• 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)
  • The enzyme displays high specific activity towards double-stranded DNA, leaving single-stranded DNA or RNA undamaged in standard conditions. (qiagen.com)
  • One unit is defined as the amount of enzyme that causes an increase in absorbance at 260 nm of 1.0 in 30 minutes at 37°C in 50 mM Tris-HCl buffer, pH 8.0 (25°C) supplemented with 5 mM MgCl 2 , 0.1 mg/mL BSA and 0.5 mg/mL herring sperm DNA as a substrate. (qiagen.com)
  • A 1.575 mL reaction volume containing herring sperm DNA as a substrate is incubated for 30 minutes at pH 8 at 37°C with an enzyme that degrades DNA to acid-soluble oligonucleotides. (qiagen.com)
  • Protean offers Non-specific Endonuclease isolated from Serratia marcescens, which is a highly processive enzyme active under a variety of conditions and temperatures - Endonuclease S. marcescens. (pharma-industry-review.com)
  • The Endonuclease S. marcescens enzyme supplied by Protean, as well as all other enzymes manufactured by the company, is produced in a certified environment under ISO 9001 and ISO 13485 standards and fully approved for use in downstream GMP certified processes. (pharma-industry-review.com)
  • The Protean Non-specific Endonuclease S. marcescens enzyme is ideally suitable for pharmaceutical and biopharmaceutical manufacturing cGMP applications. (pharma-industry-review.com)
  • Cas9 (Streptococcus pyogenes CRISPR associated protein 9) is an endonuclease enzyme that, when recruited to a specific DNA sequence by the sgRNA (single guide RNA), introduces a double stranded break into the DNA. (genprice.com)
  • Here we describe a DNA polymerase assay that allows retrieving, in a single experimental set, association and dissociation rates, as well as the catalytic rate of the enzyme. (cnrs.fr)
  • One unit is defined as the amount of enzyme which will completely degrade 1 µg of pBR322 DNA in 10 minutes at 37°C in DNase I Reaction Buffer. (neb.com)
  • EDTA should be added to a final concentration of 5 mM to protect RNA from being degraded during enzyme inactivation (3). (neb.com)
  • Monarch DNase I is optimized for use in this workflow, and is available for purchase as a component of the Monarch Total RNA Enzyme Pack, ( NEB #T2019 ). (neb.com)
  • This suggests that these mutations are not the result of mistakes by the error-prone viral reverse transcriptase (RT) enzyme but rather represent mutations that are generated by the cellular non-homologous end joining (NHEJ) machinery that repairs broken DNA (Fig. 1 ). (biomedcentral.com)
  • An enzyme capable of hydrolyzing highly polymerized DNA by splitting phosphodiester linkages, preferentially adjacent to a pyrimidine nucleotide. (umassmed.edu)
  • The enzyme has a preference for double-stranded DNA. (umassmed.edu)
  • The endonuclease activity is effective over a wide range of conditions and the enzyme possesses an exceptionally high specific activity. (sydlabs.com)
  • One unit of Dr. Nuclease corresponds approximately to the required amount of enzyme to digest 37 μg of DNA in the reaction buffer, 50 mM Tris-HCl, pH 8.0, 1 mM MgCl2, for 30 minutes at 37°C. (sydlabs.com)
  • L1 spreads through a mechanism termed target-primed reverse transcription, in which the encoded enzyme (ORF2p) nicks the target DNA to prime reverse transcription of its own or non-self RNAs2. (bvsalud.org)
  • With sequence alignments and structure modeling to guide mutagenesis, we generated enzyme variants across motifs generally conserved or specific to RT subgroups. (bvsalud.org)
  • Colicin endonucleases and the H-N-H family of homing enzymes share a common active site structural motif that has similarities to the active sites of a variety of other nucleases such as the non-specific endonuclease from Serratia and the sequence-specific His-Cys box homing enzyme I-PpoI. (gla.ac.uk)
  • Here, we show that, the H-N-H enzyme from colicin E9 (the E9 DNase) shares many of the same basic enzymological characteristics as sequence-specific H-N-H enzymes including a dependence for high concentrations of Mg2+ or Ca2+ with double-stranded substrates, a high pH optimum (pH 8-9) and inhibition by monovalent cations. (gla.ac.uk)
  • We also show that this seemingly nonspecific enzyme preferentially nicks double-stranded DNA at thymine producing 3'-hydroxy and 5'-phosphate termini, and that the enzyme does not cleave small substrates, such as dinucleotides or nucleotide analogues, which has implications for its mode of inhibition in bacteria by immunity proteins. (gla.ac.uk)
