectable cleavage at several loci that were efficiently modified by crRNA-tracrRNA duplexes bearing identical guide sequences 1 . (cdc.gov)
Furthermore, both sgRNA designs efficiently modified PVALB loci that were previously not targetable using crRNA-tracrRNA duplexes 1 ( Fig. 1b and Supplementary Fig. 1b ). (cdc.gov)
We performed northern blot analyses for the guide RNA truncations and found increased levels of expression for the longer tracrRNA sequences, suggesting that improved target cleavage was at least partially due to higher sgRNA expression or stability ( Fig. 1c ). (cdc.gov)

Both platforms require RNA-based reagents, and can lower gene expression, but they differ in more ways than they are similar. (technologynetworks.com)

A less-pronounced symmetrical reads distribution was also observed at the EMCV RNA 3′-end whereas the remaining 21- to 23-nt reads originated from discrete positive-strand regions (Fig. 1C). (biobender.com)

The discovery of the elaborate and versatile systems of RNA silencing in eukaryotes is one of the pivotal advances in biology of the last decade [ 1 - 6 ]. (biomedcentral.com)

Other restriction enzymes make staggered single-strand cuts, producing short single-stranded projections at each end of the digested DNA. (biologydiscussion.com)
Roughly speaking how stable are short sections of single-stranded RNA in exposed environments compared to double-stranded DNA? (stackexchange.com)
We found that most vsiRNAs have 5′ monophosphates, which was also confirmed by profiling short RNA libraries following either direct ligation of adapters to the 5′ end of short RNAs or after replacing any potential 5′ ends with monophosphates. (uea.ac.uk)
The Terminator exonuclease does not process double stranded RNA, and because short RNAs can quickly re-anneal at high concentration, this assay can be misleading if the substrate is not denatured and not analysed in a dilution series. (uea.ac.uk)

Adenosine-to-Inosine RNA editing by ADAR1 is proposed to destabilise duplexes formed from inverted repetitive elements within RNAs, which appear to prevent MDA5 from sensing these RNA as virus-like in the cytoplasm. (edu.au)

Resulting handheld helical models replicate the geometries in published structures and can now flex to form crossovers and allow biologically relevant zipping and unzipping to allow complex demonstrations of nanomachines undergoing strand displacement reactions. (allenpress.com)

Homologous recombination' is one of the main mechanisms used by cells to repair DNA double-strand breaks. (elifesciences.org)
Our main project is aimed at deciphering the molecular mechanisms of RNA molecular machines. (cnrs.fr)

Also binds single-stranded DNA and RNA at a site independent of the duplex site. (nih.gov)

Anatomy16

Organisms12

Diseases5

Chemicals and Drugs128

Analytical, Diagnostic and Therapeutic Techniques and Equipment27

Phenomena and Processes75

Information Science4

Health Care4

Polymerase9

RNAi20

DsRNA11

Molecules16

Interference4

Viral12

Nucleotide9

Endogenous3

SiRNAs are produced2

Proteins6

MiRNA7

Complexes8

RISC8

SiRNA3

Nucleotides2

Adenosine deaminase1

Degradation3

Antiviral2

Nucleic acid duplexes2

Enzyme5

Helix8

Sequence11

Mammalian3

Genome5

MicroRNAs3

MRNA5

Base pairs2

CRISPR RNA2

Oligonucleotide2

TRBP4

Single strands1

Nuclease2

Viruses3

Mimic1

Perfect duplexes1

Small4

Cleavage or translation1

Antisense1

Endonuclease1

Cas97

Characterization1

MicroRNA2

Genes4

Guide strand2

RNase III1

Ribosomal1

Nucleus3

Synthesis2

Ligase2

Generate1

TracrRNA3

Gene expression1

Positive-strand1

Eukaryotes1

Short4

Cytoplasm1

Structures1

Mechanisms2

Binds1