  • The method uses restriction enzyme-based fragmentation and in vitro transcription to barcode and amplify genomic DNA prior to library construction. (genomeweb.com)
  • Each enzyme works only on one specific substance (called the substrate). (nih.gov)
  • DNA is a nucleic acid which is capable of duplicating itself via the enzyme known as DNA polymerase. (wikibooks.org)
  • Single-stranded exonuclease was determined in a 50 μL reaction containing 10,000 cpm of a radiolabeled single-stranded DNA substrate and 10 μL of enzyme solution incubated for 4 hours at 37°C. (qiagen.com)
  • Double-stranded endonuclease activity was determined in a 50 μL reaction containing 0.5 μg of pBR322 DNA and 10 μL of enzyme solution incubated for 4 hours at 37°C. (qiagen.com)
  • E.coli contamination was evaluated using 5 μL samples of enzyme solution were denatured and screened in a TaqMan qPCR assay for the presence of contaminating E.coli genomic DNA using oligonucleotide primers corresponding to the 16S rRNA locus. (qiagen.com)
  • The conversion from single-stranded to double-stranded form is carried out by the host's own DNA polymerase. (wikipedia.org)
  • The host's RNA polymerase binds to the viral genome and syntheses RNA. (wikipedia.org)
  • The ERCC5 protein may also function in other cellular processes, including RNA polymerase II transcription, and transcription-coupled DNA repair. (nih.gov)
  • Fluorescence energy transfer between the primer and the beta subunit of the DNA polymerase III holoenzyme. (colorado.edu)
  • Comparison of the strengths of the two dnaA promoters in an in vitro transcription system using methylated and unmethylated DNA templates suggests that the effect of methylation on dnaA2P is probably at the level of RNA polymerase/DNA interaction. (jax.org)
  • Studies of genes transcribed by RNA polymerase II (Pol II) have shown that open and closed chromatin structures are dynamically regulated through multiple mechanisms, including histone modifications, histone variant incorporation, and DNA methylation (reviewed in reference 17 ). (asm.org)
  • May also be involved in transcription-coupled repair of this kind of damage, in transcription by RNA polymerase II, and perhaps in other processes too. (abcam.cn)
  • The activity of gp2 is regulated by two other viral proteins: gp5 (single strand binding protein) and gp1# New viral genomes are produced via the rolling circle mechanism. (wikipedia.org)
  • The core microprocessor component DiGeorge syndrome critical region 8 (DGCR8) is a nonspecific RNA-binding protein. (musc.edu)
  • Presumably, this process involves the interaction between the host's bromodomain-containing viroid RNA-binding protein 1 (VIRP1) and the viroid's TR domain (6). (degruyter.com)
  • the section of RNA which binds to the genomic DNA is 18-20 nucleotides. (bmj.com)
  • We successfully inactivated VEEV genomic RNA utilizing these two protocols. (bvsalud.org)
  • Our cDNA synthesis method also inactivated the genomic RNA of eastern and western equine encephalitis viruses (EEEV and WEEV). (bvsalud.org)
  • We also tested whether the purified VEEV genomic RNA can produce infectious virions in the absence of transfection. (bvsalud.org)
  • This includes rapid methods that directly incorporate sequencing adapters into genomic DNA by engineered transposases, such as the indexed Nextera kits sold by Illumina. (genomeweb.com)
  • The CUTseq workflow digests genomic DNA using a type-II restriction endonuclease that leaves staggered ends, which are then ligated to specialized double-stranded DNA adapters that contain a sample-specific barcode sequence, a unique molecular identifier, an Illumina sequencing adapter, and a T7 promoter sequence. (genomeweb.com)
  • The researchers chose from a list of commercially available restriction enzymes, settling on NlaIII and HindIII, which respectively cut genomic DNA on average every 136 and 2,274 base pairs. (genomeweb.com)
  • The disorders are characterized by a defect in DNA repair mechanisms or genomic stability, and patients with these disorders show increased predisposition to cancer. (medscape.com)
  • Cas9-guide RNA complexes are also effective genome engineering agents in animals and plants. (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)
  • 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)
  • 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)
  • RNA-guided human genome engineering via Cas9. (nature.com)
  • Genome engineering of Drosophila with the CRISPR RNA-guided Cas9 nuclease. (nature.com)
  • CRISPR/Cas9 is a gene-editing technology which involves two essential components: a guide RNA to match a desired target gene, and Cas9 (CRISPR-associated protein 9)-an endonuclease which causes a double-stranded DNA break, allowing modifications to the genome (see figure 1 ). (bmj.com)
  • Cas9, one of the associated proteins, is an endonuclease that cuts both strands of DNA. (bmj.com)
  • Cas9 is directed to its target by a section of RNA. (bmj.com)
  • In order to cut, a specific sequence of DNA of between 2 and 5 nucleotides (the exact sequence depends upon the bacteria which produces the Cas9) must lie at the 3' end of the guide RNA: this is called the protospacer adjacent motif (PAM). (bmj.com)
  • It is the latter which allows precise genome editing: the homologous section of DNA with the required sequence change may be delivered with the Cas9 nuclease and sgRNA, theoretically allowing changes as precise as a single base-pair. (bmj.com)
  • One of the most exciting applications of CRISPR/Cas9 is its potential use to treat genetic disorders caused by single gene mutations. (bmj.com)
  • In this report, we described the application of CRISPR (clustered regularly interspaced short palindromic repeat)/Cas9 (endonuclease) system for efficient genetic editing in E. tenella , and showed that the CRISPR/Cas9 system mediates site-specific double-strand DNA breaks with a single guide RNA. (biomedcentral.com)
  • The CRISPR/Cas9 system introduces site-specific double-strand DNA breaks (DSBs) with endonuclease Cas9 in a target sequence that is homologous to the single guide RNA (sgRNA). (biomedcentral.com)
  • Cas9 is an endonuclease that cleaves double-stranded DNA in a sequence- specific manner. (biomedcentral.com)
  • Cas9 associates with a guide RNA of which the first 20 nucleotides pair with the target DNA. (biomedcentral.com)
  • In addition to this single guide RNA (sgRNA), Cas9 also needs to recognize a multi-nucleotide region that is adjacent to the 3′ end of the target DNA, which is termed PAM (protospacer adjacent motif). (biomedcentral.com)
  • Several labs have designed sgRNAs to program Cas9 to cleave different regions of HIV-1 DNA that include either essential viral genes or the viral long terminal repeat (LTR). (biomedcentral.com)
  • Despite the promising possibility that CRISPR/Cas9 could be used to inactivate or even delete proviral DNA from HIV-1 infected cells, an important unanswered question is whether and how HIV-1 might escape from the programmed CRISPR/Cas9 attack, a topic that is fundamental to attempts aimed at HIV treatment and prevention, including the use of small molecule-based antiretroviral therapy and HIV vaccines. (biomedcentral.com)
  • Rapid escape was observed when non-conserved HIV-1 sequences were attacked, but it did take longer for HIV-1 to escape from Cas9/sgRNAs that targeted the more conserved viral DNA sequences [ 12 ]. (biomedcentral.com)
  • The majority of the resistance mutations appeared to cluster at the site at which Cas9 was designed to cleave the viral DNA, even though the sgRNA binding site is much bigger. (biomedcentral.com)
  • Some mutations abrogate the function of viral DNA and will not be selected, while others will be selected because they are not deleterious to the virus, yet generate resistance to Cas9/sgRNA attack because the target DNA sequence is changed. (biomedcentral.com)
  • Here, we report the first application of single Cas9 nickase (Cas9n) to induce gene insertion at a selected locus in cattle. (biomedcentral.com)
  • Research studies have reported that an extended secondary DNA on the guide crRNA for Cas12a or a hairpin RNA structure added to the sgRNA for Cas9 increases the efficiency and specificity of gene editing. (biorxiv.org)
  • The SpCas9 expression and sgRNA (specific to eyfp ) production, which were controlled by His4 and EtU6 promoter, were constructed in one plasmid. (biomedcentral.com)
  • Indeed, when the targeted viral DNA regions were sequenced, mutations were identified that interfered with sgRNA recognition. (biomedcentral.com)
  • The CRISPR/Cas bacterial immune system cleaves bacteriophage and plasmid DNA. (nature.com)
  • It's non-specific and cleaves DNA and RNA into smaller fragments, acting on both single stranded and double stranded nuclei acids as well as linear and circular forms of nucleic acids. (sigmaaldrich.com)
  • DNase I, (RNase-free) is an endonuclease that nonspecifically cleaves DNA to release di-, tri- and oligonucleotide products with 5´-phosphorylated and 3´-hydroxylated ends (1,2). (neb.com)
  • The Non-specific nuclease, Benzonase - Endonuclease S. marcescens, has no proteolytic activity and is perfect for the removal of nucleic acids from protein samples or as an effective sonication alternative. (pharma-industry-review.com)
  • Serratia marcescens nuclease has potent digestive activity toward both single and double-stranded DNA and RNA of any origin. (pharma-industry-review.com)
  • Stereochemical course of DNA hydrolysis by nuclease S1. (ox.ac.uk)
  • Similar to MilliporeSigma Benzonase nuclease, a genetically engineered endonuclease from Serratia marcescens, Syd Labs recombinant Dr. Nuclease degrades all forms of DNA and RNA while having no proteolytic activity. (sydlabs.com)
  • Dr. Nuclease is a recombinant endonuclease produced in E. coli. (sydlabs.com)
  • Dr. Nuclease acts as an endonuclease that degrades both DNA and RNA in single-stranded, double-stranded, linear, circular, and super-coiled forms. (sydlabs.com)
  • Dr. Nuclease eliminates DNA/RNA containments in various products with ultra-speed and efficacy. (sydlabs.com)
  • Endonuclease G (ENDOG) is a nuclear-encoded mitochondrial-localized nuclease. (mdpi.com)
  • S1 nuclease is an endonuclease that is active against single-stranded DNA and RNA molecules. (rockland.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)
  • To determine how Rad1-Rad10 catalyzes inter-strand crosslink repair (ICLR), we examined sensitivity to ICLs from yeast deleted for SAW1 and SLX4, which encode proteins that interact physically with Rad1-Rad10 and bind stalled replication forks. (nih.gov)
  • With virtually no proteolytic activity this Non-specific Endonuclease is an excellent tool for removal of nucleic acid contamination from purified proteins, commonly from recombinant DNA products, and reduction of viscosity of bacterial lysates for the improvement of downstream processed to mitigate protein degradation during drug manufacturing. (pharma-industry-review.com)
  • Class 2 CRISPR/Cas (Clustered Regularly Interspaced Short Palindromic Repeats/CRISPR-associated proteins) systems, such as Cas12a (Cpf1, subtype V-A) and Cas13a (C2c2, subtype VI), are capable of nonspecific cleavage of ssDNA (single-stranded DNA) and RNA, respectively, in addition to successful gene editing. (biorxiv.org)
  • Genes are small blocks of DNA that tell the cell which proteins it should create. (wikibooks.org)
  • RNA alternative splicing (AS) is an important post-transcriptional mechanism enabling single genes to produce multiple proteins. (nature.com)
  • The spliceosome complex, composed of at least 170 proteins and several small nuclear RNAs (snRNAs), is the key structure responsible for splicing in eukaryotes 10 . (nature.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)
  • Viroids are non-encapsidated, single-stranded (ss), 250-400 nucleotide (nt)-long circular RNA molecules that do not encode proteins (1, 2). (degruyter.com)
  • Results from RNA sequencing revealed that AEG‑1 modulated neuronal morphology and development by regulating the expression of numerous genes, such as ubiquitin C, C‑X‑C motif chemokine ligand 1, MMP9, Notch1, neuropilin 1 and ephrin type‑A receptor 4. (spandidos-publications.com)
  • Subsequent repair of the DSBs is carried out by the host cell through either non-homologous end-joining pathway (NHEJ), leading to insertion and deletion mutations in the targeted genes, or homologous direct repair (HDR) in the presence of a DNA donor template. (biomedcentral.com)
  • Mapping, gene -- Determination of the relative positions of genes on a chromosome (or other DNA molecule) and of the distance, in linkage units or physical units, between them. (nih.gov)
  • While the selective inactivation of Ophiostoma genes by insertional mutagenesis remains a challenge, an alternative approach based on RNA interference is now available for down-regulating the expression of targeted genes. (sisef.it)
  • Finally, we demonstrate that the E9 DNase also degrades RNA in the absence of metal ions. (gla.ac.uk)
  • There are six steps in the life cycle Adsorption to the host via specific receptor(s) Movement of the viral DNA into the host cell Conversion of the single strand form to a double stranded intermediate Replication of the viral genome Synthesis of the new virons Release of the new virons from the host A typical replication cycle normally take 10-15 minutes to complete. (wikipedia.org)
  • RNA-programmed genome editing in human cells. (nature.com)
  • The main reason for the existence of latently infected cells is that proviral DNA becomes integrated into the cellular genome. (biomedcentral.com)
  • An integrated encyclopedia of DNA elements in the human genome. (umassmed.edu)
  • The viral genome of positive-strand RNA viruses is infectious, as it produces infectious virus upon introduction into a cell. (bvsalud.org)
  • In this study, we tested the inactivation of the viral genome after RNA fragmentation or cDNA synthesis, using the Trinidad Donkey and TC-83 strains of VEEV. (bvsalud.org)
  • Ironically, the H-N-H motif of the E9 DNase although resembling the zinc binding site of a metalloenzyme does not support zinc-mediated hydrolysis of any DNA substrate. (gla.ac.uk)
  • Add 0.5 µL UDG (G5020L) to a reaction with uracil-containing DNA substrate (up to 0.1 µg) in a 20 µL total reaction. (qiagen.com)
  • Although its primary substrate is single-stranded, it can also occasionally introduce single-stranded breaks in double-stranded DNA or RNA, or DNA-RNA hybrids. (rockland.com)
  • A split prime editor with untethered reverse transcriptase and circular RNA template. (umassmed.edu)
  • Benzonase endonuclease is an endonuclease that's normally expressed in the bacterium Serratia marcescens . (sigmaaldrich.com)
  • A family of enzymes that catalyze the endonucleolytic cleavage of RNA. (bvsalud.org)
  • This catalyzes endonucleolytic cleavage of DNA yielding 5'-phosphodi- and oligonucleotide end-products. (umassmed.edu)
  • The E9 DNase will also bind single-stranded DNA above a certain length and in a sequence-independent manner, with transition metals such as Ni2+ optimal for cleavage but Mg2+ a poor cofactor. (gla.ac.uk)
  • We speculate that chemical modifications of the crRNA can potentially change its nature of binding and subsequently alter this collateral cleavage due to conformational changes of the Cas12a dynamic endonuclease domain. (biorxiv.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)
  • These new single strand DNA sequences become templates for further DNA and RNA synthesis. (wikipedia.org)
  • Endonucleases that remove 5' DNA sequences from a DNA structure called a DNA flap. (musc.edu)
  • Artificial nucleases that cleave DNA at a defined distance from specific DNA sequences recognized by TRANSCRIPTION ACTIVATOR-LIKE EFFECTORS . (nih.gov)
  • 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)
  • It begins at a specific sequence within the DNA which is predicted to have a hairpin formation. (wikipedia.org)
  • Among them, an RNA-binding domain bends the template backbone to allow engagement of an RNA hairpin stem with the L1 ORF2p C-terminal segment. (bvsalud.org)
  • In molecular biology, it is used in removing single stranded tails from DNA molecules to create blunt ended molecules and opening hairpin loops generated during synthesis of double stranded cDNA. (rockland.com)
  • Inside the cell, enzymes create RNA and DNA by facilitating the reaction of ribose with adenosine. (nih.gov)
  • Furthermore, double-strand DNA has relatively small grooves where damaging enzymes can't attach, making it more difficult for them to 'attack' the DNA. (wikibooks.org)
  • Double-stranded RNA , on the other hand, has much larger grooves, and therefore, it is more subject to being broken down by enzymes. (wikibooks.org)
  • In eukaryotes, DNA methylation refers to the addition of a methyl group to the fifth atom in the six-atom ring of cytosine residues. (degruyter.com)
  • HR is inefficient in many cell types and thus a site-specific double-strand break (DSB) is often introduced by site-specific homing endonucleases or artificial endonucleases, such as zinc finger and TALE nucleases. (biomedcentral.com)
  • 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)
  • The ataxia telangiectasia Rad3-related (ATR) protein responds to UV damage, whereas the ataxia telangiectasia mutated (ATM) protein responds to double-strand breaks (DSBs) caused by ionizing radiation and radiomimetic compounds. (medscape.com)
  • By removing nucleic acids from the sample, this reduces DNA fouling as DNA binds to the resins and ensures maximal binding capacity for virus during chromatography to get the best yields. (sigmaaldrich.com)
  • The bases of each strand bind very specifically, A binds with T and C binds with G no other combination exists at least in DNA. (wikibooks.org)
  • dsDNase HL (500 U) is a 43.3 kDa heat-labile recombinant endonuclease derived from a cold water eukaryotic organism expressed in Pichia pastoris . (qiagen.com)
  • Gene transcription is by the host's cellular machinery each gene having a specific promoter. (wikipedia.org)
  • Regulation of nucleosome density is therefore an important mechanism to enable the transcription machinery to access the DNA. (asm.org)
  • Here we purified full-length L1 ORF2p and biochemically reconstituted robust target-primed reverse transcription with template RNA and target-site DNA. (bvsalud.org)
  • Cell-free system -- A mixture of cytoplasmic and/or nuclear components from cells used for in vitro protein synthesis, transcription, DNA replication, or other purposes. (nih.gov)
  • They are composed of an endodeoxyribonuclease fused to DNA-binding domains of the transcription activator-like effectors. (nih.gov)
  • The simplest way to do this is to use the Benzonase ® endonuclease. (sigmaaldrich.com)
  • Benzonase ® endonuclease is expressed in E. coli W3110, a mutant strain of K12. (sigmaaldrich.com)
  • Once these nucleic acids become broken down, Benzonase ® endonuclease and small DNA fragments can be easily removed by tangential flow filtration. (sigmaaldrich.com)
  • Whether for developing viral vaccines, viral vectors for vaccine, cell and gene therapy, or oncolytic viruses, Benzonase ® endonuclease removes nucleic acid contamination from the final product to meet regulatory standards. (sigmaaldrich.com)
  • To learn more about optimizing Benzonase ® endonuclease for your process, see our application note " Optimization Strategy and Process Economics of DNA Digestion in Viral Vector Production for Gene Therapy " and data sheet " Optimization of Benzonase ® endonuclease use in virus purification . (sigmaaldrich.com)
  • However, the Benzonase ® endonuclease Safety Plus Emprove ® Expert is produced from a chemically defined medium and each batch is tested for the absence of adventitious viruses and mycoplasma. (sigmaaldrich.com)
  • To learn more about switching from the standard Benzonase ® endonuclease to the Benzonase ® endonuclease Safety Plus Emprove ® Expert, download the data sheet or read our regulatory bulletin . (sigmaaldrich.com)
  • Benzonase ® endonuclease intensifies downstream processes by increasing efficiency of these steps and results in higher recovery of viral particles. (sigmaaldrich.com)
  • article{, title = {Comprehensive features of natural and in vitro selected GNRA tetraloop-binding receptors}, author = { C. Geary and S. Baudrey and L. Jaeger}, year = {2008}, date = {2008-01-01}, journal = {Nucleic Acids Res}, volume = {36}, number = {4}, pages = {1138-52}, abstract = {Specific recognitions of GNRA tetraloops by small helical receptors are among the most widespread long-range packing interactions in large ribozymes. (cnrs.fr)
  • The CRISPR/Cas12a RNA-guided complexes have a tremendous potential for nucleic acid detection due to its ability to indiscriminately cleave ssDNA once bound to a target DNA. (biorxiv.org)
  • CRISPR RNA maturation by trans-encoded small RNA and host factor RNase III. (nature.com)
  • DNase I acts on single- and double-stranded DNA, chromatin and RNA:DNA hybrids. (neb.com)
  • We do not recommend using NEB's DNase I as a substitute for Monarch DNase I in the RNA isolation workflow when using the Monarch Total RNA Miniprep Kit ( NEB #T2010 ). (neb.com)
  • Flap endonucleases cleave the downstream strand of the overlap flap structure precisely after the first base-paired nucleotide, creating a ligatable nick. (musc.edu)
  • The ERCC5 gene encodes a single-stranded structure-specific DNA endonuclease involved in DNA excision repair following UV-induced damage. (nih.gov)
  • The promoter/regulatory region of the dnaA gene, whose gene product is required for the initiation of DNA replication in Escherichia coli K-12, contains an unusually large number of Dam methylation sites. (jax.org)
  • Subsequently, we demonstrate that a single Cas9n-induced single-strand break can stimulate the insertion of the natural resistance-associated macrophage protein-1 ( NRAMP1 ) gene with reduced, but still considerable, off-target effects. (biomedcentral.com)
  • The protein is produced by a recombinant E. coli strain carrying the recombinant thermolabile uracil DNA glycosylase gene isolated from a marine bacteria. (qiagen.com)
  • 9 , 10 In addition, chemically modified Cas12a guided-RNA has also been shown to facilitate improved gene correction in mammalian cells through both viral-and non-viral methods compared to the wild-type guide RNA. (biorxiv.org)
  • 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)
  • Methods employed to knockdown or knockout gene products can answer specific questions about gene function, in addition to helping identify and develop therapeutics. (technologynetworks.com)
  • Both platforms require RNA-based reagents, and can lower gene expression, but they differ in more ways than they are similar. (technologynetworks.com)
  • In contrast to RNAi, CRISPR-based gene manipulation requires a guide RNA and a programmable Cas endonuclease protein. (technologynetworks.com)
  • Achieving a mechanistic and experimental middle ground between CRISPR-mediated gene knockout, whereby gene expression is reduced at the DNA level, and RNAi, in which target knockdown is not permanent, is CRISPRi. (technologynetworks.com)
  • The genomes are non-segmented, circular, positive-sense, single-stranded DNA 4.4-8.5 kilobases in length. (wikipedia.org)
  • Viroids are pathogenic circular, non-coding, single-stranded RNA molecules. (degruyter.com)
  • 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)
  • A programmable dual-RNA-guided DNA endonuclease in adaptive bacterial immunity. (nature.com)
  • That is to say why has evolution favored a DNA world over an RNA world given that the two molecules are so similar structurally? (wikibooks.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)
  • Upon inoculation, mature Pospiviroidae RNA molecules enter the plant cell nucleus. (degruyter.com)
  • Complete degradation is defined as the reduction of the majority of DNA fragments to tetranucleotides or smaller. (neb.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)
  • When the RNA fragments complex with a complementary (target) mRNA sequence and an endogenous silencing complex, mRNA is fragmented, preventing its translation. (technologynetworks.com)
  • This is initiated when a viral endonuclease (gp2) nicks the double stranded intermediate. (wikipedia.org)
  • The DNA flap structure occurs in double-stranded DNA containing a single-stranded break where the 5' portion of the downstream strand is too long and overlaps the 3' end of the upstream strand. (musc.edu)
  • Repair after the DNA cut may occur via two pathways: non-homologous end joining, typically leading to a random insertion/deletion of DNA, or homology directed repair where a homologous piece of DNA is used as a repair template. (bmj.com)
  • This double stranded break is repaired in mammalian cells either through Non-Homologous End Joining or Homologous Recombination. (genprice.com)
  • Once detected by the cell, blunt-ended DSBs are repaired by the non-homologous end joining (NHEJ) pathway, which is notorious for adding or removing stretches of DNA during repair. (technologynetworks.com)
  • Application areas include degradation of DNA after cell lysis, viscosity reduction of samples caused by HMW nucleic acids, DNA and RNA removal from protein samples, replacement of sonication or another mechanical DNA shearing process, as well as the prevention of cell clumping. (pharma-industry-review.com)
  • We report cryo-electron microscopy structures of the complete human L1 ORF2p bound to structured template RNAs and initiating cDNA synthesis. (bvsalud.org)
  • Overall, this work introduces RNA fragmentation and cDNA synthesis as reliable methods for the inactivation of samples containing the genomes of positive-strand RNA viruses. (bvsalud.org)
  • Several retroelement and retroviral reverse transcriptases (RTs) support NTA and also template jumping, by which the RT performs continuous complementary DNA (cDNA) synthesis using physically separate templates. (bvsalud.org)
  • Low-temperature setup at 50°C of the cDNA synthesis step causes delayed C q values because the newly amplified DNA containing dUTP is cleaved by UDG. (qiagen.com)
  • In mammalian cells, active and silent rDNA promoters are characterized by specific histone modifications, DNA methylation, and positioning of the promoter-bound nucleosome (reviewed in reference 22 ). (asm.org)
  • RNAi using dsRNA has been found to evoke a double-stranded RNA immune response in mammalian cells which can affect cell viability. (technologynetworks.com)
  • ERCC5 makes the 3'incision in DNA nucleotide excision repair (NER) and acts as a cofactor for a DNA glycosylase that removes oxidized pyrimidines from DNA. (nih.gov)
  • Makes the 3'incision in DNA nucleotide excision repair (NER). (abcam.cn)
  • The deoxyribose sugars form the structural backbone for DNA via a phosphodiester bond between the 3' carbon of one nucleotide and the 5' carbon of the next. (wikibooks.org)
  • Our high quality reagents are available for every workflow, including popular DNA assembly methods such as NEBuilder ® HiFi DNA Assembly and NEBridge ® Golden Gate Assembly . (neb.com)
  • 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)
  • Here, we developed a platform with engineered crRNAs and optimized conditions that enabled us to detect DNA, DNA/RNA heteroduplex and methylated DNA with higher sensitivity, achieving a limit of detection of in femtomolar range without any target pre-amplification step. (biorxiv.org)
  • 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)
  • The nuclear localization sequence (nls) of His4 was introduced into the N-terminal of Streptococcus pyogenes (SpCas9) to target the nucleus of the endonuclease SpCas9. (biomedcentral.com)
  • The absence of this Hydroxyl group is fundamental in determining the way in which DNA is able to condense itself within the nucleus of a cell. (wikibooks.org)
  • Members of the Pospiviroidae family replicate in the nucleus through double-stranded RNA intermediates, attracting the host RNA silencing machinery. (degruyter.com)
  • When PSTVd enters the plant cell, a specific signal seems to direct it into the nucleus. (degruyter.com)
  • DNA methylation differentially enhances the expression of one of the two E. coli dnaA promoters in vivo and in vitro. (jax.org)
  • Importantly, RNAi-based knockdown is temporary, and effect duration is contingent upon RNA turnover (both for endogenous mRNA and exogenous RNAi modulators). (technologynetworks.com)
  • Each of the four bases on DNA, Adenine (A), Cytosine (C), Guanine (G), and Thymine (T) is bonded covalently to a deoxyribose sugar. (wikibooks.org)
  • DNA is more chemically stable than RNA because it lacks the hydroxyl group on the 2' carbon. (wikibooks.org)
  • Although it is clear that switching among BESs does not involve DNA rearrangements and that regulation is probably epigenetic, it remains unknown why BESs are transcribed by Pol I and what roles are played by chromatin structure and histone modifications. (asm.org)
  • Some of this RNA is translated and the remainder is used to initiate DNA replication. (wikipedia.org)
  • Although its precise biological function remains unclear, its proximity to mitochondrial DNA (mtDNA) makes it an excellent candidate to participate in mtDNA replication, metabolism and maintenance. (mdpi.com)
  • Indeed, several roles for ENDOG have been hypothesized, including maturation of RNA primers during mtDNA replication, splicing of polycistronic transcripts and mtDNA repair. (mdpi.com)
  • RNA splicing plays important roles in viral replication and virus-host interactions 38 . (nature.com)
  • There is no activity shown on RNA substrates, making it usable for RT-PCR. (qiagen.com)
  • If performing high-volume, repetitive assays can benefit from adding Uracil-DNA Glycosylase (UDG) to their workflow to exclude carryover contamination. (qiagen.com)
  • Moreover, structure and biochemical reconstitutions demonstrate an unexpected target-site requirement: L1 ORF2p relies on upstream single-stranded DNA to position the adjacent duplex in the endonuclease active site for nicking of the longer DNA strand, with a single nick generating a staggered DNA break. (bvsalud.org)
  • When sufficient gp5 has accumulated within the cell, further DNA synthesis is halted and viron assembly begins. (wikipedia.org)
  • The template polyadenosine tract is recognized in a sequence-specific manner by five distinct domains. (bvsalud.org)